HK40107230A - Therapeutic and diagnostic methods and compositions for cancer - Google Patents

Description

Methods and compositions for the treatment and diagnosis of cancer

sequence list

This application contains a sequence list, which has been submitted electronically in ASCII format and is incorporated herein by reference in its entirety. The ASCII copy was created on April 27, 2022, named 50474-256WO4_Sequence_Listing_4_28_22_ST25, and is 9,636 bytes in size.

Technical Field

This invention relates to methods and compositions for treating and diagnosing cancer (e.g., non-small cell lung cancer (NSCLC)) in patients, for example, by administering a treatment regimen comprising, alone or in combination with, a PD-1 axis binding antagonist (e.g., atezolizumab) and/or an NK cell-directed therapy agent, including a taxane (e.g., nab-paclitaxel or paclitaxel), a platinum-based chemotherapy agent (e.g., carboplatin), and/or an anti-angiogenic agent (e.g., bevacizumab), to a patient.

Background Technology

Cancer remains one of the deadliest threats to human health. In the United States, cancer afflicts nearly 1.3 million new patients each year, making it the second leading cause of death after heart disease, accounting for about a quarter of all deaths. Solid tumors are the primary cause of these deaths. For example, lung cancer is the leading cause of cancer death worldwide. It is estimated that in 2014, there were 224,210 new cases of lung cancer (116,000 men and 108,210 women) and 159,260 deaths in the United States. Similar data from Europe estimates 214,000 new cases of lung cancer and 268,000 deaths in 2012. Non-squamous cell carcinoma (NSCLC) is one of the two main types of lung cancer, accounting for approximately 85% of all lung cancer cases. The two main histological types of NSCLC are adenocarcinoma (accounting for more than half of all cases) and squamous cell carcinoma (accounting for about 25% of all cases).

Therefore, there is a need in this field for improved cancer therapies (e.g., NSCLC).

Summary of the Invention

The present invention particularly provides methods, compositions, uses, and articles for treating and diagnosing cancer.

On one hand, the present invention is characterized by a method for treating a patient with non-small cell lung cancer (NSCLC) whose genome has been identified as containing at least one copy of HLA-C1, the method comprising administering to the patient an effective amount of a treatment regimen comprising a PD-1 axis binding antagonist.

In another aspect, the present invention is characterized by a PD-1 axis binding antagonist for treating NSCLC in patients with this need, whose genome has been identified as containing at least one copy of HLA-C1.

In some respects, the patient's genome further contains at least one copy of KIR2DL3.

In another aspect, the present invention is characterized by a method for treating NSCLC in patients who require this treatment, the patients’ genomes having been identified to contain at least one copy of HLA-C1 and at least one copy of KIR2DL3, the method comprising administering to the patient an effective amount of a treatment regimen comprising a PD-1 axis binding antagonist.

In another aspect, the present invention is characterized by a PD-1 axis binding antagonist for treating NSCLC in patients with this need, whose genome has been identified to contain at least one copy of HLA-C1 and at least one copy of KIR2DL3.

In another aspect, the present invention is characterized by a method for treating NSCLC in patients who require this treatment, the patients’ genomes of which have been identified to contain at least one copy of HLA-Bw4, the method comprising administering to the patients an effective amount of a treatment regimen comprising a PD-1 axis binding antagonist.

In another aspect, the present invention is characterized by a PD-1 axis binding antagonist for treating NSCLC in patients with this need, whose genome has been identified as containing at least one copy of HLA-Bw4.

In some respects, the patient’s genome further contains at least one copy of KIR3DL1.

In another aspect, the present invention is characterized by a method for treating NSCLC in patients who require this treatment, the patients’ genomes of which have been identified to contain at least one copy of HLA-Bw4 and at least one copy of KIR3DL1, the method comprising administering to the patients an effective amount of a treatment regimen comprising a PD-1 axis binding antagonist.

In another aspect, the present invention is characterized by a PD-1 axis binding antagonist for treating NSCLC in patients with this need, whose genome has been identified as containing at least one copy of HLA-Bw4 and at least one copy of KIR3DL1.

In another aspect, the present invention is characterized by a method for treating NSCLC in patients with such need, the method comprising: (a) determining whether the patient’s genome contains at least one copy of HLA-C1, wherein the presence of at least one copy of HLA-C1 in the patient’s genome indicates that the patient may benefit from a treatment regimen comprising a PD-1 axis binding antagonist; and (b) administering to the patient an effective amount of a treatment regimen comprising a PD-1 axis binding antagonist based on the presence of at least one copy of HLA-C1 in the patient’s genome.

In another aspect, the present invention is characterized by a PD-1 axis binding antagonist in a method for treating NSCLC in patients with such need, the method comprising: (a) determining whether the patient’s genome contains at least one copy of HLA-C1, wherein the presence of at least one copy of HLA-C1 in the patient’s genome indicates that the patient may benefit from a treatment regimen comprising a PD-1 axis binding antagonist; and (b) administering an effective amount of the treatment regimen comprising a PD-1 axis binding antagonist to the patient based on the presence of at least one copy of HLA-C1 in the patient’s genome.

In some respects, step (a) further includes determining whether the patient’s genome contains at least one copy of KIR2DL3.

In another aspect, the present invention is characterized by a method for treating NSCLC in patients with such need, the method comprising: (a) determining whether the patient’s genome contains at least one copy of HLA-C1 and at least one copy of KIR2DL3, wherein the presence of at least one copy of HLA-C1 and at least one copy of KIR2DL3 in the patient’s genome indicates that the patient may benefit from a treatment regimen comprising a PD-1 axis binding antagonist; and (b) administering an effective amount of a treatment regimen comprising a PD-1 axis binding antagonist to the patient based on the presence of at least one copy of HLA-C1 and at least one copy of KIR2DL3 in the patient’s genome.

In another aspect, the present invention is characterized by a PD-1 axis binding antagonist for treating NSCLC in patients with such need, the method comprising: (a) determining whether the patient’s genome contains at least one copy of HLA-C1 and at least one copy of KIR2DL3, wherein the presence of at least one copy of HLA-C1 and at least one copy of KIR2DL3 in the patient’s genome indicates that the patient may benefit from a treatment regimen comprising a PD-1 axis binding antagonist; and (b) administering an effective amount of the treatment regimen comprising a PD-1 axis binding antagonist to the patient based on the presence of at least one copy of HLA-C1 and at least one copy of KIR2DL3 in the patient’s genome.

In another aspect, the present invention is characterized by a method for treating NSCLC in patients with such need, the method comprising: (a) determining whether the patient’s genome contains at least one copy of HLA-Bw4, wherein the presence of at least one copy of HLA-Bw4 in the patient’s genome indicates that the patient may benefit from a treatment regimen comprising a PD-1 axis binding antagonist; and (b) administering to the patient an effective amount of a treatment regimen comprising a PD-1 axis binding antagonist based on the presence of at least one copy of HLA-Bw4 in the patient’s genome.

In another aspect, the present invention is characterized by a PD-1 axis binding antagonist for treating NSCLC in patients with such need, the method comprising: (a) determining whether the patient’s genome contains at least one copy of HLA-Bw4, wherein the presence of at least one copy of HLA-Bw4 in the patient’s genome indicates that the patient may benefit from a treatment regimen comprising a PD-1 axis binding antagonist; and (b) administering an effective amount of the treatment regimen comprising a PD-1 axis binding antagonist to the patient based on the presence of at least one copy of HLA-Bw4 in the patient’s genome.

In some respects, step (a) further includes determining whether the patient’s genome contains at least one copy of KIR3DL1.

In another aspect, the present invention is characterized by a method for treating NSCLC in patients with such need, the method comprising: (a) determining whether the patient’s genome contains at least one copy of HLA-Bw4 and at least one copy of KIR3DL1, wherein the presence of at least one copy of HLA-Bw4 and at least one copy of KIR3DL1 in the patient’s genome indicates that the patient may benefit from a treatment regimen comprising a PD-1 axis binding antagonist; and (b) administering to the patient an effective amount of a treatment regimen comprising a PD-1 axis binding antagonist based on the presence of at least one copy of HLA-Bw4 and at least one copy of KIR3DL1 in the patient’s genome.

In another aspect, the present invention is characterized by a PD-1 axis binding antagonist for treating NSCLC in patients with such need, the method comprising: (a) determining whether the patient’s genome contains at least one copy of HLA-Bw4 and at least one copy of KIR3DL1, wherein the presence of at least one copy of HLA-Bw4 and at least one copy of KIR3DL1 in the patient’s genome indicates that the patient may benefit from a treatment regimen comprising a PD-1 axis binding antagonist; and (b) administering an effective amount of the treatment regimen comprising a PD-1 axis binding antagonist to the patient based on the presence of at least one copy of HLA-Bw4 and at least one copy of KIR3DL1 in the patient’s genome.

In another aspect, the present invention is characterized by a method for identifying patients with NSCLC who may benefit from a treatment regimen including a PD-1 axis binding antagonist, the method comprising determining whether the patient’s genome contains at least one copy of HLA-C1, wherein the presence of at least one copy of HLA-C1 in the patient’s genome identifies the patient as a patient who may benefit from treatment using a treatment regimen including a PD-1 axis binding antagonist.

In another aspect, the present invention is characterized by a method for identifying patients with NSCLC who may benefit from a treatment regimen including a PD-1 axis binding antagonist, the method comprising: (a) fragmenting a DNA sample obtained from the patient to generate fragmented DNA, adding an adaptor to the fragmented DNA to generate one or more libraries, and sequencing the one or more libraries to perform germline whole-genome sequencing (WGS) or whole-exome sequencing (WES); and (b) identifying the patient as a patient who may benefit from a treatment regimen including a PD-1 axis binding antagonist by determining whether the patient's genome contains at least one copy of HLA-C1, wherein the presence of at least one copy of HLA-C1 in the patient's genome identifies the patient as a patient who may benefit from treatment using a treatment regimen including a PD-1 axis binding antagonist.

In some aspects, the method further includes determining whether the patient's genome contains at least one copy of KIR2DL3.

In another aspect, the present invention is characterized by a method for identifying patients with NSCLC who may benefit from a treatment regimen including a PD-1 axis binding antagonist, the method comprising determining whether the patient’s genome contains at least one copy of HLA-C1 and at least one copy of KIR2DL3, wherein the presence of at least one copy of HLA-C1 and at least one copy of KIR2DL3 in the patient’s genome identifies the patient as a patient who may benefit from treatment using a treatment regimen including a PD-1 axis binding antagonist.

In another aspect, the present invention is characterized by a method for identifying patients with NSCLC who may benefit from a treatment regimen including a PD-1 axis binding antagonist, the method comprising: (a) performing germline WGS or WES by fragmenting a DNA sample obtained from the patient to generate fragmented DNA, adding an adaptor to the fragmented DNA to generate one or more libraries, and sequencing the one or more libraries; and (b) identifying the patient as a patient who may benefit from a treatment regimen including a PD-1 axis binding antagonist by determining whether the patient's genome contains at least one copy of HLA-C1 and at least one copy of KIR2DL3, wherein the presence of at least one copy of HLA-C1 and at least one copy of KIR2DL3 in the patient's genome identifies the patient as a patient who may benefit from treatment using a treatment regimen including a PD-1 axis binding antagonist.

In another aspect, the present invention is characterized by a method for identifying patients with NSCLC who may benefit from a treatment regimen including a PD-1 axis binding antagonist, the method comprising determining whether the patient’s genome contains at least one copy of HLA-Bw4, wherein the presence of at least one copy of HLA-Bw4 in the patient’s genome identifies the patient as a patient who may benefit from treatment using a treatment regimen including a PD-1 axis binding antagonist.

In another aspect, the present invention is characterized by a method for identifying a patient with NSCLC who may benefit from a treatment regimen including a PD-1 axis binding antagonist, the method comprising: (a) performing germline WGS or WES by fragmenting a DNA sample obtained from the patient to generate fragmented DNA, adding an adaptor to the fragmented DNA to generate one or more libraries, and sequencing the one or more libraries; and (b) identifying the patient as a patient who may benefit from a treatment regimen including a PD-1 axis binding antagonist by determining whether the patient's genome contains at least one copy of HLA-Bw4, wherein the presence of at least one copy of HLA-Bw4 in the patient's genome identifies the patient as a patient who may benefit from treatment using a treatment regimen including a PD-1 axis binding antagonist.

In some aspects, the method further includes determining whether the patient's genome contains at least one copy of KIR3DL1.

In another aspect, the present invention is characterized by a method for identifying patients with NSCLC who may benefit from a treatment regimen including a PD-1 axis binding antagonist, the method comprising determining whether the patient’s genome contains at least one copy of HLA-Bw4 and at least one copy of KIR3DL1, wherein the presence of at least one copy of HLA-Bw4 and at least one copy of KIR3DL1 in the patient’s genome identifies the patient as a patient who may benefit from treatment using a treatment regimen including a PD-1 axis binding antagonist.

In another aspect, the present invention is characterized by a method for identifying patients with NSCLC who may benefit from a treatment regimen including a PD-1 axis binding antagonist, the method comprising: (a) performing germline WGS or WES by fragmenting a DNA sample obtained from the patient to generate fragmented DNA, adding an adaptor to the fragmented DNA to generate one or more libraries, and sequencing the one or more libraries; and (b) identifying the patient as a patient who may benefit from a treatment regimen including a PD-1 axis binding antagonist by determining whether the patient's genome contains at least one copy of HLA-Bw4 and at least one copy of KIR3DL1, wherein the presence of at least one copy of HLA-Bw4 and at least one copy of KIR3DL1 in the patient's genome identifies the patient as a patient who may benefit from treatment using a treatment regimen including a PD-1 axis binding antagonist.

In another aspect, the present invention is characterized by a method for selecting a therapy for a patient with NSCLC, the method comprising: (a) determining whether the patient’s genome contains at least one copy of HLA-C1, wherein the presence of at least one copy of HLA-C1 in the patient’s genome indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist; and (b) selecting a treatment regimen including a PD-1 axis binding antagonist based on the presence of at least one copy of HLA-C1 in the patient’s genome.

In some aspects, the method further includes determining whether the patient's genome contains at least one copy of KIR2DL3.

In another aspect, the present invention is characterized by a method for selecting a therapy for a patient with NSCLC, the method comprising: (a) determining whether the patient’s genome contains at least one copy of HLA-C1 and at least one copy of KIR2DL3, wherein the presence of at least one copy of HLA-C1 and at least one copy of KIR2DL3 in the patient’s genome indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist; and (b) selecting a treatment regimen including a PD-1 axis binding antagonist based on the presence of at least one copy of HLA-C1 and at least one copy of KIR2DL3 in the patient’s genome.

In another aspect, the present invention is characterized by a method for selecting a therapy for a patient with NSCLC, the method comprising: (a) determining whether the patient’s genome contains at least one copy of HLA-Bw4, wherein the presence of at least one copy of HLA-Bw4 in the patient’s genome indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist; and (b) selecting a treatment regimen including a PD-1 axis binding antagonist based on the presence of at least one copy of HLA-Bw4 in the patient’s genome.

In some aspects, the method further includes determining whether the patient's genome contains at least one copy of KIR3DL1.

In another aspect, the present invention is characterized by a method for selecting a therapy for a patient with NSCLC, the method comprising: (a) determining whether the patient’s genome contains at least one copy of HLA-Bw4 and at least one copy of KIR3DL1, wherein the presence of at least one copy of HLA-Bw4 and at least one copy of KIR3DL1 in the patient’s genome indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist; and (b) selecting a treatment regimen including a PD-1 axis binding antagonist based on the presence of at least one copy of HLA-Bw4 and at least one copy of KIR3DL1 in the patient’s genome.

In some respects, the method further includes administering an effective dose of a treatment regimen, including a PD-1 axis binding antagonist, to the patient.

In some aspects, the method further includes using next-generation sequencing, Sanger sequencing, polymerase chain reaction (PCR)-based assays, or single nucleotide polymorphism (SNP) arrays to determine the presence of HLA-C1, HLA-Bw4, KIR2DL3, and/or KIR3DL1 in the patient's genome.

In some respects, the method further includes next-generation sequencing, which includes germline whole-genome sequencing or germline whole-exome sequencing.

In some respects, the method further includes PCR-based assays, including quantitative PCR (qPCR), typing using sequence-specific primers (SSP), or typing using sequence-specific oligonucleotide probes (SSO).

In another aspect, the present invention is characterized by a method for treating NSCLC in a patient who has been identified as having an increased level of NK cell infiltration relative to a reference level of natural killer (NK) cell infiltration in a tumor sample obtained from the patient, the method comprising administering to the patient an effective amount of a treatment regimen comprising a PD-1 axis binding antagonist.

On the other hand, the present invention is characterized by a PD-1 axis binding antagonist for treating NSCLC in patients who have been identified as having an increased level of NK cell infiltration in tumor samples obtained from the patient relative to a reference level of NK cell infiltration.

In another aspect, the present invention is characterized by a method for treating NSCLC in a patient with such need, the method comprising: (a) determining whether a tumor sample obtained from the patient has an increased level of NK cell infiltration relative to a reference level of NK cell infiltration, wherein an increased level of NK cell infiltration in the tumor sample obtained from the patient relative to a reference level of NK cell infiltration indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist; and (b) administering an effective amount of a treatment regimen including a PD-1 axis binding antagonist to the patient based on the increased level of NK cell infiltration in the tumor sample obtained from the patient relative to a reference level of NK cell infiltration.

In another aspect, the present invention is characterized by a PD-1 axis binding antagonist in a method for treating NSCLC in a patient with such need, the method comprising: (a) determining whether a tumor sample obtained from the patient has an increased level of NK cell infiltration relative to a reference level of NK cell infiltration, wherein an increased level of NK cell infiltration in the tumor sample obtained from the patient relative to a reference level of NK cell infiltration indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist; and (b) administering an effective amount of a treatment regimen including a PD-1 axis binding antagonist to the patient based on the increased level of NK cell infiltration in the tumor sample obtained from the patient relative to a reference level of NK cell infiltration.

In another aspect, the present invention is characterized by a method for identifying patients with NSCLC who may benefit from a treatment regimen including a PD-1 axis binding antagonist, the method comprising determining whether a tumor sample obtained from the patient has an increased level of NK cell infiltration relative to a reference level of NK cell infiltration, wherein an increased level of NK cell infiltration relative to a reference level of NK cell infiltration in a tumor sample obtained from the patient indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist.

In another aspect, the present invention is characterized by a method for identifying a patient with NSCLC who may benefit from a treatment regimen including a PD-1 axis binding antagonist, the method comprising: (a) contacting a tumor sample obtained from the patient with one or more antibody or nucleotide probes bound to one or more NK cell markers to determine the level of NK cell infiltration in the tumor sample; and (b) determining whether the tumor sample obtained from the patient has an increased level of NK cell infiltration relative to a reference level of NK cell infiltration, wherein an increased level of NK cell infiltration in the tumor sample obtained from the patient relative to a reference level of NK cell infiltration indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist.

In another aspect, the present invention is characterized by a method for selecting a therapy for a patient with NSCLC, the method comprising: (a) determining whether a tumor sample obtained from the patient has an increased level of NK cell infiltration relative to a reference level of NK cell infiltration, wherein an increased level of NK cell infiltration in the tumor sample obtained from the patient indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist; and (b) selecting a treatment regimen including a PD-1 axis binding antagonist based on the increased level of NK cell infiltration in the tumor sample obtained from the patient relative to a reference level of NK cell infiltration.

In some respects, the method further includes administering an effective dose of a treatment regimen, including a PD-1 axis binding antagonist, to the patient.

In some respects, the level of NK cell infiltration is determined by identifying the expression level of NK cell gene signatures or by counting the number of NK cells in a tumor sample.

In some respects, the NK cell genetic signature includes one or more of the following genes: CD160, CD244, CTSW, FASLG, GZMA, GZMB, GZMH, IL18RAP, IL2RB, KIR2DL4, KLRB1, KLRC3, KLRD1, KRLF1, KLRK1, NCR1, NKG7, PRF1, XCL1, and XCL2.

In some respects, the NK cell gene signature contains at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least ten, at least eleven, at least twelve, at least thirteen, at least fourteen, at least fifteen, at least sixteen, at least seventeen, at least eighteen, at least nineteen, or all twenty of the genes.

In some respects, the reference level for NK cell infiltration is the median level.

In some respects, the median level is the median level in the NSCLC patient population.

In some respects, the benefits lie in improved overall survival (OS) or improved progression-free survival (PFS).

In some respects, the benefits lie in the improved OS.

In some respects, the benefit lies in improved PFS.

In some respects, the improvement is relative to treatment regimens that do not include PD-1 axis binding antagonists.

In some respects, NSCLC is either non-squamous NSCLC or squamous NSCLC.

In some respects, NSCLC is non-squamous NSCLC.

In some respects, non-squamous NSCLC is metastatic non-squamous NSCLC.

In some respects, NSCLC is squamous NSCLC.

In some respects, squamous NSCLC is metastatic squamous NSCLC.

In some respects, the patient is a chemotherapy newcomer.

In some respects, the treatment plan is a first-line treatment.

In some respects, PD-1 axis binding antagonists are selected from the group consisting of: PD-L1 binding antagonists, PD-1 binding antagonists and PD-L2 binding antagonists.

In some respects, PD-1 axis binding antagonists are PD-L1 binding antagonists.

In some respects, PD-L1 binding antagonists are anti-PD-L1 antibodies.

In some respects, the anti-PD-L1 antibody comprises the hypervariable region (HVR)-H1, HVR-H2, and HVR-H3 sequences of (a) GFTFSDSWIH (SEQ ID NO:3), AWISPYGGSTYYADSVKG (SEQ ID NO:4), and RHWPGGFDY (SEQ ID NO:5), and the HVR-L1, HVR-L2, and HVR-L3 sequences of (b) RASQDVSTAVA (SEQ ID NO:6), SASFLYS (SEQ ID NO:7), and QQYLYHPAT (SEQ ID NO:8).

In some respects, anti-PD-L1 antibodies contain (a)VH, which comprises the following amino acid sequence:

EVQLVESGGGLVQPGGSLRLSCAASGFTFSDSWIHWVRQAPGKGLEWVAWISPYGGSTYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARRHWPGGFDYWGQGTLVTVSS (SEQ ID NO: 9), and (b) VL, which contains the following amino acid sequence:

DIQMTQSPSSSLSASVGDRVTITCRASQDVSTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQYLYHPATFGQGTKVEIKR(SEQ ID NO:10).

In some cases, anti-PD-L1 antibodies include atezolizumab, durvalumab, acitumb, or MDX-1105.

In some respects, the anti-PD-L1 antibody is atezolizumab.

In some cases, anti-PD-L1 antibodies are administered intravenously or subcutaneously.

In some cases, atezolizumab is administered intravenously at a dose of 840 mg every two weeks.

In some cases, atezolizumab is administered intravenously at a dose of 1200 mg every three weeks.

In some cases, atezolizumab is administered intravenously at a dose of 1680 mg every four weeks.

In some respects, PD-1 axis binding antagonists are PD-1 binding antagonists.

In some respects, PD-1 binding antagonists are anti-PD-1 antibodies.

In some respects, anti-PD-1 antibodies include nivolumab, pembrolizumab, MEDI-0680, spartazumab, cimiprizumab, camrelizumab, sintilimab, tislelizumab, toripalimab, or dotalimab.

In some aspects, the treatment regimen further includes taxanes.

In some respects, taxane is nab-paclitaxel or paclitaxel.

In some respects, taxane is nab-paclitaxel.

In some respects, taxane is paclitaxel.

In some aspects, the treatment regimen further includes platinum-based chemotherapy agents.

In some cases, the platinum-based chemotherapy agent is carboplatin.

In some aspects, the treatment plan further includes anti-angiogenic agents.

In some respects, anti-angiogenic agents are anti-VEGF antibodies.

In some respects, the anti-VEGF antibody is bevacizumab.

In some respects, NSCLC is metastatic non-squamous NSCLC, and treatment options include atezolizumab, nab-paclitaxel, and carboplatin.

In some respects, atezolizumab was administered intravenously (IV) at a dose of 1200 mg on day 1 of each 21-day cycle; nab-paclitaxel was administered IV at a dose of 100 mg/ ^m² on days 1, 8, and 15 of each 21-day cycle; and carboplatin was administered at an area under the concentration curve (AUC) of 6 mg/mL/min on day 1 of each 21-day cycle.

In some respects, NSCLC is metastatic non-squamous NSCLC, and treatment options include atezolizumab, paclitaxel, and carboplatin.

In some respects, atezolizumab was administered as an IV infusion at a dose of 1200 mg on day 1 of each 21-day cycle; paclitaxel was administered as an IV infusion at a dose of 200 mg/ ^m² on day 1 of each 21-day cycle; and carboplatin was administered at an AUC of 6 mg/mL/min on day 1 of each 21-day cycle.

In some respects, NSCLC is metastatic non-squamous NSCLC, and treatment options include atezolizumab, bevacizumab, paclitaxel, and carboplatin.

In some respects, atezolizumab was administered as an IV infusion at a dose of 1200 mg on day 1 of each 21-day cycle; bevacizumab was administered as an IV infusion at a dose of 15 mg/kg on day 1 of each 21-day cycle; paclitaxel was administered as an IV infusion at a dose of 200 mg/ ^m² on day 1 of each 21-day cycle; and carboplatin was administered at an AUC of 6 mg/mL/min on day 1 of each 21-day cycle.

In some respects, NSCLC is metastatic squamous NSCLC, and treatment options include atezolizumab, nab-paclitaxel, and carboplatin.

In some respects, atezolizumab was administered as an IV infusion at a dose of 1200 mg on day 1 of each 21-day cycle; nab-paclitaxel was administered as an IV infusion at a dose of 100 mg/ ^m² on days 1, 8, and 15 of each 21-day cycle; and carboplatin was administered at an area under the concentration curve (AUC) of 6 mg/mL/min on day 1 of each 21-day cycle.

In some respects, NSCLC is metastatic squamous NSCLC, and treatment options include atezolizumab, paclitaxel, and carboplatin.

In some respects, atezolizumab was administered as an IV infusion at a dose of 1200 mg on day 1 of each 21-day cycle; paclitaxel was administered as an IV infusion at a dose of 175 mg/ ^m² or 200 mg/ ^m² on days 1, 8, and 15 of each 21-day cycle; and carboplatin was administered at an AUC of 6 mg/mL/min on day 1 of each 21-day cycle.

In some respects, the method further includes administering additional therapeutic agents to the patient.

In some respects, the additional therapeutic agent is selected from the group consisting of: immunotherapeutic agents, cytotoxic agents, growth inhibitors, radiotherapy agents, anti-angiogenic agents, and combinations thereof.

On the other hand, the present invention is characterized by an article of manufacture for treating NSCLC in patients with such need, comprising a PD-1 axis binding antagonist and instructions for administering the PD-1 axis binding antagonist, the patient’s genome having been determined to contain at least one copy of HLA-C1.

On the other hand, the present invention is characterized by an article of manufacture for treating NSCLC in patients with such need, comprising a PD-1 axis binding antagonist and instructions for administering the PD-1 axis binding antagonist, the patient’s genome having been determined to contain at least one copy of HLA-C1 and at least one copy of KIR2DL3.

On the other hand, the present invention is characterized by an article of manufacture for treating NSCLC in patients who require such treatment, comprising a PD-1 axis binding antagonist and instructions for administering the PD-1 axis binding antagonist, the patient’s genome having been determined to contain at least one copy of HLA-Bw4.

On the other hand, the present invention is characterized by an article of manufacture for treating NSCLC in patients with such need, comprising a PD-1 axis binding antagonist and instructions for administering the PD-1 axis binding antagonist, the patient’s genome having been determined to contain at least one copy of HLA-Bw4 and at least one copy of KIR3DL1.

On the other hand, the present invention is characterized by an article of manufacture for treating NSCLC in a patient who requires such treatment, comprising a PD-1 axis binding antagonist and instructions for administering the PD-1 axis binding antagonist, the patient being identified as having an increased level of NK cell infiltration relative to a reference level of natural killer (NK) cell infiltration in a tumor sample obtained from the patient.

On the other hand, the present invention is characterized by an article of manufacture for treating NSCLC in patients who require such treatment, comprising an NK cell-directed therapeutic agent and instructions for administering the NK cell-directed therapeutic agent, the patient’s genome having been determined to lack KIR2DL3 or KIR3DL1.

Attached Figure Description

Figure 1A is a graph showing the overall survival (OS) hazard ratio (HR) for non-small cell lung cancer (NSCLC) patients who are carriers of at least one copy of either the human leukocyte antigen (HLA) allele HLA-C1 or the killer cell immunoglobulin-like receptor (KIR) gene KIR2DL3, and who were treated with atezolizumab-containing therapies in the IMpower130, IMpower131, or IMpower150 clinical trials, compared to controls. Estimates of treatment effect (TE), standard error of TE (seTE), p-value, and weights (fixed and randomized) are shown. Fixed-effects and random-effects models are shown.

Figure 1B is a graph showing the progression-free survival (PFS) HR in NSCLC patients who are carriers of at least one copy of either HLA-C1 or KIR2DL3 and who were treated with atezolizumab-containing therapies in the IMpower130, IMpower131, or IMpower150 clinical trials, compared to controls.

Figure 2A is a graph showing the OS HR of NSCLC patients who are carriers of at least one copy of either the HLA allele HLA-Bw4 or the KIR gene KIR3DL1, and who were treated with atezolizumab-containing therapies in the IMpower130, IMpower131, or IMpower150 clinical trials, compared with controls.

Figure 2B is a graph showing the PFS HR of NSCLC patients who are carriers of at least one copy of HLA-Bw4 and KIR3DL1 and who were treated with atezolizumab-containing therapies in the IMpower130, IMpower131 or IMpower150 clinical trials, compared with controls.

Figure 3A is a graph showing the OS HR of NSCLC patients who were carriers of at least one copy of HLA-C1 and were treated with atezolizumab-containing therapies in the IMpower130, IMpower131, or IMpower150 clinical trials, compared with controls.

Figure 3B is a graph showing the PFS HR of NSCLC patients who were carriers of at least one copy of HLA-C1 and were treated with atezolizumab-containing therapies in the IMpower130, IMpower131, or IMpower150 clinical trials, compared with controls.

Figure 4A is a graph showing the OS HR of NSCLC patients who are carriers of at least one copy of HLA-Bw4 and were treated with atezolizumab-containing therapies in the IMpower130, IMpower131, or IMpower150 clinical trials, compared with controls.

Figure 4B is a graph showing the PFS HR of NSCLC patients who are carriers of at least one copy of HLA-Bw4 and were treated with atezolizumab-containing therapies in the IMpower130, IMpower131, or IMpower150 clinical trials, compared with controls.

Figure 5A is a graph showing the OS HR of NSCLC and melanoma patients who were carriers of at least one copy of HLA-Bw4 and were treated with therapies containing immune checkpoint blockade (ICB) compared to controls in data from Chowell et al. (see example 1d) or MSK-IMPACT (see, for example, Zehir et al. Nat. Med. 23:703-713, 2017).

Figure 5B is a graph showing the OS HR of NSCLC and melanoma patients who were carriers of at least one copy of HLA-C1 and were treated with a therapy containing immune checkpoint blockade (ICB) in Chowell et al.’s data (see Example 1d) or MSK-IMPACT, compared with controls.

Figure 6A is a graph showing the OS HR of NSCLC patients with above-median natural killer (NK) cell scores who were treated with atezolizumab-containing therapies in the IMpower131 or IMpower150 clinical trials, compared to controls.

Figure 6B is a graph showing the OS HR of NSCLC patients with above-median NK cell scores who were treated with atezolizumab-containing therapies in the IMpower131 or IMpower150 clinical trials, compared to controls.

Figure 7A is a graph showing the OS HR of patients who had above-median NK cell scores and were treated with atezolizumab-containing therapies in the listed clinical trials, compared with controls.

Figure 7B is a graph showing the OS HR of patients who had above-median CD8A levels and were treated with atezolizumab-containing therapies in the listed clinical trials compared to controls.

Figure 8A is a graph showing the OS HR of patients with renal cell carcinoma (RCC) who are carriers of at least one copy of either HLA-C1 or KIR2DL3 and were treated with a therapy containing atezolizumab in the IMmotion151 clinical trial, compared with controls.

Figure 8B is a graph showing the PFS HR of RCC patients who are carriers of at least one copy of either HLA-C1 or KIR2DL3 and were treated with a therapy containing atezolizumab in the IMmotion151 clinical trial, compared with controls.

Figure 9A is a graph showing the OS HR of RCC patients who are carriers of at least one copy of HLA-Bw4 and KIR3DL1 and were treated with a therapy containing atezolizumab in the IMmotion151 clinical trial, compared with controls.

Figure 9B is a graph showing the PFS HR of RCC patients who are carriers of at least one copy of either HLA-Bw4 or KIR3DL1 and were treated with a therapy containing atezolizumab in the IMmotion151 clinical trial, compared with controls.

Figure 10A is a graph showing the OS HR of RCC patients who are carriers of at least one copy of HLA-C1 and were treated with a therapy containing atezolizumab in the IMmotion151 clinical trial, compared with controls.

Figure 10B is a graph showing the PFS HR of RCC patients who are carriers of at least one copy of HLA-C1 and were treated with a therapy containing atezolizumab in the IMmotion151 clinical trial, compared with controls.

Figure 11A is a graph showing the OS HR of RCC patients who are carriers of at least one copy of HLA-Bw4 and were treated with a therapy containing atezolizumab in the IMmotion151 clinical trial, compared with controls.

Figure 11B is a graph showing the PFS HR of RCC patients who are carriers of at least one copy of HLA-Bw4 and were treated with a therapy containing atezolizumab in the IMmotion151 clinical trial, compared with controls.

Figure 12A is a graph showing the OS HR of RCC patients who had above-median NK cell scores and were treated with atezolizumab-containing therapies in the IMmotion150 or IMmotion151 clinical trials, compared with controls.

Figure 12B is a graph showing the PFS HR of RCC patients who had above-median NK cell scores and were treated with atezolizumab-containing therapies in the IMmotion150 or IMmotion151 clinical trials, compared with controls.

Figure 13A is a graph showing the OS HR of RCC patients who had above-median CD8A levels and were treated with atezolizumab-containing therapies in the IMmotion150 or IMmotion151 clinical trials, compared with controls.

Figure 13B is a graph showing the PFS HR of RCC patients who had above-median CD8A levels and were treated with atezolizumab-containing therapies in the IMmotion150 or IMmotion151 clinical trials, compared with controls.

Figure 14 is a graph showing the risk of immune checkpoint inhibitor (ICI)-associated pneumonia in patients carrying the HLA class II allele HLA-DRB1*15:01 and treated with ICIs in the designated cohort compared to controls. GNE, Genentech; PICI, Parker Institute for Cancer Immunotherapy; PMC, Peter McCallum Cancer Center; OR, odds ratio; CI, confidence interval; W, weight.

Figure 15 is a plot showing the OS HR for the specified cohort, demonstrating that HLA class I loss of heterozygosity (LOH) is not associated with prognosis. The plot shows a comparison of any class I LOH with no LOH in the atezolizumab group for the specified study.

Figure 16 is a series of graphs showing that TMB does not change the effect of LOH on prognosis.

Figure 17 shows the association between type I LOH and lower CD8A expression. This figure compares any type I LOH with no LOH in the atezolizumab group for a specified study.

Figure 18 is a plot showing the OS HR for the specified cohort, illustrating the association between HLA class II LOH and poor prognosis. This plot compares any class II LOH with no LOH in the atezolizumab group for the specified study.

Detailed Implementation

This invention provides methods and compositions for the treatment and diagnosis of cancers (e.g., lung cancer (e.g., NSCLC (e.g., non-squamous NSCLC or squamous NSCLC)) or renal cell carcinoma (e.g., RCC)). The invention is based, at least in part, on the findings described herein that the presence of specific human leukocyte antigen genes (e.g., HLA-C1 or HLA-Bw4) and/or killer cell immunoglobulin-like receptor genes (e.g., KIR2DL3 or KIR3DL1) in a patient's genome is associated with improved therapeutic benefit from treatment regimens including a PD-1 axis binding antagonist (e.g., atezolizumab). The invention is also based, at least in part, on the findings described herein that elevated NK cell infiltration in tumor samples obtained from patients is associated with improved therapeutic benefit from treatment regimens including a PD-1 axis binding antagonist (e.g., atezolizumab). Furthermore, the invention is based, at least in part, on the findings described herein that patients with a genomic deficiency of one or more of KIR2DL3 or KIR3DL1 can benefit from treatment regimens including NK cell-targeted therapies.

I. Definition

The following abbreviations are used in this article:

The terms "human leukocyte antigen C" and "HLA-C" refer to the HLA class I heavy chain gene. Class I molecules play a central role in the immune system by presenting peptides derived from cytoplasmic proteins and are expressed in almost all cells. The HLA-C receptor is a heterodimer comprising the mature HLA-C gene product heavy chain and the β2-microglobulin light chain. The heavy chain is approximately 45 kDa, and its gene contains eight exons. Typically, exon 1 encodes a leader peptide, exons 2 and 3 encode α-1 and α-2 domains, both of which bind to the peptide, exon 4 encodes the α-3 domain, exon 5 encodes the transmembrane region, and exons 6 and 7 encode the cytoplasmic tail region. Polymorphisms within exons 2 and 3 are generally responsible for the peptide-binding specificity of each class I molecule. Approximately 6,600 HLA-C alleles have been described. HLA-C alleles belong to the HLA-C1 and HLA-C2 groups. Additional information about HLA-C can be found, for example, under UniProt accession number P10321.

The term "HLA-C1" refers to the HLA-C gene allele, typically characterized by an asparagine (Asn) residue at position 80 of the α-1 domain. Exemplary HLA-C1 alleles include, but are not limited to, Cw*0102, Cw*0103, Cw*0104, Cw*0105, Cw*0302, Cw*0303, Cw*0304, Cw*0305, Cw*0306, Cw*0308, Cw*0309, Cw*0310, Cw*0311, Cw*0312, Cw*0313, Cw*0314, Cw*0701, Cw*0702, Cw*0703, Cw*0704, Cw*0705, Cw*0706, Cw*0708, and Cw*0709. *0710, Cw*0711, Cw*0712, Cw*0713, Cw*0714, Cw*0715, Cw*0801, Cw*0802, Cw*0803, Cw*0804, Cw*0805, Cw*0806, Cw*0807, Cw*0808, Cw*0809, Cw*1202, Cw*1203, Cw*1206, Cw*1208, Cw*1301, Cw*1402, Cw*1403, Cw*1405, Cw*1507, Cw*1601, and Cw*1604. Other HLA-C1 alleles are known in the art. See, for example, the IPD-IMGT/HLA database (ebi.ac.uk/ipd/imgt/hla).

The term "HLA-C2" refers to the HLA-C gene allele, typically characterized by a lysine residue at position 80 of the α-1 domain. Exemplary HLA-C2 alleles include, but are not limited to, Cw*0202, Cw*0203, Cw*0204, Cw*0205, Cw*0307, Cw*0401, Cw*0403, Cw*0404, Cw*0405, Cw*0406, Cw*0407, Cw*0408, Cw*0501, Cw*0502, Cw*0503, Cw*0504, Cw*0602, Cw*0603, Cw*0604, Cw*0605, and Cw*0202. *0606, Cw*0607, Cw*0707, Cw*0709, Cw*1204, Cw*1205, Cw*1207, Cw*1404, Cw*1502, Cw*1503, Cw*1504, Cw*1505, Cw*1506, Cw*1508, Cw*1509, Cw*1510, Cw*1511, Cw*1602, Cw*1701, Cw*1702, Cw*1703, Cw*1801, and Cw*1802. Other HLA-C2 alleles are known in the art. See, for example, the IPD-IMGT/HLA database.

The term "HLA-B" refers to the HLA class I heavy chain gene. The HLA-B receptor is a heterodimer comprising the mature HLA-B gene product heavy chain and the β2-microglobulin light chain. The heavy chain is approximately 45 kDa, and its gene contains eight exons. Typically, exon 1 encodes the leader peptide, exons 2 and 3 encode the α-1 and α-2 domains, both of which bind to the peptide, exon 4 encodes the α-3 domain, exon 5 encodes the transmembrane region, and exons 6 and 7 encode the cytoplasmic tail region. Polymorphisms within exons 2 and 3 typically determine the peptide-binding specificity of each class I molecule. Additional information about HLA-B can be found, for example, under UniProt accession number P01889. The Bw4 or Bw6 epitopes are expressed by almost all HLA-B molecules; Bw4 is also present on some HLA-A proteins (e.g., HLA-A*24:02, -A*32:01, and -A*23:01).

The term "HLA-Bw4" refers to a class I HLA allele characterized by the Bw4 epitope within the α-1 helix. The Bw4 epitope is typically defined by five residues within the α-1 helix (i.e., positions 77, 80, 81, 82, and 83), which serologically distinguishes it from the Bw6 epitope. HLA-Bw4 molecules (such as HLA-B*57:01 or HLA-B*15:13) are characterized by the presence of Asn77, Ile80, Ala81, Leu82, and Arg83. Although residues 82 and 83 of the Bw4 sequence are conserved, the remaining residues can vary to produce up to eight different Bw4 motifs. As used herein, the term includes HLA-B or HLA-A molecules containing the Bw4 epitope.

Unless otherwise specified, the terms “cytotoxic cell immunoglobulin-like receptor 2DL3” and “KIR2DL3” refer to any naturally occurring KIR2DL3 from any vertebrate source, including mammals such as primates (e.g., humans) and rodents (e.g., mice and rats). The term covers “full-length” unprocessed KIR2DL3, as well as any form of KIR2DL3 produced through cellular processing. The term also covers naturally occurring variants of KIR2DL3, such as splice variants or allelic variants. KIR2DL3 is a repressive KIR gene that recognizes HLA-C molecules (e.g., HLA-C1 molecules) and certain HLA-B molecules (see, for example, Pende et al., Front. Immunol. doi:10.3389/fimmu.2019.01179,2019). KIR2DL3 is also known in the art as CD158 antigen-like family member B2, KIR-023GB, cytotoxic inhibitory receptor cl2-3, NKAT2a, NKAT2b, natural killer-associated transcript 2, p58 natural killer cell receptor clone CL-6, p58.2 MHC class I specific NK receptor, and CD158b2. Additional information about human KIR2DL3 can be found at NCBI Gene ID: 3804. The nucleotide sequence of an exemplary human KIR2DL3 is shown under NCBI Reference Sequence: NM_015868.3. The amino acid sequence encoded by the exemplary human KIR2DL3 gene is shown under UniProt accession number P43628-1.

Unless otherwise specified, the terms “killer cell immunoglobulin-like receptor 3DL1” and “KIR3DL1” refer to any naturally occurring KIR3DL1 from any vertebrate source, including mammals such as primates (e.g., humans) and rodents (e.g., mice and rats). The term covers “full-length” unprocessed KIR3DL1 as well as any form of KIR3DL1 produced through cellular processing. The term also covers naturally occurring variants of KIR3DL1, such as splice variants or allelic variants. KIR3DL1 is a repressive KIR gene that recognizes HLA-B molecules (e.g., HLA-Bw4 molecules) and some carrying allotypes of HLA-A Bw4. KIR3DL1 is also referred to in the art as CD158 antigen-like family member E, HLA-BW4-specific repressive NK cell receptor, natural killer-associated transcript 3 (NKAT-3), p70 natural killer cell receptor clones CL-2/CL-11, and CD158e. Additional information about human KIR3DL1 is available at NCBI Gene ID: 3811. The nucleotide sequence of the exemplary human KIR3DL1 is shown under NCBI Reference Sequence: NM_013289.3. The amino acid sequence encoded by the exemplary human KIR3DL1 gene is shown under UniProt Accession Number P43629-1.

The terms "natural killer cells" and "NK cells" refer to a class of lymphocytes in the innate immune system that can detect and eliminate cells such as cancer cells. NK cells include, for example, CD56 ^bright (also known as CD56 ^high ) cells, which make up the majority of NK cells and are found in the bone marrow, secondary lymphoid tissues, liver, and skin, and CD56 ^dim (also known as CD56 ^low ) cells, which are mainly found in the peripheral blood system and are characterized by cytotoxic capabilities. CD56 ^dim NK cells are usually CD16 positive and can be called CD56 ^dim CD16 ^bright NK cells; CD56 ^bright cells can be converted into CD56 ^dim cells by acquiring CD16.

The term "PD-1 axis binding antagonist" refers to a molecule that inhibits the interaction between a PD-1 axis binding partner and one or more of its binding partners to eliminate T cell dysfunction resulting from signal transduction along the PD-1 signaling axis, resulting in the restoration or enhancement of T cell function (e.g., proliferation, cytokine production, and/or target cell killing). As used herein, PD-1 axis binding antagonists include PD-L1 binding antagonists, PD-1 binding antagonists, and PD-L2 binding antagonists. In some cases, PD-1 axis binding antagonists include either PD-L1 binding antagonists or PD-1 binding antagonists. In a preferred aspect, the PD-1 axis binding antagonist is a PD-L1 binding antagonist.

The term "PD-L1 binding antagonist" refers to a molecule that reduces, blocks, inhibits, eliminates, or interferes with signal transduction resulting from the interaction of PD-L1 with one or more of its binding partners (such as PD-1 and/or B7-1). In some cases, a PD-L1 binding antagonist is a molecule that inhibits the binding of PD-L1 with its binding partners. In one specific aspect, a PD-L1 binding antagonist inhibits the binding of PD-L1 to PD-1 and/or B7-1. In some cases, PD-L1 binding antagonists include anti-PD-L1 antibodies, their antigen-binding fragments, immunoadhesins, fusion proteins, oligopeptides, and other molecules that reduce, block, inhibit, eliminate, or interfere with signal transduction resulting from the interaction of PD-L1 with one or more of its binding partners (such as PD-1 and/or B7-1). In one scenario, a PD-L1 binding antagonist reduces negative co-stimulatory signals mediated by PD-L1 signaling, either mediated by or through cell surface proteins expressed on T lymphocytes, thereby reducing dysfunction of dysfunctional T cells (e.g., enhancing effector responses to antigen recognition). In some cases, the PD-L1 binding antagonist binds to PD-L1. In some cases, the PD-L1 binding antagonist is an anti-PD-L1 antibody (e.g., an anti-PD-L1 antagonist antibody). Exemplary anti-PD-L1 antagonist antibodies include atezolizumab, MDX-1105, MEDI4736 (durvalumab), MSB0010718C (avelumab), SHR-1316, CS1001, envafolimab, TQB2450, ZKAB001, LP-002, CX-072, and IMC-001. The following are listed: KL-A167, APL-502, cosibelimab, lodapolimab, FAZ053, TG-1501, BGB-A333, BCD-135, AK-106, LDP, GR1405, HLX20, MSB2311, RC98, PDL-GEX, KD036, KY1003, YBL-007, and HS-636. In some respects, anti-PD-L1 antibodies are atezolizumab, MDX-1105, MEDI4736 (dvorumab), or MSB0010718C (averumab). In one specific respect, the PD-L1 binding antagonist is MDX-1105. In another specific respect, the PD-L1 binding antagonist is MEDI4736 (dvorumab). In another specific aspect, the PD-L1 binding antagonist is MSB0010718C (avermab). In other aspects, the PD-L1 binding antagonist can be a small molecule, such as GS-4224, INCB086550, MAX-10181, INCB090244, CA-170, or ABSK041, which in some cases can be administered orally. Other exemplary PD-L1 binding antagonists include AVA-004, MT-6035, VXM10, LYN192, GB7003, and JS-003. In a preferred aspect, the PD-L1 binding antagonist is atezolizumab.

The term "PD-1 binding antagonist" refers to a molecule that reduces, blocks, inhibits, eliminates, or interferes with signal transduction resulting from the interaction of PD-1 with one or more of its binding partners (such as PD-L1 and/or PD-L2). PD-1 (programmed cell death 1) is also referred to in the art as "programmed cell death 1," "PDCD1," "CD279," and "SLEB2." Exemplary human PD-1 is shown in UniProtKB/Swiss-Prot accession number Q15116. In some cases, a PD-1 binding antagonist is a molecule that inhibits the binding of PD-1 with one or more of its binding partners. In one specific aspect, a PD-1 binding antagonist inhibits the binding of PD-1 to PD-L1 and/or PD-L2. For example, PD-1 binding antagonists include anti-PD-1 antibodies, their antigen-binding fragments, immunoadhesins, fusion proteins, oligopeptides, and other molecules that reduce, block, inhibit, eliminate, or interfere with signal transduction resulting from the interaction of PD-1 with PD-L1 and/or PD-L2. In one case, the PD-1 binding antagonist reduces negative co-stimulatory signals mediated by PD-1 signaling, either mediated by or through cell surface proteins expressed on T lymphocytes, thereby reducing dysfunction of dysfunctional T cells (e.g., enhancing effector responses to antigen recognition). In some cases, the PD-1 binding antagonist binds to PD-1. In some cases, the PD-1 binding antagonist is an anti-PD-1 antibody (e.g., an anti-PD-1 antagonist antibody). Exemplary anti-PD-1 antagonist antibodies include nivolumab, pembrolizumab, MEDI-0680, PDR001 (spartazumab), REGN2810 (cimipril), BGB-108, palolizumab, camrelizumab, sintilimab, tislelizumab, toripalimab, dotalimab, refulimab, sasanlimab, penexazol, CS1003, HLX10, SCT-I10A, and cepalim Monoclonal antibodies, including batitimab, genolumab, BI 754091, cilimab, YBL-006, BAT1306, HX008, buglimab, AMG 404, CX-188, JTX-4014, 609A, Sym021, LZM009, F520, SG001, AM0001, ENUM 244C8, ENUM 388D4, STI-1110, AK-103, and hAb21. In one specific aspect, the PD-1 binding antagonist is MDX-1106 (nivolumab). In another specific aspect, the PD-1 binding antagonist is MK-3475 (pembrolizumab). In yet another specific aspect, the PD-1 binding antagonist is a PD-L2 fusion protein, such as AMP-224. In another specific aspect, the PD-1 binding antagonist is MED1-0680. In another specific aspect, the PD-1 binding antagonist is PDR001 (spartazolizumab). In another specific aspect, the PD-1 binding antagonist is REGN2810 (cimiprimab). In another specific aspect, the PD-1 binding antagonist is BGB-108. In another specific aspect, the PD-1 binding antagonist is palolizumab. In another specific aspect, the PD-1 binding antagonist is camrelizumab. In another specific aspect, the PD-1 binding antagonist is sintilimab. In another specific aspect, the PD-1 binding antagonist is tislelizumab. In another specific aspect, the PD-1 binding antagonist is toripalimab. Other additional exemplary PD-1 binding antagonists include BION-004, CB201, AUNP-012, ADG104, and LBL-006.

The term "PD-L2 binding antagonist" refers to a molecule that reduces, blocks, inhibits, eliminates, or interferes with signal transduction resulting from the interaction of PD-L2 with one or more of its binding partners (such as PD-1). PD-L2 (programmed cell death ligand 2) is also referred to in the art as "programmed cell death 1 ligand 2," "PDCD1LG2," "CD273," "B7-DC," "Btdc," and "PDL2." Exemplary human PD-L2 is shown in UniProtKB/Swiss-Prot accession number Q9BQ51. In some cases, a PD-L2 binding antagonist is a molecule that inhibits the binding of PD-L2 with one or more of its binding partners. In one specific aspect, a PD-L2 binding antagonist inhibits the binding of PD-L2 to PD-1. Exemplary PD-L2 antagonists include anti-PD-L2 antibodies, their antigen-binding fragments, immunoadhesins, fusion proteins, oligopeptides, and other molecules that reduce, block, inhibit, eliminate, or interfere with signaling generated by the interaction of PD-L2 with one or more of its binding partners (such as PD-1). In one aspect, the PD-L2 binding antagonist reduces negative co-stimulatory signals mediated by PD-L2 signaling, mediated by or through cell surface proteins expressed on T lymphocytes, thereby reducing dysfunction of dysfunctional T cells (e.g., enhancing effector responses to antigen recognition). In some aspects, the PD-L2 binding antagonist binds to PD-L2. In some aspects, the PD-L2 binding antagonist is an immunoadhesin. In other aspects, the PD-L2 binding antagonist is an anti-PD-L2 antagonist antibody.

The terms “programmed cell death ligand 1” and “PD-L1” refer herein to the natural sequence human PD-L1 polypeptide. The natural sequence PD-L1 polypeptide is provided under Uniprotocol accession number Q9NZQ7. For example, the natural sequence PD-L1 may have the amino acid sequence described in Uniprotocol accession number Q9NZQ7-1 (isomer 1). In another example, the natural sequence PD-L1 may have the amino acid sequence described in Uniprotocol accession number Q9NZQ7-2 (isomer 2). In yet another example, the natural sequence PD-L1 may have the amino acid sequence described in Uniprotocol accession number Q9NZQ7-3 (isomer 3). PD-L1 is also referred to in the art as “programmed cell death 1 ligand 1”, “PDCD1LG1”, “CD274”, “B7-H”, and “PDL1”.

When referring to residues in the variable domain (approximately residues 1-107 of the light chain and residues 1-113 of the heavy chain), the Kabat numbering system is typically used (e.g., Kabat et al., Sequences of Immunological Interest. 5th ed., U.S. Department of Health and Human Services, National Institutes of Health, Bethesda, MD (1991)). When referring to residues in the constant region of the immunoglobulin heavy chain, the “EU numbering system” or “EU index” is typically used (e.g., the EU index reported by Kabat et al. above). The “EU index described by Kabat” refers to the residue numbering of human IgG1 EU antibodies.

For the purposes of this article, “atezolizumab” is an Fc-engineered, humanized, non-glycosylated IgG1 kappa immunoglobulin that binds to PD-L1 and contains the heavy chain sequence of SEQ ID NO:1 and the light chain sequence of SEQ ID NO:2. Atezolizumab contains a single amino acid substitution (asparagine to alanine) at position 297 on the heavy chain (N297A), using the EU number of the amino acid residues in the Fc region, which results in a non-glycosylated antibody with minimal binding to the Fc receptor. Atezolizumab is also described in: WHO Drug Information (International Nonproprietary Names for Medicinal Substances), Proposed INN: List 112, Volume 28, Issue 4, published on January 16, 2015 (see page 485).

The terms “cancer” and “cancerous” refer to or describe a physiological condition in mammals typically characterized by uncontrolled cell growth. Cancer includes both solid tumor cancers and non-solid tumor cancers. Examples of cancer include, but are not limited to, carcinoma, lymphoma, blastoma, sarcoma, and leukemia or lymphoid malignancies. More specific examples of such cancers include, but are not limited to: bladder cancer (e.g., urothelial carcinoma (UC), including metastatic UC (mUC); muscle-invasive bladder cancer (MIBC) and non-muscle-invasive bladder cancer (NMIBC)); kidney or renal cell carcinoma (e.g., renal cell carcinoma (RCC)); lung cancer, including small cell lung cancer, non-small cell lung cancer, lung adenocarcinoma, and squamous cell carcinoma; urinary tract cancer; breast cancer (e.g., HER2+ breast cancer and triple-negative breast cancer (TNBC), where TNBC refers to estrogen receptor (ER-), progesterone receptor (PR-), and HER2 (H+) receptors). ER2- (negative); prostate cancer, such as castration-resistant prostate cancer (CRPC); peritoneal cancer; hepatocellular carcinoma; gastric/stomach cancer, including gastrointestinal cancer and gastrointestinal stromal carcinoma; pancreatic cancer (e.g., pancreatic ductal adenocarcinoma (PDAC)); glioblastoma; cervical cancer; ovarian cancer; liver cancer (e.g., hepatocellular carcinoma (HCC)); hepatocellular carcinoma; colon cancer; rectal cancer; colorectal cancer; endometrial cancer or uterine cancer; salivary gland cancer; prostate cancer; vulvar cancer; thyroid cancer; liver cancer; anal cancer; penile cancer; melanoma. This includes superficial diffuse melanoma, malignant lentigines melanoma, peripheral macular malignant melanoma, and nodular melanoma; multiple myeloma and B-cell lymphoma (including low-grade/follicular non-Hodgkin lymphoma (NHL); small lymphocytic (SL) NHL; intermediate/follicular NHL; intermediate diffuse NHL; high-grade immunoblastic NHL; high-grade lymphocytic NHL; high-grade small non-lytic cell NHL; giant mass NHL; mantle cell lymphoma; AIDS-related lymphoma; and Waldenström's macroglobulinemia). Macroglobulinemia; chronic lymphocytic leukemia (CLL); acute lymphoblastic leukemia (ALL); acute myeloid leukemia (AML); hairy cell leukemia; chronic myeloid leukemia (CML); post-transplant lymphoproliferative disorder (PTLD); and myelodysplastic syndromes (MDS), as well as abnormal angiogenesis associated with nevus hamartomatosis, edema (such as in diseases associated with brain tumors), Meigs' syndrome, brain cancer, head and neck cancer, and related metastases. In one case, the cancer is lung cancer (e.g., NSCLC, such as non-squamous NSCLC or squamous NSCLC). In another case, the cancer is kidney cancer (e.g., RCC). The cancer may be locally advanced or metastatic. In some cases, the cancer is locally advanced. In others, the cancer is metastatic. In some cases, the cancer is stage IV cancer. In some cases, the cancer may be unresectable (e.g., unresectable locally advanced or metastatic cancer).

As used herein, the term “tumor” refers to all proliferative cell growth and proliferation, whether malignant or benign, as well as all precancerous and cancerous cells and tissues. The terms “cancer,” “cancerous,” “proliferative disorder,” “proliferative lesion,” and “tumor” are not mutually exclusive in this text.

The terms "cell proliferation disorder" and "proliferative disorder" refer to conditions associated with some degree of abnormal cell proliferation. In one embodiment, the cell proliferation disorder is cancer. In another embodiment, the cell proliferation disorder is a tumor.

The terms "B-cell proliferative disorder" or "B-cell malignancy" refer to disorders associated with some degree of abnormal B-cell proliferation and include, for example, lymphoma, leukemia, myeloma, and myelodysplastic syndromes. In one embodiment, a B-cell proliferative disorder is a lymphoma, such as non-Hodgkin lymphoma (NHL), including, for example, DLBCL (e.g., relapsed or refractory DLBCL), FL (e.g., relapsed or refractory FL or transforming FL), or MCL. In another embodiment, a B-cell proliferative disorder is a leukemia, such as chronic lymphocytic leukemia (CLL). In yet another embodiment, a B-cell proliferative disorder is central nervous system lymphoma (CNSL).

As used herein, “treatment” includes effective cancer treatment with an effective amount of a therapeutic agent (e.g., a PD-1 axis binding antagonist (e.g., atezolizumab) or an NK cell-directed therapy) or a combination of therapeutic agents (e.g., a PD-1 axis antagonist and one or more additional therapeutic agents, such as taxanes (e.g., nab-paclitaxel or paclitaxel), platinum-based chemotherapy agents (e.g., carboplatin), anti-angiogenic agents (e.g., anti-VEGF antibodies, such as bevacizumab), and/or NK cell-directed therapy). Treatment in this article specifically includes adjuvant therapy, neoadjuvant therapy, non-metastatic cancer therapy (e.g., locally advanced cancer therapy), and metastatic cancer therapy. Treatment can be first-line treatment (e.g., the patient may have been previously untreated or has not received prior systemic therapy), or second-line or subsequent treatment.

In this document, “effective amount” refers to the amount of a therapeutic agent (e.g., a PD-1 axis binding antagonist (e.g., atezolizumab) or an NK cell-directed therapy that achieves the therapeutic outcome) or a combination of therapeutic agents (e.g., a PD-1 axis antagonist and one or more additional therapeutic agents, such as taxanes (e.g., nab-paclitaxel or paclitaxel), platinum-based chemotherapy agents (e.g., carboplatin), anti-angiogenic agents (e.g., bevacizumab), and/or NK cell-directed therapy). In some instances, the effective amount of a therapeutic agent or combination of therapeutic agents is the amount of a drug or combination of drugs that achieves the clinical endpoint of improved survival (e.g., disease-free survival (DFS), progression-free survival (PFS), and/or overall survival (OS)), improved overall response rate (ORR), complete response (CR), pathological complete response (pCR), partial response (PR), and/or improved duration of response (DOR). Improvement (e.g., in terms of response rate (e.g., ORR, CR, and/or PR), survival (e.g., PFS and/or OS) or DOR) can be relative to a suitable reference treatment, such as treatment excluding a PD-1 axis binding antagonist and/or treatment excluding taxanes (e.g., nab-paclitaxel or paclitaxel), platinum-based chemotherapy agents (e.g., carboplatin), anti-angiogenic agents (e.g., bevacizumab), and/or NK cell-directed therapy agents. In some respects, improvement can be relative to treatment using a regimen that does not include a PD-1 axis binding antagonist.

As used in this article, "complete remission" and "CR" refer to the disappearance of all target lesions.

As used in this article, "partial remission" and "PR" refer to a reduction of at least 30% in the SLD of the target lesion, with reference to the sum of the longest diameters (SLD) at baseline before treatment.

As used in this article, “overall response rate”, “objective response rate” and “ORR” are interchangeable and refer to the sum of complete response rate and partial response rate.

As used in this article, “progression-free survival” and “PFS” refer to the length of time during and after treatment when cancer does not worsen. PFS can include the amount of time a patient has achieved complete remission (CR) or partial remission (PR), and the amount of time a patient has experienced disease stabilization. In some instances, PFS can be determined using the Recognition of Clinical Efficacy in Solid Tumors (RECIST) version 1.1. For example, in some cases, PFS is defined as the time between the randomization date and the date of first recorded disease progression or death, whichever occurs first.

As used in this article, “overall survival” and “OS” refer to the length of time a patient remains alive from the date of diagnosis or the start of treatment for a disease (e.g., cancer). For example, in some cases, OS is defined as the time between the randomization date and the date of death from any cause.

As used in this article, the terms “duration of response” and “DOR” refer to the length of time from the time of recording to the tumor response until disease progression or death (whichever occurs first).

As used herein, the term "chemotherapeutic agent" refers to a compound that can be used to treat cancer (e.g., NSCLC). Examples of chemotherapeutic agents include EGFR inhibitors (including small molecule inhibitors such as erlotinib (Genentech/OSIPharm.); PD 183805 (CI 1033, 2-acrylamide, N-[4-[(3-chloro-4-fluorophenyl)amino]-7-[3-(4-morpholinyl)propoxy]-6-quinazolinyl]-, dihydrochloride, Pfizer Inc.); ZD1839, gefitinib 4-(3'-chloro-4'-fluoroaniline)-7-methoxy-6-(3-morpholinopropoxy)quinazolin, AstraZeneca); ZM 105180 ((6-amino-4-(3-methylphenyl-amino)-quinazoline, Zeneca); BIBX-1382 (N8-(3-chloro-4-fluoro-phenyl)-N2-(1-methyl-piperidin-4-yl)-pyrimidinyl[5,4-d]pyrimidin-2,8-diamine, Boehringer Ingelheim); PKI-166 ((R)-4-[4-[(1-phenylethyl)amino]-1H-pyrrolidone[2,3-d]pyrimidin-6-yl]-phenol); (R)-6-(4-hydroxyphenyl)-4-[(1-phenylethyl)amino]-7H- Pyrrolo[2,3-d]pyrimidine); CL-387785(N-[4-[(3-bromophenyl)amino]-6-quinazolinyl]-2-butynamide); EKB-569(N-[4-[(3-chloro-4-fluorophenyl)amino]-3-cyano-7-ethoxy-6-quinolinyl]-4-(dimethylamino)-2-butenamide)(Wyeth); AG1478(Pfizer); AG1571(SU 5271; Pfizer); and dual EGFR/HER2 tyrosine kinase inhibitors, such as lapatinib (GSK572016 or N-[ 3-Chloro-4-[(3-fluorophenyl)methoxy]phenyl]-6[5[[[2-methylsulfonyl)ethyl]amino]methyl]-2-furanyl]-4-quinazolinamine); tyrosine kinase inhibitors (e.g., EGFR inhibitors; small molecule HER2 tyrosine kinase inhibitors, such as TAK165 (Takeda); CP-724,714, oral selective inhibitors of ErbB2 receptor tyrosine kinases (Pfizer and OSI); dual HER inhibitors that preferentially bind to EGFR but simultaneously inhibit cells overexpressing HER2 and EGFR, such as EKB 569 (available from Wy eth); PKI-166 (Novartis); pan-HER inhibitors, such as cananetinib (CI-1033; Pharmacia); Raf-1 inhibitors, such as the antisense agent ISIS-5132 (ISIS Pharmaceuticals) that inhibits Raf-1 signaling; non-HER-targeting tyrosine kinase inhibitors, such as imatinib mesylate (Glaxo SmithKline); multi-targeting tyrosine kinase inhibitors, such as sunitinib (Pfizer); VEGF receptor tyrosine kinase inhibitors, such as vatalani (eth); PTK787/ZK222584 (Novartis/Schering AG); MAPK extracellular kinase I inhibitor CI-1040 (Pharmacia); quinazolines, such as PD 153035, 4-(3-chloroaniline)quinazoline; pyridopyrimidines; pyrimidines; pyrrolopyrimidines, such as CGP 59326, CGP 60261 and CGP 62706; pyrrolopyrimidines, 4-(phenylamino)-7H-pyrrolo[2,3-d]pyrimidine; curcumin (difluoroformylmethane, 4,5-bis(4-fluoroaniline) Phthalimide; Tyrosine containing a nitrothiophene moiety; PD-0183805 (Warner-Lamber); antisense molecules (e.g., molecules that bind to HER-encoding nucleic acids); quinoxalines (US Patent No. 5,804,396); tyrosine phosphorylation inhibitors (US Patent No. 5,804,396); ZD6474 (Astra Zeneca); PTK-787 (Novartis/Schering AG); pan-HER inhibitors, such as CI-1033 (Pfizer); Affinitac ( ISIS 3521; Isis/Lilly); PKI 166 (Novartis); GW2016 (Glaxo SmithKline); CI-1033 (Pfizer); EKB-569 (Wyeth); Semaxinib (Pfizer); ZD6474 (AstraZeneca); PTK-787 (Novartis/Schering AG); INC-1C11 (Imclone) and rapamycin (sirolimus); proteasome inhibitors, such as bortezomib ( Millennium Pharm.); Disulfiram; Epigallocatexin; Halosporamide A; Carfilzomib; 17-AAG (Geldmycin); Rhizocarpine; Lactate Dehydrogenase A (LDH-A); Fulvestrant (AstraZeneca); Letrozole (Novartis), Finazine (Novartis); Oxaliplatin (Sanofi); 5-FU (5-fluorouracil); Formicoyltetrahydrofolate; Lonafanib (SCH66336); Sorafenib (Bayer Labs); AG1478, Alkylating agents, such as thiotepa and cyclophosphamide; Alkyl sulfonates, such as busulfan, indomethacin, and piperosulfan; azacyclopropane derivatives, such as benzotipane, carboquinone, metopepane, and urotepiperazine; ethylamines and methylmelamines, including hexamethylmelamine, triethylmelamine, triethylphosphamide, triethylthiophosphamide, and tris(hydroxymethylmelamine); anomeric lactones (especially bratasine and bratasineone); camptothecin (including topotecan and irinotecan); nematostatin; carlistatin; CC-1065 (including its synthetic analogues adorelasin, carzelecanin, and bizelecanin); nostocins (especially nostocin 1 and nostocin 8); corticosteroids. (Including prednisone and prednisolone); cyproterone acetate; 5α-reductase (including finasteride and dutasteride); vorinostat, romidesin, ubiquitin, valproic acid, moxistat; interleukin, talc, ducamycin (including synthetic analogs KW-2189 and CB1-TM1); eleutheroscin; hydatidine; styraxol; spongistatin; nitrogen mustards, such as chlorambucil, chlorpheniramine, chlorphosphatamide, estradiol, ifosfamide, methoxyfenozide, melphalan, neonitrogen, benzyl mustard cholesterol, prednisone, trelophosphamide, uramustine; nitrosoureas, such as carmustine, chlorambucil... Ureapromycin, formustine, lomustine, nimustine, and lanimustine; antibiotics, such as enediyne antibiotics (e.g., chachimycin, especially chachimycin γ1 and chachimycin ω1); danendomycin, including danendomycin A; bisphosphonates, such as clophosphonates; esmicin; and neo-cancer suppressant chromophores and associated chromophores (enediyne antibiotic chromophores), aclarubicin, actinomycin, amiodarone, azoserine, actinomycin, carrubicin, erythromycin, carcinomacin, chromomycin, actinomycin D, detoxin, 6-azido-5-oxo-L-leucine, morpholino-doxamycin, cyanomorpholino- - Doxorubicin, 2-pyrrolidine-doxorubicin and deoxydoxorubicin), epirubicin, isopycin, idarubicin, maceralomycin, mitomycin, such as mitomycin C, mycophenolic acid, nogamycin, olivomycin, pepromycin, methylmitomycin, puromycin, triterpenoid doxorubicin, rhodopsin, streptozotocin, streptozotocin, tuberculin, ubenimex, fenestrated statin, zorubicin; antimetabolites, such as methotrexate and 5-fluorouracil (5-FU); folic acid analogs, such as folate, methotrexate, pteroxate, trimethopterin; purine analogs, such as fludarabine, 6-mercaptopurine, thioimidine, thiopurine, thiouracil Guanine; pyrimidine analogues, such as ancitabine, azacitidine, 6-azouridine, carmoflurane, araciclovir, dideoxyuridine, deoxyfluorouridine, enoxabin, fluorouridine; androgens, such as capprotestone, drotalonone propionate, cyclothionol, meandrolone, testosterone; antiadrenergic drugs, such as aminoglutethimide, mitotane, trelostan; folic acid supplements, such as folinic acid; acetoglucan lactone; aldehyde phosphoramide glycoside; aminolevulinic acid; enuracil; acridine; betributazone; bismuth subcitrate; edaraxazole; desphosphonamide; colchicine; iminoquinone; ileonisyl; eletate; epothilone; ethoxyphenidate; gallium nitrate; hydroxyurea Lentinan; Clonidamine; Maytansin alkaloids, such as maytansin and anthraquinone; Mitoguanidine hydrazone; Mitoantrone; Mopiperol; Diamine nitrazepam; Pentostatin; Methamidomus acid; Pirarubicin; Loxoantrone; Podophyllotoxin; 2-Ethylhydrazine; Methylbenzylhydrazine; Polysaccharide iron complex (JHS Natural Products); Razosen; Rhizomycin; Schizotypalin; Germanium spiroamine; Alternaria ketoacid; Triaminoquinone; 2,2',2”-Trichlorotriethylamine; Trichoderma toxins (especially T-2mycin, Veracrulin A, Erythromycin A and Serpentin); Uranium; Vincaine; Dacarbazine; Mannitol mustard; dibromomannitol; dibromoeutherol; piperobromane; gasitocin; arabinoside (“Ara-C”); cyclophosphamide; thiotepa; chlorambucil; gemcitabine; 6-thioguanine; mercaptopurine; methotrexate; etoposide (VP-16); ifosfamide; mitoxantrone; novalong; teniposide; edastrexate; daunorubicin; aminopterin; capecitabine ibandronate; CPT-11; topoisomerase inhibitor RFS 2000; difluoromethylornithine (DMFO); retinoids, such as retinoic acid; and pharmaceutical salts, acids, prodrugs, and derivatives of any of the above.

Chemotherapy agents also include: (i) anti-hormonal agents that modulate or inhibit the effects of hormones on tumors, such as anti-estrogens and selective estrogen receptor modulators (SERMs), including, for example, tamoxifen (including tamoxifen citrate), raloxifene, droloxifene, iodoxyfene, 4-hydroxytamoxifen, trioxifene, raloxifene hydrochloride, LY117018, onapristone, and (toremifine citrate); (ii) aromatase inhibitors that inhibit aromatase. Preparations that regulate the production of estrogen by the adrenal glands, such as, for example, 4(5)-imidazole, aminoglutethimide, (medroxyprogesterone acetate), (exemestane; Pfizer), formestanie, fadrozole, (vorozole), (letrozole; Novartis), and (anastrozole; AstraZeneca); (iii) antiandrogens, such as flutamide, nilutamide, bicalutamide, leuprolide, and goserelin; Buserelin, tripterelin, medroxyprogesterone acetate, diethylstilbestrol, Premarin, fluorometholone, all trans-retinoic acid, fenretinide, and trisatabolin (a 1,3-dioxane cytosine analog); (iv) protein kinase inhibitors; (v) lipid kinase inhibitors; (vi) antisense oligonucleotides, especially those that inhibit gene expression in signaling pathways associated with abnormal cell proliferation, such as, for example, PKC-α, Ralf, and H-Ras; (vii) ribozymes, such as VEGF expression inhibitors (e.g., and HER2 expression inhibitors). Preparations; (viii) vaccines, such as gene therapy vaccines, and (ix) growth inhibitors, including vinblastine (e.g., vincristine and vinblastine), (vinorelbine), taxanes (e.g., paclitaxel, albumin-bound paclitaxel, and docetaxel), topoisomerase II inhibitors (e.g., doxorubicin, epirubicin, donomycin, etoposide, and bleomycin) and DNA alkylating agents (e.g., tamoxigenin, prednisone, dacarbazine, dichloromethyldiethylamine, cisplatin, methotrexate, 5-fluorouracil, and ara-C); and (x) pharmaceutical salts, acids, prodrugs, and derivatives of any of the above.

As used herein, the term "cytotoxic agent" means any agent that is harmful to cells (e.g., causing cell death, inhibiting proliferation, or otherwise impairing cell function). Cytotoxic agents include, but are not limited to, radioisotopes (e.g., radioisotopes of At ²¹¹ , I ¹³¹ , I ¹²⁵ , Y ⁹⁰ , Re ¹⁸⁶ , Re ¹⁸⁸ , Sm ¹⁵³ , Bi ²¹² , P ³² , Pb ²¹² , and Lu); chemotherapeutic agents; enzymes and fragments thereof, such as lysozymes; and toxins, such as small molecule toxins or enzyme-active toxins of bacterial, fungal, plant, or animal origin, including fragments and/or variants thereof. Exemplary cytotoxic agents may be selected from anti-microtubule agents, platinum coordination complexes, alkylating agents, antibiotics, topoisomerase II inhibitors, antimetabolites, topoisomerase I inhibitors, hormones and hormone analogs, signal transduction pathway inhibitors, non-receptor tyrosine kinase angiogenesis inhibitors, immunotherapeutic agents, pro-apoptotic agents, LDH-A inhibitors, fatty acid biosynthesis inhibitors, cell cycle signaling inhibitors, HDAC inhibitors, proteasome inhibitors, and cancer metabolism inhibitors. In one instance, the cytotoxic agent is a platinum-based chemotherapeutic agent (e.g., carboplatin or cisplatin). In one instance, the cytotoxic agent is an EGFR antagonist, such as N-(3-ethynylphenyl)-6,7-bis(2-methoxyethoxy)quinazoline-4-amine (e.g., erlotinib). In one instance, the cytotoxic agent is a RAF inhibitor, such as a BRAF and/or CRAF inhibitor. In one instance, the RAF inhibitor is vemurafenib. In one instance, the cytotoxic agent is a PI3K inhibitor.

As used herein, “taxane” is an agent (e.g., a diterpene) that can bind to tubulin to promote microtubule assembly and stabilization and/or prevent microtubule depolymerization. Exemplary taxanes include, but are not limited to, paclitaxel (i.e., CAS#33069-62-4), docetaxel (i.e., CAS#114977-28-5), larotaxel, cabazitaxel, miratataxel, testatataxel, and/or orataxel. Taxanes included herein also include taxoids 10-deacetylated baccatin III and/or their derivatives. In some embodiments, taxanes are albumin-coated nanoparticles (e.g., albumin-bound (nab)-paclitaxel (i.e., and/or nab-docetaxel (ABI-008)). In some embodiments, taxanes are nab-paclitaxel. In some embodiments, taxanes are formulated in (e.g.,) and/or (such as polysorbate 80 (e.g.,)). In some embodiments, taxane is taxane encapsulated in liposomes. In some embodiments, taxane is a prodrug form and/or conjugated form of taxane (e.g., DHA covalently conjugated with paclitaxel, polyglutamate paclitaxel, and/or linoleic acid paclitaxel). In some embodiments, paclitaxel is formulated to be substantially surfactant-free (e.g., in the absence of and/or (such as) paclitaxel).

Chemotherapy agents also include “platinum-based” chemotherapeutic agents, which contain organic compounds in which platinum is a component of the molecule. Typically, platinum-based chemotherapeutic agents are coordination complexes of platinum. Platinum-based chemotherapeutic agents are sometimes referred to in the art as “platinum-based drugs.” Examples of platinum-based chemotherapeutic agents include, but are not limited to, cisplatin, carboplatin, oxaliplatin, nedaplatin, triplatinum tetranitrate, phenanthriplatin, picoplatin, lipoplatin, and satraplatin. Platinum-based chemotherapeutic agents (e.g., cisplatin or carboplatin) may be administered in combination with one or more additional chemotherapeutic agents (e.g., nucleoside analogs, such as gemcitabine).

As used herein, “platinum-based chemotherapy” refers to a chemotherapy regimen that includes platinum-based chemotherapeutic agents. For example, platinum-based chemotherapy may include a combination of platinum-based chemotherapeutic agents (e.g., cisplatin or carboplatin) with one or more additional chemotherapeutic agents (e.g., nucleoside analogs (e.g., gemcitabine)).

"Anti-angiogenic agents" or "angiogenesis inhibitors" refer to small molecular weight substances, polynucleotides, polypeptides, isolated proteins, recombinant proteins, antibodies, or their conjugates or fusion proteins that directly or indirectly inhibit angiogenesis, vascularization, or adverse vascular permeability. It should be understood that anti-angiogenic agents include those agents that bind to and block the angiogenic activity of angiogenic factors or their receptors. Examples include anti-angiogenic antibodies or other antagonists against agents defined above, such as antibodies against VEGF-A or VEGF-A receptors (e.g., KDR receptors or Flt-1 receptors), and anti-PDGFR inhibitors such as GLEEVEC ^™ (imatinib mesylate). Anti-angiogenic agents also include natural angiogenesis inhibitors, such as angiostatin, endostatin, etc. See, for example, Klagsbrun and D'Amore, Annu. Rev. Physiol., 53:217-39 (1991); Streit and Detmar, Oncogene, 22:3172-3179 (2003) (for example, Table 3 lists anti-angiogenic therapies for malignant melanoma); Ferrara and Alitalo, Nature Medicine 5(12):1359-1364 (1999); Tonini et al., Oncogene, 22:6549-6556 (2003) and Sato Int. J. Clin. Oncol., 8:200-206 (2003).

"Anti-VEGF antibody" is an antibody that binds to VEGF with sufficient affinity and specificity. In some embodiments, the antibody will have a sufficiently high binding affinity to VEGF; for example, the antibody may bind hVEGF with a Kd value between 100 nM and 1 pM. Antibody affinity can be determined, for example, by surface plasmon resonance-based assays (such as those described in PCT application publication WO2005/012359), enzyme-linked immunosorbent assays (ELISA), and competitive assays (e.g., radioimmunoassay (RIA)).

In some embodiments, anti-VEGF antibodies can be used as therapeutic agents targeting and interfering with VEGF activity in diseases or conditions in which it is involved. Furthermore, other bioactivity assays can be performed on the antibody, for example, to evaluate its effectiveness as a therapeutic agent. Such assays are known in the art and depend on the intended use of the target antigen and the antibody. Examples include HUVEC inhibition assays; tumor cell growth inhibition assays (e.g., as described in WO 89/06692); antibody-dependent cytotoxicity (ADCC) and complement-mediated cytotoxicity (CDC) assays (US Patent No. 5,500,362); and agonist activity or hematopoietic activity assays (see WO 95/27062). Anti-VEGF antibodies generally do not bind to other VEGF homologs (such as VEGF-B or VEGF-C) or other growth factors (such as P1GF, PDGF, or bFGF). In one embodiment, the anti-VEGF antibody is a monoclonal antibody that binds to the same epitope as monoclonal anti-VEGF antibody A4.6.1 generated from hybridoma ATCC HB 10709. In another embodiment, the anti-VEGF antibody is a recombinant humanized anti-VEGF monoclonal antibody produced according to Presta et al. (Cancer Res. 57:4593-4599, 1997), including but not limited to an antibody called bevacizumab (BV).

The anti-VEGF antibody “bevacizumab”, also known as “rhuMAb VEGF”, “BV”, or a recombinant humanized anti-VEGF monoclonal antibody produced by Presta et al. (Cancer Res. 57:4593-4599, 1997), comprises a mutated human IgG1 framework region and an antigen-binding complementarity-determining region derived from mouse anti-hVEGF monoclonal antibody A.4.6.1 that blocks the binding of human VEGF to its receptor. Approximately 93% of the amino acid sequence of bevacizumab, including the majority of the framework region, is derived from human IgG1, and approximately 7% of the sequence is derived from mouse antibody A4.6.1. Bevacizumab has a molecular weight of approximately 149,000 Daltons and is glycosylated. Bevacizumab and other humanized anti-VEGF antibodies are further described in U.S. Patent No. 6,884,879, issued February 26, 2005, the entire disclosure of which is expressly incorporated herein by reference. Other preferred antibodies include G6 or B20 series antibodies (e.g., G6-31, B20-4.1), as described in PCT application publication number WO 2005/012359. For other preferred antibodies, see U.S. Patent Nos. 7,060,269, 6,582,959, 6,703,020, and 6,054,297; WO98/45332; WO 96/30046; WO94/10202; EP 0666868B1; U.S. Patent Application Publication Nos. 2006009360, 20050186208, 20030206899, 20030190317, 20030203409, and 20050112126; and Popkov et al. (Journal of Immunological Methods 288:149-164, 2004). Other preferred antibodies include antibodies that bind to functional epitopes on human VEGF containing residues F17, M18, D19, Y21, Y25, Q89, 191, K101, E103, and C104, or alternatively, containing residues F17, Y21, Q22, Y25, D63, 183, and Q89.

The term “NK cell-targeted therapy” refers to an agent that includes NK cells or regulates the number, activity, or function of NK cells. In some cases, NK cell-targeted therapy includes adoptive cell transfer (e.g., using allogeneic NK cells, autologous NK cells, off-the-shelf NK cells, or chimeric antigen receptor (CAR)-NK cells), cytokine therapy, NK cell conjugates (e.g., bispecific killer cell conjugates (BiKE), trispecific killer cell conjugates (TriKE), or tetraspecific killer cell conjugates (TetraKE)), NK cell checkpoint receptor antagonists, or oncolytic viruses. Exemplary NK cell-targeted therapy agents are described, for example, in Hodgins et al., J. Clin. Invest. 129(9):3499-3510, 2019.

The term "NK cell conjugate" refers to a molecule that, for example, causes NK cells and tumor cells to aggregate by binding to one or more targets on the surface of NK cells (e.g., proteins, such as receptors) (e.g., CD16, NKG2D, SLAM family proteins, NKp30, NKp44, or NKp46) and one or more targets on the surface of tumor cells (e.g., proteins, such as receptors) (e.g., tumor antigens, including CD30, CD33, EGFR, BCMA, or any tumor antigens described in Table C). NK cell conjugates can be multispecific, such as bispecific, trispecific, or tetraspecific. For a specific target, NK cell conjugates can be multivalent, such as bivalent, trivalent, tetravalent, pentavalent, or hexavalent. For example, an NK cell conjugate for CD16A can be at least bivalent, i.e., containing at least two CD16A antigen-binding moieties. In some instances, NK cell conjugates include at least a first targeting domain that binds to an epitope on NK cells and at least a second targeting domain that binds to a different target (e.g., a tumor antigen (e.g., any tumor antigen described in Table C)). Exemplary NK cell conjugates are described, for example, in WO 2019/198051; Reusch et al., mAbs, 6(3):727-738; 2014; US7129330B1; US9035026B2; WO0111059A1; Treder et al., Journal of Clinical Oncology, 34(15suppl), 2016; and Ellwanger et al., J Immunother Cancer, 3(Suppl 2):219, 2015. In some embodiments, the NK cell binder is a nanoparticle-based NK cell binder, such as a nanoparticle-based trispecific NK cell binder (nano-TriNKE); see, for example, Au et al., Science Advances 6(27):eaba8564, 2020. Exemplary NK cell binders include, for example, IPH6101 (Innate Pharma/Sanofi).

The term "patient" refers to a human patient. For example, a patient can be an adult.

The term "antibody" in this article specifically covers monoclonal antibodies (including full-length monoclonal antibodies), polyclonal antibodies, multispecific antibodies (e.g., bispecific antibodies), and antibody fragments, provided they exhibit the desired biological activity. In one case, the antibody is a full-length monoclonal antibody.

As used herein, the term IgG “isotype” or “subclass” refers to any subclass of immunoglobulins defined by the chemical and antigenic characteristics of the immunoglobulin constant region.

Antibodies (immunoglobulins) can be classified into different categories based on the amino acid sequence of their heavy chain constant domains. Immunoglobulins are mainly divided into five classes: IgA, IgD, IgE, IgG, and IgM, and some of them can be further subdivided into subclasses (isotypes), such as IgG1, IgG2, IgG3, IgG4, IgA1, and IgA2. The heavy chain constant domains corresponding to different classes of immunoglobulins are called α, γ, ε, γ, and μ, respectively. The subunit structures and three-dimensional conformations of different types of immunoglobulins are well known and are generally described in references such as Abbas et al., Cellular and Mol. Immunology, 4th edition (W.B. Saunders, Co., 2000). Antibodies can be part of a larger fusion molecule formed by the covalent or non-covalent association of an antibody with one or more other proteins or peptides.

The terms “full-length antibody,” “intact antibody,” and “whole antibody” are used interchangeably in this document and refer to an antibody in its essentially complete form, rather than an antibody fragment as defined below. The term refers to an antibody containing the Fc region.

The term "Fc region" used herein is used to define the C-terminal region of an immunoglobulin heavy chain that comprises at least a portion of a constant region. This term includes both native sequence Fc regions and variant Fc regions. In one aspect, the human IgG heavy chain Fc region extends from Cys226 or Pro230 to the C-terminus of the heavy chain. However, antibodies produced by host cells can undergo post-translational cleavage of one or more (particularly one or two) amino acids from the C-terminus of the heavy chain. Therefore, antibodies produced by host cells by expressing a specific nucleic acid molecule encoding the full-length heavy chain can comprise the full-length heavy chain, or said antibodies can comprise cleaved variants of the full-length heavy chain. This could be the case where the last two C-terminal amino acids of the heavy chain are glycine (G446) and lysine (K447). Therefore, the C-terminal lysine (Lys447) or C-terminal glycine (Gly446) and lysine (Lys447) of the Fc region may or may not be present. Unless otherwise indicated, the amino acid sequence of the heavy chain including the Fc region is represented herein as lacking a C-terminal lysine (Lys447). In one aspect, a heavy chain including the Fc region as specified herein is included in an antibody disclosed herein, the heavy chain containing an additional C-terminal glycine-lysine dipeptide (G446 and K447). In another aspect, a heavy chain including the Fc region as specified herein is included in an antibody disclosed herein, the heavy chain containing an additional C-terminal glycine residue (G446). In another aspect, a heavy chain including the Fc region as specified herein is included in an antibody disclosed herein, the heavy chain containing an additional C-terminal lysine residue (K447). In one embodiment, the Fc region contains a single amino acid substitution of N297A from the heavy chain. Unless otherwise specified herein, the amino acid residues in the Fc region or constant region are numbered according to the EU numbering system, also known as the EU index, as described in Kabat et al., Sequences of Proteins of Immunological Interest, 5th edition, Public Health Service, National Institutes of Health, Bethesda, MD, 1991.

"Naked antibody" refers to an antibody that is not conjugated to a heterologous moiety (e.g., a cytotoxic moiety) or a radiolabeled part. Naked antibodies may be present in pharmaceutical compositions.

An "antibody fragment" comprises a portion of a complete antibody, preferably including its antigen-binding region. - In some cases, the antibody fragments described herein are antigen-binding fragments. Examples of antibody fragments include Fab, Fab', F(ab') ₂ , and Fv fragments; bisomatic antibodies; linear antibodies; single-chain antibody molecules (e.g., scFv); and multispecific antibodies formed from antibody fragments.

As used herein, the term "monoclonal antibody" refers to an antibody obtained from a substantially homogeneous group of antibodies, meaning that, apart from possible variant antibodies (e.g., those containing naturally occurring mutations or generated during the production of the monoclonal antibody formulation, such variants are typically present in small quantities), the individual antibodies comprising this group are identical and/or bind to the same epitopes. In contrast to polyclonal antibody formulations, which typically comprise different antibodies targeting different determinants (epitaxes), each monoclonal antibody in a monoclonal antibody formulation targets a single determinant on the antigen. Therefore, the modifier "monoclonal" indicates that the antibody is characterized by being obtained from a substantially homogeneous group of antibodies and should not be interpreted as requiring the antibody to be produced by any particular method. For example, the monoclonal antibodies according to the invention can be prepared by a variety of techniques, including but not limited to hybridoma methods, recombinant DNA methods, phage display methods, and methods utilizing transgenic animals containing all or part of the human immunoglobulin loci.

As used herein, the term "hypervariant region" or "HVR" refers to the regions within the variable domain of an antibody that are hypervariable in sequence and determine antigen-binding specificity, such as the "complementarity-determining region" ("CDR").

Typically, an antibody contains six CDRs; three in the VH (CDR-H1, CDR-H2, CDR-H3) and three in the VL (CDR-L1, CDR-L2, CDR-L3). Exemplary CDRs in this document include:

(a) Highly variable rings appearing at the following amino acid residues: 26 to 32 (L1), 50 to 52 (L2), 91 to 96 (L3), 26 to 32 (H1), 53 to 55 (H2) and 96 to 101 (H3) (Chothia and Lesk, J.Mol.Biol.196:901-917(1987));

(b) CDRs present at amino acid residues 24-34 (L1), 50-56 (L2), 89-97 (L3), 31-35b (H1), 50-65 (H2), and 95-102 (H3) (Kabat et al., Sequences of Proteins of Immunological Interest, 5th ed., Public Health Service, National Institutes of Health, Bethesda, MD (1991)); and

(c) Antigen contacts appearing at the following amino acid residues: 27c to 36 (L1), 46 to 55 (L2), 89 to 96 (L3), 30 to 35b (H1), 47 to 58 (H2), and 93 to 101 (H3) (MacCallum et al., J. Mol. Biol. 262:732-745 (1996)). Unless otherwise specified, the CDR is determined according to the method described by Kabat et al., ibid. Those skilled in the art will understand that the CDR name may also be determined according to the method described by Chothia, ibid., McCallum, or any other scientifically accepted nomenclature system.

"Frame" or "FR" refers to the variable domain residues other than the complementarity-determining region (CDR). A variable domain FR typically consists of four FR domains: FR1, FR2, FR3, and FR4. Therefore, the CDR and FR sequences usually appear in the VH (or VL) as follows: FR1-CDR-H1(CDR-L1)-FR2-CDR-H2(CDR-L2)-FR3-CDR-H3(CDR-L3)-FR4.

The terms “Kabat-described variable domain residue numbering” or “Kabat-described amino acid position numbering” and their variations refer to the numbering system proposed in the aforementioned Kabat et al. literature for heavy chain or light chain variable domains. Using this numbering system, the actual linear amino acid sequence may contain fewer or additional amino acids, corresponding to shortening or insertion of the FR or HVR of the variable domain. For example, the heavy chain variable domain may include a single amino acid insertion fragment (residue 52a according to Kabat numbering) after residue 52 of H2, and insertion residues after heavy chain FR residue 82 (e.g., residues 82a, 82b, and 82c, etc., according to Kabat numbering). The Kabat number of residues for a given antibody can be determined by comparing the antibody sequence with homologous regions of a “standard” Kabat-numbered sequence.

The term "packaging insert" is used to refer to the instruction leaflet typically included in the commercial packaging of a therapeutic product, which contains information concerning the indications, usage, dosage, administration, combination therapy, contraindications, and/or warnings related to the use of such therapeutic products.

As used herein, “in combination with” means administering a treatment modality in addition to another modality of treatment, such as a regimen that includes administration of a PD-1 axis binding antagonist (e.g., atezolizumab) and taxanes (e.g., nab-paclitaxel or paclitaxel), platinum-based chemotherapy agents (e.g., carboplatin), anti-angiogenic agents (e.g., anti-VEGF antibodies, such as bevacizumab), and/or NK cell-targeted therapy agents. Thus, “in combination with” means administering another modality of treatment before, during, or after administering a previous modality of treatment to a patient.

A drug administered "concurrently" with one or more other drugs is administered on the same day as treatment with one or more other drugs within the same treatment cycle, and optionally concurrently with one or more other drugs. For example, in cancer treatment administered every 3 weeks, the concurrently administered drugs are each administered on day 1 of the 3-week cycle.

The term "detection" includes any detection method, including direct and indirect detection.

As used herein, the term "biomarker" refers to an indicator that can be detected in a sample, such as a predictive, diagnostic, and/or prognostic indicator, for example, an HLA gene (e.g., HLA-C1 or HLA-Bw4), a KIR gene (e.g., KIR2DL3 or KIR3DL1), NK cell infiltration, or NK cell signature (e.g., NK cell signature including one or more of the following genes: CD160, CD244, CTSW, FASLG, GZMA, GZMB, GZMH, IL18RAP, IL2RB, KIR2DL4, KLRB1, KLRC3, KLRD1, KRLF1, KLRK1, NCR1, NKG7, PRF1, XCL1, and XCL2). Biomarkers can be used as indicators of a specific subtype of a disease or disorder (e.g., cancer) characterized by certain features, molecular features, pathological features, histological features, and/or clinical features. In some embodiments, the biomarker is a gene. Biomarkers include, but are not limited to, polynucleotides (e.g., DNA and/or RNA), polynucleotide copy number alterations (e.g., DNA copy number), peptides, peptide and polynucleotide modifications (e.g., post-translational modifications), carbohydrates and/or glycolipid-based molecular markers.

Unless otherwise specified, as used herein, the term "CD160" refers to any naturally occurring CD160 (differentiation cluster 160; also known as NK1; BY55; and NK28) from any vertebrate source, including mammals such as primates (e.g., humans) and rodents (e.g., mice and rats). The term covers "full-length" unprocessed CD160, as well as any form of CD160 produced by cellular processing. The term also covers naturally occurring variants of CD160, such as splice variants or allelic variants. An exemplary human CD160 nucleic acid sequence is shown under NCBI reference sequence: NM_007053.4. An exemplary protein encoded by human CD160 is shown under UniProt accession number Q6FH89.

Unless otherwise specified, as used herein, the term "CD244" refers to any naturally occurring CD244 (differentiation cluster 244; also known as natural killer cell receptor 2B4; NAIL; NKR2B4; Nmrk; and SLAMF4) from any vertebrate source, including mammals such as primates (e.g., humans) and rodents (e.g., mice and rats). The term covers "full-length" unprocessed CD244, as well as any form of CD244 produced by cellular processing. The term also covers naturally occurring variants of CD244, such as splice variants or allelic variants. An exemplary nucleic acid sequence of human CD244 is shown under NCBI Reference Sequence: NM_016382.4. An exemplary amino acid sequence of a protein encoded by human CD244 is shown under UniProt Accession Number Q07763.

Unless otherwise specified, as used herein, the term "CTSW" refers to any naturally occurring CTSW (cathepsin W; also known as LYPN) from any vertebrate source, including mammals such as primates (e.g., humans) and rodents (e.g., mice and rats). The term covers "full-length" unprocessed CTSW, as well as any form of CTSW produced through cellular processing. The term also covers naturally occurring variants of CTSW, such as splice variants or allelic variants. An exemplary human CTSW nucleic acid sequence is shown under NCBI reference sequence: NM_001335.4. An exemplary protein encoded by human CTSW is shown under UniProt accession number P56202.

Unless otherwise specified, as used herein, the term "FASLG" refers to any naturally occurring FASLG (Fas ligand; also known as FAS; CD95L; and CD178) from any vertebrate source, including mammals such as primates (e.g., humans) and rodents (e.g., mice and rats). The term covers "full-length" unprocessed FASLG, as well as any form of FASLG produced through cellular processing. The term also covers naturally occurring variants of FASLG, such as splice variants or allelic variants. An exemplary human FASLG nucleic acid sequence is shown under NCBI reference sequence: NM_000639.3. An exemplary protein encoded by human FASLG is shown under UniProt accession number P48023.

Unless otherwise specified, as used herein, the term “GZMA” refers to any naturally occurring GZMA (granzyme A; also known as CTLA3; and HFSP) from any vertebrate source, including mammals such as primates (e.g., humans) and rodents (e.g., mice and rats). The term covers “full-length” unprocessed GZMA, as well as any form of GZMA produced through cellular processing. The term also covers naturally occurring variants of GZMA, such as splice variants or allelic variants. An exemplary human GZMA nucleic acid sequence is shown under NCBI reference sequence: NM_006144.4. An exemplary protein encoded by human GZMA amino acid sequence is shown under UniProt accession number P12544.

Unless otherwise specified, as used herein, the term "GZMB" refers to any naturally occurring GZMB (granzyme B; also known as CGL1 and CSPB) from any vertebrate source, including mammals such as primates (e.g., humans) and rodents (e.g., mice and rats). The term covers "full-length" unprocessed GZMB, as well as any form of GZMB produced through cellular processing. The term also covers naturally occurring variants of GZMB, such as splice variants or allelic variants. An exemplary nucleic acid sequence of human GZMB is shown under NCBI reference sequence: NM_004131.6. An exemplary amino acid sequence of a protein encoded by human GZMB is shown under UniProt accession number P10144.

Unless otherwise specified, as used herein, the term "GZMH" refers to any naturally occurring GZMH (granzyme H; also known as CGL2; CTSGL2; and CSPC) from any vertebrate source, including mammals such as primates (e.g., humans) and rodents (e.g., mice and rats). The term covers "full-length" unprocessed GZMH, as well as any form of GZMH produced through cellular processing. The term also covers naturally occurring variants of GZMH, such as splice variants or allelic variants. An exemplary human GZMH nucleic acid sequence is shown under NCBI reference sequence: NM_033423.5. An exemplary protein encoded by human GZMH is shown under UniProt accession number P20718.

Unless otherwise specified, as used herein, the term "IL18RAP" refers to any naturally occurring IL18RAP (interleukin-18 receptor helper protein; also known as CDw218b) from any vertebrate source, including mammals such as primates (e.g., humans) and rodents (e.g., mice and rats). The term covers "full-length" unprocessed IL18RAP, as well as any form of IL18RAP produced by cellular processing. The term also covers naturally occurring variants of IL18RAP, such as splice variants or allelic variants. An exemplary nucleic acid sequence of human IL18RAP is shown under NCBI reference sequence: NM_003853.4. An exemplary amino acid sequence of a protein encoded by human IL18RAP is shown under UniProt accession number O95256.

Unless otherwise specified, as used herein, the term "IL2RB" refers to any naturally occurring IL2RB (interleukin-2 receptor subunit β; also known as IL15RB; CD122; and P70-75) from any vertebrate source, including mammals such as primates (e.g., humans) and rodents (e.g., mice and rats). The term covers "full-length" unprocessed IL2RB, as well as any form of IL2RB produced by cellular processing. The term also covers naturally occurring variants of IL2RB, such as splice variants or allelic variants. An exemplary nucleic acid sequence of human IL2RB is shown under NCBI reference sequence: NM_000878.5. The amino acid sequence of an exemplary protein encoded by human IL2RB is shown under UniProt accession number P14784.

Unless otherwise specified, as used herein, the term "KIR2DL4" refers to any naturally occurring KIR2DL4 (cytotoxic cell immunoglobulin-like receptor 2DL4; also known as CD158D and KIR103AS) from any vertebrate source, including mammals such as primates (e.g., humans) and rodents (e.g., mice and rats). The term covers "full-length" unprocessed KIR2DL4, as well as any form of KIR2DL4 produced by cellular processing. The term also covers naturally occurring variants of KIR2DL4, such as splice variants or allelic variants. An exemplary nucleic acid sequence of human KIR2DL4 is shown under NCBI Reference Sequence: NM_002255.6. An exemplary amino acid sequence of a protein encoded by human KIR2DL4 is shown under UniProt Accession Number Q99706.

Unless otherwise specified, as used herein, the term "KLRB1" refers to any native KLRB1 (member 1 of the cytotoxic lectin-like receptor subfamily B; also known as NKR-P1A and CD161) from any vertebrate source, including mammals such as primates (e.g., humans) and rodents (e.g., mice and rats). The term covers "full-length" unprocessed KLRB1, as well as any form of KLRB1 produced by cellular processing. The term also covers naturally occurring variants of KLRB1, such as splice variants or allelic variants. An exemplary nucleic acid sequence of human KLRB1 is shown under NCBI reference sequence: NM_002258.3. An exemplary amino acid sequence of a protein encoded by human KLRB1 is shown under UniProt accession number Q12918.

Unless otherwise specified, as used herein, the term "KLRC3" refers to any naturally occurring KLRC3 (killer cell lectin-like receptor C3; also known as NKG2E) from any vertebrate source, including mammals such as primates (e.g., humans) and rodents (e.g., mice and rats). The term covers "full-length" unprocessed KLRC3 as well as any form of KLRC3 produced by cellular processing. The term also covers naturally occurring variants of KLRC3, such as splice variants or allelic variants. An exemplary human KLRC3 nucleic acid sequence is shown under NCBI reference sequence: NM_002261.3. An exemplary protein encoded by human KLRC3 has an amino acid sequence shown under UniProt accession number Q07444.

Unless otherwise specified, as used herein, the term "KLRD1" refers to any naturally occurring KLRD1 (killer cell lectin-like receptor D1; also known as CD94) from any vertebrate source, including mammals such as primates (e.g., humans) and rodents (e.g., mice and rats). The term covers "full-length" unprocessed KLRD1, as well as any form of KLRD1 produced by cellular processing. The term also covers naturally occurring variants of KLRD1, such as splice variants or allelic variants. An exemplary nucleic acid sequence of human KLRD1 is shown under NCBI reference sequence: NM_002262.5. An exemplary amino acid sequence of a protein encoded by human KLRD1 is shown under UniProt accession number Q13241.

Unless otherwise specified, as used herein, the term "KLRF1" refers to any naturally occurring KLRF1 (member F of the cytotoxic lectin-like receptor subfamily; also known as CLEC5C) from any vertebrate source, including mammals such as primates (e.g., humans) and rodents (e.g., mice and rats). The term covers "full-length" unprocessed KLRF1, as well as any form of KLRF1 produced by cellular processing. The term also covers naturally occurring variants of KLRF1, such as splice variants or allelic variants. An exemplary nucleic acid sequence of human KLRF1 is shown under NCBI reference sequence: NM_016523.3. An exemplary amino acid sequence of a protein encoded by human KLRF1 is shown under UniProt accession number Q9NZS2.

Unless otherwise specified, as used herein, the term "KLRK1" refers to any naturally occurring KLRK1 (K member 1 of the cytotoxic lectin-like receptor subfamily; also known as NKG2D) from any vertebrate source, including mammals such as primates (e.g., humans) and rodents (e.g., mice and rats). The term covers "full-length" unprocessed KLRK1, as well as any form of KLRK1 produced by cellular processing. The term also covers naturally occurring variants of KLRK1, such as splice variants or allelic variants. An exemplary nucleic acid sequence of human KLRK1 is shown under NCBI reference sequence: NM_007360.4. An exemplary amino acid sequence of a protein encoded by human KLRK1 is shown under UniProt accession number P26718.

Unless otherwise specified, as used herein, the term “NCR1” means any naturally occurring NCR1 (natural cytotoxic trigger receptor 1; also known as CD335; NKP46; and LY94) from any vertebrate source, including mammals such as primates (e.g., humans) and rodents (e.g., mice and rats). The term covers “full-length” unprocessed NCR1, as well as any form of NCR1 produced by cellular processing. The term also covers naturally occurring variants of NCR1, such as splice variants or allelic variants. An exemplary nucleic acid sequence of human NCR1 is shown under NCBI Reference Sequence: NM_004829.7. An exemplary amino acid sequence of a protein encoded by human NCR1 is shown under UniProt accession number O76036.

Unless otherwise specified, as used herein, the term "NKG7" refers to any naturally occurring NKG7 (natural killer cell granule protein 7; also known as GIG1; GMP-17; and p15-TIA-1) from any vertebrate source, including mammals such as primates (e.g., humans) and rodents (e.g., mice and rats). The term covers "full-length" unprocessed NKG7, as well as any form of NKG7 produced by cellular processing. The term also covers naturally occurring variants of NKG7, such as splice variants or allelic variants. An exemplary nucleic acid sequence of human NKG7 is shown under NCBI Reference Sequence: NM_005601.4. An exemplary amino acid sequence of a protein encoded by human NKG7 is shown under UniProt Accession Number Q16617.

Unless otherwise specified, as used herein, the term "PRF1" refers to any naturally occurring PRF1 (perforin-1; also known as PFP) from any vertebrate source, including mammals such as primates (e.g., humans) and rodents (e.g., mice and rats). The term covers "full-length" unprocessed PRF1, as well as any form of PRF1 produced by cellular processing. The term also covers naturally occurring variants of PRF1, such as splice variants or allelic variants. An exemplary nucleic acid sequence of human PRF1 is shown under NCBI reference sequence: NM_005041.6. An exemplary amino acid sequence of a protein encoded by human PRF1 is shown under UniProt accession number P14222.

Unless otherwise specified, as used herein, the term “XCL1” refers to any naturally occurring XCL1 (chemokine (C motif) ligand; also known as LTN and SCYC1) from any vertebrate source, including mammals such as primates (e.g., humans) and rodents (e.g., mice and rats). The term covers “full-length” unprocessed XCL1, as well as any form of XCL1 produced by cellular processing. The term also covers naturally occurring variants of XCL1, such as splice variants or allelic variants. An exemplary nucleic acid sequence of human XCL1 is shown under NCBI reference sequence: NM_002995.3. An exemplary amino acid sequence of a protein encoded by human XCL1 is shown under UniProt accession number P47992.

Unless otherwise specified, as used herein, the term “XCL2” refers to any naturally occurring XCL2 (chemokine (C motif) ligand 2; also known as SCM1B and SCYC2) from any vertebrate source, including mammals such as primates (e.g., humans) and rodents (e.g., mice and rats). The term covers “full-length” unprocessed XCL2, as well as any form of XCL2 produced by cellular processing. The term also covers naturally occurring variants of XCL2, such as splice variants or allelic variants. An exemplary nucleic acid sequence of human XCL2 is shown under NCBI reference sequence: NM_003175.4. An exemplary amino acid sequence of a protein encoded by human XCL2 is shown under UniProt accession number Q9UBD3.

The “amount” or “level” of a biomarker associated with increased clinical benefit to an individual is the detectable level in a biological sample. These can be measured by methods known to those skilled in the art and disclosed herein. The expression level or amount of the biomarker being assessed can be used to determine the response to treatment.

Generally, the terms “level of expression” or “expression level” are used interchangeably and typically refer to the amount of a biomarker in a biological sample. “Expression” generally refers to the process of converting information (e.g., gene-encoded and/or epigenetic information) into structures that are present and function in the cell. Therefore, as used herein, “expression” can refer to transcription into a polynucleotide, translation into a polypeptide, or even polynucleotide and/or polypeptide modification (e.g., post-translational modification of a polypeptide). Fragments of transcribed polynucleotides, translated polypeptides, or polynucleotide and/or polypeptide modifications (e.g., post-translational modifications of a polypeptide) should also be considered expressed, regardless of whether they originate from transcripts generated through alternative splicing or degradation, or from post-translational processing of polypeptides (e.g., through proteolysis). “Expressed genes” include those transcribed into polynucleotides such as mRNA and then translated into polypeptides, as well as those transcribed into RNA but not translated into polypeptides (e.g., transfer RNA and ribosomal RNA).

"Increased expression", "increased expression level", "increased level", "elevated expression", "elevated expression level" or "elevated level" refers to an increase in the expression or level of a biomarker in an individual relative to one or more individuals or internal controls such as those without a disease or condition (e.g., cancer) or a housekeeping biomarker.

"Decreased expression," "decreased expression level," "lower level," "decreased expression," or "lower level" refers to an increase or decrease in the expression or level of a biomarker in an individual relative to one or more individuals or internal controls (e.g., housekeeping biomarkers) who do not have a disease or condition (e.g., cancer). In some embodiments, decreased expression means little or no expression.

The term "housekeeping biomarker" refers to a biomarker or group of biomarkers (e.g., polynucleotides and/or peptides) that are generally similarly present in all cell types. In some embodiments, a housekeeping biomarker is a "housekeeping gene." A "housekeeping gene" herein refers to a gene or group of genes that encode proteins whose activity is essential for maintaining cellular function, and housekeeping genes are generally similarly present in all cell types.

As used herein, the term “diagnosis” refers to the identification or classification of a molecular or pathological state, disease, or symptom (e.g., cancer (e.g., NSCLC)). For example, “diagnosis” can refer to the identification of a specific type of cancer. “Diagnosis” can also refer to the classification of a specific subtype of cancer, for example, by histopathological criteria or molecular characteristics (e.g., a subtype characterized by the expression of a biomarker or a combination of biomarkers (e.g., a specific gene or a protein encoded by said gene)).

As used herein, the term "sample" refers to a composition obtained or derived from a target subject and/or individual that contains, for example, cells and/or other molecular entities to be characterized and/or identified based on physical, biochemical, chemical, and/or physiological characteristics. For example, the phrase "disease sample" and variations thereof refer to any sample obtained from a target subject that is expected or known to contain cells and/or molecular entities to be characterized. Samples include, but are not limited to, tissue samples, primary or cultured cells or cell lines, cell supernatants, cell lysates, platelets, serum, plasma, vitreous fluid, lymph, synovial fluid, follicular fluid, semen, amniotic fluid, breast milk, whole blood, blood-derived cells, urine, cerebrospinal fluid, saliva, sputum, tears, sweat, mucus, tumor lysis products, and tissue culture media, tissue extracts such as homogenized tissue, tumor tissue, cell extracts, and combinations thereof.

A “tissue sample” or “cell sample” refers to a collection of similar cells obtained from a subject’s or individual’s tissue. The source of a tissue or cell sample can be solid tissue from fresh, frozen, and/or preserved organs, tissue samples, biopsies, and/or aspirates; blood or any blood component, such as plasma; body fluids, such as cerebrospinal fluid, amniotic fluid, peritoneal fluid, or interstitial fluid; or cells from any time during the subject’s pregnancy or development. A tissue sample can also be primary or cultured cells or cell lines. Optionally, a tissue or cell sample is obtained from diseased tissue/organ. For example, a “tumor sample” is a tissue sample obtained from a tumor (e.g., a liver tumor) or other cancerous tissue. A tissue sample can contain a mixed population of cell types (e.g., tumor cells and non-tumor cells, cancer cells and non-cancer cells). A tissue sample can contain compounds that are naturally occurring and do not mix with tissues, such as preservatives, anticoagulants, buffers, fixatives, nutrients, antibiotics, etc.

As used herein, “tumor-infiltrating immune cells” refers to any immune cell present in a tumor or its sample. Tumor-infiltrating immune cells include, but are not limited to, intratumoral immune cells, peritumoral immune cells, other tumor stromal cells (e.g., fibroblasts), or any combination thereof. Such tumor-infiltrating immune cells can be, for example, T lymphocytes (such as CD8+ T lymphocytes and/or CD4+ T lymphocytes), B lymphocytes or other bone marrow lineage cells, including granulocytes (e.g., neutrophils, eosinophils, and basophils), monocytes, macrophages, dendritic cells (e.g., finger dendritic cells), histiocytes, and natural killer cells.

As used herein, “tumor cell” means any tumor cell present in a tumor or its sample. Using methods known in the art and/or those described herein, tumor cells can be distinguished from other cells that may be present in a tumor sample, such as stromal cells and tumor-infiltrating immune cells.

As used herein, “reference sample,” “reference cell,” “reference tissue,” “control sample,” “control cell,” or “control tissue” refers to a sample, cell, tissue, standard, or level used for comparative purposes. In one embodiment, the reference sample, reference cell, reference tissue, control sample, control cell, or control tissue is obtained from a healthy and/or disease-free site (e.g., tissue or cell) of the same subject or individual's body. For example, the reference sample, reference cell, reference tissue, control sample, control cell, or control tissue may be a healthy and/or disease-free cell or tissue adjacent to a diseased cell or tissue (e.g., a cell or tissue adjacent to a tumor). In another embodiment, the reference sample is obtained from untreated body tissue and/or cells of the same subject or individual. In yet another embodiment, the reference sample, reference cell, reference tissue, control sample, control cell, or control tissue is obtained from a healthy and/or disease-free body site (e.g., tissue or cell) of an individual who is not a subject or study individual. In yet another embodiment, the reference sample, reference cell, reference tissue, control sample, control cell, or control tissue is obtained from untreated body tissue and/or cells of an individual who is not a subject or study individual.

For the purposes of this article, a “slice” of a tissue sample refers to a single portion or sheet of a tissue sample, such as a thin slice of tissue or cells cut from a tissue sample (e.g., a tumor sample). It should be understood that multiple portions of a tissue sample can be obtained and analyzed, provided that the same portion of the tissue sample can be analyzed at the morphological and molecular levels, or that analysis can be performed on peptides (e.g., by immunohistochemistry) and/or polynucleotides (e.g., by in situ hybridization).

"Association" or "relevance" means comparing the performance and/or results of a first analysis or protocol with the performance and/or results of a second analysis or protocol in any way. For example, the results of the first analysis or protocol may be used when performing the second protocol, and/or the results of the first analysis or protocol may be used to determine whether the second analysis or protocol should be performed. Regarding examples of peptide analyses or protocols, the results of peptide expression analyses or protocols may be used to determine whether a specific treatment regimen should be implemented. Regarding examples of polynucleotide analyses or protocols, the results of polynucleotide expression analyses or protocols may be used to determine whether a specific treatment regimen should be implemented.

The phrase “based on” as used in this article refers to information about one or more biomarkers that is provided in information such as informing treatment decisions, packaging inserts, or marketing/promotional guidelines.

As used herein, the term “adverse event” or “AE” refers to any adverse and unexpected indication (including abnormal laboratory findings), symptom, or illness that is temporarily associated with the use of a medical treatment or procedure that may or may not be considered related to the medical treatment or procedure. Adverse events can be classified by “grade” as defined in the National Cancer Institute Common Terminology Standard for Adverse Events v5.0 (NIH CTCAE). In some respects, AEs are low-grade AEs, such as Grade 1 or Grade 2 AEs. Grade 1 includes asymptomatic or mildly symptomatic AEs. Grade 2 includes moderate AEs that limit age-appropriate assistive activities of daily living (e.g., preparing meals, grocery shopping, or clothing) and indicate a local or non-invasive intervention. In other cases, AEs are high-grade AEs, such as Grade 3, Grade 4, or Grade 5 AEs. Grade 3 includes serious or medically significant AEs that are not immediately life-threatening and indicate hospitalization or prolonged hospitalization. Grade 4 includes AEs with life-threatening consequences and indicate the need for urgent intervention. Grade 5 includes AEs that result in or are related to death.

As used herein, the term “immune-mediated adverse event” or “imAE” refers to an adverse event or “adverse event of particular concern” (“AESI”) classified by the NIH CTCAE with a presumed immune-related etiology. In some respects, an imAE is an AES that occurs as a result of immune checkpoint inhibitor therapy. In some respects, an imAE affects the respiratory tract, the endocrine system (“endocrine imAE”), the skin (“dermatological imAE” or “skin imAE”), or the gastrointestinal tract (“GI imAE”). In some respects, an imAE is pneumonia.

As used herein, the term "immune checkpoint inhibitor" refers to a therapeutic agent that targets at least one immune checkpoint protein to alter the regulation of the immune response, such as downregulating, inhibiting, upregulating, or activating the immune response. The term "immune checkpoint blockade" may be used to refer to therapies that include immune checkpoint inhibitors. Immune checkpoint proteins are known in the art and include, but are not limited to, programmed cell death ligand 1 (PD-L1), TIGIT, cytotoxic T-lymphocyte antigen 4 (CTLA-4), programmed cell death 1 (PD-1), programmed cell death ligand 2 (PD-L2), V-domain Ig inhibitor of T cell activation (VISTA), B7-H2, B7-H3, B7-H4, B7-H6, 2B4, ICOS, HVEM, CD160, gp49B, PIR-B, KIR family receptors, TIM-1, TIM-3, TIM-4, LAG-3, BTLA, SIRPα (CD47), CD48, 2B4 (CD244), B7.1, B7.2, ILT-2, ILT-4, LAG-3, BTLA, IDO, OX40, and A2aR. In some respects, immune checkpoint proteins can be expressed on the surface of activated T cells. Therapeutic agents that can be used as immune checkpoint inhibitors in the methods of the present invention include, but are not limited to, agents targeting one or more of PD-L1, TIGIT, PD-1, CTLA-4, PD-L2, VISTA, B7-H2, B7-H3, B7-H4, B7-H6, 2B4, ICOS, HVEM, CD160, gp49B, PIR-B, KIR family receptors, TIM-1, TIM-3, TIM-4, LAG-3, BTLA, SIRPα (CD47), CD48, 2B4 (CD244), B7.1, B7.2, ILT-2, ILT-4, LAG-3, BTLA, IDO, OX40, and A2aR. In some aspects, immune checkpoint inhibitors enhance or inhibit the function of one or more targeted immune checkpoint proteins. In some aspects, immune checkpoint inhibitors are PD-1 axis binding antagonists, such as atezolizumab, as described herein.

II. Methods and compositions for the treatment and diagnosis of lung cancer

This article provides methods for the treatment and diagnosis of cancer (e.g., NSCLC) in which patients can be identified, selected, and/or given a treatment regimen comprising a PD-1 axis binding antagonist (e.g., atezolizumab) based on their genotype, which contains HLA or KIR genes or HLA/KIR pairs associated with improved NK cell education, such as at least one copy of HLA-C1, at least one copy of HLA-Bw4, at least one copy of KIR2DL3, and/or at least one copy of KIR3DL1. For example, in some instances, this article provides methods for the treatment and diagnosis of cancer (e.g., NSCLC) in which patients can be identified, selected, and/or given a treatment regimen comprising a PD-1 axis binding antagonist (e.g., atezolizumab) based on their genotype, which contains at least one copy of HLA-C1 and/or at least one copy of KIR2DL3. In another instance, this article provides a treatment and diagnostic approach for cancer (e.g., NSCLC) in which patients can be identified, selected, and/or given a treatment regimen comprising a PD-1 axis binding antagonist (e.g., atezolizumab) based on their genotype containing at least one copy of HLA-Bw4 and/or at least one copy of KIR3DL1. Not wishing to be bound by theory, such patients may have increased NK cell activity or function, for example, due to improved NK cell education. Therefore, such patients may also benefit from NK cell-targeted therapies, either alone or in combination with a PD-1 axis binding antagonist (e.g., atezolizumab).

This article also provides methods for the treatment and diagnosis of cancer, in which patients can be identified, selected, and/or treated with regimens including PD-1 axis-binding antagonists (e.g., atezolizumab) based on an increase in NK cell infiltration levels in tumor samples relative to a reference level of NK cell infiltration. Not wishing to be bound by theory, such patients may have increased NK cell activity or function, for example, due to improved NK cell education. Therefore, such patients may also benefit from NK cell-targeted therapies, either alone or in combination with PD-1 axis-binding antagonists.

An in vitro method for NK cell education is also provided, in which NK cells expressing KIR2DL3 or KIR3DL1 can be contacted with cells expressing HLA-C1 or HLA-Bw4, respectively. The resulting NK cells can be used, for example, for adoptive cell therapy targeting patients with, for example, an HLA loss phenotype.

In one instance, this article provides a method for treating cancer (e.g., NSCLC) in a patient whose genome has been identified as containing at least one copy of HLA-C1, the method comprising administering to the patient an effective amount of a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab). In some cases, the patient's genome further contains at least one copy of KIR2DL3.

In another instance, this article provides a PD-1 axis binding antagonist (e.g., atezolizumab) for treating cancers (e.g., NSCLC) in patients with this need, whose genome has been identified as containing at least one copy of HLA-C1. In some cases, the patient's genome further contains at least one copy of KIR2DL3.

In another instance, this article provides a method for treating cancer (e.g., NSCLC) in a patient whose genome has been identified as containing at least one copy of HLA-C1 and at least one copy of KIR2DL3, the method comprising administering to the patient an effective amount of a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab).

In another instance, this article provides a PD-1 axis binding antagonist (e.g., atezolizumab) for treating cancer (e.g., NSCLC) in patients with this need whose genome has been identified as containing at least one copy of HLA-C1 and at least one copy of KIR2DL3.

In another instance, this article provides a method for treating cancer (e.g., NSCLC) in a patient whose genome has been identified as containing at least one copy of HLA-Bw4, the method comprising administering to the patient an effective dose of a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab). In some cases, the patient's genome further contains at least one copy of KIR3DL1.

In another instance, this article provides a PD-1 axis binding antagonist (e.g., atezolizumab) for treating cancers (e.g., NSCLC) in patients with this need, whose genome has been identified as containing at least one copy of HLA-Bw4. In some cases, the patient's genome further contains at least one copy of KIR3DL1.

In another instance, this article provides a method for treating cancer (e.g., NSCLC) in a patient whose genome has been identified as containing at least one copy of HLA-Bw4 and at least one copy of KIR3DL1, the method comprising administering to the patient an effective amount of a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab).

In another instance, this article provides a PD-1 axis binding antagonist (e.g., atezolizumab) for treating cancer (e.g., NSCLC) in patients with this need whose genome has been identified as containing at least one copy of HLA-Bw4 and at least one copy of KIR3DL1.

In another instance, this document provides a method for treating cancer (e.g., NSCLC) in a patient with this need, the method comprising: (a) determining whether the patient's genome contains at least one copy of HLA-C1, wherein the presence of at least one copy of HLA-C1 in the patient's genome indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab); and (b) administering an effective amount of the treatment regimen including the PD-1 axis binding antagonist to the patient based on the presence of at least one copy of HLA-C1 in the patient's genome. In some cases, step (a) further comprises determining whether the patient's genome contains at least one copy of KIR2DL3.

In another example, this document provides a method for treating cancer (e.g., NSCLC) in patients with this need, using a PD-1 axis binding antagonist (e.g., atezolizumab), the method comprising: (a) determining whether the patient's genome contains at least one copy of HLA-C1, wherein the presence of at least one copy of HLA-C1 in the patient's genome indicates that the patient may benefit from a treatment regimen comprising a PD-1 axis binding antagonist; and (b) administering an effective amount of the treatment regimen comprising a PD-1 axis binding antagonist to the patient based on the presence of at least one copy of HLA-C1 in the patient's genome. In some cases, step (a) further comprises determining whether the patient's genome contains at least one copy of KIR2DL3.

In another instance, this article provides a method for treating cancer (e.g., NSCLC) in a patient with this need, the method comprising: (a) determining whether the patient’s genome contains at least one copy of HLA-C1 and at least one copy of KIR2DL3, wherein the presence of at least one copy of HLA-C1 and at least one copy of KIR2DL3 in the patient’s genome indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab); and (b) administering an effective amount of the treatment regimen including the PD-1 axis binding antagonist to the patient based on the presence of at least one copy of HLA-C1 and at least one copy of KIR2DL3 in the patient’s genome.

In another instance, this article provides a PD-1 axis binding antagonist (e.g., atezolizumab) for treating cancer (e.g., NSCLC) in patients with this need, the method comprising: (a) determining whether the patient’s genome contains at least one copy of HLA-C1 and at least one copy of KIR2DL3, wherein the presence of at least one copy of HLA-C1 and at least one copy of KIR2DL3 in the patient’s genome indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist; and (b) administering an effective amount of the treatment regimen including a PD-1 axis binding antagonist to the patient based on the presence of at least one copy of HLA-C1 and at least one copy of KIR2DL3 in the patient’s genome.

In another instance, this document provides a method for treating cancer (e.g., NSCLC) in a patient with this need, the method comprising: (a) determining whether the patient's genome contains at least one copy of HLA-Bw4, wherein the presence of at least one copy of HLA-Bw4 in the patient's genome indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab); and (b) administering an effective amount of the treatment regimen including the PD-1 axis binding antagonist to the patient based on the presence of at least one copy of HLA-Bw4 in the patient's genome. In some cases, step (a) further comprises determining whether the patient's genome contains at least one copy of KIR3DL1.

In another instance, this document provides a PD-1 axis binding antagonist (e.g., atezolizumab) for treating cancer (e.g., NSCLC) in patients with this need, the method comprising: (a) determining whether the patient's genome contains at least one copy of HLA-Bw4, wherein the presence of at least one copy of HLA-Bw4 in the patient's genome indicates that the patient may benefit from a treatment regimen comprising a PD-1 axis binding antagonist; and (b) administering an effective amount of the treatment regimen comprising a PD-1 axis binding antagonist to the patient based on the presence of at least one copy of HLA-Bw4 in the patient's genome. In some cases, step (a) further comprises determining whether the patient's genome contains at least one copy of KIR3DL1.

In another instance, this article provides a method for treating cancer (e.g., NSCLC) in a patient with this need, the method comprising: (a) determining whether the patient’s genome contains at least one copy of HLA-Bw4 and at least one copy of KIR3DL1, wherein the presence of at least one copy of HLA-Bw4 and at least one copy of KIR3DL1 in the patient’s genome indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab); and (b) administering an effective amount of the treatment regimen including the PD-1 axis binding antagonist to the patient based on the presence of at least one copy of HLA-Bw4 and at least one copy of KIR3DL1 in the patient’s genome.

In another instance, this article provides a PD-1 axis binding antagonist (e.g., atezolizumab) for treating cancer (e.g., NSCLC) in patients with this need, the method comprising: (a) determining whether the patient’s genome contains at least one copy of HLA-Bw4 and at least one copy of KIR3DL1, wherein the presence of at least one copy of HLA-Bw4 and at least one copy of KIR3DL1 in the patient’s genome indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist; and (b) administering an effective amount of the treatment regimen including a PD-1 axis binding antagonist to the patient based on the presence of at least one copy of HLA-Bw4 and at least one copy of KIR3DL1 in the patient’s genome.

In another instance, this article provides a method for identifying patients with cancer (e.g., NSCLC) who may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab), the method comprising determining whether the patient's genome contains at least one copy of HLA-C1, wherein the presence of at least one copy of HLA-C1 in the patient's genome identifies the patient as a patient who may benefit from treatment with a treatment regimen including a PD-1 axis binding antagonist. In some cases, the method further comprises determining whether the patient's genome contains at least one copy of KIR2DL3.

In another instance, this document provides a method for identifying patients with cancer (e.g., NSCLC) who may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab), the method comprising: (a) performing germline whole-genome sequencing (WGS) or whole-exome sequencing (WES) by fragmenting a DNA sample obtained from the patient to generate fragmented DNA, adding an adaptor to the fragmented DNA to generate one or more libraries, and sequencing the one or more libraries; and (b) identifying the patient as a patient who may benefit from a treatment regimen including a PD-1 axis binding antagonist by determining whether the patient's genome contains at least one copy of HLA-C1, wherein the presence of at least one copy of HLA-C1 in the patient's genome identifies the patient as a patient who may benefit from treatment using a treatment regimen including a PD-1 axis binding antagonist. In some cases, the method further includes determining whether the patient's genome contains at least one copy of KIR2DL3.

In another instance, this article provides a method for identifying patients with cancer (e.g., NSCLC) who may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab), the method comprising determining whether the patient’s genome contains at least one copy of HLA-C1 and at least one copy of KIR2DL3, wherein the presence of at least one copy of HLA-C1 and at least one copy of KIR2DL3 in the patient’s genome identifies the patient as a patient who may benefit from treatment using a treatment regimen including a PD-1 axis binding antagonist.

In another instance, this article provides a method for identifying a patient with cancer (e.g., NSCLC) who may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab), the method comprising: (a) performing germline WGS or WES by fragmenting a DNA sample obtained from the patient to generate fragmented DNA, adding an adaptor to the fragmented DNA to generate one or more libraries, and sequencing the one or more libraries; and (b) identifying the patient as a patient who may benefit from a treatment regimen including a PD-1 axis binding antagonist by determining whether the patient's genome contains at least one copy of HLA-C1 and at least one copy of KIR2DL3, wherein the presence of at least one copy of HLA-C1 and at least one copy of KIR2DL3 in the patient's genome identifies the patient as a patient who may benefit from treatment using a treatment regimen including a PD-1 axis binding antagonist.

In another instance, this article provides a method for identifying patients with cancer (e.g., NSCLC) who may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab), the method comprising determining whether the patient's genome contains at least one copy of HLA-Bw4, wherein the presence of at least one copy of HLA-Bw4 in the patient's genome identifies the patient as a patient who may benefit from treatment using a treatment regimen including a PD-1 axis binding antagonist. In some cases, the method further comprises determining whether the patient's genome contains at least one copy of KIR3DL1.

In another instance, this document provides a method for identifying patients with cancer (e.g., NSCLC) who may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab), the method comprising: (a) performing germline WGS or WES by fragmenting a DNA sample obtained from the patient to generate fragmented DNA, adding an adaptor to the fragmented DNA to generate one or more libraries, and sequencing the one or more libraries; and (b) identifying the patient as a patient who may benefit from a treatment regimen including a PD-1 axis binding antagonist by determining whether the patient's genome contains at least one copy of HLA-Bw4, wherein the presence of at least one copy of HLA-Bw4 in the patient's genome identifies the patient as a patient who may benefit from treatment with a treatment regimen including a PD-1 axis binding antagonist. In some cases, the method further includes determining whether the patient's genome contains at least one copy of KIR3DL1.

In another instance, this article provides a method for identifying patients with cancer (e.g., NSCLC) who may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab), the method comprising determining whether the patient’s genome contains at least one copy of HLA-Bw4 and at least one copy of KIR3DL1, wherein the presence of at least one copy of HLA-Bw4 and at least one copy of KIR3DL1 in the patient’s genome identifies the patient as a patient who may benefit from treatment using a treatment regimen including a PD-1 axis binding antagonist.

In another instance, this article provides a method for identifying a patient with cancer (e.g., NSCLC) who may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab), the method comprising: (a) performing germline WGS or WES by fragmenting a DNA sample obtained from the patient to generate fragmented DNA, adding an adaptor to the fragmented DNA to generate one or more libraries, and sequencing the one or more libraries; and (b) identifying the patient as a patient who may benefit from a treatment regimen including a PD-1 axis binding antagonist by determining whether the patient's genome contains at least one copy of HLA-Bw4 and at least one copy of KIR3DL1, wherein the presence of at least one copy of HLA-Bw4 and at least one copy of KIR3DL1 in the patient's genome identifies the patient as a patient who may benefit from treatment using a treatment regimen including a PD-1 axis binding antagonist.

In another instance, this article provides a method for selecting a therapy for a patient with cancer (e.g., NSCLC), the method comprising: (a) determining whether the patient's genome contains at least one copy of HLA-C1, wherein the presence of at least one copy of HLA-C1 in the patient's genome indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab); and (b) selecting a treatment regimen including a PD-1 axis binding antagonist based on the presence of at least one copy of HLA-C1 in the patient's genome. In some cases, the method further comprises determining whether the patient's genome contains at least one copy of KIR2DL3.

In another instance, this article provides a method for selecting a therapy for a patient with cancer (e.g., NSCLC), the method comprising: (a) determining whether the patient’s genome contains at least one copy of HLA-C1 and at least one copy of KIR2DL3, wherein the presence of at least one copy of HLA-C1 and at least one copy of KIR2DL3 in the patient’s genome indicates that the patient may benefit from a treatment regimen that includes a PD-1 axis binding antagonist (e.g., atezolizumab); and (b) selecting a treatment regimen that includes a PD-1 axis binding antagonist based on the presence of at least one copy of HLA-C1 and at least one copy of KIR2DL3 in the patient’s genome.

In another instance, this article provides a method for selecting a therapy for a patient with cancer (e.g., NSCLC), the method comprising: (a) determining whether the patient's genome contains at least one copy of HLA-Bw4, wherein the presence of at least one copy of HLA-Bw4 in the patient's genome indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab); and (b) selecting a treatment regimen including a PD-1 axis binding antagonist based on the presence of at least one copy of HLA-Bw4 in the patient's genome. In some cases, the method further comprises determining whether the patient's genome contains at least one copy of KIR3DL1.

In another instance, this article provides a method for selecting a therapy for a patient with cancer (e.g., NSCLC), the method comprising: (a) determining whether the patient’s genome contains at least one copy of HLA-Bw4 and at least one copy of KIR3DL1, wherein the presence of at least one copy of HLA-Bw4 and at least one copy of KIR3DL1 in the patient’s genome indicates that the patient may benefit from a treatment regimen that includes a PD-1 axis binding antagonist (e.g., atezolizumab); and (b) selecting a treatment regimen that includes a PD-1 axis binding antagonist based on the presence of at least one copy of HLA-Bw4 and at least one copy of KIR3DL1 in the patient’s genome.

Any of the foregoing examples may further include treatment regimens that administer an effective amount of a PD-1 axis binding antagonist (e.g., atezolizumab) to the patient.

In any of the instances described herein, any suitable method may be used to determine the presence of HLA-C1, HLA-Bw4, KIR2DL3, and/or KIR3DL1 in a patient's genome. For example, in some cases, next-generation sequencing, Sanger sequencing, polymerase chain reaction (PCR)-based assays, or single nucleotide polymorphism (SNP) arrays are used to determine the presence of HLA-C1, HLA-Bw4, KIR2DL3, and/or KIR3DL1 in a patient's genome. In some cases, next-generation sequencing includes germline whole-genome sequencing or germline whole-exome sequencing. In some cases, PCR-based assays include quantitative PCR (qPCR), genotyping using sequence-specific primers (SSPs), or genotyping using sequence-specific oligonucleotide probes (SSOs).

In another instance, this article provides a method for treating cancer (e.g., NSCLC) in a patient who has been identified as having an increased level of NK cell infiltration relative to a reference level of natural killer (NK) cell infiltration in a tumor sample obtained from the patient, the method comprising administering to the patient an effective amount of a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab).

In another instance, this article provides a PD-1 axis binding antagonist for treating cancer (e.g., NSCLC) in patients who have been identified as having increased levels of NK cell infiltration relative to a reference level of NK cell infiltration in tumor samples obtained from the patient.

In another instance, this article provides a method for treating cancer (e.g., NSCLC) in a patient with this need, the method comprising: (a) determining whether a tumor sample obtained from the patient has an increased level of NK cell infiltration relative to a reference level of NK cell infiltration, wherein an increased level of NK cell infiltration in the tumor sample obtained from the patient relative to a reference level of NK cell infiltration indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab); and (b) administering an effective amount of the treatment regimen including a PD-1 axis binding antagonist to the patient based on the increased level of NK cell infiltration in the tumor sample obtained from the patient relative to a reference level of NK cell infiltration.

In another instance, this article provides a method for treating cancer (e.g., NSCLC) in a patient with this need, using a PD-1 axis binding antagonist (e.g., atezolizumab), the method comprising: (a) determining whether a tumor sample obtained from the patient has an increased level of NK cell infiltration relative to a reference level of NK cell infiltration, wherein an increased level of NK cell infiltration in the tumor sample obtained from the patient indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist; and (b) administering an effective amount of the treatment regimen including a PD-1 axis binding antagonist to the patient based on the increased level of NK cell infiltration in the tumor sample obtained from the patient relative to a reference level of NK cell infiltration.

In another instance, this article provides a method for identifying patients with cancer (e.g., NSCLC) who may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab), the method comprising determining whether a tumor sample obtained from the patient has an increased level of NK cell infiltration relative to a reference level of NK cell infiltration, wherein an increased level of NK cell infiltration relative to a reference level of NK cell infiltration in a tumor sample obtained from the patient indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist.

In another instance, this article provides a method for identifying patients with cancer (e.g., NSCLC) who may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab), the method comprising: (a) contacting a tumor sample obtained from the patient with one or more antibody or nucleotide probes conjugated to one or more NK cell markers to determine the level of NK cell infiltration in the tumor sample; and (b) determining whether the tumor sample obtained from the patient has an increased level of NK cell infiltration relative to a reference level of NK cell infiltration, wherein an increased level of NK cell infiltration relative to a reference level of NK cell infiltration in the tumor sample obtained from the patient indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist. Any suitable antibody or nucleotide probe can be used, for example, an antibody or nucleotide probe that binds to any NK cell marker described herein or known in the art, such as one or more of the following genes (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or all 20): CD160, CD244, CTSW, FASLG, GZMA, GZMB, GZMH, IL18RAP, IL2RB, KIR2DL4, KLRB1, KLRC3, KLRD1, KRLF1, KLRK1, NCR1, NKG7, PRF1, XCL1 and XCL2.

In another instance, this article provides a method for selecting a therapy for a patient with cancer (e.g., NSCLC), the method comprising: (a) determining whether a tumor sample obtained from the patient has an increased level of NK cell infiltration relative to a reference level of NK cell infiltration, wherein an increased level of NK cell infiltration in a tumor sample obtained from the patient indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab); and (b) selecting a treatment regimen including a PD-1 axis binding antagonist based on the increased level of NK cell infiltration in a tumor sample obtained from the patient relative to a reference level of NK cell infiltration.

Any example described herein may include a treatment regimen that administers an effective amount of a PD-1 axis binding antagonist (e.g., atezolizumab) to a patient.

In any of the instances described herein, the level of NK cell infiltration can be determined using any suitable method. For example, in some cases, the level of NK cell infiltration can be determined by, for example, by immunofluorescence, immunohistochemistry, Western blotting, flow cytometry, or any other suitable method, by determining the expression level of NK cell gene signatures, by counting the number of NK cells in a tumor sample, or by detecting the presence or level of one or more NK cell markers. Any suitable NK cell marker or combination of NK cell markers can be used. In some aspects, NK cell markers are costimulatory receptors, such as TRAIL, CD16a, CD16b, NKG2D, NKG2C, 4-1BB, OX40, CD27, 2B4, DNAM-1, NKp30, NKp46, NKp44, NKp80, KIR2DS1, and KIR2DS2. In some aspects, NK cell receptors are costimulatory receptors. In some aspects, co-inhibitory receptors are NKG2A or KIR, such as KIR3DL1, KIR2DL1, KIR2DL2, or KIR2DL3.

In any of the instances described herein, the NK cell genetic signature may include one or more of the following genes (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or all 20): CD160, CD244, CTSW, FASLG, GZMA, GZMB, GZMH, IL18RAP, IL2RB, KIR2DL4, KLRB1, KLRC3, KLRD1, KRLF1, KLRK1, NCR1, NKG7, PRF1, XCL1, and XCL2. In some cases, the NK cell genetic signature contains at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least ten, at least eleven, at least twelve, at least thirteen, at least fourteen, at least fifteen, at least sixteen, at least seventeen, at least eighteen, at least nineteen, or all twenty of the genes in question. In some cases, the reference level for NK cell infiltration is the median level. In some cases, the median level is the median level in a patient population with cancer (e.g., NSCLC).

In some instances, the patient's genome contains at least one copy of HLA-C1 (e.g., 1 or 2 copies) or at least one copy of HLA-Bw4 (e.g., 1 or 2 copies). In some cases, the patient's genome contains at least one copy of HLA-C1 (e.g., 1 or 2 copies). In some cases, the patient's genome contains at least one copy of HLA-Bw4 (e.g., 1 or 2 copies).

In some instances, the patient's genome contains at least one copy of KIR2DL3 (e.g., 1 or 2 copies) or at least one copy of KIR3DL1 (e.g., 1 or 2 copies). In some cases, the patient's genome contains at least one copy of KIR2DL3 (e.g., 1 or 2 copies). In some cases, the patient's genome contains at least one copy of KIR3DL1 (e.g., 1 or 2 copies).

Any instance disclosed herein, including any of the foregoing instances, may further include a treatment regimen that administers an effective amount of an NK cell-targeted therapeutic agent (e.g., an NK cell conjugate) to a patient. Any suitable NK cell-targeted therapeutic agent may be used, such as any NK cell-targeted therapeutic agent described in Section V below. In some instances, any NK cell-targeted therapy described in Hodgins et al., J. Clin. Invest. 129(9):3499-3510, 2019, may be used. In some cases, NK cell-targeted therapeutic agents include allogeneic NK cells, autologous NK cells, off-the-shelf NK cells, chimeric antigen receptor (CAR)-NK cells, cytokine therapy, NK cell conjugates (e.g., bispecific killer cell conjugates (BiKE), trispecific killer cell conjugates (TriKE), or tetraspecific killer cell conjugates (TetraKE)), NK cell checkpoint receptor antagonists, or oncolytic viruses.

In another instance, this article provides a method for treating cancer (e.g., NSCLC) in a patient whose genome has been identified as containing at least one copy of HLA-C1, the method comprising administering to the patient an effective amount of a treatment regimen including an NK cell-targeted therapeutic agent (e.g., an NK cell binder). In some cases, the patient's genome further contains at least one copy of KIR2DL3.

In another instance, this article provides an NK cell-targeted therapeutic agent (e.g., an NK cell conjugate) for treating cancer (e.g., NSCLC) in patients with this need, whose genome has been identified as containing at least one copy of HLA-C1. In some cases, the patient's genome further contains at least one copy of KIR2DL3.

In another instance, this article provides a method for treating cancer (e.g., NSCLC) in a patient whose genome has been identified as containing at least one copy of HLA-C1 and at least one copy of KIR2DL3, the method comprising administering to the patient an effective amount of a treatment regimen including an NK cell-targeted therapeutic agent (e.g., an NK cell conjugate).

In another instance, this article provides an NK cell-targeted therapeutic agent (e.g., an NK cell conjugate) for treating cancer (e.g., NSCLC) in patients with this need whose genome has been identified as containing at least one copy of HLA-C1 and at least one copy of KIR2DL3.

In another instance, this article provides a method for treating cancer (e.g., NSCLC) in a patient whose genome has been identified as containing at least one copy of HLA-Bw4, the method comprising administering to the patient an effective amount of a treatment regimen including an NK cell-targeted therapeutic agent (e.g., an NK cell binder). In some cases, the patient's genome further contains at least one copy of KIR3DL1.

In another instance, this article provides an NK cell-targeted therapeutic agent (e.g., an NK cell conjugate) for treating cancer (e.g., NSCLC) in patients with this need, whose genome has been identified as containing at least one copy of HLA-Bw4. In some cases, the patient's genome further contains at least one copy of KIR3DL1.

In another instance, this article provides a method for treating cancer (e.g., NSCLC) in a patient whose genome has been identified as containing at least one copy of HLA-Bw4 and at least one copy of KIR3DL1, the method comprising administering to the patient an effective amount of a treatment regimen including an NK cell-targeted therapeutic agent (e.g., an NK cell conjugate).

In another instance, this article provides an NK cell-targeted therapeutic agent (e.g., an NK cell conjugate) for treating cancer (e.g., NSCLC) in patients with this need whose genome has been identified as containing at least one copy of HLA-Bw4 and at least one copy of KIR3DL1.

In another instance, this document provides a method for treating cancer (e.g., NSCLC) in a patient with this need, the method comprising: (a) determining whether the patient's genome contains at least one copy of HLA-C1, wherein the presence of at least one copy of HLA-C1 in the patient's genome indicates that the patient may benefit from a treatment regimen including an NK cell-targeted therapeutic agent (e.g., an NK cell conjugate); and (b) administering an effective amount of the treatment regimen including the NK cell-targeted therapeutic agent to the patient based on the presence of at least one copy of HLA-C1 in the patient's genome. In some cases, step (a) further comprises determining whether the patient's genome contains at least one copy of KIR2DL3.

In another example, this document provides an NK cell-targeted therapeutic agent (e.g., an NK cell binder) in a method for treating cancer (e.g., NSCLC) in a patient with this need, the method comprising: (a) determining whether the patient's genome contains at least one copy of HLA-C1, wherein the presence of at least one copy of HLA-C1 in the patient's genome indicates that the patient may benefit from a treatment regimen including an NK cell-targeted therapeutic agent; and (b) administering an effective amount of the treatment regimen including the NK cell-targeted therapeutic agent to the patient based on the presence of at least one copy of HLA-C1 in the patient's genome. In some cases, step (a) further comprises determining whether the patient's genome contains at least one copy of KIR2DL3.

In another instance, this article provides a method for treating cancer (e.g., NSCLC) in a patient with this need, the method comprising: (a) determining whether the patient’s genome contains at least one copy of HLA-C1 and at least one copy of KIR2DL3, wherein the presence of at least one copy of HLA-C1 and at least one copy of KIR2DL3 in the patient’s genome indicates that the patient may benefit from a treatment regimen including an NK cell-targeted therapeutic agent (e.g., an NK cell conjugate); and (b) administering an effective amount of the treatment regimen including the NK cell-targeted therapeutic agent to the patient based on the presence of at least one copy of HLA-C1 and at least one copy of KIR2DL3 in the patient’s genome.

In another instance, this article provides an NK cell-targeted therapeutic agent (e.g., an NK cell conjugate) for treating cancer (e.g., NSCLC) in patients with this need, the method comprising: (a) determining whether the patient's genome contains at least one copy of HLA-C1 and at least one copy of KIR2DL3, wherein the presence of at least one copy of HLA-C1 and at least one copy of KIR2DL3 in the patient's genome indicates that the patient may benefit from a treatment regimen including an NK cell-targeted therapeutic agent; and (b) administering an effective amount of the treatment regimen including the NK cell-targeted therapeutic agent to the patient based on the presence of at least one copy of HLA-C1 and at least one copy of KIR2DL3 in the patient's genome.

In another instance, this document provides a method for treating cancer (e.g., NSCLC) in a patient with this need, the method comprising: (a) determining whether the patient's genome contains at least one copy of HLA-Bw4, wherein the presence of at least one copy of HLA-Bw4 in the patient's genome indicates that the patient may benefit from a treatment regimen including an NK cell-targeted therapeutic agent (e.g., an NK cell conjugate); and (b) administering an effective amount of the treatment regimen including the NK cell-targeted therapeutic agent to the patient based on the presence of at least one copy of HLA-Bw4 in the patient's genome. In some cases, step (a) further comprises determining whether the patient's genome contains at least one copy of KIR3DL1.

In another example, this document provides an NK cell-directed therapeutic agent (e.g., an NK cell binder) for treating cancer (e.g., NSCLC) in patients with this need, the method comprising: (a) determining whether the patient's genome contains at least one copy of HLA-Bw4, wherein the presence of at least one copy of HLA-Bw4 in the patient's genome indicates that the patient may benefit from a treatment regimen comprising an NK cell-directed therapeutic agent; and (b) administering an effective amount of the treatment regimen comprising an NK cell-directed therapeutic agent to the patient based on the presence of at least one copy of HLA-Bw4 in the patient's genome. In some cases, step (a) further comprises determining whether the patient's genome contains at least one copy of KIR3DL1.

In another instance, this document provides a method for treating cancer (e.g., NSCLC) in a patient with this need, the method comprising: (a) determining whether the patient's genome contains at least one copy of HLA-Bw4 and at least one copy of KIR3DL1, wherein the presence of at least one copy of HLA-Bw4 and at least one copy of KIR3DL1 in the patient's genome indicates that the patient may benefit from a treatment regimen including an NK cell-targeted therapeutic agent (e.g., an NK cell conjugate); and (b) administering an effective amount of the treatment regimen including the NK cell-targeted therapeutic agent to the patient based on the presence of at least one copy of HLA-Bw4 and at least one copy of KIR3DL1 in the patient's genome.

In another instance, this document provides an NK cell-targeted therapeutic agent (e.g., an NK cell conjugate) for treating cancer (e.g., NSCLC) in patients with this need, the method comprising: (a) determining whether the patient's genome contains at least one copy of HLA-Bw4 and at least one copy of KIR3DL1, wherein the presence of at least one copy of HLA-Bw4 and at least one copy of KIR3DL1 in the patient's genome indicates that the patient may benefit from a treatment regimen including an NK cell-targeted therapeutic agent; and (b) administering an effective amount of the treatment regimen including the NK cell-targeted therapeutic agent to the patient based on the presence of at least one copy of HLA-Bw4 and at least one copy of KIR3DL1 in the patient's genome.

In another example, this document provides a method for identifying patients with cancer (e.g., NSCLC) who may benefit from a treatment regimen including NK cell-targeted therapeutic agents (e.g., NK cell binders), the method comprising determining whether the patient's genome contains at least one copy of HLA-C1, wherein the presence of at least one copy of HLA-C1 in the patient's genome identifies the patient as a patient who may benefit from treatment using a treatment regimen including NK cell-targeted therapeutic agents. In some cases, the method further comprises determining whether the patient's genome contains at least one copy of KIR2DL3.

In another example, this document provides a method for identifying a patient with cancer (e.g., NSCLC) who may benefit from a treatment regimen including an NK cell-targeted therapy (e.g., an NK cell binder), the method comprising: (a) performing germline whole-genome sequencing (WGS) or whole-exome sequencing (WES) by fragmenting a DNA sample obtained from the patient to produce fragmented DNA, adding an adaptor to the fragmented DNA to produce one or more libraries, and sequencing the one or more libraries; and (b) identifying the patient as a patient who may benefit from a treatment regimen including an NK cell-targeted therapy by determining whether the patient's genome contains at least one copy of HLA-C1, wherein the presence of at least one copy of HLA-C1 in the patient's genome identifies the patient as a patient who may benefit from treatment using a treatment regimen including an NK cell-targeted therapy. In some cases, the method further comprises determining whether the patient's genome contains at least one copy of KIR2DL3.

In another instance, this article provides a method for identifying a patient with cancer (e.g., NSCLC) who may benefit from a treatment regimen including an NK cell-targeted therapy (e.g., an NK cell conjugate), the method comprising determining whether the patient’s genome contains at least one copy of HLA-C1 and at least one copy of KIR2DL3, wherein the presence of at least one copy of HLA-C1 and at least one copy of KIR2DL3 in the patient’s genome identifies the patient as a patient who may benefit from treatment using a treatment regimen including an NK cell-targeted therapy.

In another instance, this document provides a method for identifying a patient with cancer (e.g., NSCLC) who may benefit from a treatment regimen including NK cell-targeted therapy (e.g., NK cell binders), the method comprising: (a) performing germline WGS or WES by fragmenting a DNA sample obtained from the patient to generate fragmented DNA, adding an adaptor to the fragmented DNA to generate one or more libraries, and sequencing the one or more libraries; and (b) identifying the patient as a patient who may benefit from a treatment regimen including NK cell-targeted therapy by determining whether the patient's genome contains at least one copy of HLA-C1 and at least one copy of KIR2DL3, wherein the presence of at least one copy of HLA-C1 and at least one copy of KIR2DL3 in the patient's genome identifies the patient as a patient who may benefit from treatment using a treatment regimen including NK cell-targeted therapy.

In another instance, this document provides a method for identifying patients with cancer (e.g., NSCLC) who may benefit from a treatment regimen including NK cell-targeted therapeutic agents (e.g., NK cell binders), the method comprising determining whether the patient's genome contains at least one copy of HLA-Bw4, wherein the presence of at least one copy of HLA-Bw4 in the patient's genome identifies the patient as a patient who may benefit from treatment using a treatment regimen including NK cell-targeted therapeutic agents. In some cases, the method further comprises determining whether the patient's genome contains at least one copy of KIR3DL1.

In another example, this document provides a method for identifying a patient with cancer (e.g., NSCLC) who may benefit from a treatment regimen including an NK cell-targeted therapy (e.g., an NK cell binder), the method comprising: (a) performing germline WGS or WES by fragmenting a DNA sample obtained from the patient to generate fragmented DNA, adding an adaptor to the fragmented DNA to generate one or more libraries, and sequencing the one or more libraries; and (b) identifying the patient as a patient who may benefit from a treatment regimen including an NK cell-targeted therapy by determining whether the patient's genome contains at least one copy of HLA-Bw4, wherein the presence of at least one copy of HLA-Bw4 in the patient's genome identifies the patient as a patient who may benefit from treatment using a treatment regimen including an NK cell-targeted therapy. In some cases, the method further includes determining whether the patient's genome contains at least one copy of KIR3DL1.

In another instance, this article provides a method for identifying patients with cancer (e.g., NSCLC) who may benefit from a treatment regimen including NK cell-targeted therapy (e.g., NK cell conjugates), the method comprising determining whether the patient’s genome contains at least one copy of HLA-Bw4 and at least one copy of KIR3DL1, wherein the presence of at least one copy of HLA-Bw4 and at least one copy of KIR3DL1 in the patient’s genome identifies the patient as a patient who may benefit from treatment using a treatment regimen including NK cell-targeted therapy.

In another instance, this document provides a method for identifying a patient with cancer (e.g., NSCLC) who may benefit from a treatment regimen including NK cell-directed therapy (e.g., NK cell binders), the method comprising: (a) performing germline WGS or WES by fragmenting a DNA sample obtained from the patient to generate fragmented DNA, adding an adaptor to the fragmented DNA to generate one or more libraries, and sequencing the one or more libraries; and (b) identifying the patient as a patient who may benefit from a treatment regimen including NK cell-directed therapy by determining whether the patient's genome contains at least one copy of HLA-Bw4 and at least one copy of KIR3DL1, wherein the presence of at least one copy of HLA-Bw4 and at least one copy of KIR3DL1 in the patient's genome identifies the patient as a patient who may benefit from treatment using a treatment regimen including NK cell-directed therapy.

In another example, this article provides a method for selecting a therapy for a patient with cancer (e.g., NSCLC), the method comprising: (a) determining whether the patient's genome contains at least one copy of HLA-C1, wherein the presence of at least one copy of HLA-C1 in the patient's genome indicates that the patient may benefit from a treatment regimen including an NK cell-targeted therapeutic agent (e.g., an NK cell conjugate); and (b) selecting a treatment regimen including an NK cell-targeted therapeutic agent based on the presence of at least one copy of HLA-C1 in the patient's genome. In some cases, the method further comprises determining whether the patient's genome contains at least one copy of KIR2DL3.

In another instance, this article provides a method for selecting a therapy for a patient with cancer (e.g., NSCLC), the method comprising: (a) determining whether the patient’s genome contains at least one copy of HLA-C1 and at least one copy of KIR2DL3, wherein the presence of at least one copy of HLA-C1 and at least one copy of KIR2DL3 in the patient’s genome indicates that the patient may benefit from a treatment regimen including an NK cell-targeted therapy (e.g., an NK cell conjugate); and (b) selecting a treatment regimen including an NK cell-targeted therapy based on the presence of at least one copy of HLA-C1 and at least one copy of KIR2DL3 in the patient’s genome.

In another example, this document provides a method for selecting a therapy for a patient with cancer (e.g., NSCLC), the method comprising: (a) determining whether the patient's genome contains at least one copy of HLA-Bw4, wherein the presence of at least one copy of HLA-Bw4 in the patient's genome indicates that the patient may benefit from a treatment regimen including an NK cell-targeted therapeutic agent (e.g., an NK cell conjugate); and (b) selecting a treatment regimen including an NK cell-targeted therapeutic agent based on the presence of at least one copy of HLA-Bw4 in the patient's genome. In some cases, the method further comprises determining whether the patient's genome contains at least one copy of KIR3DL1.

In another instance, this article provides a method for selecting a therapy for a patient with cancer (e.g., NSCLC), the method comprising: (a) determining whether the patient’s genome contains at least one copy of HLA-Bw4 and at least one copy of KIR3DL1, wherein the presence of at least one copy of HLA-Bw4 and at least one copy of KIR3DL1 in the patient’s genome indicates that the patient may benefit from a treatment regimen including an NK cell-targeted therapy agent (e.g., an NK cell conjugate); and (b) selecting a treatment regimen including an NK cell-targeted therapy agent based on the presence of at least one copy of HLA-Bw4 and at least one copy of KIR3DL1 in the patient’s genome.

In any of the instances described herein, any suitable method may be used to determine the presence of HLA-C1, HLA-Bw4, KIR2DL3, and/or KIR3DL1 in a patient's genome. For example, in some cases, next-generation sequencing, Sanger sequencing, polymerase chain reaction (PCR)-based assays, or single nucleotide polymorphism (SNP) arrays are used to determine the presence of HLA-C1, HLA-Bw4, KIR2DL3, and/or KIR3DL1 in a patient's genome. In some cases, next-generation sequencing includes germline whole-genome sequencing or germline whole-exome sequencing. In some cases, PCR-based assays include quantitative PCR (qPCR), genotyping using sequence-specific primers (SSPs), or genotyping using sequence-specific oligonucleotide probes (SSOs).

Any example described herein may include a treatment regimen that administers an effective amount of an NK cell-targeted therapeutic agent (e.g., an NK cell binder) to a patient.

In another instance, this article provides a method for treating cancer (e.g., NSCLC) in a patient who has been identified as having an increased level of NK cell infiltration relative to a reference level of natural killer (NK) cell infiltration in a tumor sample obtained from the patient, the method comprising administering to the patient an effective amount of a treatment regimen comprising an NK cell-targeted therapeutic agent (e.g., an NK cell binder).

In another instance, this article provides an NK cell-targeted therapeutic agent (e.g., an NK cell binder) for treating cancer (e.g., NSCLC) in a patient who has been identified as having an increased level of NK cell infiltration in a tumor sample obtained from that patient relative to a reference level of NK cell infiltration.

In another instance, this article provides a method for treating cancer (e.g., NSCLC) in a patient with this need, the method comprising: (a) determining whether a tumor sample obtained from the patient has an increased level of NK cell infiltration relative to a reference level of NK cell infiltration, wherein an increased level of NK cell infiltration in the tumor sample obtained from the patient relative to a reference level of NK cell infiltration indicates that the patient may benefit from a treatment regimen including an NK cell-targeted therapeutic agent (e.g., an NK cell binder); and (b) administering an effective amount of the treatment regimen including the NK cell-targeted therapeutic agent to the patient based on the increased level of NK cell infiltration in the tumor sample obtained from the patient relative to a reference level of NK cell infiltration.

In another instance, this document provides an NK cell-targeted therapeutic agent (e.g., an NK cell binder) in a method for treating cancer (e.g., NSCLC) in a patient with this need, the method comprising: (a) determining whether a tumor sample obtained from the patient has an increased level of NK cell infiltration relative to a reference level of NK cell infiltration, wherein an increased level of NK cell infiltration in the tumor sample obtained from the patient relative to a reference level of NK cell infiltration indicates that the patient may benefit from a treatment regimen including the NK cell-targeted therapeutic agent; and (b) administering an effective amount of the treatment regimen including the NK cell-targeted therapeutic agent to the patient based on the increased level of NK cell infiltration in the tumor sample obtained from the patient relative to a reference level of NK cell infiltration.

In another instance, this article provides a method for identifying a patient with cancer (e.g., NSCLC) who may benefit from a treatment regimen including an NK cell-targeted therapeutic agent (e.g., an NK cell binder), the method comprising determining whether a tumor sample obtained from the patient has an increased level of NK cell infiltration relative to a reference level of NK cell infiltration, wherein an increased level of NK cell infiltration relative to a reference level of NK cell infiltration in a tumor sample obtained from the patient indicates that the patient may benefit from a treatment regimen including an NK cell-targeted therapeutic agent.

In another instance, this article provides a method for identifying a patient with cancer (e.g., NSCLC) who may benefit from a treatment regimen including an NK cell-targeted therapeutic agent (e.g., an NK cell conjugate), the method comprising: (a) contacting a tumor sample obtained from the patient with one or more antibody or nucleotide probes conjugated to one or more NK cell markers to determine the level of NK cell infiltration in the tumor sample; and (b) determining whether the tumor sample obtained from the patient has an increased level of NK cell infiltration relative to a reference level of NK cell infiltration, wherein an increased level of NK cell infiltration relative to a reference level of NK cell infiltration in the tumor sample obtained from the patient indicates that the patient may benefit from a treatment regimen including an NK cell-targeted therapeutic agent.

Any suitable antibody or nucleotide probe can be used, for example, an antibody or nucleotide probe that binds to any NK cell marker described herein or known in the art, such as one or more of the following genes (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or all 20): CD160, CD244, CTSW, FASLG, GZMA, GZMB, GZMH, IL18RAP, IL2RB, KIR2DL4, KLRB1, KLRC3, KLRD1, KRLF1, KLRK1, NCR1, NKG7, PRF1, XCL1 and XCL2.

In another instance, this article provides a method for selecting a therapy for a patient with cancer (e.g., NSCLC), the method comprising: (a) determining whether a tumor sample obtained from the patient has an increased level of NK cell infiltration relative to a reference level of NK cell infiltration, wherein an increased level of NK cell infiltration in the tumor sample obtained from the patient indicates that the patient may benefit from a treatment regimen including an NK cell-targeted therapeutic agent (e.g., an NK cell binder); and (b) selecting a treatment regimen including an NK cell-targeted therapeutic agent based on the increased level of NK cell infiltration in the tumor sample obtained from the patient relative to a reference level of NK cell infiltration.

Any example described herein may include a treatment regimen that administers an effective amount of an NK cell-targeted therapeutic agent (e.g., an NK cell binder) to a patient.

In any of the instances described herein, the level of NK cell infiltration can be determined using any suitable method. For example, in some cases, the level of NK cell infiltration can be determined by, for example, by immunofluorescence, immunohistochemistry, Western blotting, flow cytometry, or any other suitable method, by determining the expression level of NK cell gene signatures, by counting the number of NK cells in a tumor sample, or by detecting the presence or level of one or more NK cell markers. Any suitable NK cell marker or combination of NK cell markers can be used. In some aspects, NK cell markers are costimulatory receptors, such as TRAIL, CD16a, CD16b, NKG2D, NKG2C, 4-1BB, OX40, CD27, 2B4, DNAM-1, NKp30, NKp46, NKp44, NKp80, KIR2DS1, and KIR2DS2. In some aspects, NK cell receptors are costimulatory receptors. In some aspects, co-inhibitory receptors are NKG2A or KIR, such as KIR3DL1, KIR2DL1, KIR2DL2, or KIR2DL3.

In any of the instances described herein, the NK cell genetic signature may include one or more of the following genes (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or all 20): CD160, CD244, CTSW, FASLG, GZMA, GZMB, GZMH, IL18RAP, IL2RB, KIR2DL4, KLRB1, KLRC3, KLRD1, KRLF1, KLRK1, NCR1, NKG7, PRF1, XCL1, and XCL2. In some cases, the NK cell genetic signature contains at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least ten, at least eleven, at least twelve, at least thirteen, at least fourteen, at least fifteen, at least sixteen, at least seventeen, at least eighteen, at least nineteen, or all twenty of the genes in question. In some cases, the reference level for NK cell infiltration is the median level. In some cases, the median level is the median level in a patient population with cancer (e.g., NSCLC).

In some instances, the patient's genome contains at least one copy of HLA-C1 (e.g., 1 or 2 copies) or at least one copy of HLA-Bw4 (e.g., 1 or 2 copies). In some cases, the patient's genome contains at least one copy of HLA-C1 (e.g., 1 or 2 copies). In some cases, the patient's genome contains at least one copy of HLA-Bw4 (e.g., 1 or 2 copies).

In some instances, the patient's genome contains at least one copy of KIR2DL3 (e.g., 1 or 2 copies) or at least one copy of KIR3DL1 (e.g., 1 or 2 copies). In some cases, the patient's genome contains at least one copy of KIR2DL3 (e.g., 1 or 2 copies). In some cases, the patient's genome contains at least one copy of KIR3DL1 (e.g., 1 or 2 copies).

Any suitable NK cell-directed therapy may be used, such as any NK cell-directed therapy described in Section V below. Any suitable NK cell-directed therapy may be used, including any NK cell-directed therapy described herein (see, for example, Section V below). In some instances, any NK cell-directed therapy described in Hodgins et al. J. Clin. Invest. 129(9):3499-3510, 2019 may be used. In some cases, NK cell-directed therapy includes allogeneic NK cells, autologous NK cells, off-the-shelf NK cells, chimeric antigen receptor (CAR)-NK cells, cytokine therapy, NK cell conjugates (e.g., bispecific killer cell conjugates (BiKE), trispecific killer cell conjugates (TriKE), or tetraspecific killer cell conjugates (TetraKE)), NK cell checkpoint receptor antagonists, or oncolytic viruses.

Any of the aforementioned instances of administering NK cell-targeted therapeutic agents to a patient may further include administering a PD-1 axis binding antagonist (e.g., atezolizumab) to a patient.

This article also provides in vitro methods for NK cell education. For example, such methods may include contacting NK cells expressing KIR2DL3 or KIR3DL1 with cells expressing HLA-C1 or HLA-Bw4, for example, under conditions and for a duration sufficient for NK cell education. Such educated NK cells can be used for adoptive cell therapy, for example, in patients with an HLA loss phenotype.

For example, this article provides an in vitro method for NK cell education, which includes contacting NK cells expressing KIR2DL3 with cells expressing HLA-C1, for example, under conditions and for a duration sufficient for NK cell education.

In another instance, this article provides an in vitro method for NK cell education, which involves contacting NK cells expressing KIR3DL1 with cells expressing HLA-Bw4, for example, under conditions and for a duration sufficient for NK cell education.

These NK cells can endogenously express KIR2DL3 or KIR3DL1, or they can be engineered to express KIR2DL3 or KIR3DL1 (e.g., using gene editing or transduction (e.g., lentiviral transduction)). Any suitable engineering method can be used.

In some instances, in vitro-educated NK cells, as described herein, can be used for adoptive cell therapy. For example, in some instances, in vitro-educated NK cells, as described herein, can be used to treat patients with an HLA loss phenotype (e.g., NSCLC patients). In some instances, in vitro-educated NK cells, as described herein, can be used to treat patients with cancer (e.g., NSCLC) whose genome lacks HLA-C1, HLA-Bw4, KIR2DL3, and/or KIR3DL1. In some instances, the patient's genome lacks HLA-C1. In some instances, the patient's genome lacks HLA-Bw4. In some instances, the patient's genome lacks KIR2DL3. In some instances, the patient's genome lacks KIR3DL1.

In another instance, this article provides a method for treating cancer (e.g., NSCLC) in patients whose genome has been identified as lacking KIR2DL3 or KIR3DL1, the method comprising administering to the patient an effective dose of a treatment regimen including an NK cell-targeted therapeutic agent.

In another instance, this article provides an NK cell-targeted therapeutic agent for treating cancer (e.g., NSCLC) in patients with this need whose genome has been identified as lacking KIR2DL3 or KIR3DL1.

In another instance, this article provides a method for treating cancer (e.g., NSCLC) in a patient with this need, the method comprising: (a) determining whether the patient's genome lacks KIR2DL3 or KIR3DL1, wherein the lack of KIR2DL3 or KIR3DL1 in the patient's genome indicates that the patient may benefit from a treatment regimen including an NK cell-targeted therapy; and (b) administering an effective amount of the treatment regimen including an NK cell-targeted therapy to the patient based on the lack of KIR2DL3 or KIR3DL1 in the patient's genome.

In another instance, this document provides an NK cell-targeted therapeutic agent in a method for treating cancer (e.g., NSCLC) in a patient with this need, the method comprising: (a) determining whether the patient's genome lacks KIR2DL3 or KIR3DL1, wherein the lack of KIR2DL3 or KIR3DL1 in the patient's genome indicates that the patient may benefit from a treatment regimen including an NK cell-targeted therapeutic agent; and (b) administering an effective amount of the treatment regimen including the NK cell-targeted therapeutic agent to the patient based on the lack of KIR2DL3 or KIR3DL1 in the patient's genome.

In another instance, this article provides a method for identifying patients with cancer (e.g., NSCLC) who may benefit from a treatment regimen including NK cell-targeted therapy agents, the method comprising determining whether the patient’s genome lacks KIR2DL3 or KIR3DL1, wherein the lack of KIR2DL3 or KIR3DL1 in the patient’s genome identifies the patient as a patient who may benefit from a treatment regimen including NK cell-targeted therapy agents.

In another instance, this document provides a method for identifying a patient with cancer (e.g., NSCLC) who may benefit from a treatment regimen including NK cell-directed therapy, the method comprising: (a) performing germline WGS or WES by fragmenting a DNA sample obtained from the patient to generate fragmented DNA, adding an adaptor to the fragmented DNA to generate one or more libraries, and sequencing the one or more libraries; and (b) identifying the patient as a patient who may benefit from a treatment regimen including NK cell-directed therapy by determining whether the patient's genome lacks KIR2DL3 or KIR3DL1, wherein the lack of KIR2DL3 or KIR3DL1 in the patient's genome identifies the patient as a patient who may benefit from treatment using a treatment regimen including NK cell-directed therapy.

In another instance, this article provides a method for selecting a therapy for a patient with cancer (e.g., NSCLC), the method comprising: (a) determining whether the patient’s genome lacks KIR2DL3 or KIR3DL1, wherein the lack of KIR2DL3 or KIR3DL1 in the patient’s genome identifies the patient as potentially eligible for treatment using a treatment regimen that includes an NK cell-targeted therapy; and (b) selecting a treatment regimen that includes an NK cell-targeted therapy based on the lack of KIR2DL3 or KIR3DL1 in the patient’s genome.

Any suitable NK cell-directed therapy may be used, including any NK cell-directed therapy described herein (see, for example, Section V below). In some instances, any NK cell-directed therapy described in Hodgins et al. J. Clin. Invest. 129(9):3499-3510, 2019 may be used. In some cases, NK cell-directed therapeutic agents include allogeneic NK cells, autologous NK cells, off-the-shelf NK cells, chimeric antigen receptor (CAR)-NK cells, cytokine therapy, NK cell conjugates (e.g., bispecific killer cell conjugates (BiKE), trispecific killer cell conjugates (TriKE), or tetraspecific killer cell conjugates (TetraKE)), NK cell checkpoint receptor antagonists, or oncolytic viruses.

In some instances, NK cell-directed therapeutic agents include allogeneic NK cells, autologous NK cells, off-the-shelf NK cells, or combinations thereof. In some cases, NK cell-directed therapeutic agents contain allogeneic NK cells. In other cases, NK cell-directed therapeutic agents contain autologous NK cells. In still other cases, NK cell-directed therapeutic agents contain off-the-shelf NK cells.

In some instances, allogeneic NK cells, autologous NK cells, or off-the-shelf NK cells are engineered to express KIR2DL3 or KIR3DL1. For example, in some cases, allogeneic NK cells, autologous NK cells, or off-the-shelf NK cells are engineered to express KIR2DL3. In other cases, allogeneic NK cells, autologous NK cells, or off-the-shelf NK cells are engineered to express KIR3DL1.

In some instances, the patient's genome contains at least one copy of HLA-C1 (e.g., 1 or 2 copies) or at least one copy of HLA-Bw4 (e.g., 1 or 2 copies). In some cases, the patient's genome contains at least one copy of HLA-C1 (e.g., 1 or 2 copies). In some cases, the patient's genome contains at least one copy of HLA-Bw4 (e.g., 1 or 2 copies).

In some instances, the patient's genome contains at least one copy of KIR2DL3 (e.g., 1 or 2 copies) or at least one copy of KIR3DL1 (e.g., 1 or 2 copies). In some cases, the patient's genome contains at least one copy of KIR2DL3 (e.g., 1 or 2 copies). In some cases, the patient's genome contains at least one copy of KIR3DL1 (e.g., 1 or 2 copies).

In some instances, treatment with allogeneic NK cells, autologous NK cells, or off-the-shelf NK cells engineered to express KIR2DL3 or KIR3DL1 has enabled patients to benefit from treatment regimens that include PD-1 axis binding antagonists (e.g., atezolizumab).

Any of the foregoing examples may further include, for example, administering a treatment regimen to a patient, including a PD-1 axis binding antagonist (e.g., atezolizumab), before, during, or after treatment regimens that include NK cell-targeted therapies.

In some instances, the benefit is in terms of improved overall survival (OS) or improved progression-free survival (PFS). In some cases, the benefit is in terms of improved OS. In some cases, the benefit is in terms of improved PFS. In some cases, the improvement is relative to treatment regimens that do not include a PD-1 axis binding antagonist (e.g., atezolizumab).

Cancer can be any suitable cancer. For example, in some instances, the cancer is lung cancer (e.g., NSCLC), kidney cancer (e.g., renal cell carcinoma), or melanoma.

In some cases, the cancer is NSCLC. In some cases, the NSCLC is non-squamous NSCLC or squamous NSCLC. In some cases, the NSCLC is non-squamous NSCLC. In some cases, the non-squamous NSCLC is locally advanced or metastatic non-squamous NSCLC. In some cases, the non-squamous NSCLC is metastatic non-squamous NSCLC. In other cases, the NSCLC is squamous NSCLC. In some cases, the squamous NSCLC is locally advanced or metastatic squamous NSCLC. In some cases, the squamous NSCLC is metastatic squamous NSCLC.

For example, in one instance, this article provides a method for treating NSCLC in a patient whose genome has been determined to contain at least one copy of HLA-C1, the method comprising administering to the patient an effective amount of a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab). In some cases, the patient's genome further contains at least one copy of KIR2DL3.

In another instance, this article provides a PD-1 axis binding antagonist (e.g., atezolizumab) for treating NSCLC in patients with this need whose genome has been identified as containing at least one copy of HLA-C1. In some cases, the patient's genome further contains at least one copy of KIR2DL3.

In another instance, this article provides a method for treating NSCLC in patients with this need whose genome has been identified as containing at least one copy of HLA-C1 and at least one copy of KIR2DL3, the method comprising administering to the patient an effective amount of a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab).

In another instance, this article provides a PD-1 axis binding antagonist (e.g., atezolizumab) for treating NSCLC in patients with this need whose genome has been identified as containing at least one copy of HLA-C1 and at least one copy of KIR2DL3.

In another instance, this article provides a method for treating NSCLC in patients with this need whose genome has been identified as containing at least one copy of HLA-Bw4, the method comprising administering to the patient an effective dose of a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab). In some cases, the patient's genome further contains at least one copy of KIR3DL1.

In another instance, this article provides a PD-1 axis binding antagonist (e.g., atezolizumab) for treating NSCLC in patients with this need whose genome has been identified as containing at least one copy of HLA-Bw4. In some cases, the patient's genome further contains at least one copy of KIR3DL1.

In another instance, this article provides a method for treating NSCLC in patients with this need whose genome has been identified as containing at least one copy of HLA-Bw4 and at least one copy of KIR3DL1, the method comprising administering to the patient an effective amount of a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab).

In another instance, this article provides a PD-1 axis binding antagonist (e.g., atezolizumab) for treating NSCLC in patients with this need whose genome has been identified as containing at least one copy of HLA-Bw4 and at least one copy of KIR3DL1.

In another instance, this document provides a method for treating NSCLC in patients with this need, the method comprising: (a) determining whether the patient's genome contains at least one copy of HLA-C1, wherein the presence of at least one copy of HLA-C1 in the patient's genome indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab); and (b) administering an effective amount of the treatment regimen including the PD-1 axis binding antagonist to the patient based on the presence of at least one copy of HLA-C1 in the patient's genome. In some cases, step (a) further comprises determining whether the patient's genome contains at least one copy of KIR2DL3.

In another example, this document provides a method for treating NSCLC in patients with this need using a PD-1 axis binding antagonist (e.g., atezolizumab), the method comprising: (a) determining whether the patient's genome contains at least one copy of HLA-C1, wherein the presence of at least one copy of HLA-C1 in the patient's genome indicates that the patient may benefit from a treatment regimen comprising a PD-1 axis binding antagonist; and (b) administering an effective amount of the treatment regimen comprising a PD-1 axis binding antagonist to the patient based on the presence of at least one copy of HLA-C1 in the patient's genome. In some cases, step (a) further comprises determining whether the patient's genome contains at least one copy of KIR2DL3.

In another instance, this article provides a method for treating NSCLC in patients with this need, the method comprising: (a) determining whether the patient’s genome contains at least one copy of HLA-C1 and at least one copy of KIR2DL3, wherein the presence of at least one copy of HLA-C1 and at least one copy of KIR2DL3 in the patient’s genome indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab); and (b) administering an effective amount of the treatment regimen including a PD-1 axis binding antagonist to the patient based on the presence of at least one copy of HLA-C1 and at least one copy of KIR2DL3 in the patient’s genome.

In another instance, this article provides a PD-1 axis binding antagonist (e.g., atezolizumab) for treating NSCLC in patients with this need, the method comprising: (a) determining whether the patient’s genome contains at least one copy of HLA-C1 and at least one copy of KIR2DL3, wherein the presence of at least one copy of HLA-C1 and at least one copy of KIR2DL3 in the patient’s genome indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist; and (b) administering an effective amount of the treatment regimen including a PD-1 axis binding antagonist to the patient based on the presence of at least one copy of HLA-C1 and at least one copy of KIR2DL3 in the patient’s genome.

In another instance, this document provides a method for treating NSCLC in patients with this need, the method comprising: (a) determining whether the patient's genome contains at least one copy of HLA-Bw4, wherein the presence of at least one copy of HLA-Bw4 in the patient's genome indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab); and (b) administering an effective amount of the treatment regimen including the PD-1 axis binding antagonist to the patient based on the presence of at least one copy of HLA-Bw4 in the patient's genome. In some cases, step (a) further comprises determining whether the patient's genome contains at least one copy of KIR3DL1.

In another example, this article provides a PD-1 axis binding antagonist (e.g., atezolizumab) for treating NSCLC in patients with this need, the method comprising: (a) determining whether the patient's genome contains at least one copy of HLA-Bw4, wherein the presence of at least one copy of HLA-Bw4 in the patient's genome indicates that the patient may benefit from a treatment regimen comprising a PD-1 axis binding antagonist; and (b) administering an effective amount of the treatment regimen comprising a PD-1 axis binding antagonist to the patient based on the presence of at least one copy of HLA-Bw4 in the patient's genome. In some cases, step (a) further comprises determining whether the patient's genome contains at least one copy of KIR3DL1.

In another instance, this article provides a method for treating NSCLC in patients with this need, the method comprising: (a) determining whether the patient’s genome contains at least one copy of HLA-Bw4 and at least one copy of KIR3DL1, wherein the presence of at least one copy of HLA-Bw4 and at least one copy of KIR3DL1 in the patient’s genome indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab); and (b) administering an effective amount of a treatment regimen including a PD-1 axis binding antagonist to the patient based on the presence of at least one copy of HLA-Bw4 and at least one copy of KIR3DL1 in the patient’s genome.

In another instance, this article provides a PD-1 axis binding antagonist for treating NSCLC in patients with this need, the method comprising: (a) determining whether the patient’s genome contains at least one copy of HLA-Bw4 and at least one copy of KIR3DL1, wherein the presence of at least one copy of HLA-Bw4 and at least one copy of KIR3DL1 in the patient’s genome indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab); and (b) administering an effective amount of the treatment regimen including the PD-1 axis binding antagonist to the patient based on the presence of at least one copy of HLA-Bw4 and at least one copy of KIR3DL1 in the patient’s genome.

In another instance, this article provides a method for identifying patients with NSCLC who may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab), the method comprising determining whether the patient's genome contains at least one copy of HLA-C1, wherein the presence of at least one copy of HLA-C1 in the patient's genome identifies the patient as a patient who may benefit from treatment with a treatment regimen including a PD-1 axis binding antagonist. In some cases, the method further comprises determining whether the patient's genome contains at least one copy of KIR2DL3.

In another instance, this document provides a method for identifying patients with NSCLC who may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab), the method comprising: (a) performing germline WGS or WES by fragmenting a DNA sample obtained from the patient to generate fragmented DNA, adding an adaptor to the fragmented DNA to generate one or more libraries, and sequencing the one or more libraries; and (b) identifying the patient as a patient who may benefit from a treatment regimen including a PD-1 axis binding antagonist by determining whether the patient's genome contains at least one copy of HLA-C1, wherein the presence of at least one copy of HLA-C1 in the patient's genome identifies the patient as a patient who may benefit from treatment with a treatment regimen including a PD-1 axis binding antagonist. In some cases, the method further comprises determining whether the patient's genome contains at least one copy of KIR2DL3.

In another instance, this article provides a method for identifying patients with NSCLC who may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab), the method comprising determining whether the patient’s genome contains at least one copy of HLA-C1 and at least one copy of KIR2DL3, wherein the presence of at least one copy of HLA-C1 and at least one copy of KIR2DL3 in the patient’s genome identifies the patient as a patient who may benefit from treatment with a treatment regimen including a PD-1 axis binding antagonist.

In another instance, this article provides a method for identifying patients with NSCLC who may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab), the method comprising: (a) performing germline WGS or WES by fragmenting a DNA sample obtained from the patient to generate fragmented DNA, adding an adaptor to the fragmented DNA to generate one or more libraries, and sequencing the one or more libraries; and (b) identifying the patient as a patient who may benefit from a treatment regimen including a PD-1 axis binding antagonist by determining whether the patient's genome contains at least one copy of HLA-C1 and at least one copy of KIR2DL3, wherein the presence of at least one copy of HLA-C1 and at least one copy of KIR2DL3 in the patient's genome identifies the patient as a patient who may benefit from treatment using a treatment regimen including a PD-1 axis binding antagonist.

In another instance, this article provides a method for identifying patients with NSCLC who may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab), the method comprising determining whether the patient's genome contains at least one copy of HLA-Bw4, wherein the presence of at least one copy of HLA-Bw4 in the patient's genome identifies the patient as a patient who may benefit from treatment with a treatment regimen including a PD-1 axis binding antagonist. In some cases, the method further comprises determining whether the patient's genome contains at least one copy of KIR3DL1.

In another instance, this document provides a method for identifying patients with NSCLC who may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab), the method comprising: (a) performing germline WGS or WES by fragmenting a DNA sample obtained from the patient to generate fragmented DNA, adding an adaptor to the fragmented DNA to generate one or more libraries, and sequencing the one or more libraries; and (b) identifying the patient as a patient who may benefit from a treatment regimen including a PD-1 axis binding antagonist by determining whether the patient's genome contains at least one copy of HLA-Bw4, wherein the presence of at least one copy of HLA-Bw4 in the patient's genome identifies the patient as a patient who may benefit from treatment with a treatment regimen including a PD-1 axis binding antagonist. In some cases, the method further includes determining whether the patient's genome contains at least one copy of KIR3DL1.

In another instance, this article provides a method for identifying patients with NSCLC who may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab), the method comprising determining whether the patient’s genome contains at least one copy of HLA-Bw4 and at least one copy of KIR3DL1, wherein the presence of at least one copy of HLA-Bw4 and at least one copy of KIR3DL1 in the patient’s genome identifies the patient as a patient who may benefit from treatment using a treatment regimen including a PD-1 axis binding antagonist.

In another instance, this article provides a method for identifying patients with NSCLC who may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab), the method comprising: (a) performing germline WGS or WES by fragmenting a DNA sample obtained from the patient to generate fragmented DNA, adding an adaptor to the fragmented DNA to generate one or more libraries, and sequencing the one or more libraries; and (b) identifying the patient as a patient who may benefit from a treatment regimen including a PD-1 axis binding antagonist by determining whether the patient's genome contains at least one copy of HLA-Bw4 and at least one copy of KIR3DL1, wherein the presence of at least one copy of HLA-Bw4 and at least one copy of KIR3DL1 in the patient's genome identifies the patient as a patient who may benefit from treatment using a treatment regimen including a PD-1 axis binding antagonist.

In another instance, this paper provides a method for selecting a therapy for a patient with NSCLC, the method comprising: (a) determining whether the patient's genome contains at least one copy of HLA-C1, wherein the presence of at least one copy of HLA-C1 in the patient's genome indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab); and (b) selecting a treatment regimen including a PD-1 axis binding antagonist based on the presence of at least one copy of HLA-C1 in the patient's genome. In some cases, the method further comprises determining whether the patient's genome contains at least one copy of KIR2DL3.

In another instance, this article provides a method for selecting a therapy for a patient with NSCLC, the method comprising: (a) determining whether the patient’s genome contains at least one copy of HLA-C1 and at least one copy of KIR2DL3, wherein the presence of at least one copy of HLA-C1 and at least one copy of KIR2DL3 in the patient’s genome indicates that the patient may benefit from a treatment regimen that includes a PD-1 axis binding antagonist (e.g., atezolizumab); and (b) selecting a treatment regimen that includes a PD-1 axis binding antagonist based on the presence of at least one copy of HLA-C1 and at least one copy of KIR2DL3 in the patient’s genome.

In another instance, this paper provides a method for selecting a therapy for a patient with NSCLC, the method comprising: (a) determining whether the patient's genome contains at least one copy of HLA-Bw4, wherein the presence of at least one copy of HLA-Bw4 in the patient's genome indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab); and (b) selecting a treatment regimen including a PD-1 axis binding antagonist based on the presence of at least one copy of HLA-Bw4 in the patient's genome. In some cases, the method further comprises determining whether the patient's genome contains at least one copy of KIR3DL1.

In another instance, this article provides a method for selecting a therapy for a patient with NSCLC, the method comprising: (a) determining whether the patient’s genome contains at least one copy of HLA-Bw4 and at least one copy of KIR3DL1, wherein the presence of at least one copy of HLA-Bw4 and at least one copy of KIR3DL1 in the patient’s genome indicates that the patient may benefit from a treatment regimen that includes a PD-1 axis binding antagonist (e.g., atezolizumab); and (b) selecting a treatment regimen that includes a PD-1 axis binding antagonist based on the presence of at least one copy of HLA-Bw4 and at least one copy of KIR3DL1 in the patient’s genome.

Any of the foregoing examples may further include treatment regimens that administer an effective amount of a PD-1 axis binding antagonist to the patient.

In any of the instances described herein, any suitable method may be used to determine the presence of HLA-C1, HLA-Bw4, KIR2DL3, and/or KIR3DL1 in a patient's genome. For example, in some cases, next-generation sequencing, Sanger sequencing, polymerase chain reaction (PCR)-based assays, or single nucleotide polymorphism (SNP) arrays are used to determine the presence of HLA-C1, HLA-Bw4, KIR2DL3, and/or KIR3DL1 in a patient's genome. In some cases, next-generation sequencing includes germline whole-genome sequencing or germline whole-exome sequencing. In some cases, PCR-based assays include quantitative PCR (qPCR), genotyping using sequence-specific primers (SSPs), or genotyping using sequence-specific oligonucleotide probes (SSOs).

In another instance, this article provides a method for treating NSCLC in a patient who has been identified as having an increased level of NK cell infiltration in a tumor sample obtained from the patient relative to a reference level of NK cell infiltration, the method comprising administering to the patient an effective amount of a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab).

In another instance, this article provides a PD-1 axis binding antagonist (e.g., atezolizumab) for treating NSCLC in patients who have been identified as having increased NK cell infiltration levels relative to a reference level of NK cell infiltration in tumor samples obtained from the patient.

In another instance, this article provides a method for treating NSCLC in a patient with this need, the method comprising: (a) determining whether a tumor sample obtained from the patient has an increased level of NK cell infiltration relative to a reference level of NK cell infiltration, wherein an increased level of NK cell infiltration in the tumor sample obtained from the patient relative to a reference level of NK cell infiltration indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab); and (b) administering an effective amount of the treatment regimen including a PD-1 axis binding antagonist to the patient based on the increased level of NK cell infiltration in the tumor sample obtained from the patient relative to a reference level of NK cell infiltration.

In another instance, this article provides a method for treating NSCLC in patients with this need using a PD-1 axis binding antagonist (e.g., atezolizumab), the method comprising: (a) determining whether a tumor sample obtained from the patient has an increased level of NK cell infiltration relative to a reference level of NK cell infiltration, wherein an increased level of NK cell infiltration in the tumor sample obtained from the patient relative to a reference level of NK cell infiltration indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist; and (b) administering an effective amount of a treatment regimen including a PD-1 axis binding antagonist to the patient based on the increased level of NK cell infiltration in the tumor sample obtained from the patient relative to a reference level of NK cell infiltration.

In another instance, this article provides a method for identifying patients with NSCLC who may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab), the method comprising determining whether a tumor sample obtained from the patient has an increased level of NK cell infiltration relative to a reference level of NK cell infiltration, wherein an increased level of NK cell infiltration relative to a reference level of NK cell infiltration in a tumor sample obtained from the patient indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist.

In another instance, this article provides a method for identifying patients with NSCLC who may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab), the method comprising: (a) contacting a tumor sample obtained from the patient with one or more antibody or nucleotide probes bound to one or more NK cell markers to determine the level of NK cell infiltration in the tumor sample; and (b) determining whether the tumor sample obtained from the patient has an increased level of NK cell infiltration relative to a reference level of NK cell infiltration, wherein an increased level of NK cell infiltration relative to a reference level of NK cell infiltration in the tumor sample obtained from the patient indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist.

In another instance, this article provides a method for selecting a therapy for a patient with NSCLC, the method comprising: (a) determining whether a tumor sample obtained from the patient has an increased level of NK cell infiltration relative to a reference level of NK cell infiltration, wherein an increased level of NK cell infiltration in a tumor sample obtained from the patient relative to a reference level of NK cell infiltration indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab); and (b) selecting a treatment regimen including a PD-1 axis binding antagonist based on the increased level of NK cell infiltration in a tumor sample obtained from the patient relative to a reference level of NK cell infiltration.

Any example described herein may include a treatment regimen that administers an effective amount of a PD-1 axis binding antagonist (e.g., atezolizumab) to a patient.

In any of the instances described herein, the level of NK cell infiltration can be determined using any suitable method. For example, in some cases, the level of NK cell infiltration can be determined by means of immunofluorescence, immunohistochemistry, Western blotting, flow cytometry, or any other suitable method, by determining the expression level of NK cell gene signatures, by counting the number of NK cells in a tumor sample, or by detecting the presence or level of one or more NK cell markers.

In any of the instances described herein, the NK cell genetic signature may include one or more of the following genes (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or all 20): CD160, CD244, CTSW, FASLG, GZMA, GZMB, GZMH, IL18RAP, IL2RB, KIR2DL4, KLRB1, KLRC3, KLRD1, KRLF1, KLRK1, NCR1, NKG7, PRF1, XCL1, and XCL2. In some cases, the NK cell gene signature contains at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least ten, at least eleven, at least twelve, at least thirteen, at least fourteen, at least fifteen, at least sixteen, at least seventeen, at least eighteen, at least nineteen, or all twenty of the genes in question. In some cases, the reference level for NK cell infiltration is the median level. In some cases, the median level is the median level within the NSCLC patient population.

In another instance, this article provides a method for treating NSCLC in patients whose genome has been identified as lacking KIR2DL3 or KIR3DL1, the method comprising administering to the patient an effective dose of a treatment regimen including an NK cell-targeted therapeutic agent.

In another instance, this article provides an NK cell-targeted therapeutic agent for treating NSCLC in patients whose genome has been identified as lacking KIR2DL3 or KIR3DL1.

In another instance, this article provides a method for treating NSCLC in patients with this need, the method comprising: (a) determining whether the patient's genome lacks KIR2DL3 or KIR3DL1, wherein the lack of KIR2DL3 or KIR3DL1 in the patient's genome indicates that the patient may benefit from a treatment regimen including an NK cell-targeted therapy; and (b) administering an effective amount of the treatment regimen including an NK cell-targeted therapy to the patient based on the lack of KIR2DL3 or KIR3DL1 in the patient's genome.

In another instance, this document provides an NK cell-targeted therapeutic agent in a method for treating NSCLC in patients with this need, the method comprising: (a) determining whether the patient's genome lacks KIR2DL3 or KIR3DL1, wherein the lack of KIR2DL3 or KIR3DL1 in the patient's genome indicates that the patient may benefit from a treatment regimen including an NK cell-targeted therapeutic agent; and (b) administering an effective amount of a treatment regimen including an NK cell-targeted therapeutic agent to the patient based on the lack of KIR2DL3 or KIR3DL1 in the patient's genome.

In another instance, this article provides a method for identifying patients with NSCLC who may benefit from a treatment regimen including NK cell-targeted therapies, the method comprising determining whether the patient’s genome lacks KIR2DL3 or KIR3DL1, wherein the lack of KIR2DL3 or KIR3DL1 in the patient’s genome identifies the patient as a patient who may benefit from treatment using a treatment regimen including NK cell-targeted therapies.

In another instance, this article provides a method for identifying patients with NSCLC who may benefit from a treatment regimen including NK cell-directed therapy, the method comprising: (a) performing germline WGS or WES by fragmenting a DNA sample obtained from the patient to generate fragmented DNA, adding an adaptor to the fragmented DNA to generate one or more libraries, and sequencing the one or more libraries; and (b) identifying the patient as a patient who may benefit from a treatment regimen including NK cell-directed therapy by determining whether the patient's genome lacks KIR2DL3 or KIR3DL1, wherein the lack of KIR2DL3 or KIR3DL1 in the patient's genome identifies the patient as a patient who may benefit from treatment using a treatment regimen including NK cell-directed therapy.

In another instance, this article provides a method for selecting a therapy for a patient with cancer (e.g., NSCLC), the method comprising: (a) determining whether the patient’s genome lacks KIR2DL3 or KIR3DL1, wherein the lack of KIR2DL3 or KIR3DL1 in the patient’s genome identifies the patient as potentially eligible for treatment using a treatment regimen that includes an NK cell-targeted therapy; and (b) selecting a treatment regimen that includes an NK cell-targeted therapy based on the lack of KIR2DL3 or KIR3DL1 in the patient’s genome.

Any suitable NK cell-directed therapy may be used, including any NK cell-directed therapy described herein (see, for example, Section V below). In some instances, any NK cell-directed therapy described in Hodgins et al. J. Clin. Invest. 129(9):3499-3510, 2019 may be used. In some cases, NK cell-directed therapeutic agents include allogeneic NK cells, autologous NK cells, off-the-shelf NK cells, chimeric antigen receptor (CAR)-NK cells, cytokine therapy, NK cell conjugates (e.g., bispecific killer cell conjugates (BiKE), trispecific killer cell conjugates (TriKE), or tetraspecific killer cell conjugates (TetraKE)), NK cell checkpoint receptor antagonists, or oncolytic viruses.

In some instances, NK cell-directed therapeutic agents include allogeneic NK cells, autologous NK cells, off-the-shelf NK cells, or combinations thereof. In some cases, NK cell-directed therapeutic agents contain allogeneic NK cells. In other cases, NK cell-directed therapeutic agents contain autologous NK cells. In still other cases, NK cell-directed therapeutic agents contain off-the-shelf NK cells.

In some instances, allogeneic NK cells, autologous NK cells, or off-the-shelf NK cells are engineered to express KIR2DL3 or KIR3DL1. For example, in some cases, allogeneic NK cells, autologous NK cells, or off-the-shelf NK cells are engineered to express KIR2DL3. In other cases, allogeneic NK cells, autologous NK cells, or off-the-shelf NK cells are engineered to express KIR3DL1.

In some instances, the patient's genome contains at least one copy of HLA-C1 (e.g., 1 or 2 copies) or at least one copy of HLA-Bw4 (e.g., 1 or 2 copies). In some cases, the patient's genome contains at least one copy of HLA-C1 (e.g., 1 or 2 copies). In some cases, the patient's genome contains at least one copy of HLA-Bw4 (e.g., 1 or 2 copies).

In some instances, treatment with allogeneic NK cells, autologous NK cells, or off-the-shelf NK cells engineered to express KIR2DL3 or KIR3DL1 has enabled patients to benefit from treatment regimens that include PD-1 axis binding antagonists (e.g., atezolizumab).

Any of the foregoing examples may further include, for example, administering a treatment regimen to a patient, including a PD-1 axis binding antagonist (e.g., atezolizumab), before, during, or after treatment regimens that include NK cell-targeted therapies.

In some instances, the benefit is in terms of improved overall survival (OS) or improved progression-free survival (PFS). In some cases, the benefit is in terms of improved OS. In some cases, the benefit is in terms of improved PFS. In some cases, the improvement is relative to treatment regimens that do not include a PD-1 axis binding antagonist (e.g., atezolizumab).

In some cases, the cancer is kidney cancer. In other cases, kidney cancer is renal cell carcinoma (RCC). In still other cases, RCC is locally advanced or metastatic.

For example, this article provides a method for treating renal cell carcinoma (e.g., RCC) in patients whose genome has been identified as containing at least one copy of HLA-C1, the method comprising administering to the patient an effective dose of a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab). In some cases, the patient's genome further contains at least one copy of KIR2DL3.

In another instance, this article provides a PD-1 axis binding antagonist (e.g., atezolizumab) for the treatment of patients with renal cell carcinoma (e.g., RCC) in need, whose genome has been identified as containing at least one copy of HLA-C1. In some cases, the patient's genome further contains at least one copy of KIR2DL3.

In another instance, this article provides a method for treating renal cell carcinoma (e.g., RCC) in a patient whose genome has been identified as containing at least one copy of HLA-C1 and at least one copy of KIR2DL3, the method comprising administering to the patient an effective dose of a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab).

In another instance, this article provides a PD-1 axis binding antagonist (e.g., atezolizumab) for the treatment of patients with renal cell carcinoma (e.g., RCC) in need of this treatment, whose genome has been identified as containing at least one copy of HLA-C1 and at least one copy of KIR2DL3.

In another instance, this article provides a method for treating renal cell carcinoma (e.g., RCC) in a patient whose genome has been identified as containing at least one copy of HLA-Bw4, the method comprising administering to the patient an effective dose of a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab). In some cases, the patient's genome further contains at least one copy of KIR3DL1.

In another instance, this article provides a PD-1 axis binding antagonist (e.g., atezolizumab) for the treatment of patients with renal cell carcinoma (e.g., RCC) in need, whose genome has been identified as containing at least one copy of HLA-Bw4. In some cases, the patient's genome further contains at least one copy of KIR3DL1.

In another instance, this article provides a method for treating renal cell carcinoma (e.g., RCC) in a patient whose genome has been identified as containing at least one copy of HLA-Bw4 and at least one copy of KIR3DL1, the method comprising administering to the patient an effective amount of a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab).

In another instance, this article provides a PD-1 axis binding antagonist (e.g., atezolizumab) for the treatment of patients with renal cell carcinoma (e.g., RCC) in need of treatment whose genome has been identified as containing at least one copy of HLA-Bw4 and at least one copy of KIR3DL1.

In another instance, this article provides a method for treating renal cell carcinoma (e.g., RCC) in a patient with this need, the method comprising: (a) determining whether the patient's genome contains at least one copy of HLA-C1, wherein the presence of at least one copy of HLA-C1 in the patient's genome indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab); and (b) administering an effective amount of the treatment regimen including the PD-1 axis binding antagonist to the patient based on the presence of at least one copy of HLA-C1 in the patient's genome. In some cases, step (a) further comprises determining whether the patient's genome contains at least one copy of KIR2DL3.

In another example, this article provides a method for treating renal cell carcinoma (e.g., RCC) in patients with this need, using a PD-1 axis binding antagonist (e.g., atezolizumab), the method comprising: (a) determining whether the patient's genome contains at least one copy of HLA-C1, wherein the presence of at least one copy of HLA-C1 in the patient's genome indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist; and (b) administering an effective amount of the treatment regimen including a PD-1 axis binding antagonist to the patient based on the presence of at least one copy of HLA-C1 in the patient's genome. In some cases, step (a) further comprises determining whether the patient's genome contains at least one copy of KIR2DL3.

In another instance, this article provides a method for treating renal cell carcinoma (e.g., RCC) in a patient with this need, the method comprising: (a) determining whether the patient’s genome contains at least one copy of HLA-C1 and at least one copy of KIR2DL3, wherein the presence of at least one copy of HLA-C1 and at least one copy of KIR2DL3 in the patient’s genome indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab); and (b) administering an effective amount of a treatment regimen including a PD-1 axis binding antagonist to the patient based on the presence of at least one copy of HLA-C1 and at least one copy of KIR2DL3 in the patient’s genome.

In another instance, this article provides a PD-1 axis binding antagonist (e.g., atezolizumab) for treating renal cell carcinoma (e.g., RCC) in patients with this need, the method comprising: (a) determining whether the patient’s genome contains at least one copy of HLA-C1 and at least one copy of KIR2DL3, wherein the presence of at least one copy of HLA-C1 and at least one copy of KIR2DL3 in the patient’s genome indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist; and (b) administering an effective amount of the treatment regimen including a PD-1 axis binding antagonist to the patient based on the presence of at least one copy of HLA-C1 and at least one copy of KIR2DL3 in the patient’s genome.

In another instance, this article provides a method for treating renal cell carcinoma (e.g., RCC) in a patient with this need, the method comprising: (a) determining whether the patient's genome contains at least one copy of HLA-Bw4, wherein the presence of at least one copy of HLA-Bw4 in the patient's genome indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab); and (b) administering an effective amount of the treatment regimen including the PD-1 axis binding antagonist to the patient based on the presence of at least one copy of HLA-Bw4 in the patient's genome. In some cases, step (a) further comprises determining whether the patient's genome contains at least one copy of KIR3DL1.

In another example, this article provides a PD-1 axis binding antagonist (e.g., atezolizumab) for treating renal cell carcinoma (e.g., RCC) in patients with this need, the method comprising: (a) determining whether the patient's genome contains at least one copy of HLA-Bw4, wherein the presence of at least one copy of HLA-Bw4 in the patient's genome indicates that the patient may benefit from a treatment regimen comprising a PD-1 axis binding antagonist; and (b) administering an effective amount of the treatment regimen comprising a PD-1 axis binding antagonist to the patient based on the presence of at least one copy of HLA-Bw4 in the patient's genome. In some cases, step (a) further comprises determining whether the patient's genome contains at least one copy of KIR3DL1.

In another instance, this article provides a method for treating renal cell carcinoma (e.g., RCC) in a patient with this need, the method comprising: (a) determining whether the patient’s genome contains at least one copy of HLA-Bw4 and at least one copy of KIR3DL1, wherein the presence of at least one copy of HLA-Bw4 and at least one copy of KIR3DL1 in the patient’s genome indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab); and (b) administering an effective amount of a treatment regimen including a PD-1 axis binding antagonist to the patient based on the presence of at least one copy of HLA-Bw4 and at least one copy of KIR3DL1 in the patient’s genome.

In another instance, this article provides a PD-1 axis binding antagonist (e.g., atezolizumab) for treating renal cell carcinoma (e.g., RCC) in patients with this need, the method comprising: (a) determining whether the patient’s genome contains at least one copy of HLA-Bw4 and at least one copy of KIR3DL1, wherein the presence of at least one copy of HLA-Bw4 and at least one copy of KIR3DL1 in the patient’s genome indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist; and (b) administering an effective amount of the treatment regimen including a PD-1 axis binding antagonist to the patient based on the presence of at least one copy of HLA-Bw4 and at least one copy of KIR3DL1 in the patient’s genome.

In another instance, this article provides a method for identifying patients with renal cell carcinoma (e.g., RCC) who may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab). This method includes determining whether the patient's genome contains at least one copy of HLA-C1, wherein the presence of at least one copy of HLA-C1 in the patient's genome identifies the patient as a patient who may benefit from treatment with a regimen including a PD-1 axis binding antagonist. In some cases, the method further includes determining whether the patient's genome contains at least one copy of KIR2DL3.

In another instance, this document provides a method for identifying a patient with renal cell carcinoma (e.g., RCC) who may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab), the method comprising: (a) performing germline WGS or WES by fragmenting a DNA sample obtained from the patient to generate fragmented DNA, adding an adaptor to the fragmented DNA to generate one or more libraries, and sequencing the one or more libraries; and (b) identifying the patient as a patient who may benefit from a treatment regimen including a PD-1 axis binding antagonist by determining whether the patient's genome contains at least one copy of HLA-C1, wherein the presence of at least one copy of HLA-C1 in the patient's genome identifies the patient as a patient who may benefit from treatment with a treatment regimen including a PD-1 axis binding antagonist. In some cases, the method further comprises determining whether the patient's genome contains at least one copy of KIR2DL3.

In another instance, this article provides a method for identifying patients with renal cell carcinoma (e.g., RCC) who may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab), the method comprising determining whether the patient’s genome contains at least one copy of HLA-C1 and at least one copy of KIR2DL3, wherein the presence of at least one copy of HLA-C1 and at least one copy of KIR2DL3 in the patient’s genome identifies the patient as a patient who may benefit from treatment with a treatment regimen including a PD-1 axis binding antagonist.

In another instance, this article provides a method for identifying patients with renal cell carcinoma (e.g., RCC) who may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab), the method comprising: (a) performing germline WGS or WES by fragmenting a DNA sample obtained from the patient to generate fragmented DNA, adding an adaptor to the fragmented DNA to generate one or more libraries, and sequencing the one or more libraries; and (b) identifying the patient as a patient who may benefit from a treatment regimen including a PD-1 axis binding antagonist by determining whether the patient's genome contains at least one copy of HLA-C1 and at least one copy of KIR2DL3, wherein the presence of at least one copy of HLA-C1 and at least one copy of KIR2DL3 in the patient's genome identifies the patient as a patient who may benefit from treatment using a treatment regimen including a PD-1 axis binding antagonist.

In another instance, this article provides a method for identifying patients with renal cell carcinoma (e.g., RCC) who may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab). This method includes determining whether the patient's genome contains at least one copy of HLA-Bw4, wherein the presence of at least one copy of HLA-Bw4 in the patient's genome identifies the patient as a potential beneficiary of treatment with a regimen including a PD-1 axis binding antagonist. In some cases, the method further includes determining whether the patient's genome contains at least one copy of KIR3DL1.

In another instance, this document provides a method for identifying a patient with renal cell carcinoma (e.g., RCC) who may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab), the method comprising: (a) performing germline WGS or WES by fragmenting a DNA sample obtained from the patient to generate fragmented DNA, adding an adaptor to the fragmented DNA to generate one or more libraries, and sequencing the one or more libraries; and (b) identifying the patient as a patient who may benefit from a treatment regimen including a PD-1 axis binding antagonist by determining whether the patient's genome contains at least one copy of HLA-Bw4, wherein the presence of at least one copy of HLA-Bw4 in the patient's genome identifies the patient as a patient who may benefit from treatment with a treatment regimen including a PD-1 axis binding antagonist. In some cases, the method further includes determining whether the patient's genome contains at least one copy of KIR3DL1.

In another instance, this article provides a method for identifying patients with renal cell carcinoma (e.g., RCC) who may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab), the method comprising determining whether the patient’s genome contains at least one copy of HLA-Bw4 and at least one copy of KIR3DL1, wherein the presence of at least one copy of HLA-Bw4 and at least one copy of KIR3DL1 in the patient’s genome identifies the patient as a patient who may benefit from treatment using a treatment regimen including a PD-1 axis binding antagonist.

In another instance, this article provides a method for identifying patients with renal cell carcinoma (e.g., RCC) who may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab), the method comprising: (a) performing germline WGS or WES by fragmenting a DNA sample obtained from the patient to generate fragmented DNA, adding an adaptor to the fragmented DNA to generate one or more libraries, and sequencing the one or more libraries; and (b) identifying the patient as a patient who may benefit from a treatment regimen including a PD-1 axis binding antagonist by determining whether the patient's genome contains at least one copy of HLA-Bw4 and at least one copy of KIR3DL1, wherein the presence of at least one copy of HLA-Bw4 and at least one copy of KIR3DL1 in the patient's genome identifies the patient as a patient who may benefit from treatment using a treatment regimen including a PD-1 axis binding antagonist.

In another instance, this article provides a method for selecting a therapy for a patient with renal cell carcinoma (e.g., RCC), the method comprising: (a) determining whether the patient's genome contains at least one copy of HLA-C1, wherein the presence of at least one copy of HLA-C1 in the patient's genome indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab); and (b) selecting a treatment regimen including a PD-1 axis binding antagonist based on the presence of at least one copy of HLA-C1 in the patient's genome. In some cases, the method further comprises determining whether the patient's genome contains at least one copy of KIR2DL3.

In another instance, this article provides a method for selecting a therapy for a patient with renal cell carcinoma (e.g., RCC), the method comprising: (a) determining whether the patient’s genome contains at least one copy of HLA-C1 and at least one copy of KIR2DL3, wherein the presence of at least one copy of HLA-C1 and at least one copy of KIR2DL3 in the patient’s genome indicates that the patient may benefit from a treatment regimen that includes a PD-1 axis binding antagonist (e.g., atezolizumab); and (b) selecting a treatment regimen that includes a PD-1 axis binding antagonist based on the presence of at least one copy of HLA-C1 and at least one copy of KIR2DL3 in the patient’s genome.

In another example, this article provides a method for selecting a therapy for a patient with renal cell carcinoma (e.g., RCC), the method comprising: (a) determining whether the patient's genome contains at least one copy of HLA-Bw4, wherein the presence of at least one copy of HLA-Bw4 in the patient's genome indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab); and (b) selecting a treatment regimen including a PD-1 axis binding antagonist based on the presence of at least one copy of HLA-Bw4 in the patient's genome. In some cases, the method further comprises determining whether the patient's genome contains at least one copy of KIR3DL1.

In another instance, this article provides a method for selecting a therapy for a patient with renal cell carcinoma (e.g., RCC), the method comprising: (a) determining whether the patient’s genome contains at least one copy of HLA-Bw4 and at least one copy of KIR3DL1, wherein the presence of at least one copy of HLA-Bw4 and at least one copy of KIR3DL1 in the patient’s genome indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab); and (b) selecting a treatment regimen including a PD-1 axis binding antagonist based on the presence of at least one copy of HLA-Bw4 and at least one copy of KIR3DL1 in the patient’s genome.

Any of the foregoing examples may further include treatment regimens that administer an effective amount of a PD-1 axis binding antagonist (e.g., atezolizumab) to the patient.

In any of the instances described herein, any suitable method may be used to determine the presence of HLA-C1, HLA-Bw4, KIR2DL3, and/or KIR3DL1 in a patient's genome. For example, in some cases, next-generation sequencing, Sanger sequencing, polymerase chain reaction (PCR)-based assays, or single nucleotide polymorphism (SNP) arrays are used to determine the presence of HLA-C1, HLA-Bw4, KIR2DL3, and/or KIR3DL1 in a patient's genome. In some cases, next-generation sequencing includes germline whole-genome sequencing or germline whole-exome sequencing. In some cases, PCR-based assays include quantitative PCR (qPCR), genotyping using sequence-specific primers (SSPs), or genotyping using sequence-specific oligonucleotide probes (SSOs).

In another instance, this article provides a method for treating renal cell carcinoma (e.g., RCC) in a patient who has been identified as having an increased level of NK cell infiltration relative to a reference level of natural killer (NK) cell infiltration in a tumor sample obtained from the patient, the method comprising administering to the patient an effective amount of a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab).

In another instance, this article provides a PD-1 axis binding antagonist (e.g., atezolizumab) for the treatment of patients with renal cell carcinoma (e.g., RCC) who have been identified as having increased NK cell infiltration levels relative to a reference level of NK cell infiltration in tumor samples obtained from the patient.

In another instance, this article provides a method for treating renal cell carcinoma (e.g., RCC) in a patient with this need, the method comprising: (a) determining whether a tumor sample obtained from the patient has an increased level of NK cell infiltration relative to a reference level of NK cell infiltration, wherein an increased level of NK cell infiltration in the tumor sample obtained from the patient relative to a reference level of NK cell infiltration indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab); and (b) administering an effective amount of the treatment regimen including a PD-1 axis binding antagonist to the patient based on the increased level of NK cell infiltration in the tumor sample obtained from the patient relative to a reference level of NK cell infiltration.

In another instance, this article provides a method for treating renal cell carcinoma (e.g., RCC) in a patient with this need, using a PD-1 axis binding antagonist (e.g., atezolizumab), the method comprising: (a) determining whether a tumor sample obtained from the patient has an increased level of NK cell infiltration relative to a reference level of NK cell infiltration, wherein an increased level of NK cell infiltration in the tumor sample obtained from the patient indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist; and (b) administering an effective amount of the treatment regimen including a PD-1 axis binding antagonist to the patient based on the increased level of NK cell infiltration in the tumor sample obtained from the patient relative to a reference level of NK cell infiltration.

In another instance, this article provides a method for identifying patients with renal cell carcinoma (e.g., RCC) who may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab), the method comprising determining whether a tumor sample obtained from the patient has an increased level of NK cell infiltration relative to a reference level of NK cell infiltration, wherein an increased level of NK cell infiltration relative to a reference level of NK cell infiltration in a tumor sample obtained from the patient indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist.

In another instance, this article provides a method for identifying patients with renal cell carcinoma (e.g., RCC) who may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab), the method comprising: (a) contacting a tumor sample obtained from the patient with one or more antibody or nucleotide probes conjugated to one or more NK cell markers to determine the level of NK cell infiltration in the tumor sample; and (b) determining whether the tumor sample obtained from the patient has an increased level of NK cell infiltration relative to a reference level of NK cell infiltration, wherein an increased level of NK cell infiltration relative to a reference level of NK cell infiltration in the tumor sample obtained from the patient indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist.

In another instance, this article provides a method for selecting a therapy for a patient with renal cell carcinoma (e.g., RCC), the method comprising: (a) determining whether a tumor sample obtained from the patient has an increased level of NK cell infiltration relative to a reference level of NK cell infiltration, wherein an increased level of NK cell infiltration in a tumor sample obtained from the patient indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist (e.g., atezolizumab); and (b) selecting a treatment regimen including a PD-1 axis binding antagonist based on the increased level of NK cell infiltration in a tumor sample obtained from the patient relative to a reference level of NK cell infiltration.

Any example described herein may include a treatment regimen that administers an effective amount of a PD-1 axis binding antagonist (e.g., atezolizumab) to a patient.

In any of the instances described herein, the level of NK cell infiltration can be determined using any suitable method. For example, in some cases, the level of NK cell infiltration can be determined by means of immunofluorescence, immunohistochemistry, Western blotting, flow cytometry, or any other suitable method, by determining the expression level of NK cell gene signatures, by counting the number of NK cells in a tumor sample, or by detecting the presence or level of one or more NK cell markers.

In any of the instances described herein, the NK cell genetic signature may include one or more of the following genes (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or all 20): CD160, CD244, CTSW, FASLG, GZMA, GZMB, GZMH, IL18RAP, IL2RB, KIR2DL4, KLRB1, KLRC3, KLRD1, KRLF1, KLRK1, NCR1, NKG7, PRF1, XCL1, and XCL2. In some cases, the NK cell gene signature contains at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least ten, at least eleven, at least twelve, at least thirteen, at least fourteen, at least fifteen, at least sixteen, at least seventeen, at least eighteen, at least nineteen, or all twenty of the genes in question. In some cases, the reference level for NK cell infiltration is the median level. In some cases, the median level is the median level in a patient population with renal cell carcinoma (e.g., RCC).

In another instance, this article provides a method for treating renal cell carcinoma (e.g., RCC) in patients whose genome has been identified as lacking KIR2DL3 or KIR3DL1, the method comprising administering to the patient an effective dose of a treatment regimen including an NK cell-targeted therapeutic agent.

In another instance, this article provides an NK cell-targeted therapeutic agent for treating renal cell carcinoma (e.g., RCC) in patients with this need whose genome has been identified as lacking KIR2DL3 or KIR3DL1.

In another instance, this article provides a method for treating renal cell carcinoma (e.g., RCC) in a patient with this need, the method comprising: (a) determining whether the patient's genome lacks KIR2DL3 or KIR3DL1, wherein the lack of KIR2DL3 or KIR3DL1 in the patient's genome indicates that the patient may benefit from a treatment regimen including an NK cell-targeted therapy; and (b) administering an effective amount of the treatment regimen including an NK cell-targeted therapy to the patient based on the lack of KIR2DL3 or KIR3DL1 in the patient's genome.

In another instance, this document provides an NK cell-directed therapeutic agent in a method for treating renal cell carcinoma (e.g., RCC) in a patient with such need, the method comprising: (a) determining whether the patient's genome lacks KIR2DL3 or KIR3DL1, wherein the lack of KIR2DL3 or KIR3DL1 in the patient's genome indicates that the patient may benefit from a treatment regimen including an NK cell-directed therapeutic agent; and (b) administering an effective amount of the treatment regimen including the NK cell-directed therapeutic agent to the patient based on the lack of KIR2DL3 or KIR3DL1 in the patient's genome.

In another instance, this article provides a method for identifying patients with renal cell carcinoma (e.g., RCC) who may benefit from a treatment regimen including NK cell-targeted therapy agents, the method comprising determining whether the patient’s genome lacks KIR2DL3 or KIR3DL1, wherein the lack of KIR2DL3 or KIR3DL1 in the patient’s genome identifies the patient as a patient who may benefit from a treatment regimen including NK cell-targeted therapy agents.

In another instance, this article provides a method for identifying patients with renal cell carcinoma (e.g., RCC) who may benefit from a treatment regimen including NK cell-directed therapy, the method comprising: (a) performing germline WGS or WES by fragmenting a DNA sample obtained from the patient to generate fragmented DNA, adding an adaptor to the fragmented DNA to generate one or more libraries, and sequencing the one or more libraries; and (b) identifying the patient as a patient who may benefit from a treatment regimen including NK cell-directed therapy by determining whether the patient's genome lacks KIR2DL3 or KIR3DL1, wherein the lack of KIR2DL3 or KIR3DL1 in the patient's genome identifies the patient as a patient who may benefit from treatment using a treatment regimen including NK cell-directed therapy.

In another instance, this article provides a method for selecting a therapy for a patient with renal cell carcinoma (e.g., RCC), the method comprising: (a) determining whether the patient’s genome lacks KIR2DL3 or KIR3DL1, wherein the lack of KIR2DL3 or KIR3DL1 in the patient’s genome identifies the patient as a potential beneficiary of a treatment regimen that includes an NK cell-targeted therapy; and (b) selecting a treatment regimen that includes an NK cell-targeted therapy based on the lack of KIR2DL3 or KIR3DL1 in the patient’s genome.

Any suitable NK cell-directed therapy may be used, including any NK cell-directed therapy described herein (see, for example, Section V below). In some instances, any NK cell-directed therapy described in Hodgins et al. J. Clin. Invest. 129(9):3499-3510, 2019 may be used. In some cases, NK cell-directed therapeutic agents include allogeneic NK cells, autologous NK cells, off-the-shelf NK cells, chimeric antigen receptor (CAR)-NK cells, cytokine therapy, NK cell conjugates (e.g., bispecific killer cell conjugates (BiKE), trispecific killer cell conjugates (TriKE), or tetraspecific killer cell conjugates (TetraKE)), NK cell checkpoint receptor antagonists, or oncolytic viruses.

In some instances, NK cell-directed therapeutic agents include allogeneic NK cells, autologous NK cells, off-the-shelf NK cells, or combinations thereof. In some cases, NK cell-directed therapeutic agents contain allogeneic NK cells. In other cases, NK cell-directed therapeutic agents contain autologous NK cells. In still other cases, NK cell-directed therapeutic agents contain off-the-shelf NK cells.

In some instances, allogeneic NK cells, autologous NK cells, or off-the-shelf NK cells are engineered to express KIR2DL3 or KIR3DL1. For example, in some cases, allogeneic NK cells, autologous NK cells, or off-the-shelf NK cells are engineered to express KIR2DL3. In other cases, allogeneic NK cells, autologous NK cells, or off-the-shelf NK cells are engineered to express KIR3DL1.

In some instances, the patient's genome contains at least one copy of HLA-C1 (e.g., 1 or 2 copies) or at least one copy of HLA-Bw4 (e.g., 1 or 2 copies). In some cases, the patient's genome contains at least one copy of HLA-C1 (e.g., 1 or 2 copies). In some cases, the patient's genome contains at least one copy of HLA-Bw4 (e.g., 1 or 2 copies).

In some instances, treatment with allogeneic NK cells, autologous NK cells, or off-the-shelf NK cells engineered to express KIR2DL3 or KIR3DL1 has enabled patients to benefit from treatment regimens that include PD-1 axis binding antagonists (e.g., atezolizumab).

Any of the foregoing examples may further include, for example, administering a treatment regimen to a patient, including a PD-1 axis binding antagonist (e.g., atezolizumab), before, during, or after treatment regimens that include NK cell-targeted therapies.

In some instances, the benefit is in terms of improved overall survival (OS) or improved progression-free survival (PFS). In some cases, the benefit is in terms of improved OS. In some cases, the benefit is in terms of improved PFS. In some cases, the improvement is relative to treatment regimens that do not include a PD-1 axis binding antagonist.

In any of the instances described in this article, the patient may be a chemotherapy-naïve individual.

In any of the instances described in this article, the treatment plan can be a first-line treatment plan.

Any suitable PD-1 axis binding antagonist can be used, including any PD-1 axis binding antagonist described herein (see, for example, Section IV below). In some instances, the PD-1 axis binding antagonist is selected from the group consisting of PD-L1 binding antagonists, PD-1 binding antagonists, and PD-L2 binding antagonists.

In some instances, the PD-1 axis binding antagonist is a PD-L1 binding antagonist. In some cases, the PD-L1 binding antagonist is an anti-PD-L1 antibody. In some cases, the anti-PD-L1 antibody comprises the hypervariable region (HVR)-H1, HVR-H2, and HVR-H3 sequences of (a) GFTFSDSWIH (SEQ ID NO:3), AWISPYGGSTYYADSVKG (SEQ ID NO:4), and RHWPGGFDY (SEQ ID NO:5), and (b) the HVR-L1, HVR-L2, and HVR-L3 sequences of (b) RASQDVSTAVA (SEQ ID NO:6), SASFLYS (SEQ ID NO:7), and QQYLYHPAT (SEQ ID NO:8). In some cases, the anti-PD-L1 antibody comprises (a) VH, which contains the amino acid sequence of SEQ ID NO:9, and (b) VL, which contains the amino acid sequence of SEQ ID NO:10. In some cases, the anti-PD-L1 antibody is atezolizumab, durvalumab, acimetab, or MDX-1105. In some cases, the anti-PD-L1 antibody is atezolizumab. In some cases, the anti-PD-L1 antibody is administered intravenously or subcutaneously. In some cases, atezolizumab is administered intravenously at a dose of 840 mg every two weeks. In some cases, atezolizumab is administered intravenously at a dose of 1200 mg every three weeks. In some cases, atezolizumab is administered intravenously at a dose of 1680 mg every four weeks.

In other instances, the PD-1 axis binding antagonist is a PD-1 binding antagonist. In some cases, the PD-1 binding antagonist is an anti-PD-1 antibody. In some cases, the anti-PD-1 antibody is nivolumab, pembrolizumab, MEDI-0680, spartazolizumab, cimiprizumab, camrelizumab, sintilimab, tislelizumab, toripalimab, or dotalimab.

In some instances, a PD-1 axis binding antagonist is administered in combination with an effective amount of one or more additional therapeutic agents. For example, in some embodiments, the treatment regimen includes taxanes (e.g., nab-paclitaxel or paclitaxel), platinum-based chemotherapy agents (e.g., carboplatin), anti-angiogenic agents (e.g., anti-VEGF antibodies, such as atezolizumab), NK cell-directed therapy (e.g., NK cell conjugates), or combinations thereof.

In some instances, the treatment regimen further includes taxanes (e.g., nab-paclitaxel or paclitaxel). In some cases, the taxane is nab-paclitaxel. In some cases, the taxane is paclitaxel.

In some instances, the treatment regimen further includes platinum-based chemotherapy agents. In some cases, the platinum-based chemotherapy agent is carboplatin.

In some cases, the treatment regimen further includes an anti-angiogenic agent. In some cases, the anti-angiogenic agent is an anti-VEGF antibody. In some cases, the anti-VEGF antibody is bevacizumab.

Any instance described herein may further include the administration of additional therapeutic agents to the patient. In some cases, the additional therapeutic agent is selected from the group consisting of: immunotherapeutic agents, cytotoxic agents, growth inhibitors, radiotherapy agents, anti-angiogenic agents, and combinations thereof. In some cases, the immunotherapeutic agent is an NK cell-targeting agent, including any NK cell-targeting agent described herein.

In any of the foregoing examples, each dosing cycle can have any suitable length, such as about 7 days, about 14 days, about 21 days, about 28 days, or longer. In some cases, each dosing cycle is about 21 days.

The preferred patient is a human being.

As a general suggestion, the therapeutically effective dose of a PD-1 axis binding antagonist (e.g., atezolizumab) administered to humans will be in the range of about 0.01 to about 50 mg/kg of patient body weight, whether administered once or multiple times.

In some exemplary embodiments, the PD-1 axis binding antagonist is administered at a dose of about 0.01 to about 45 mg/kg, about 0.01 to about 40 mg/kg, about 0.01 to about 35 mg/kg, about 0.01 to about 30 mg/kg, about 0.01 to about 25 mg/kg, about 0.01 to about 20 mg/kg, about 0.01 to about 15 mg/kg, about 0.01 to about 10 mg/kg, about 0.01 to about 5 mg/kg, or about 0.01 to about 1 mg/kg, for example, daily, weekly, every two weeks, every three weeks, or every four weeks.

In one case, the PD-1 axis binding antagonist is administered to a person at a dose of about 100 mg, about 200 mg, about 300 mg, about 400 mg, about 500 mg, about 600 mg, about 700 mg, about 800 mg, about 900 mg, about 1000 mg, about 1100 mg, about 1200 mg, about 1300 mg, about 1400 mg, or about 1500 mg. In some cases, the PD-1 axis binding antagonist may be administered every three weeks at a dose of about 1000 mg to about 1400 mg (e.g., about 1100 mg to about 1300 mg every three weeks, or about 1150 mg to about 1250 mg every three weeks).

In some cases, patients are given a total of 1 to 50 doses of PD-1 axis-binding antagonists, for example, 1 to 50 doses, 1 to 45 doses, 1 to 40 doses, 1 to 35 doses, 1 to 30 doses, 1 to 25 doses, 1 to 20 doses, 1 to 15 doses, 1 to 10 doses, 1 to 5 doses, 2 to 50 doses, 2 to 45 doses, 2 to 40 doses, 2 to 35 doses, 2 to 30 doses, 2 to 25 doses, 2 to 20 doses, 2 to 15 doses, 2 to 10 doses. 2 to 5 doses, 3 to 50 doses, 3 to 45 doses, 3 to 40 doses, 3 to 35 doses, 3 to 30 doses, 3 to 25 doses, 3 to 20 doses, 3 to 15 doses, 3 to 10 doses, 3 to 5 doses, 4 to 50 doses, 4 to 45 doses, 4 to 40 doses, 4 to 35 doses, 4 to 30 doses, 4 to 25 doses, 4 to 20 doses, 4 to 15 doses, 4 to 10 doses, 4 to 5 doses, 5 to 50 doses, 5 to 45 doses, 5 to 40 doses Dosage, 5 to 35 doses, 5 to 30 doses, 5 to 25 doses, 5 to 20 doses, 5 to 15 doses, 5 to 10 doses, 10 to 50 doses, 10 to 45 doses, 10 to 40 doses, 10 to 35 doses, 10 to 30 doses, 10 to 25 doses, 10 to 20 doses, 10 to 15 doses, 15 to 50 doses, 15 to 45 doses, 15 to 40 doses, 15 to 35 doses, 15 to 30 doses, 15 to 25 doses, 15 to 20 doses, 20 Up to 50 doses, 20 to 45 doses, 20 to 40 doses, 20 to 35 doses, 20 to 30 doses, 20 to 25 doses, 25 to 50 doses, 25 to 45 doses, 25 to 40 doses, 25 to 35 doses, 25 to 30 doses, 30 to 45 doses, 30 to 40 doses, 30 to 35 doses, 35 to 50 doses, 35 to 45 doses, 35 to 40 doses, 40 to 50 doses, 40 to 45 doses, or 45 to 50 doses. In certain cases, the dosage may be administered intravenously.

In some cases, atezolizumab is administered intravenously to patients at a dose of approximately 840 mg every 2 weeks, approximately 1200 mg every 3 weeks, or approximately 1680 mg every 4 weeks.

PD-1 axis binding antagonists and/or any additional therapeutic agents (e.g., taxanes (e.g., nab-paclitaxel or paclitaxel), platinum-based chemotherapy agents (e.g., carboplatin), anti-angiogenic agents (e.g., anti-VEGF antibodies such as bevacizumab), and/or NK cell-directed therapies (e.g., NK cell conjugates)) can be administered in any suitable manner known in the art. For example, PD-1 axis binding antagonists and/or any additional therapeutic agents can be administered sequentially (on different days) or simultaneously (on the same day or within the same treatment cycle). In some cases, PD-1 axis binding antagonists are administered before additional therapeutic agents. In some cases, PD-1 axis binding antagonists are administered after additional therapeutic agents. In some cases, PD-1 axis binding antagonists and/or additional therapeutic agents can be administered on the same day. In some cases, PD-1 axis binding antagonists can be administered before additional therapeutic agents administered on the same day. For example, PD-1 axis binding antagonists can be administered on the same day before chemotherapy. In another example, a PD-1 axis binding antagonist may be administered on the same day before chemotherapy and another drug (e.g., bevacizumab). In other cases, a PD-1 axis binding antagonist may be administered after an additional treatment administered on the same day. In other cases, a PD-1 axis binding antagonist is administered at the same time as an additional treatment. In some cases, a PD-1 axis binding antagonist and an additional treatment are in separate compositions. In some cases, a PD-1 axis binding antagonist and an additional treatment are in the same composition. In some cases, a PD-1 axis binding antagonist is administered via an intravenous line separate from any other treatment administered to the patient on the same day.

PD-1 axis binding antagonists and any additional therapeutic agents can be administered via the same route of administration or via different routes. In some cases, PD-1 axis binding antagonists are administered intravenously, intramuscularly, subcutaneously, topically, orally, percutaneously, intraperitoneally, intraorbitally, implanted, inhaled, intrathecally, intraventricularly, or intranasally. In some cases, additional therapeutic agents are administered intravenously, intramuscularly, subcutaneously, topically, orally, transdermally, intraperitoneally, intraorbitally, implanted, inhaled, intrathecally, intraventricularly, or intranasally.

In preferred embodiments, the PD-1 axis binding antagonist is administered intravenously. In one example, atezolizumab may be administered intravenously over 60 minutes; if the first infusion is tolerated, all subsequent infusions may be delivered over 30 minutes. In some examples, the PD-1 axis binding antagonist is not administered as an intravenous bolus or rapid injection. In some instances, intravenous administration of taxanes (e.g., nab-paclitaxel or paclitaxel), platinum-based chemotherapy agents (e.g., carboplatin), anti-angiogenic agents (e.g., anti-VEGF antibodies, such as bevacizumab), and/or NK cell-targeted therapy (e.g., NK cell conjugates) is performed.

In some cases, the NSCLC is metastatic non-squamous NSCLC, and the treatment regimen includes atezolizumab, nab-paclitaxel, and carboplatin. In some cases, atezolizumab is administered intravenously (IV) at a dose of 1200 mg on day 1 of each 21-day cycle; nab-paclitaxel is administered IV at a dose of 100 mg/ ^m² on days 1, 8, and 15 of each 21-day cycle; and carboplatin is administered at an area under the concentration curve (AUC) of 6 mg/mL/min on day 1 of each 21-day cycle.

In some cases, the NSCLC is metastatic non-squamous NSCLC, and the treatment regimen includes atezolizumab, paclitaxel, and carboplatin. In some cases, atezolizumab is administered as an IV infusion at a dose of 1200 mg on day 1 of each 21-day cycle; paclitaxel is administered as an IV infusion at a dose of 200 mg/ ^m² on day 1 of each 21-day cycle; and carboplatin is administered at an AUC of 6 mg/mL/min on day 1 of each 21-day cycle.

In some cases, the NSCLC is metastatic non-squamous NSCLC, and the treatment regimen includes atezolizumab, bevacizumab, paclitaxel, and carboplatin. In some cases, atezolizumab is administered as an IV infusion at a dose of 1200 mg on day 1 of each 21-day cycle; bevacizumab is administered as an IV infusion at a dose of 15 mg/kg on day 1 of each 21-day cycle; paclitaxel is administered as an IV infusion at a dose of 200 mg/ ^m² on day 1 of each 21-day cycle; and carboplatin is administered at an AUC of 6 mg/mL/min on day 1 of each 21-day cycle.

In some cases, the NSCLC is metastatic squamous NSCLC, and the treatment regimen includes atezolizumab, nab-paclitaxel, and carboplatin. In some cases, atezolizumab is administered as an IV infusion at a dose of 1200 mg on day 1 of each 21-day cycle; nab-paclitaxel is administered as an IV infusion at a dose of 100 mg/ ^m² on days 1, 8, and 15 of each 21-day cycle; and carboplatin is administered at an area under the concentration curve (AUC) of 6 mg/mL/min on day 1 of each 21-day cycle.

In some cases, the NSCLC is metastatic squamous NSCLC, and the treatment regimen includes atezolizumab, paclitaxel, and carboplatin. In some cases, atezolizumab is administered as an IV infusion at a dose of 1200 mg on day 1 of each 21-day cycle; paclitaxel is administered as an IV infusion at a dose of 175 mg/ ^m² or 200 mg/ ^m² on days 1, 8, and 15 of each 21-day cycle; and carboplatin is administered at an AUC of 6 mg/mL/min on day 1 of each 21-day cycle.

In some cases, the renal cell carcinoma is metastatic RCC, and the treatment regimen includes atezolizumab and bevacizumab. In some cases, atezolizumab is administered as an IV infusion at a dose of 1200 mg on days 1 and 22 of each 42-day cycle; and bevacizumab is administered as an IV infusion at a dose of 15 mg/mk on days 1 and 22 of each 42-day cycle.

This article also provides methods for treating a patient with cancer (e.g., NSCLC), comprising administering to the patient a treatment regimen comprising an effective amount of a PD-1 axis binding antagonist (e.g., atezolizumab) and/or taxanes (e.g., nab-paclitaxel or paclitaxel), a platinum-based chemotherapy agent (e.g., carboplatin), an anti-angiogenic agent (e.g., an anti-VEGF antibody, such as bevacizumab), and/or an NK cell-directed therapy (e.g., an NK cell conjugate) in combination with another anticancer agent or cancer therapy. For example, a PD-1 axis binding antagonist may be administered in combination with: additional chemotherapy or chemotherapeutic agents (see definition above); targeted therapy or targeted therapeutic agents; immunotherapy or immunotherapeutic agents, such as monoclonal antibodies; one or more cytotoxic agents (see definition above); or combinations thereof. For example, PD-1 axis-binding antagonists can be administered in combination with bevacizumab, paclitaxel, protein-bound paclitaxel (e.g., albumin-bound paclitaxel), carboplatin, cisplatin, pemetrexed, gemcitabine, etoposide, cobimetinib, vemurafenib, or combinations thereof. PD-1 axis-binding antagonists are anti-PD-L1 antibodies (e.g., atezolizumab) or anti-PD-1 antibodies.

For example, when administered with or without bevacizumab in conjunction with chemotherapy, atezolizumab can be administered at a dose of 1200 mg every 3 weeks before chemotherapy and bevacizumab. In another example, after completing 4 to 6 cycles of chemotherapy, and if bevacizumab is discontinued, atezolizumab can be administered at a dose of 840 mg every 2 weeks, 1200 mg every 3 weeks, or 1680 mg every 4 weeks. In another example, atezolizumab can be administered at a dose of 840 mg, followed by 100 mg/ ^m² of protein-bound paclitaxel (e.g., albumin-bound paclitaxel); for each 28-day cycle, atezolizumab is administered on days 1 and 15, and protein-bound paclitaxel is administered on days 1, 8, and 15. In another example, when administered with carboplatin and etoposide, atezolizumab can be administered at a dose of 1200 mg every 3 weeks before chemotherapy. In another example, after completing four cycles of carboplatin and etoposide, atezolizumab can be administered at a dose of 840 mg every 2 weeks, 1200 mg every 3 weeks, or 1680 mg every 4 weeks. In yet another example, after completing a 28-day cycle of cobimetinib and vemurafenib, atezolizumab can be administered at a dose of 840 mg every 2 weeks, together with cobimetinib at a dose of 60 mg orally once daily (for 21 days, followed by a 7-day break) and vemurafenib at a dose of 720 mg orally twice daily.

In some cases, the treatment may further include additional therapies. Any suitable additional therapies known in the art or described herein may be used. Additional therapies may include radiation therapy, surgery, gene therapy, DNA therapy, viral therapy, RNA therapy, immunotherapy, bone marrow transplantation, nanotherapy, monoclonal antibody therapy, gamma radiation, or a combination of the above.

In some cases, additional treatment may involve the administration of side effect limiters (e.g., agents designed to reduce the occurrence and/or severity of treatment side effects, such as antinausea agents, corticosteroids (e.g., prednisone or equivalents, for example, at a dose of 1 to 2 mg/kg/day), hormone replacement drugs, etc.).

III. Assessment of PD-L1 expression

PD-L1 expression in patients treated according to any of the methods and compositions available for use herein can be assessed. The methods and compositions available for use may include determining the level of PD-L1 expression in a biological sample (e.g., a tumor sample) obtained from the patient. In other examples, the level of PD-L1 expression in a biological sample (e.g., a tumor sample) obtained from the patient has been determined before or after treatment initiation. PD-L1 expression can be determined using any suitable method. For example, PD-L1 expression can be determined as described in U.S. Patent Application Publications US2018/0030138 and US2018/0037655, which are incorporated herein by reference in their entirety. Any suitable tumor sample can be used, such as formalin-fixed and paraffin-embedded (FFPE) tumor samples, archived tumor samples, fresh tumor samples, or frozen tumor samples.

For example, PD-L1 expression can be determined as the percentage of tumor-infiltrating immune cells expressing a detectable level of PD-L1 in a tumor sample, as the percentage of tumor-infiltrating immune cells expressing a detectable level of PD-L1 in the tumor sample, and/or as the percentage of tumor cells expressing a detectable level of PD-L1 in the tumor sample. It should be understood that in any of the foregoing examples, the percentage of tumor-infiltrating immune cells in a tumor sample can be the percentage of the tumor area covered by tumor-infiltrating immune cells in a section of a tumor sample obtained from a patient, for example, as assessed by IHC using an anti-PD-L1 antibody (e.g., SP142 antibody). Any suitable anti-PD-L1 antibody can be used, including, for example, SP142 (Ventana), SP263 (Ventana), 22C3 (Dako), 28-8 (Dako), E1L3N (CellSignaling Technology), 4059 (ProSci, Inc.), h5H1 (Advanced Cell Diagnostics), and 9A11. In some examples, the anti-PD-L1 antibody is SP142. In other examples, the anti-PD-L1 antibody is SP263.

In some examples, tumor samples obtained from patients showed detectable PD-L1 expression levels in less than 1% of tumor cells, 1% or more of tumor cells, 1% to less than 5% of tumor cells, 5% or more of tumor cells, 5% to less than 50% of tumor cells, or 50% or more of tumor cells.

In some examples, tumor samples obtained from patients showed detectable PD-L1 expression levels in tumor-infiltrating immune cells that comprised less than 1% of the tumor sample, more than 1% of the tumor sample, 1% to less than 5% of the tumor sample, more than 5% of the tumor sample, 5% to less than 10% of the tumor sample, or more than 10% of the tumor sample.

In some embodiments, tumor samples can be scored based on PD-L1 positivity in tumor-infiltrating immune cells and/or tumor cells according to the diagnostic assessment criteria shown in Table 1 and/or Table 2, respectively.

Table 1. Diagnostic criteria for tumor-infiltrating immune cells (IC) using IHC

Table 2. Diagnostic criteria for tumor cell (TC) IHC

IV. PD-1 Axial Binding Antagonists

PD-1 axis binding antagonists may include PD-L1 binding antagonists, PD-1 binding antagonists, and PD-L2 binding antagonists. Any suitable PD-1 axis binding antagonist can be used.

A. PD-L1 binding antagonists

In some cases, PD-L1 binding antagonists inhibit the binding of PD-L1 to one or more of its ligand-binding partners. In other cases, PD-L1 binding antagonists inhibit the binding of PD-L1 to PD-1. In still other cases, PD-L1 binding antagonists inhibit the binding of PD-L1 to B7-1. In some cases, PD-L1 binding antagonists inhibit the binding of PD-L1 to both PD-1 and B7-1. PD-L1 binding antagonists can be, but are not limited to, antibodies, their antigen-binding fragments, immunoadhesins, fusion proteins, oligopeptides, or small molecules. In some cases, PD-L1 binding antagonists are small molecules that inhibit PD-L1 (e.g., GS-4224, INCB086550, MAX-10181, INCB090244, CA-170, or ABSK041). In some cases, PD-L1 binding antagonists are small molecules that inhibit both PD-L1 and VISTA. In some cases, the PD-L1 binding antagonist is CA-170 (also known as AUPM-170). In some cases, the PD-L1 binding antagonist is a small molecule that inhibits both PD-L1 and TIM3. In some cases, this small molecule is a compound described in WO 2015/033301 and WO 2015/033299.

In some cases, PD-L1 binding antagonists are anti-PD-L1 antibodies. Various anti-PD-L1 antibodies are considered and described herein. In any case herein, isolated anti-PD-L1 antibodies can bind to human PD-L1 (e.g., human PD-L1 as shown in UniProtKB/Swiss-Prot accession number Q9NZQ7-1, or a variant thereof). In some cases, anti-PD-L1 antibodies are capable of inhibiting binding between PD-L1 and PD-1 and/or between PD-L1 and B7-1. In some cases, anti-PD-L1 antibodies are monoclonal antibodies. In some cases, anti-PD-L1 antibodies are antibody fragments selected from the group consisting of Fab, Fab'-SH, Fv, scFv, and (Fab')2 fragments. In some cases, anti-PD-L1 antibodies are humanized antibodies. In some cases, anti-PD-L1 antibodies are human antibodies. Exemplary anti-PD-L1 antibodies include atezolizumab, MDX-1105, MEDI4736 (dvorumab), MSB0010718C (avimab), SHR-1316, CS1001, envorimab, TQB2450, ZKAB001, LP-002, CX-072, IMC-001, KL-A167, APL-502, cochilimumab, lodalimumab, FAZ053, TG-1501, BGB-A333, BCD-135, AK-106, LDP, GR1405, HLX20, MSB2311, RC98, PDL-GEX, KD036, KY1003, YBL-007, and HS-636. Examples of anti-PD-L1 antibodies that can be used in the methods of the present invention and methods for their preparation are described in International Patent Application Publication No. WO2010/077634 and U.S. Patent No. 8,217,149, each of which is incorporated herein by reference in its entirety.

In some cases, anti-PD-L1 antibodies contain:

(a) HVR-H1, HVR-H2, and HVR-H3 sequences of GFTFSDSWIH (SEQ ID NO:3), AWISPYGGSTYYADSVKG (SEQ ID NO:4), and RHWPGGFDY (SEQ ID NO:5), respectively, and

(b) HVR-L1, HVR-L2 and HVR-L3 sequences of RASQDVSTAVA (SEQ ID NO:6), SASFLYS (SEQ ID NO:7) and QQYLYHPAT (SEQ ID NO:8), respectively.

In one embodiment, the anti-PD-L1 antibody comprises:

(a) Heavy chain variable region (VH) containing the following amino acid sequence:

EVQLVESGGGLVQPGGSLRLSCAASGFTFSDSWIHWVRQAPGKGLEWVAWISPYGGSTYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARRHWPGGFDYWGQGTLVTVSS(SEQ ID NO:9) and

(b) Light chain variable region (VL) containing the following amino acid sequence:

DIQMTQSPSSSLSASVGDRVTITCRASQDVSTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQYLYHPATFGQGTKVEIKR(SEQ ID NO:10).

In some cases, the anti-PD-L1 antibody comprises (a) VH, which comprises an amino acid sequence having at least 95% sequence identity (e.g., at least 95%, 96%, 97%, 98%, or 99% sequence identity) with the sequence of SEQ ID NO:9, or comprises the sequence of SEQ ID NO:9; (b) VL, which comprises an amino acid sequence having at least 95% sequence identity (e.g., at least 95%, 96%, 97%, 98%, or 99% sequence identity) with the sequence of SEQ ID NO:10, or comprises the sequence of SEQ ID NO:10; or (c) VH as described in (a) and VL as described in (b).

In one embodiment, the anti-PD-L1 antibody comprises atezolizumab, which includes:

(a) The following heavy chain amino acid sequence:

EVQLVESGGGLVQPGGSLRLSCAASGFTFSDSWIHWVRQAPGKGLEWVAWISPYGGSTYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARRHWPGGFDYWGQGTLVT VSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTCPPC PAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYASTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPR EPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPG(SEQ ID NO:1) and

(b) The following light chain amino acid sequence:

DIQMTQSPSSSLSASVGDRVTITCRASQDVSTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQYLYHPATFGQGTKVEIKRTVAAP SVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC(SEQ IDNO:2).

In some cases, the anti-PD-L1 antibody is avermab (CAS Registry No.: 1537032-82-8). Avermab, also known as MSB0010718C, is a human monoclonal IgG1 anti-PD-L1 antibody (Merck KGaA, Pfizer).

In some cases, the anti-PD-L1 antibody is durvalumab (CAS Registry No.: 1428935-60-7). Durvalumab, also known as MEDI4736, is the Fc-optimized human monoclonal IgG1 kappa anti-PD-L1 antibody described in WO 2011/066389 and US 2013/034559 (MedImmune, AstraZeneca).

In some cases, the anti-PD-L1 antibody is MDX-1105 (Bristol Myers Squibb). MDX-1105, also known as BMS-936559, is the anti-PD-L1 antibody described in WO 2007/005874.

In some cases, the anti-PD-L1 antibody is LY3300054 (Eli Lilly).

In some cases, the anti-PD-L1 antibody is STI-A1014 (Sorrento Biosciences). STI-A1014 is a human anti-PD-L1 antibody.

In some cases, the anti-PD-L1 antibody is KN035 (Suzhou Alphamab). KN035 is a single-domain antibody (dAB) generated from a camel phage display library.

In some cases, anti-PD-L1 antibodies contain a cleavable moiety or linker that, when cleaved (e.g., by proteases in the tumor microenvironment), activates the antibody antigen-binding domain to bind its antigen, for example, by removing the non-binding spatial moiety. In some cases, the anti-PD-L1 antibody is CX-072 (CytomX Therapeutics).

In some cases, anti-PD-L1 antibodies comprise six HVR sequences (e.g., three heavy chain HVRs and three light chain HVRs) and/or heavy chain variable domains and light chain variable domains from the anti-PD-L1 antibodies described in the following patents: US20160108123, WO 2016/000619, WO 2012/145493, US Patent No. 9,205,148, WO 2013/181634, or WO 2016/061142.

In a more specific context, anti-PD-L1 antibodies exhibit reduced or minimal effector function. More specifically, minimal effector function arises from "effectless Fc mutations" or glycosylation-free mutations. In a further specific case, the effectless Fc mutation is an N297A or D265A/N297A substitution in the constant region. In a further specific case, the effectless Fc mutation is an N297A substitution in the constant region. In some cases, isolated anti-PD-L1 antibodies are glycosylated. Antibody glycosylation is typically N-linked or O-linked. N-linking refers to the carbohydrate moiety being linked to the asparagine residue side chain. The tripeptide sequences asparagine-X-serine and asparagine-X-threonine (where X is any amino acid other than proline) are recognition sequences for the enzymatic linking of the carbohydrate moiety to the asparagine side chain. Therefore, the presence of either of these tripeptide sequences in the polypeptide creates a potential glycosylation site. O-glycosylation refers to the linkage of one of the sugars N-acetylgalactosamine, galactose, or xylose to a hydroxy amino acid (most commonly serine or threonine, although 5-hydroxyproline or 5-hydroxylysine can also be used). Glycosylation sites can be conveniently removed from antibodies by altering the amino acid sequence to remove one of the aforementioned tripeptide sequences (for N-linked glycosylation sites). Mutation can be achieved by substituting an asparagine, serine, or threonine residue within the glycosylation site with another amino acid residue (e.g., glycine, alanine, or a conserved substitution).

B. PD-1 binding antagonists

In some cases, PD-1 axis binding antagonists are PD-1 binding antagonists. For example, in some cases, PD-1 binding antagonists inhibit the binding of PD-1 to one or more of its ligand-binding partners. In some cases, PD-1 binding antagonists inhibit the binding of PD-1 to PD-L1. In other cases, PD-1 binding antagonists inhibit the binding of PD-1 to PD-L2. In still other cases, PD-1 binding antagonists inhibit the binding of PD-1 to both PD-L1 and PD-L2. PD-1 binding antagonists can be, but are not limited to, antibodies, their antigen-binding fragments, immunoadhesins, fusion proteins, oligopeptides, or small molecules. In some cases, PD-1 binding antagonists are immunoadhesins (e.g., immunoadhesins containing an extracellular or PD-1-binding portion of PD-L1 or PD-L2 fused to a constant region (e.g., the Fc region of an immunoglobulin sequence). For example, in some cases, PD-1 binding antagonists are Fc fusion proteins. In some cases, the PD-1 binding antagonist is AMP-224. AMP-224, also known as B7-DCIg, is the PD-L2-Fc fusion soluble receptor described in WO 2010/027827 and WO 2011/066342. In some cases, the PD-1 binding antagonist is a peptide or a small molecule compound. In some cases, the PD-1 binding antagonist is AUNP-12 (Pierre Fabre/Aurigene). See, for example, WO 2012/168944, WO 2015/036927, WO 2015/044900, WO 2015/033303, WO 2013/144704, WO 2013/132317 and WO 2011/161699. In some cases, PD-1 binding antagonists are small molecules that inhibit PD-1.

In some cases, the PD-1 binding antagonist is an anti-PD-1 antibody. A variety of anti-PD-1 antibodies can be used in the methods and uses disclosed herein. In any of the cases herein, the PD-1 antibody can bind to human PD-1 or a variant thereof. In some cases, the anti-PD-1 antibody is a monoclonal antibody. In some cases, the anti-PD-1 antibody is an antibody fragment selected from the group consisting of: Fab, Fab', Fab'-SH, Fv, scFv, and (Fab') ₂ fragments. In some cases, the anti-PD-1 antibody is a humanized antibody. In other cases, the anti-PD-1 antibody is a human antibody. Exemplary anti-PD-1 antagonist antibodies include nivolumab, pembrolizumab, MEDI-0680, PDR001 (spartazumab), REGN2810 (cimiprizumab), BGB-108, palolizumab, camrelizumab, sintilimab, tislelizumab, toripalimab, dotalimab, rivanlimab, sazasanlimab, penaplimab, CS1003, HLX10, SCT-I10A, cepalimumab, baritelimab, genolimab, BI 754091, cilimab, YBL-006, BAT1306, HX008, bouglimab, and AMG. 404, CX-188, JTX-4014, 609A, Sym021, LZM009, F520, SG001, AM0001, ENUM 244C8, ENUM 388D4, STI-1110, AK-103 and hAb21.

In some cases, the anti-PD-1 antibody is nivolumab (CAS Registry No.: 946414-94-4). Nivolumab (Bristol-Myers Squibb/Ono Pharmaceutical (Ono)) is also known as MDX-1106-04, MDX-1106, ONO-4538, BMS-936558, and is the anti-PD-1 antibody described in WO 2006/121168.

In some cases, the anti-PD-1 antibody is pembrolizumab (CAS Registry No.: 1374853-91-4). Pembrolizumab (Merck) is also known as MK-3475, Merck3475, pembrolizumab, SCH-900475, and is the anti-PD-1 antibody described in WO 2009/114335.

In some cases, the anti-PD-1 antibody is MEDI-0680 (AMP-514; AstraZeneca). MEDI-0680 is a humanized IgG4 anti-PD-1 antibody.

In some cases, the anti-PD-1 antibody is PDR001 (CAS registration number 1859072-53-9; Novartis). PDR001 is a humanized IgG4 anti-PD-1 antibody that blocks the binding of PD-L1 and PD-L2 to PD-1.

In some cases, the anti-PD-1 antibody is REGN2810 (Regeneron). REGN2810 is a human anti-PD-1 antibody.

In some cases, the anti-PD-1 antibody is BGB-108 (BeiGene).

In some cases, the anti-PD-1 antibody is BGB-A317 (BeiGene).

In some cases, the anti-PD-1 antibody is JS-001 (Shanghai Junshi Biosciences). JS-001 is a humanized anti-PD-1 antibody.

In some cases, the anti-PD-1 antibody is STI-A1110 (Sorrento Biosciences). STI-A1110 is a human anti-PD-1 antibody.

In some cases, the anti-PD-1 antibody is INCSHR-1210 (Incyte). INCSHR-1210 is a human IgG4 anti-PD-1 antibody.

In some cases, the anti-PD-1 antibody is PF-06801591 (Pfizer).

In some cases, the anti-PD-1 antibody is TSR-042 (also known as ANB011; Tesaro/AnaptysBio).

In some cases, the anti-PD-1 antibody is AM0001 (ARMO Biosciences).

In some cases, the anti-PD-1 antibody is ENUM 244C8 (Enumeral Biomedical Holdings). ENUM 244C8 is an anti-PD-1 antibody that inhibits PD-1 function without preventing PD-L1 from binding to PD-1.

In some cases, the anti-PD-1 antibody is ENUM 388D4 (Enumeral Biomedical Holdings). ENUM 388D4 is an anti-PD-1 antibody that competitively inhibits the binding of PD-L1 to PD-1.

In some cases, anti-PD-1 antibodies comprise six HVR sequences (e.g., three heavy chain HVRs and three light chain HVRs) and/or heavy chain variable domains and light chain variable domains from the anti-PD-1 antibodies described in the following patents: WO 2015/112800, WO 2015/112805, WO 2015/112900, US20150210769, WO2016/089873, WO 20 15/035606、WO 2015/085847、WO 2014/206107、WO 2012/145493、US 9,205,148、WO 2015/119 930, WO 2015/119923, WO 2016/032927, WO 2014/179664, WO 2016/106160 and WO 2014/194302.

In a more specific context, anti-PD-1 antibodies exhibit reduced or minimal effector function. More specifically, minimal effector function arises from "effectless Fc mutations" or glycosylation-free mutations. In a further specific case, the effectless Fc mutation is an N297A or D265A/N297A substitution in the constant region. In some cases, the isolated anti-PD-1 antibody is glycosylated.

C. PD-L2 binding antagonists

In some cases, PD-1 axis binding antagonists are PD-L2 binding antagonists. In other cases, PD-L2 binding antagonists are molecules that inhibit the binding of PD-L2 to its ligand-binding partner. In specific instances, the PD-L2 binding ligand partner is PD-1. PD-L2 binding antagonists can be, but are not limited to, antibodies, their antigen-binding fragments, immunoadhesins, fusion proteins, oligopeptides, or small molecules.

In some cases, the PD-L2 binding antagonist is an anti-PD-L2 antibody. In any of the cases described herein, the anti-PD-L2 antibody may bind to human PD-L2 or a variant thereof. In some cases, the anti-PD-L2 antibody is a monoclonal antibody. In some cases, the anti-PD-L2 antibody is an antibody fragment selected from the group consisting of: Fab, Fab', Fab'-SH, Fv, scFv, and (Fab') ₂ fragments. In some cases, the anti-PD-L2 antibody is a humanized antibody. In other cases, the anti-PD-L2 antibody is a human antibody. In a more specific aspect, the anti-PD-L2 antibody has reduced or minimal effector function. In a more specific aspect, minimal effector function arises from an "effectless Fc mutation" or a glycosylation-free mutation. In a more specific case, the effectless Fc mutation is an N297A or D265A/N297A substitution in the constant region. In some cases, the isolated anti-PD-L2 antibody is glycosylated.

V.NK Cell Targeted Therapy

This document provides a method for treating a patient with cancer (e.g., NSCLC), comprising administering a treatment regimen to the patient including an NK cell-targeted therapeutic agent. Related compositions (e.g., pharmaceutical compositions), kits, and articles of manufacture are also provided. Any method, composition, kit, or article of manufacture described herein may include or relate to any of the pharmaceutical agents described below.

Any suitable NK cell-directed therapy can be used. In some instances, any NK cell-directed therapy described in Hodgins et al., J. Clin. Invest. 129(9):3499-3510, 2019, may be used. In some cases, NK cell-directed therapy includes allogeneic NK cells, autologous NK cells, off-the-shelf NK cells, chimeric antigen receptor (CAR)-NK cells, cytokine therapy, NK cell conjugates (e.g., bispecific killer cell conjugates (BiKE), trispecific killer cell conjugates (TriKE), or tetraspecific killer cell conjugates (TetraKE)), NK cell checkpoint receptor antagonists, or oncolytic viruses. In some cases, NK cell-directed therapy includes adoptive cell transfer (e.g., using allogeneic NK cells, autologous NK cells, off-the-shelf NK cells, or chimeric antigen receptor (CAR)-NK cells).

In some instances, NK cell-directed therapeutic agents include allogeneic NK cells, autologous NK cells, off-the-shelf NK cells, or combinations thereof. In some cases, NK cell-directed therapeutic agents contain allogeneic NK cells. In other cases, NK cell-directed therapeutic agents contain autologous NK cells. In still other cases, NK cell-directed therapeutic agents contain off-the-shelf NK cells.

Exemplary NK cells that can be used include, but are not limited to, FT500 (a generic, off-the-shelf NK cell cancer immunotherapy derived from the master clone iPSC line, see, for example, Cichocki et al., Sci. Trans. Med. 12(568): eaaz5618, 2020), FT516 (a generic, off-the-shelf NK cell cancer immunotherapy derived from the master clone iPSC line, engineered to express a high-affinity 158V, non-cleavable CD16 (hnCD16) Fc receptor, which has been modified to prevent its downregulation and enhance its binding to tumor-targeting antibodies, see, for example, Zhu et al., Blood 135(6): 399-410, 2020), and FT536 (a generic, off-the-shelf NK cell derived from the master clone engineered iPSC line). K-cell cancer immunotherapy includes four functional modifications: CAR targeting the α3 domains of MICA and MICB; a high-affinity 158V, non-cleavable CD16 (hnCD16) Fc receptor that enhances ADCC; IL-15 receptor fusion (IL-15RF) that promotes enhanced NK cell activity; and the elimination of CD38 expression that enhances NK cell metabolic adaptability, persistence, and anti-tumor function. See, for example, de Andrade et al., Cancer Immunol. Res. 8:769-80, 2020), and FT596 (an engineered, universal, off-the-shelf NK-cell cancer immunotherapy derived from a clonal master iPSC line, which has three anti-tumor functional modalities: a CAR targeting the B-cell antigen CD19; a high-affinity 158V, non-cleavable CD16 (hnCD16) Fc receptor; an IL-15 receptor fusion (IL-15RF) that promotes enhanced NK cell activity; and an elimination of CD38 expression that enhances NK cell metabolic adaptability, persistence, and anti-tumor function. CD16)Fc receptor, which has been modified to prevent its downregulation and enhance its binding to tumor-targeting antibodies; and IL-15 receptor fusion (IL-15RF) to promote enhanced NK cell activity; see, for example, Liu et al. New Engl. J. Med. 382:545-53, 2020), FT538 (a universal off-the-shelf NK cell cancer immunotherapy derived from a master clone iPSC line, which incorporates the following three functional modifications: a high-affinity 158V, non-cleavable CD16 (hnCD16)Fc receptor modified to enhance ADCC; IL-15 receptor fusion (IL-15RF) to promote enhanced NK cell activity; and ablation of CD38 expression to reduce the likelihood of NK cell cannibalism), FT573 (a universal off-the-shelf NK cell derived from a master clone engineered iPSC line). Cancer immunotherapy incorporates the following four functional modifications: a CAR targeting B7H3; a high-affinity 158V, non-cleavable CD16 (hnCD16) Fc receptor to enhance ADCC; IL-15 receptor fusion (IL-15RF) to promote enhanced NK cell activity; and elimination of CD38 expression to enhance NK cell metabolic adaptability, persistence, and anti-tumor function. FT576 (a universal, off-the-shelf NK cell cancer immunotherapy derived from the master iPSC line, incorporating the following four functional modifications: a CAR targeting BCMA; a high-affinity 158V, non-cleavable CD16 (hnCD16) Fc receptor modified to enhance ADCC; IL-15 receptor fusion (IL-15RF) to promote enhanced NK cell activity; and elimination of CD38 expression to reduce the likelihood of NK cell cannibalism).

In some instances, NK cells (e.g., allogeneic NK cells, autologous NK cells, or off-the-shelf NK cells) are engineered to express KIR2DL3 or KIR3DL1. For example, in some cases, allogeneic NK cells, autologous NK cells, or off-the-shelf NK cells are engineered to express KIR2DL3. In other cases, allogeneic NK cells, autologous NK cells, or off-the-shelf NK cells are engineered to express KIR3DL1. Any suitable method (including gene editing or transduction (e.g., lentiviral transduction)) can be used to engineer NK cells (e.g., allogeneic NK cells, autologous NK cells, or off-the-shelf NK cells) to express KIR2DL3 or KIR3DL1.

In some instances, allogeneic NK cells are derived from cell lines such as NK92 or KyHG1. In other instances, allogeneic NK cells may be derived from umbilical cord blood or iPSCs.

In some instances, NK cell-directed therapeutic agents are natural killer cells transduced with chimeric antigen receptors (CAR-NK; also known as NAR-T). In some aspects, a chimeric antigen receptor (CAR) comprises an antigen-binding domain (e.g., an antibody or fragment thereof; a T-cell receptor (TCR) or fragment thereof) that binds to a tumor antigen (e.g., tumor antigens listed in Table 3), a transmembrane domain, and one or more intracellular signaling domains, such as a primary signaling domain (e.g., CD3ζ) and/or a co-stimulatory signaling domain (e.g., CD28, 4-1BB) (WO2017-114497; Hartmann et al., EMBO Molecular Medicine, 9(9), 2017). The intracellular signaling domains can act to activate cytotoxicity.

In some instances, CARs are introduced into NK cell populations. As described in WO 2017/117112, NK cell populations can be prepared for CARs, for example, by using a flow module. NK cells can be autologous, such as those derived from a patient, or allogeneic, such as those derived from a donor. In some aspects, CAR-NK cells are introduced into the patient via intravenous or intratumoral administration.

Table 3: Exemplary Tumor Antigens

In some instances, NK cell-targeted therapeutic agents are NK cell conjugates (e.g., bispecific killer cell conjugates (BiKE), trispecific killer cell conjugates (TriKE), or tetraspecific killer cell conjugates (TetraKE)). In some cases, NK cell conjugates bind to one or more targets on the surface of NK cells (e.g., proteins, such as receptors) (e.g., CD16, NKG2D, SLAM family proteins, NKp30, NKp44, or NKp46) and one or more targets on the surface of tumor cells (e.g., proteins, such as receptors) (e.g., tumor antigens, including CD30, CD33, EGFR, BCMA, or any tumor antigens described in Table 3). Exemplary NK cell binders are described, for example, in WO 2019/198051; Reusch et al., mAbs, 6(3):727-738; 2014; US7129330B1; US9035026B2; WO0111059A1; Treder et al., Journal of Clinical Oncology, 34(15suppl), 2016; and Ellwanger et al., J Immunother Cancer, 3(Suppl 2):219, 2015. In some embodiments, the NK cell binder is a nanoparticle-based NK cell binder, such as a nanoparticle-based trispecific NK cell binder (nano-TriNKE) (see, for example, Au et al., Science Advances 6(27):eaba8564, 2020. Exemplary NK cell binders include, for example, IPH6101 (Innate Pharma/Sanofi).

NK cell conjugates can be multispecific, such as bispecific, trispecific, or tetraspecific.

For a specific target, NK cell binders can be multivalent, such as bivalent, trivalent, tetravalent, pentavalent, or hexavalent.

In some instances, NK cell conjugates are bispecific NK cell conjugates comprising a first targeting domain that binds to an epitope on NK cells and a second targeting domain that binds to a different target, such as a tumor antigen. In some aspects, bispecific NK cell conjugates comprise a first targeting domain that binds to CD16a (a protein expressed on the surface of NK cells) and a second targeting domain that binds to the tumor marker CD30. In some aspects, bispecific NK cell conjugates comprise a first targeting domain that binds to CD16a and a second targeting domain that binds to the epidermal growth factor receptor (EGFR) or EGFRvIII. In some aspects, bispecific NK cell conjugates comprise a first targeting domain that binds to NKp46 and a second targeting domain that binds to tumor antigens (e.g., tumor antigens listed in Table 3).

In some cases, any NK cell binder described in WO 2019/198051 may be used, which is incorporated herein by reference in its entirety.

Any suitable NK cell checkpoint receptor antagonist can be used. Exemplary, non-limiting examples of NK cell checkpoint receptor antagonists include, for example, KIR antagonists (e.g., anti-KIR antibodies, such as lirelurumab (IPH2102) targeting KIR2DL1-3 and KIR2DS1-2), CD94/NKG2A antagonists (e.g., anti-CD94 antibodies or protein expression blockers (PEBL) or anti-NKG2A antibodies (e.g., monarizumab (IPH2201) or PEBL)), CTLA-4 antagonists (e.g., anti-CTLA-4 antibodies), PD-1 axis binding antagonists, LAG3 antagonists (e.g., anti-LAG3 antibodies), or TIM-3 antagonists (e.g., anti-TIM-3 antibodies).

Any suitable cytokine therapy can be used. For example, cytokine therapy may include type I interferon, TLR agonists or cGAS/STING agonists, IL-2, IL-12, IL-18, IL-15, combinations thereof or variants thereof (e.g., engineered IL-2 cytokine “super-2” or engineered IL-15 cytokine ALT-803).

Any suitable oncolytic virus can be used, such as any of the oncolytic viruses described in Hodgins et al. above.

VII. Pharmaceutical compositions and formulations

This disclosure also provides pharmaceutical compositions and formulations comprising a PD-1 axis binding antagonist (e.g., atezolizumab) and optionally a pharmaceutical carrier. This disclosure also provides pharmaceutical compositions and formulations comprising taxanes (e.g., nab-paclitaxel or paclitaxel), platinum-based chemotherapeutic agents (e.g., carboplatin), anti-angiogenic agents (e.g., bevacizumab), and/or NK cell-targeting therapeutic agents (e.g., NK cell binders) and optionally a pharmaceutical carrier.

The pharmaceutical compositions and formulations described herein can be prepared as lyophilized formulations or aqueous solutions by mixing an active ingredient (e.g., a PD-1 axis binding antagonist) having the desired purity with one or more optional pharmaceutical carriers (see, for example, Remington's Pharmaceutical Sciences, 16th edition, Osol, A. ed. (1980)).

An exemplary atezolizumab formulation comprises glacial acetic acid, L-histidine, polysorbate 20, and sucrose at pH 5.8. For example, atezolizumab can be provided in a 20 mL vial containing 1200 mg of atezolizumab, formulated in glacial acetic acid (16.5 mg), L-histidine (62 mg), polysorbate 20 (8 mg), and sucrose (821.6 mg) at pH 5.8. In another example, atezolizumab can be provided in a 14 mL vial containing 840 mg of atezolizumab, formulated in glacial acetic acid (11.5 mg), L-histidine (43.4 mg), polysorbate 20 (5.6 mg), and sucrose (575.1 mg) at pH 5.8.

VIII. Products or reagent kits

On the other hand, this document provides articles or kits comprising a PD-1 axis binding antagonist (e.g., atezolizumab) and/or taxanes (e.g., nab-paclitaxel or paclitaxel), platinum-based chemotherapy agents (e.g., carboplatin), anti-angiogenic agents (e.g., bevacizumab), and/or NK cell-directed therapy agents (e.g., NK cell conjugates). In some cases, the articles or kits further comprise a packaging insert containing instructions for using the PD-1 axis binding antagonist to treat a patient’s cancer or delay cancer progression (e.g., NSCLC). In some cases, the articles or kits further comprise a packaging insert containing instructions for using a combination of a PD-1 axis binding antagonist and taxanes (e.g., nab-paclitaxel or paclitaxel), platinum-based chemotherapy agents (e.g., carboplatin), anti-angiogenic agents (e.g., bevacizumab), and/or NK cell-directed therapy agents (e.g., NK cell conjugates) to treat a patient’s cancer or delay cancer progression. Any PD-1 axis binding antagonists and/or taxanes, platinum-based chemotherapy agents, anti-angiogenic agents, and/or NK cell-targeted therapeutic agents described herein may be included in products or kits.

On the other hand, this article provides articles or kits containing NK cell-directed therapeutic agents (e.g., NK cell binders). In some cases, the articles or kits further include a packaging insert containing instructions for using the NK cell-directed therapeutic agent to treat a patient's cancer (e.g., NSCLC) or to delay the progression of cancer (e.g., NSCLC).

In some cases, PD-1 axis binding antagonists and additional therapeutic agents (e.g., taxanes (e.g., nab-paclitaxel or paclitaxel), platinum-based chemotherapy agents (e.g., carboplatin), anti-angiogenic agents (e.g., bevacizumab), and/or NK cell-targeted therapeutic agents (e.g., NK cell binders)) are housed in the same container or separate containers. Suitable containers include, for example, vials, bottles, bags, and syringes. Containers can be formed from a variety of materials, such as glass, plastics (e.g., polyvinyl chloride or polyolefins), or metal alloys (e.g., stainless steel or Hastelloy). In some cases, the container contains the formulation, and a label on or associated with the container may indicate instructions for use. The product or kit may also include other materials desired from a commercial and user perspective, including additional buffers, diluents, filters, needles, syringes, and packaging inserts with instructions for use. In some cases, the product further includes one or more other pharmaceutical agents (e.g., additional chemotherapy agents and antitumor agents). Suitable containers for one or more agents include, for example, vials, bottles, bags, and syringes.

Any product or kit may include instructions for administering a PD-1 axis binding antagonist and/or taxane (e.g., nab-paclitaxel or paclitaxel), platinum-based chemotherapy agent (e.g., carboplatin), anti-angiogenic agent (e.g., bevacizumab), and/or NK cell-targeted therapy agent (e.g., NK cell binder) to a patient according to any of the methods described herein (e.g., any of the methods set forth in Section II above).

In another instance, this article provides an article of manufacture for treating cancer (e.g., NSCLC) in a patient with this need, comprising a PD-1 axis binding antagonist and instructions for administering the PD-1 axis binding antagonist, the patient's genome having been identified as containing at least one copy of HLA-C1. In some cases, the patient's genome further contains at least one copy of KIR2DL3.

In another instance, this article provides an article for treating cancer (e.g., NSCLC) in a patient with this need, comprising a PD-1 axis binding antagonist and instructions for administering the PD-1 axis binding antagonist, the patient’s genome having been identified to contain at least one copy of HLA-C1 and at least one copy of KIR2DL3.

In another instance, this article provides an article of manufacture for treating cancer (e.g., NSCLC) in a patient with this need, comprising a PD-1 axis binding antagonist and instructions for administering the PD-1 axis binding antagonist, the patient's genome having been identified as containing at least one copy of HLA-Bw4. In some cases, the patient's genome further contains at least one copy of KIR3DL1.

In another instance, this article provides an article for treating cancer (e.g., NSCLC) in a patient with this need, comprising a PD-1 axis binding antagonist and instructions for administering the PD-1 axis binding antagonist, the patient’s genome having been identified to contain at least one copy of HLA-Bw4 and at least one copy of KIR3DL1.

In another instance, this article provides an article for treating cancer (e.g., NSCLC) in a patient with this need, comprising a PD-1 axis binding antagonist and instructions for administering the PD-1 axis binding antagonist, the patient having been identified as having an increased level of NK cell infiltration relative to a reference level of NK cell infiltration in a tumor sample obtained from the patient.

In another instance, this article provides an article for treating cancer (e.g., NSCLC) in a patient with this need, comprising an NK cell-directed therapeutic agent and instructions for administering the NK cell-directed therapeutic agent, the patient’s genome having been determined to lack KIR2DL3 or KIR3DL1.

Example

Example 1. Immunogenetic variations involved in NK cell education and NK cell infiltration are associated with the prognosis of non-small cell lung cancer patients treated with immune checkpoint blockade.

a. Introduction

Natural killer (NK) cells are important contributors to anti-tumor immune responses. In addition to NK cell abundance in tumors, various tumor immune evasion strategies targeting NK cells, and the differential distribution of NK cell subsets in different tissue types, the immunogenetic composition of the patient's genome is considered an important determinant of NK cell effectiveness.

In particular, genetic variations in the human leukocyte antigen (HLA) and killer cell immunoglobulin-like receptor (KIR) genes affect NK cell education and function. NK cell education is a dynamic process of achieving functional maturation and self-tolerance, and better NK cell education elicits a stronger response to the “lost self” phenotype. Allele-specific interactions between repressive KIR and HLA proteins contribute to NK cell education (Pende et al., Front. Immunol., 10: Article 1179, 2019). KIR3DL1+ NK cells from Bw4/Bw4 donors have been shown to exhibit increased responsiveness (IFNy production) to MHC-deficient tumors (Kim et al., PNAS, 105(8):3053-3058, 2008). KIR2DL3 and KIR3DL1 are mainly found on KIR A haplotypes, which are often associated with improved response to pathogens (Jamil and Khakoo, J Biomed Biotechnol, 2011: Article ID 298348, 2011).

b. Method

HLA allele variations and the presence of the KIR gene were inferred using germline whole-genome sequencing data from 1,395 patients in three atezolizumab (anti-PD-L1) clinical trials (IMpower130, IMpower131, and IMpower150) in non-small cell lung cancer (NSCLC). IMpower130 (NCT02367781) investigated the safety and efficacy of a treatment regimen including atezolizumab, nab-paclitaxel, and carboplatin in metastatic non-squamous NSCLC compared to a control treatment without atezolizumab. IMpower131 (NCT02367794) investigated the safety and efficacy of a treatment regimen including atezolizumab, paclitaxel, and carboplatin, or atezolizumab, nab-paclitaxel, and carboplatin, in metastatic squamous NSCLC compared to a control treatment without atezolizumab. The IMpower150 (NCT02367794) study investigated the safety and efficacy of treatment regimens including atezolizumab, paclitaxel, and carboplatin, or atezolizumab, bevacizumab, paclitaxel, and carboplatin, in metastatic non-squamous NSCLC compared to control treatments without atezolizumab. The number of patients included in the atezolizumab (atezo) and control groups in the germline analysis is shown in Table 4.

Table 4. Patient populations used for phylogenetic analysis

Research Atezo Group control group IMpower150 433 182 IMpower130 202 102 IMpower131 320 156

HLA alleles were computationally inferred from germline whole-genome sequencing data (30x coverage) using the software HLA-HD (Kawaguchi et al., Hum Mutat., 38(7):788-797, 2017). HLA alleles are described in databases such as IPD and IMGT/HLA (Robinson et al., Nucleic Acids Research, 43:D423-431, 2015).

The presence of KIR genes was computationally inferred from germline whole-genome sequencing data (30x coverage) using the software KPI (Roe et al., Front. Immunol., 11:583013, 2020). KIR genes are variable in copy number, and individuals can carry the KIR gene on chromosome 0, 1, or both chromosomes. The software method used identified the presence or absence of a particular KIR gene in an individual (0 vs. 1/2).

First, association analysis was conducted at the research level. The Cox proportional hazards model was used to study the association between genotype or genetic score (high/low defined median cutoff) and overall or progression-free survival.

The `metagen` function in R's `meta` package is used for meta-analysis (e.g., fixed-effects and random-effects meta-analysis based on estimates and their standard errors). Inverse variance is used for pooling.

As detailed in sections c-f below, the results indicate that both NK cell genotype and NK cell infiltration play important roles in patient responses to PD-L1 cancer immunotherapy.

c. HLA-KIR interaction is associated with prognostic outcomes of atezolizumab treatment in NSCLC.

Compared with patients without this NK cell educational interaction, patients treated with atezolizumab who carried at least one copy of KIR2DL3 and its ligand HLA-C1 had longer overall survival (OS) and progression-free survival (PFS) (N = 955, HR = 0.71, p = 0.0002) (Figures 1A and 1B). No association was observed in the trial's control group.

Similarly, compared with patients without this interaction, patients treated with atezolizumab who carried at least one copy of KIR3DL1 and its ligand HLA-Bw4 had longer OS and PFS (HR = 0.84, p = 0.04) (Figures 2A and 2B). No significant association was found in the chemotherapy control group of the trial (N = 440).

d. HLA-C1 carrier status is associated with the prognosis of atezolizumab treatment.

Similarly, regardless of the patient's KIR genotype, the HLA ligand set defined by KIR interactions (HLA-C1 carrier status and HLA-Bw4 carrier status) was also found to be associated with the prognosis (PFS and OS) of patients treated with atezolizumab (Figures 3A, 3B, 4A and 4B).

Furthermore, in an analysis of recently released datasets of melanoma and NSCLC patients, HLA-C1 carrier status was found to be beneficial to the prognosis of immune checkpoint blockade therapy (N = 1.55, HR = 0.74, p = 0.01, data from Chowell et al., Science, 359(6375):582-587, 2018) (Figures 5A and 5B).

e. NK cell infiltration is associated with prognosis of atezolizumab treatment.

Genetic signatures derived from RNA sequencing data (NK cell score; Cursons et al., Cancer Immunology Research, 7(7):1162-1174, 2019) were used to find that high (above median) NK cell infiltration was associated with longer overall survival (OS) in patients treated with atezolizumab (N=619, HR=0.75, p=0.01) (Figure 6A). The genetic signature included the following 20 genes: CD160, CD244, CTSW, FASLG, GZMA, GZMB, GZMH, IL18RAP, IL2RB, KIR2DL4, KLRB1, KLRC3, KLRD1, KLRF1, KLRK1, NCR1, NKG7, PRF1, XCL1, and XCL2. The measurement of the genetic signature was as described in Cursons et al., Cancer Immunology Research, 7(7):1162-1174, 2019. Association analysis was performed as described in Example 1b above. Similarly, no significant association was found in the control group (N = 288) (Figure 6B).

It is noteworthy that T cell and NK cell infiltration are related (Figures 7A and 7B).

The number of patients included in the atezolizumab and control groups in the NK score RNAseq analysis is shown in Table 5.

Table 5. Patient populations used for RNAseq analysis

Research Atezo Group control group IMpower150 360 151 IMpower131 259 137

Example 2. Assessing the immunogenetic variations involved in NK cell education and NK cell infiltration and their relationship to the prognosis of renal cell carcinoma patients treated with immune checkpoint blockade.

a. Method

HLA allele variants and the presence of the KIR gene were inferred using germline whole-genome sequencing data from the atezolizumab (anti-PD-L1) clinical trial IMmotion151, as described in Example 1. IMmotion151 (NCT02420821) investigated the safety and efficacy of a treatment regimen including atezolizumab and bevacizumab compared to a control treatment including sunitinib in participants with unresectable, locally advanced, or metastatic renal cell carcinoma (RCC).

For NK cell characterization analysis, data from IMmotion150 were also included. IMmotion150 (NCT01984242) investigated the safety and efficacy of treatment regimens including atezolizumab and bevacizumab in participants with unresectable, locally advanced, or metastatic renal cell carcinoma (RCC) compared to control therapy including sunitinib.

b. Association between HLA-KIR interaction in RCC and prognosis of atezolizumab treatment

Compared to patients without this NK cell educational interaction, patients with atezolizumab treated with atezolizumab carrying at least one copy of KIR2DL3 and its ligand HLA-C1 had the following risks of OS and PFS, as shown in Figures 8A and 8B.

Compared to patients without this NK cell educational interaction, patients with atezolizumab treated with atezolizumab carrying at least one copy of KIR3DL1 and its ligand HLA-Bw4 had the following risks of OS and PFS, as shown in Figures 9A and 9B.

c. Association between HLA-C1 or HLA-Bw4 carrier status in RCC and prognosis of atezolizumab treatment

The OS and PFS risks of patients with at least one copy of HLA-C1 treated with atezolizumab are shown in Figures 10A and 10B.

The OS and PFS risks of patients with at least one copy of HLA-Bw4 treated with atezolizumab are shown in Figures 11A and 11B.

d. Association between NK cell infiltration and atezolizumab treatment prognosis in RCC

The OS and PFS risks of patients treated with atezolizumab with high (above median) NK cell infiltration scores as determined in Example 1 are shown in Figures 12A and 12B.

The OS and PFS risks of patients with high (above median) CD8A expression levels treated with atezolizumab are shown in Figures 13A and 13B.

e. Conclusion

A trend toward improved response in RCC patients treated with atezolizumab in the IMmotion151 clinical trial was observed, relating to HLA-KIR genotype and NK cell infiltration, as described in Example 1 for NSCLC. The effect estimates for RCC were within a similar range to those described in Example 1 for the NSCLC trial.

Example 3. Immunogenetic variations involved in NK cell education and NK cell infiltration are associated with the prognosis of non-small cell lung cancer patients treated with immune checkpoint blockade.

Immune-mediated adverse events (imAEs) commonly occur in patients treated with immune checkpoint inhibitors (ICIs), and pneumonia is known to occur in 3–5% of patients treated with anti-PD-1/PD-L1 antibodies (Wang et al., Thorac Cancer, 11:191–197, 2020). Most cases are Grade 1 or 2 events and can be managed with immunosuppressive therapy, but a small percentage of patients experience high-grade events that can be fatal (Naidoo et al., J Clin Oncol, 35:709–717, 2016). In nine Genentech (GNE) clinical trials with available whole-genome sequencing data, pneumonia occurred in 72 out of 1761 patients treated with atezolizumab (anti-PD-L1) (Table 6). The included trials are IMmotion151 (WO29637), IMpassion130 (WO29522), IMpower110 (GO29431), IMpower130 (GO29537), IMpower131 (GO29437), IMpower132 (GO29438), IMpower133 (GO30081), IMpower150 (GO29436), and IMvigor211 (GO29294); these studies included patients with renal cell carcinoma (RCC), triple-negative breast cancer (TNBC), non-squamous or squamous non-small cell lung cancer (NSCLC), small cell lung cancer (SCLC), and bladder urothelial carcinoma.

Table 6. Survey Cohort

GNE, Genentech; PICI, Parker Institute for Cancer Immunotherapy; PMC, Peter McCallum Cancer Center.

HLA genotyping was inferred using HLA-HD (Kawaguchi et al., Hum Mutat, 38:788-797, 2017), and an association study involving 87 alleles was conducted, with a carrier frequency >2%. Two HLA class II alleles, belonging to a common haplotype, showed a significant association with pneumonia risk after multiple adjustments (HLA-DRB1*15:01, HLA-DQA1*01:02), with HLA-DRB1*15:01 showing the strongest association (p = 0.0002, odds ratio (OR) = 2.51). No association was identified in the control group (N = 1192). To confirm these results and test whether the association is generalized across different classes of ICI, two additional cohorts were genotyped using the Illumina genome-wide SNP array (GSA v3) and then HLA imputation was performed using HIBAG (Zheng et al., Pharmacogenomics:14:192-200, 2014): the cohorts were (1) 20 cancer patients with pneumonia treated with ICI and 20 matched controls without pneumonia from the pilot study of the AEROSMITH trial at the Parker Cancer Immunotherapy Institute (PICI), and (2) 15 melanoma patients with pneumonia treated with ICI and 149 patients without pneumonia from the Peter McCallum Cancer Center (PMC) (Table 6). In the PICI pilot cohort, although the odds ratios (ORs) were comparable (p = 0.26, OR = 2.75), HLA-DRB1*15:01 did not reach statistical significance, but this allele was significantly associated with the risk of pneumonia in the PMC cohort (p = 0.03, OR = 3.92). Meta-analysis of the three cohorts yielded a highly significant p-value of 1.2 x ^10⁻⁵ (OR = 2.67, Figure 14), indicating that this association is generalizable in ICI. Importantly, the same class II haplotype has previously been shown to be associated with different inflammatory phenotypes of the lungs, including fibrotic phenotypes (Tian et al., Nat Commun, 8:599, 2017; Fingerlin et al., BMC Genet., 17:74, 2016; Voorter et al., Hum Immunol, 66:826-835, 2005; Furukawa et al., PLoS One, 7:e33133, 2012).

In summary, these findings confirm that HLA class II allele variants are a potential risk factor for ICI-associated pneumonia.

Example 4. HLA class II loss of heterozygosity (LOH) is associated with poor prognosis of atezolizumab treatment.

The analysis presented in this example demonstrates that HLA class II loss, rather than HLA class I loss, is associated with poor prognosis after atezolizumab treatment.

The loss or reduction of HLA expression may be due to genetic or epigenetic modifications or indirect regulation, and may be a result of the evolutionary trajectory of tumors evading antitumor immune responses. The antigen-specific signal provided by the binding of the TCR to antigenic peptides complexed with MHC is also known as "signal 1". Most treatments in cancer immunology rely on functional antigen presentation, making the loss or downregulation of HLA expression an effective immune evasion strategy for tumors. In principle, HLA loss or downregulation should be counteracted by NK cells, which may be influenced by the differential distribution of NK cell subsets in different tissue types, NK cell abundance in tumors, tumor immune evasion strategies that modulate NK cell effectiveness, and the immunogenomic composition of the patient's tumor.

HLA class I and II LOH were computationally inferred from tumor whole-exome sequencing (WES) data from clinical trials in which patients were administered atezolizumab. The included trials were IMpower131 (GO29437), IMpower133 (GO30081), IMpower150 (GO29436), POPLAR (NCT01903993), and IMmotion150 (NCT01984242); these studies included patients with NSCLC, SCLC, or mRCC.

HLA class I locotype loss of hemorrhage (LOH) was not associated with prognosis. Atezolizumab-treated LOH patients did not show worse overall survival (OS) compared to patients without LOH (Figure 15). Similar results were obtained in patients who had lost their complete class I haplotype. A summary of indications, clinical trials, patient numbers, and the percentage of LOH patients is shown in Table 7. No significant association was observed in the trial's control group.

Table 7. Percentage of LOH in clinical trials

Indications Test Name N %LOH (any), all groups NSCLC IMpower131 344 twenty four% SCLC IMpower133 190 26% NSCLC IMpower150 544 16% NSCLC POPLAR 148 41% mRCC IMmotion150 205 62%

Furthermore, tumor mutational burden (TMB) did not alter the prognostic impact of type I LOH (Figure 16). No difference in the effect of LOH on lung cancer was observed between low and high TMB settings. LOH was not more frequent at intermediate TMB levels. However, type I LOH was associated with lower CD8A expression (Figure 17). Without being bound by theory, these data suggest that these observations reflect a selective process leading to reduced CD8+ T cell infiltration.

Surprisingly, HLA class II loss was associated with prognosis. In particular, in the meta-analysis, LOH calls to HLA class II genes showed an association with shorter OS (Figure 18). Without being bound by theory, this may be consistent with the finding that optimal antitumor responses require tumor cells expressing both HLA class I and class II neoantigens.

Other embodiments

Although the invention has been described in considerable detail above by way of example and instance for the purpose of clear understanding, such description and instance should not be construed as limiting the scope of the invention.

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Mount Sinai Icahn School of Medicine

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Claims (113)

1. A method for treating a patient with non-small cell lung cancer (NSCLC) who has this need, the patient’s genome having been identified as containing at least one copy of HLA-C1, the method comprising administering to the patient an effective amount of a treatment regimen comprising a PD-1 axis binding antagonist. 2. The method of claim 1, wherein the patient’s genome further comprises at least one copy of KIR2DL3. 3. A method for treating NSCLC in a patient with this need, the patient's genome having been identified as containing at least one copy of HLA-C1 and at least one copy of KIR2DL3, the method comprising administering to the patient an effective amount of a treatment regimen comprising a PD-1 axis binding antagonist. 4. A method for treating NSCLC in a patient with this need, the patient's genome having been identified as containing at least one copy of HLA-Bw4, the method comprising administering to the patient an effective amount of a treatment regimen comprising a PD-1 axis binding antagonist. 5. The method of claim 4, wherein the patient’s genome further comprises at least one copy of KIR3DL1. 6. A method for treating NSCLC in a patient with this need, the patient's genome having been identified as containing at least one copy of HLA-Bw4 and at least one copy of KIR3DL1, the method comprising administering to the patient an effective amount of a treatment regimen comprising a PD-1 axis binding antagonist. 7. A method for treating NSCLC in patients with this need, the method comprising: (a) Determining whether the patient's genome contains at least one copy of HLA-C1, wherein the presence of at least one copy of HLA-C1 in the patient's genome indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist; and (b) Based on the presence of at least one copy of HLA-C1 in the patient's genome, administer an effective amount of a treatment regimen including a PD-1 axis binding antagonist to the patient. 8. The method of claim 7, wherein step (a) further comprises determining whether the patient’s genome contains at least one copy of KIR2DL3. 9. A method for treating NSCLC in patients with this need, the method comprising: (a) Determining whether the patient's genome contains at least one copy of HLA-C1 and at least one copy of KIR2DL3, wherein the presence of at least one copy of HLA-C1 and at least one copy of KIR2DL3 in the patient's genome indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist; and (b) Based on the presence of at least one copy of HLA-C1 and at least one copy of KIR2DL3 in the patient's genome, administer an effective amount of a treatment regimen including a PD-1 axis binding antagonist to the patient. 10. A method for treating NSCLC in patients with this need, the method comprising: (a) Determining whether the patient's genome contains at least one copy of HLA-Bw4, wherein the presence of at least one copy of HLA-Bw4 in the patient's genome indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist; and (b) Based on the presence of at least one copy of HLA-Bw4 in the patient's genome, administer an effective amount of a treatment regimen including a PD-1 axis binding antagonist to the patient. 11. The method of claim 10, wherein step (a) further comprises determining whether the patient’s genome contains at least one copy of KIR3DL1. 12. A method for treating NSCLC in patients with this need, the method comprising: (a) Determining whether the patient's genome contains at least one copy of HLA-Bw4 and at least one copy of KIR3DL1, wherein the presence of at least one copy of HLA-Bw4 and at least one copy of KIR3DL1 in the patient's genome indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist; and (b) Based on the presence of at least one copy of HLA-Bw4 and at least one copy of KIR3DL1 in the patient's genome, administer an effective amount of a treatment regimen including a PD-1 axis binding antagonist to the patient. 13. A method for identifying a patient with NSCLC who may benefit from a treatment regimen including a PD-1 axis binding antagonist, the method comprising determining whether the patient’s genome contains at least one copy of HLA-C1, wherein the presence of at least one copy of HLA-C1 in the patient’s genome identifies the patient as a patient who may benefit from treatment using a treatment regimen including a PD-1 axis binding antagonist. 14. A method for identifying patients with NSCLC who may benefit from a treatment regimen including a PD-1 axis binding antagonist, the method comprising: (a) Germ-based whole-genome sequencing (WGS) or whole-exome sequencing (WES) is performed by fragmenting a DNA sample obtained from the patient to generate fragmented DNA, adding an adaptor to the fragmented DNA to generate one or more libraries, and sequencing the one or more libraries. (b) Identifying a patient as a patient who may benefit from a treatment regimen including a PD-1 axis binding antagonist by determining whether the patient’s genome contains at least one copy of HLA-C1, wherein the presence of at least one copy of HLA-C1 in the patient’s genome identifies the patient as a patient who may benefit from treatment using a treatment regimen including a PD-1 axis binding antagonist. 15. The method of claim 13 or 14, further comprising determining whether the patient’s genome contains at least one copy of KIR2DL3. 16. A method for identifying a patient with NSCLC who may benefit from a treatment regimen including a PD-1 axis binding antagonist, the method comprising determining whether the patient’s genome contains at least one copy of HLA-C1 and at least one copy of KIR2DL3, wherein the presence of at least one copy of HLA-C1 and at least one copy of KIR2DL3 in the patient’s genome identifies the patient as a patient who may benefit from treatment using a treatment regimen including a PD-1 axis binding antagonist. 17. A method for identifying patients with NSCLC who may benefit from a treatment regimen including a PD-1 axis binding antagonist, the method comprising: (a) Germ-based WGS or WES is performed by fragmenting a DNA sample obtained from the patient to generate fragmented DNA, adding an adaptor to the fragmented DNA to generate one or more libraries, and sequencing the one or more libraries; and (b) Identifying a patient as a potential recipient of a treatment regimen comprising a PD-1 axis binding antagonist by determining whether the patient’s genome contains at least one copy of HLA-C1 and at least one copy of KIR2DL3, wherein the presence of at least one copy of HLA-C1 and at least one copy of KIR2DL3 in the patient’s genome identifies the patient as a potential recipient of treatment with a treatment regimen comprising a PD-1 axis binding antagonist. 18. A method for identifying a patient with NSCLC who may benefit from a treatment regimen including a PD-1 axis binding antagonist, the method comprising determining whether the patient’s genome contains at least one copy of HLA-Bw4, wherein the presence of at least one copy of HLA-Bw4 in the patient’s genome identifies the patient as a patient who may benefit from treatment using a treatment regimen including a PD-1 axis binding antagonist. 19. A method for identifying patients with NSCLC who may benefit from a treatment regimen including a PD-1 axis binding antagonist, the method comprising: (a) Germ-based WGS or WES is performed by fragmenting a DNA sample obtained from the patient to generate fragmented DNA, adding an adaptor to the fragmented DNA to generate one or more libraries, and sequencing the one or more libraries; and (b) Identifying a patient as a patient who may benefit from a treatment regimen including a PD-1 axis binding antagonist by determining whether the patient’s genome contains at least one copy of HLA-Bw4, wherein the presence of at least one copy of HLA-Bw4 in the patient’s genome identifies the patient as a patient who may benefit from treatment using a treatment regimen including a PD-1 axis binding antagonist. 20. The method of claim 18 or 19, further comprising determining whether the patient’s genome contains at least one copy of KIR3DL1. 21. A method for identifying a patient with NSCLC who may benefit from a treatment regimen including a PD-1 axis binding antagonist, the method comprising determining whether the patient’s genome contains at least one copy of HLA-Bw4 and at least one copy of KIR3DL1, wherein the presence of at least one copy of HLA-Bw4 and at least one copy of KIR3DL1 in the patient’s genome identifies the patient as a patient who may benefit from treatment using a treatment regimen including a PD-1 axis binding antagonist. 22. A method for identifying patients with NSCLC who may benefit from a treatment regimen including a PD-1 axis binding antagonist, the method comprising: (a) Germ-based WGS or WES is performed by fragmenting a DNA sample obtained from the patient to generate fragmented DNA, adding an adaptor to the fragmented DNA to generate one or more libraries, and sequencing the one or more libraries; and (b) Identifying a patient as a potential recipient of a treatment regimen comprising a PD-1 axis binding antagonist by determining whether the patient’s genome contains at least one copy of HLA-Bw4 and at least one copy of KIR3DL1, wherein the presence of at least one copy of HLA-Bw4 and at least one copy of KIR3DL1 in the patient’s genome identifies the patient as a potential recipient of treatment with a treatment regimen comprising a PD-1 axis binding antagonist. 23. A method for selecting a therapy for a patient with NSCLC, the method comprising: (a) Determining whether the patient's genome contains at least one copy of HLA-C1, wherein the presence of at least one copy of HLA-C1 in the patient's genome indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist; and (b) Based on the presence of at least one copy of HLA-C1 in the patient’s genome, select a treatment regimen that includes a PD-1 axis binding antagonist. 24. The method of claim 23, further comprising determining whether the patient’s genome contains at least one copy of KIR2DL3. 25. A method for selecting a therapy for a patient with NSCLC, the method comprising: (a) Determining whether the patient's genome contains at least one copy of HLA-C1 and at least one copy of KIR2DL3, wherein the presence of at least one copy of HLA-C1 and at least one copy of KIR2DL3 in the patient's genome indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist; and (b) Based on the presence of at least one copy of HLA-C1 and at least one copy of KIR2DL3 in the patient’s genome, select a treatment regimen that includes a PD-1 axis binding antagonist. 26. A method for selecting a therapy for a patient with NSCLC, the method comprising: (a) Determining whether the patient's genome contains at least one copy of HLA-Bw4, wherein the presence of at least one copy of HLA-Bw4 in the patient's genome indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist; and (b) Based on the presence of at least one copy of HLA-Bw4 in the patient’s genome, select a treatment regimen that includes a PD-1 axis binding antagonist. 27. The method of claim 26, further comprising determining whether the patient’s genome contains at least one copy of KIR3DL1. 28. A method for selecting a therapy for a patient with NSCLC, the method comprising: (a) Determining whether the patient's genome contains at least one copy of HLA-Bw4 and at least one copy of KIR3DL1, wherein the presence of at least one copy of HLA-Bw4 and at least one copy of KIR3DL1 in the patient's genome indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist; and (b) Based on the presence of at least one copy of HLA-Bw4 and at least one copy of KIR3DL1 in the patient’s genome, select a treatment regimen that includes a PD-1 axis binding antagonist. 29. The method according to any one of claims 13 to 28, further comprising administering to the patient an effective amount of a treatment regimen comprising a PD-1 axis binding antagonist. 30. The method according to any one of claims 1 to 29, wherein next-generation sequencing, Sanger sequencing, polymerase chain reaction (PCR)-based assays, or single nucleotide polymorphism (SNP) arrays are used to determine the presence of HLA-C1, HLA-Bw4, KIR2DL3, and/or KIR3DL1 in the patient's genome. 31. The method of claim 30, wherein the next-generation sequencing comprises germline whole-genome sequencing or germline whole-exome sequencing. 32. The method of claim 30, wherein the PCR-based assay comprises quantitative PCR (qPCR), typing using sequence-specific primers (SSP), or typing using sequence-specific oligonucleotide probes (SSO). 33. A method for treating NSCLC in a patient who requires this treatment, the patient having been identified as having an increased level of NK cell infiltration in a tumor sample obtained from the patient relative to a reference level of natural killer (NK) cell infiltration, the method comprising administering to the patient an effective amount of a treatment regimen comprising a PD-1 axis binding antagonist. 34. A method for treating NSCLC in patients with this need, the method comprising: (a) Determining whether a tumor sample obtained from the patient has an increased level of NK cell infiltration relative to a reference level of NK cell infiltration, wherein the increased level of NK cell infiltration in the tumor sample obtained from the patient relative to the reference level of NK cell infiltration indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist; and (b) Based on the increased level of NK cell infiltration in the tumor sample obtained from the patient relative to the reference level of NK cell infiltration, administer an effective amount of a treatment regimen including a PD-1 axis binding antagonist to the patient. 35. A method for identifying a patient with NSCLC who may benefit from a treatment regimen including a PD-1 axis binding antagonist, the method comprising determining whether a tumor sample obtained from the patient has an increased level of NK cell infiltration relative to a reference level of NK cell infiltration, wherein the increased level of NK cell infiltration in the tumor sample obtained from the patient relative to the reference level of NK cell infiltration indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist. 36. A method for identifying patients with NSCLC who may benefit from a treatment regimen including a PD-1 axis binding antagonist, the method comprising: (a) contacting a tumor sample obtained from the patient with one or more antibody or nucleotide probes to determine the level of NK cell infiltration in the tumor sample, wherein the one or more antibody or nucleotide probes are bound to one or more NK cell markers; and (b) Determine whether a tumor sample obtained from the patient has an increased level of NK cell infiltration relative to a reference level of NK cell infiltration, wherein the increased level of NK cell infiltration in the tumor sample obtained from the patient relative to the reference level of NK cell infiltration indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist. 37. A method for selecting a therapy for a patient with NSCLC, the method comprising: (a) Determining whether a tumor sample obtained from the patient has an increased level of NK cell infiltration relative to a reference level of NK cell infiltration, wherein the increased level of NK cell infiltration in the tumor sample obtained from the patient relative to the reference level of NK cell infiltration indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist; and (b) Based on the increased level of NK cell infiltration in the tumor sample obtained from the patient relative to the reference level of NK cell infiltration, a treatment regimen including a PD-1 axis binding antagonist is selected. 38. The method according to any one of claims 35 to 37, further comprising administering to the patient an effective amount of a treatment regimen comprising a PD-1 axis binding antagonist. 39. The method according to any one of claims 33 to 38, wherein the level of NK cell infiltration is determined by determining the expression level of NK cell gene signatures or by counting the number of NK cells in the tumor sample. 40. The method of claim 39, wherein the NK cell gene signature comprises one or more of the following genes: CD160, CD244, CTSW, FASLG, GZMA, GZMB, GZMH, IL18RAP, IL2RB, KIR2DL4, KLRB1, KLRC3, KLRD1, KRLF1, KLRK1, NCR1, NKG7, PRF1, XCL1, and XCL2. 41. The method of claim 40, wherein the NK cell gene features comprise at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least ten, at least eleven, at least twelve, at least thirteen, at least fourteen, at least fifteen, at least sixteen, at least seventeen, at least eighteen, at least nineteen, or all twenty of the genes. 42. The method according to any one of claims 33 to 41, wherein the reference level for NK cell infiltration is the median level. 43. The method of claim 42, wherein the median level is the median level in the NSCLC patient population. 44. The method according to any one of claims 7 to 32 and 34 to 43, wherein the benefit is in terms of improved total survival (OS) or improved progression-free survival (PFS). 45. The method of claim 44, wherein the benefit is in terms of improved OS. 46. The method of claim 44, wherein the benefit is in terms of improved PFS. 47. The method according to any one of claims 44 to 46, wherein the improvement is relative to treatment using a treatment regimen that does not include the PD-1 axis binding antagonist. 48. The method according to any one of claims 1 to 47, wherein the NSCLC is a non-squamous NSCLC or a squamous NSCLC. 49. The method of claim 48, wherein the NSCLC is a non-squamous NSCLC. 50. The method of claim 49, wherein the non-squamous NSCLC is metastatic non-squamous NSCLC. 51. The method of claim 48, wherein the NSCLC is a scaly NSCLC. 52. The method of claim 51, wherein the scaly NSCLC is a metastatic scaly NSCLC. 53. The method according to any one of claims 1 to 52, wherein the patient is a chemotherapy-naïve patient. 54. The method according to any one of claims 1 to 53, wherein the treatment regimen is a first-line treatment regimen. 55. The method according to any one of claims 1 to 54, wherein the PD-1 axis binding antagonist is selected from PD-L1 binding antagonists, PD-1 binding antagonists and PD-L2 binding antagonists. 56. The method of claim 55, wherein the PD-1 axis binding antagonist is a PD-L1 binding antagonist. 57. The method of claim 56, wherein the PD-L1 binding antagonist is an anti-PD-L1 antibody. 58. The method of claim 57, wherein the anti-PD-L1 antibody comprises (a) the hypervariable region (HVR)-H1, HVR-H2, and HVR-H3 sequences of each of GFTFSDSWIH (SEQ ID NO:3), AWISPYGGSTYYADSVKG (SEQ ID NO:4), and RHWPGGFDY (SEQ ID NO:5), and (b) the HVR-L1, HVR-L2, and HVR-L3 sequences of each of RASQDVSTAVA (SEQ ID NO:6), SASFLYS (SEQ ID NO:7), and QQYLYHPAT (SEQ ID NO:8). 59. The method of claim 57 or 58, wherein the anti-PD-L1 antibody comprises: (a) VH, which contains the following amino acid sequence: EVQLVESGGGLVQPGGSLRLSCAASGFTFSDSWIHWVRQAPGKGLEWVAWISPYGGSTYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARRHWPGGFDYWGQGTLVTVSS(SEQID NO:9), and (b) VL, which contains the following amino acid sequence: DIQMTQSPSSSLSASVGDRVTITCRASQDVSTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQYLYHPATFGQGTKVEIKR(SEQ ID NO:10). 60. The method of claim 57, wherein the anti-PD-L1 antibody is atezolizumab, durvalumab, acimetidine, or MDX-1105. 61. The method according to any one of claims 57 to 60, wherein the anti-PD-L1 antibody is atezolizumab. 62. The method according to any one of claims 57 to 61, wherein the anti-PD-L1 antibody is administered intravenously or subcutaneously. 63. The method of claim 61, wherein the atezolizumab is administered intravenously at a dose of 840 mg every two weeks. 64. The method of claim 61, wherein the atezolizumab is administered intravenously at a dose of 1200 mg every three weeks. 65. The method of claim 61, wherein the atezolizumab is administered intravenously at a dose of 1680 mg every four weeks. 66. The method of claim 55, wherein the PD-1 axis binding antagonist is a PD-1 binding antagonist. 67. The method of claim 66, wherein the PD-1 binding antagonist is an anti-PD-1 antibody. 68. The method of claim 67, wherein the anti-PD-1 antibody is nivolumab, pembrolizumab, MEDI0680, spartazolizumab, cimiprizumab, camrelizumab, sintilimab, tislelizumab, toripalimab, or dotalimab. 69. The method according to any one of claims 1 to 68, wherein the treatment regimen further comprises taxane. 70. The method of claim 69, wherein the taxane is nab-paclitaxel or paclitaxel. 71. The method according to claim 70, wherein the taxane is nab-paclitaxel. 72. The method according to claim 70, wherein the taxane is paclitaxel. 73. The method according to any one of claims 1 to 72, wherein the treatment regimen further comprises a platinum-based chemotherapeutic agent. 74. The method of claim 73, wherein the platinum-based chemotherapeutic agent is carboplatin. 75. The method according to any one of claims 1 to 74, wherein the treatment regimen further comprises an anti-angiogenic agent. 76. The method of claim 75, wherein the anti-angiogenic agent is an anti-VEGF antibody. 77. The method of claim 76, wherein the anti-VEGF antibody is bevacizumab. 78. The method according to any one of claims 1 to 50 and 53 to 77, wherein the NSCLC is metastatic non-squamous NSCLC, and the treatment regimen comprises atezolizumab, nab-paclitaxel, and carboplatin. 79. The method of claim 78, wherein atezolizumab is administered intravenously (IV) at a dose of 1200 mg on day 1 of each 21-day cycle; nab-paclitaxel is administered IV at a dose of 100 mg/ ^m² on days 1, 8, and 15 of each 21-day cycle; and carboplatin is administered at an area under the concentration curve (AUC) of 6 mg/mL/min on day 1 of each 21-day cycle. 80. The method according to any one of claims 1 to 50 and 53 to 77, wherein the NSCLC is metastatic non-squamous NSCLC, and the treatment regimen comprises atezolizumab, paclitaxel, and carboplatin. 81. The method of claim 80, wherein atezolizumab is administered by intravenous infusion at a dose of 1200 mg on day 1 of each 21-day cycle; paclitaxel is administered by intravenous infusion at a dose of 200 mg/ ^m² on day 1 of each 21-day cycle; and carboplatin is administered at an AUC of 6 mg/mL/min on day 1 of each 21-day cycle. 82. The method according to any one of claims 1 to 50 and 53 to 77, wherein the NSCLC is metastatic non-squamous NSCLC, and the treatment regimen comprises atezolizumab, bevacizumab, paclitaxel, and carboplatin. 83. The method of claim 82, wherein atezolizumab is administered intravenously at a dose of 1200 mg on day 1 of each 21-day cycle; bevacizumab is administered intravenously at a dose of 15 mg/kg on day 1 of each 21-day cycle; paclitaxel is administered intravenously at a dose of 200 mg/ ^m² on day 1 of each 21-day cycle; and carboplatin is administered at an AUC of 6 mg/mL/min on day 1 of each 21-day cycle. 84. The method according to any one of claims 1 to 48 and 51 to 77, wherein the NSCLC is metastatic squamous NSCLC, and the treatment regimen comprises atezolizumab, nab-paclitaxel, and carboplatin. 85. The method of claim 84, wherein atezolizumab is administered via IV infusion at a dose of 1200 mg on day 1 of each 21-day cycle; nab-paclitaxel is administered via IV infusion at a dose of 100 mg/ ^m² on days 1, 8, and 15 of each 21-day cycle; and carboplatin is administered at an area under the concentration curve (AUC) of 6 mg/mL/min on day 1 of each 21-day cycle. 86. The method according to any one of claims 1 to 48 and 51 to 77, wherein the NSCLC is metastatic squamous NSCLC, and the treatment regimen comprises atezolizumab, paclitaxel, and carboplatin. 87. The method of claim 86, wherein atezolizumab is administered by intravenous infusion at a dose of 1200 mg on day 1 of each 21-day cycle; paclitaxel is administered by intravenous infusion at a dose of 175 mg/ ^m² or 200 mg/ ^m² on days 1, 8, and 15 of each 21-day cycle; and carboplatin is administered at an AUC of 6 mg/mL/min on day 1 of each 21-day cycle. 88. The method according to any one of claims 1 to 87, further comprising administering an additional therapeutic agent to the patient. 89. The method of claim 88, wherein the additional therapeutic agent is selected from the group consisting of: immunotherapeutic agents, cytotoxic agents, growth inhibitors, radiotherapy agents, anti-angiogenic agents, and combinations thereof. 90. A PD-1 axis binding antagonist for use in the treatment of NSCLC in patients with this need, whose genome has been identified as containing at least one copy of HLA-C1. 91. The PD-1 axis binding antagonist of claim 90, wherein the patient’s genome further comprises at least one copy of KIR2DL3. 92. A PD-1 axis binding antagonist for use in the treatment of NSCLC in patients with this need, whose genome has been identified as containing at least one copy of HLA-C1 and at least one copy of KIR2DL3. 93. A PD-1 axis binding antagonist for use in the treatment of NSCLC in patients with this need, whose genome has been identified as containing at least one copy of HLA-Bw4. 94. The PD-1 axis binding antagonist of claim 93, wherein the patient’s genome further comprises at least one copy of KIR3DL1. 95. A PD-1 axis binding antagonist for use in the treatment of NSCLC in patients with this need, whose genome has been identified as containing at least one copy of HLA-Bw4 and at least one copy of KIR3DL1. 96. A PD-1 axis binding antagonist used in a method of treating NSCLC in patients with this need, the method comprising: (a) Determining whether the patient's genome contains at least one copy of HLA-C1, wherein the presence of at least one copy of HLA-C1 in the patient's genome indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist; and (b) Based on the presence of at least one copy of HLA-C1 in the patient's genome, administer an effective amount of a treatment regimen including a PD-1 axis binding antagonist to the patient. 97. The PD-1 axis binding antagonist of claim 96, wherein step (a) further comprises determining whether the patient’s genome contains at least one copy of KIR2DL3. 98. A PD-1 axis binding antagonist for use in the treatment of NSCLC in patients with this need, comprising: (a) Determining whether the patient's genome contains at least one copy of HLA-C1 and at least one copy of KIR2DL3, wherein the presence of at least one copy of HLA-C1 and at least one copy of KIR2DL3 in the patient's genome indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist; and (b) Based on the presence of at least one copy of HLA-C1 and at least one copy of KIR2DL3 in the patient's genome, administer an effective amount of a treatment regimen including a PD-1 axis binding antagonist to the patient. 99. A PD-1 axis binding antagonist for use in the treatment of NSCLC in patients with this need, comprising: (a) Determining whether the patient's genome contains at least one copy of HLA-Bw4, wherein the presence of at least one copy of HLA-Bw4 in the patient's genome indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist; and (b) Based on the presence of at least one copy of HLA-Bw4 in the patient's genome, administer an effective amount of a treatment regimen including a PD-1 axis binding antagonist to the patient. 100. The PD-1 axis binding antagonist of claim 99, wherein step (a) further comprises determining whether the patient’s genome contains at least one copy of KIR3DL1. 101. A PD-1 axis binding antagonist for use in the treatment of NSCLC in patients with this need, comprising: (a) Determining whether the patient's genome contains at least one copy of HLA-Bw4 and at least one copy of KIR3DL1, wherein the presence of at least one copy of HLA-Bw4 and at least one copy of KIR3DL1 in the patient's genome indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist; and (b) Based on the presence of at least one copy of HLA-Bw4 and at least one copy of KIR3DL1 in the patient's genome, administer an effective amount of a treatment regimen including a PD-1 axis binding antagonist to the patient. 102. A PD-1 axis binding antagonist for use in the treatment of NSCLC in patients who have been identified as having increased levels of NK cell infiltration in tumor samples obtained from the patients, relative to a reference level of NK cell infiltration. 103. A PD-1 axis binding antagonist used in a method of treating NSCLC in patients with this need, the method comprising: (a) Determining whether a tumor sample obtained from the patient has an increased level of NK cell infiltration relative to a reference level of NK cell infiltration, wherein the increased level of NK cell infiltration in the tumor sample obtained from the patient relative to the reference level of NK cell infiltration indicates that the patient may benefit from a treatment regimen including a PD-1 axis binding antagonist; and (b) Based on the increased level of NK cell infiltration in the tumor sample obtained from the patient relative to the reference level of NK cell infiltration, administer an effective amount of a treatment regimen including a PD-1 axis binding antagonist to the patient. 104. An NK cell-targeted therapeutic agent for use in the treatment of NSCLC in patients with this need, whose genome has been determined to lack KIR2DL3 or KIR3DL1. 105. An NK cell-targeted therapeutic agent for use in a method of treating NSCLC in patients with this need, the method comprising: (a) Determining whether the patient's genome lacks KIR2DL3 or KIR3DL1, wherein the lack of KIR2DL3 or KIR3DL1 in the patient's genome indicates that the patient may benefit from a treatment regimen including NK cell-targeted therapies; and (b) Based on the deficiency of KIR2DL3 or KIR3DL1 in the patient's genome, administer an effective amount of a treatment regimen including NK cell-targeted therapy to the patient. 106. An article of manufacture for treating NSCLC in patients with this need, comprising a PD-1 axis binding antagonist and instructions for administering said PD-1 axis binding antagonist, said patient’s genome having been determined to contain at least one copy of HLA-C1. 107. The article of manufacture according to claim 106, wherein the patient’s genome further comprises at least one copy of KIR2DL3. 108. An article of manufacture for treating NSCLC in patients with this need, comprising a PD-1 axis binding antagonist and instructions for administering the PD-1 axis binding antagonist, wherein the patient’s genome has been determined to contain at least one copy of HLA-C1 and at least one copy of KIR2DL3. 109. An article of manufacture for treating NSCLC in patients with this need, comprising a PD-1 axis binding antagonist and instructions for administering the PD-1 axis binding antagonist, wherein the patient’s genome has been determined to contain at least one copy of HLA-Bw4. 110. The article of manufacture according to claim 109, wherein the patient’s genome further comprises at least one copy of KIR3DL1. 111. An article of manufacture for treating NSCLC in patients with this need, comprising a PD-1 axis binding antagonist and instructions for administering said PD-1 axis binding antagonist, wherein the patient’s genome has been determined to contain at least one copy of HLA-Bw4 and at least one copy of KIR3DL1. 112. An article of manufacture for treating NSCLC in a patient with such need, comprising a PD-1 axis binding antagonist and instructions for administering the PD-1 axis binding antagonist, wherein the patient has been identified as having an increased level of NK cell infiltration in a tumor sample obtained from the patient relative to a reference level of natural killer (NK) cell infiltration. 113. An article of manufacture for treating NSCLC in patients with this need, comprising an NK cell-directed therapeutic agent and instructions for administering the NK cell-directed therapeutic agent, wherein the patient’s genome has been determined to lack KIR2DL3 or KIR3DL1.