CN117545857A

CN117545857A - Methods and compositions for the treatment and diagnosis of cancer

Info

Publication number: CN117545857A
Application number: CN202280044766.2A
Authority: CN
Inventors: C·哈默; A·霍洛维茨
Original assignee: Genentech Inc; Icahn School of Medicine at Mount Sinai
Current assignee: Genentech Inc; Icahn School of Medicine at Mount Sinai
Priority date: 2021-04-30
Filing date: 2022-04-29
Publication date: 2024-02-09

Abstract

The present invention provides methods and compositions for treating cancer (e.g., NSCLC) in a patient, for example, by administering a treatment regimen comprising a PD-1 axis binding antagonist (e.g., alemtuzumab) or an NK cell-directed therapeutic to the patient. Also provided are compositions (e.g., PD-1 axis binding antagonists (e.g., alemtuzumab) or NK cell-directed therapeutic agents, pharmaceutical compositions thereof, kits thereof, and articles of manufacture thereof) for treating cancer (e.g., NSCLC) in a patient. Also provided are methods for identifying cancer (e.g., NSCLC) patients who may benefit from treatment with a treatment regimen comprising a PD-1 axis binding antagonist (e.g., alemtuzumab) or an NK cell-directed therapeutic. Methods of selecting therapies for cancer patients are also provided.

Description

Methods and compositions for the treatment and diagnosis of cancer

Sequence listing

The present application contains a sequence listing that has been electronically submitted in ASCII format and is incorporated by reference herein in its entirety. The ASCII copy was created at 2022, month 4, and 27, named 50474-256wo4_sequence_listing_4_28_22_st25, and was 9,636 bytes in size.

Technical Field

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

Background

Cancer remains one of the most fatal threats to human health. In the united states, cancer affects nearly 130 million new patients annually, the second leading cause of death next to heart disease, accounting for about 1/4 of the deaths. Solid tumors are the leading cause of these deaths. For example, lung cancer is a leading cause of cancer death worldwide. It is estimated that there were 224,210 new lung cancer cases (116,000 men and 108,210 women) and 159,260 deaths in the united states in 2014. Similar data from europe estimated 214,000 new lung cancer cases and 268,000 deaths in 2012. NSCLC is one of two major types of lung cancer, accounting for about 85% of all lung cancer cases. The two major histological types of NSCLC are adenocarcinoma (accounting for more than half of cases) and squamous cell carcinoma (accounting for about 25% of cases).

Accordingly, there is a need in the art for improved cancer (e.g., NSCLC) therapies.

Disclosure of Invention

The invention provides, inter alia, methods, compositions of use, uses, and articles of manufacture for the treatment and diagnosis of cancer.

In one aspect, the invention features a method of treating non-small cell lung cancer (NSCLC) in a patient in need thereof 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 comprising a PD-1 axis binding antagonist.

In another aspect, the invention features a PD-1 axis binding antagonist for treating NSCLC in a patient in need thereof whose genome has been determined to contain at least one copy of HLA-C1.

In some aspects, the patient's genome further comprises at least one copy of KIR2DL 3.

In another aspect, the invention features a method of treating NSCLC in a patient in need thereof whose genome has been determined 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 invention features a PD-1 axis binding antagonist for treating NSCLC in a patient in need thereof whose genome has been determined to comprise at least one copy of HLA-C1 and at least one copy of KIR2DL 3.

In another aspect, the invention features a method of treating NSCLC in a patient in need thereof whose genome has been determined to contain 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.

In another aspect, the invention features a PD-1 axis binding antagonist for treating NSCLC in a patient in need thereof whose genome has been determined to contain at least one copy of HLA-Bw 4.

In some aspects, the patient's genome further comprises at least one copy of KIR3DL 1.

In another aspect, the invention features a method of treating NSCLC in a patient in need thereof whose genome has been determined to contain at least one copy of HLA-Bw4 and at least one copy of KIR3DL1, comprising administering to the patient an effective amount of a treatment regimen comprising a PD-1 axis binding antagonist.

In another aspect, the invention features a PD-1 axis binding antagonist for treating NSCLC in a patient in need thereof whose genome has been determined to comprise at least one copy of HLA-Bw4 and at least one copy of KIR3DL 1.

In another aspect, the invention features a method of treating NSCLC in a patient in need thereof, the method comprising: (a) Determining whether the patient's genome comprises 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 is likely to 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 genome of the patient.

In another aspect, the invention features a PD-1 axis binding antagonist for use in a method of treating NSCLC in a patient in need thereof, the method comprising: (a) Determining whether the patient's genome comprises 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 is likely to 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 genome of the patient.

In some aspects, step (a) further comprises determining whether the patient's genome comprises at least one copy of KIR2DL 3.

In another aspect, the invention features a method of treating NSCLC in a patient in need thereof, the method comprising: (a) Determining whether the patient's genome comprises 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 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 and at least one copy of KIR2DL3 in the genome of the patient.

In another aspect, the invention features a PD-1 axis binding antagonist for use in treating NSCLC in a patient in need thereof, the method comprising: (a) Determining whether the patient's genome comprises 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 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 and at least one copy of KIR2DL3 in the genome of the patient.

In another aspect, the invention features a method of treating NSCLC in a patient in need thereof, the method comprising: (a) Determining whether the patient's genome comprises 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 genome of the patient.

In another aspect, the invention features a PD-1 axis binding antagonist for use in treating NSCLC in a patient in need thereof, the method comprising: (a) Determining whether the patient's genome comprises 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 genome of the patient.

In some aspects, step (a) further comprises determining whether the patient's genome comprises at least one copy of KIR3DL 1.

In another aspect, the invention features a method of treating NSCLC in a patient in need thereof, the method comprising: (a) Determining whether the patient's genome comprises 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 genome of the patient.

In another aspect, the invention features a PD-1 axis binding antagonist for use in treating NSCLC in a patient in need thereof, the method comprising: (a) Determining whether the patient's genome comprises 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 genome of the patient.

In another aspect, the invention features a method of identifying a patient having NSCLC who may benefit from a treatment regimen that includes a PD-1 axis binding antagonist, the method including determining whether the patient's genome comprises 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 that includes a PD-1 axis binding antagonist.

In another aspect, the invention features a method of identifying a patient having NSCLC who may benefit from a treatment regimen that includes a PD-1 axis binding antagonist, the method comprising: (a) Germline Whole Genome Sequencing (WGS) or Whole Exome Sequencing (WES) by fragmenting a DNA sample obtained from the patient to produce fragmented DNA, adding adaptors 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 comprising a PD-1 axis binding antagonist by determining whether the patient's genome comprises 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 comprising a PD-1 axis binding antagonist.

In some aspects, the method further comprises determining whether the patient's genome comprises at least one copy of KIR2DL 3.

In another aspect, the invention features a method of identifying a patient having NSCLC who may benefit from a treatment regimen that includes a PD-1 axis binding antagonist, the method including determining whether the patient's genome comprises at least one copy of HLA-C1 and at least one copy of KIR2DL3, wherein the presence of the at least one copy of HLA-C1 and the 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 that includes a PD-1 axis binding antagonist.

In another aspect, the invention features a method of identifying a patient having NSCLC who may benefit from a treatment regimen that includes a PD-1 axis binding antagonist, the method comprising: (a) Germline WGS or WES is performed by fragmenting a DNA sample obtained from the patient to produce fragmented DNA, adding adaptors 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 comprising a PD-1 axis binding antagonist by determining whether the patient's genome comprises 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 comprising a PD-1 axis binding antagonist.

In another aspect, the invention features a method of identifying a patient having NSCLC who may benefit from a treatment regimen that includes a PD-1 axis binding antagonist, the method including determining whether the patient's genome includes 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 that includes a PD-1 axis binding antagonist.

In another aspect, the invention features a method of identifying a patient having NSCLC who may benefit from a treatment regimen that includes a PD-1 axis binding antagonist, the method comprising: (a) Germline WGS or WES is performed by fragmenting a DNA sample obtained from the patient to produce fragmented DNA, adding adaptors 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 comprising a PD-1 axis binding antagonist by determining whether the patient's genome comprises 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 comprising a PD-1 axis binding antagonist.

In some aspects, the method further comprises determining whether the patient's genome comprises at least one copy of KIR3DL 1.

In another aspect, the invention features a method of identifying a patient having NSCLC who may benefit from a treatment regimen that includes a PD-1 axis binding antagonist, the method including determining whether the patient's genome includes 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 that includes a PD-1 axis binding antagonist.

In another aspect, the invention features a method of identifying a patient having NSCLC who may benefit from a treatment regimen that includes a PD-1 axis binding antagonist, the method comprising: (a) Germline WGS or WES is performed by fragmenting a DNA sample obtained from the patient to produce fragmented DNA, adding adaptors 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 comprising a PD-1 axis binding antagonist by determining whether the patient's genome comprises 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 comprising a PD-1 axis binding antagonist.

In another aspect, the invention features a method of selecting a therapy for a patient having NSCLC, the method including: (a) Determining whether the patient's genome comprises 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 is likely to benefit from a treatment regimen comprising a PD-1 axis binding antagonist; and (b) selecting a treatment regimen comprising a PD-1 axis binding antagonist based on the presence of at least one copy of HLA-C1 in the genome of the patient.

In another aspect, the invention features a method of selecting a therapy for a patient having NSCLC, the method including: (a) Determining whether the patient's genome comprises 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) selecting a treatment regimen comprising 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 genome of the patient.

In another aspect, the invention features a method of selecting a therapy for a patient having NSCLC, the method including: (a) Determining whether the patient's genome comprises 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) selecting a treatment regimen comprising a PD-1 axis binding antagonist based on the presence of at least one copy of HLA-Bw4 in the genome of the patient.

In another aspect, the invention features a method of selecting a therapy for a patient having NSCLC, the method including: (a) Determining whether the patient's genome comprises 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) selecting 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 genome of the patient.

In some aspects, the method further comprises administering to the patient an effective amount of a treatment regimen comprising a PD-1 axis binding antagonist.

In some aspects, the method further comprises determining the presence of HLA-C1, HLA-Bw4, KIR2DL3, and/or KIR3DL1 in the genome of the patient using next generation sequencing, sanger sequencing, polymerase Chain Reaction (PCR) based assays, or Single Nucleotide Polymorphism (SNP) arrays.

In some aspects, the method further comprises next generation sequencing, including germline whole genome sequencing or germline whole exome sequencing.

In some aspects, the method further comprises a PCR-based assay comprising quantitative PCR (qPCR), typing using sequence-specific primers (SSP), or typing using sequence-specific oligonucleotide probes (SSO).

In another aspect, the invention features a method of treating NSCLC in a patient in need thereof, the patient having been determined to have an increased level of Natural Killer (NK) cell infiltration relative to a reference level of 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.

In another aspect, the invention features a PD-1 axis binding antagonist for treating NSCLC in a patient in need thereof who has been determined to have an increased NK cell infiltration level relative to a reference level of NK cell infiltration in a tumor sample obtained from the patient.

In another aspect, the invention features a method of treating NSCLC in a patient in need thereof, the method comprising: (a) Determining whether a tumor sample obtained from the patient has an increased NK cell infiltration level relative to a reference level of NK cell infiltration, wherein an increase in NK cell infiltration level relative to the reference level of NK cell infiltration in the tumor sample obtained from the patient indicates that the patient is likely to 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 an increase in NK cell infiltration level relative to a reference level of NK cell infiltration in a tumor sample obtained from the patient.

In another aspect, the invention features a PD-1 axis binding antagonist for use in a method of treating NSCLC in a patient in need thereof, the method comprising: (a) Determining whether a tumor sample obtained from the patient has an increased NK cell infiltration level relative to a reference level of NK cell infiltration, wherein an increase in NK cell infiltration level relative to the reference level of NK cell infiltration in the tumor sample obtained from the patient indicates that the patient is likely to 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 an increase in NK cell infiltration level relative to a reference level of NK cell infiltration in a tumor sample obtained from the patient.

In another aspect, the invention features a method of identifying a patient having NSCLC who may benefit from a treatment regimen that includes a PD-1 axis binding antagonist, the method including determining whether a tumor sample obtained from the patient has an increased NK cell infiltration level relative to a reference level of NK cell infiltration, wherein an increase in NK cell infiltration level 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 that includes a PD-1 axis binding antagonist.

In another aspect, the invention features a method of identifying a patient having NSCLC who may benefit from a treatment regimen that includes a PD-1 axis binding antagonist, the method comprising: (a) Contacting a tumor sample obtained from the patient with one or more antibodies or nucleotide probes that bind 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 NK cell infiltration level relative to a reference level of NK cell infiltration, wherein an increase in NK cell infiltration level relative to the reference level of NK cell infiltration in the tumor sample obtained from the patient indicates that the patient is likely to benefit from a treatment regimen comprising a PD-1 axis binding antagonist.

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

In some aspects, the level of NK cell infiltration is determined by determining the expression level of the NK cell gene signature or by counting the number of NK cells in the tumor sample.

In some aspects, 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, KRRF 1, KLRK1, NCR1, NKG7, PRF1, XCL1 and XCL2.

In some aspects, the NK cell gene signature comprises 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 aspects, the reference level of NK cell infiltration is a median level.

In some aspects, the median level is a median level in a population of NSCLC patients.

In some aspects, the benefit is in terms of improved Overall Survival (OS) or improved Progression Free Survival (PFS).

In some aspects, benefits are in terms of improved OS.

In some aspects, the benefit is in terms of improved PFS.

In some aspects, the improvement is relative to treatment using a treatment regimen that does not include a PD-1 axis binding antagonist.

In some aspects, the NSCLC is non-squamous NSCLC or squamous NSCLC.

In some aspects, the NSCLC is non-squamous NSCLC.

In some aspects, the non-squamous NSCLC is metastatic non-squamous NSCLC.

In some aspects, the NSCLC is squamous NSCLC.

In some aspects, the squamous NSCLC is metastatic squamous NSCLC.

In some aspects, the patient is a primary treatment for chemotherapy.

In some aspects, the treatment regimen is a first-line treatment regimen.

In some aspects, 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 aspects, the PD-1 axis binding antagonist is a PD-L1 binding antagonist.

In some aspects, the PD-L1 binding antagonist is an anti-PD-L1 antibody.

In some aspects, 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).

In some aspects, an anti-PD-L1 antibody comprises (a) a VH comprising the amino acid sequence:

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

DIQMTQSPSSLSASVGDRVTITCRASQDVSTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQYLYHPATFGQGTKVEIKR(SEQ ID NO:10)。

in some aspects, the anti-PD-L1 antibody is alemtuzumab, dewaruzumab, avermectin, or MDX-1105.

In some aspects, the anti-PD-L1 antibody is alemtuzumab.

In some aspects, the anti-PD-L1 antibody is administered intravenously or subcutaneously.

In some aspects, the alemtuzumab is administered intravenously at a dose of 840mg every two weeks.

In some aspects, the alemtuzumab is administered intravenously at a dose of 1200mg every three weeks.

In some aspects, the alemtuzumab is administered intravenously every four weeks at a dose of 1680 mg.

In some aspects, the PD-1 axis binding antagonist is a PD-1 binding antagonist.

In some aspects, the PD-1 binding antagonist is an anti-PD-1 antibody.

In some aspects, the anti-PD-1 antibody is na Wu Shankang, pamil mab, MEDI-0680, swamp mab, cimaprab Li Shan, carlizumab, singdi Li Shan, tirelimumab, terpride Li Shan, or multi-tarolimumab.

In some aspects, the treatment regimen further comprises a taxane.

In some aspects, the taxane is nab-paclitaxel or paclitaxel.

In some aspects, the taxane is nab-paclitaxel.

In some aspects, the taxane is paclitaxel.

In some aspects, the treatment regimen further comprises a platinum-based chemotherapeutic agent.

In some aspects, the platinum-based chemotherapeutic agent is carboplatin.

In some aspects, the treatment regimen further comprises an anti-angiogenic agent.

In some aspects, the anti-angiogenic agent is an anti-VEGF antibody.

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

In some aspects, the NSCLC is metastatic non-squamous NSCLC and the treatment regimen comprises alemtuzumab, nab-paclitaxel, and carboplatin.

In some aspects, the alemtuzumab is administered as an Intravenous (IV) infusion at a dose of 1200mg on day 1 of each 21-day cycle; nab-paclitaxel at 100mg/m on days 1, 8 and 15 of each 21-day cycle ² Is administered as an IV infusion; and carboplatin was administered at 6mg/mL/min concentration curve area under Area (AUC) on day 1 of each 21 day cycle.

In some aspects, the NSCLC is metastatic non-squamous NSCLC and the treatment regimen includes alemtuzumab, paclitaxel, and carboplatin.

In some aspects, the alemtuzumab is administered as an IV infusion at a dose of 1200mg on day 1 of each 21-day cycle; paclitaxel at 200mg/m on day 1 of each 21-day cycle ² Is administered as an IV infusion; and carboplatin was administered at AUC of 6mg/mL/min on day 1 of each 21-day cycle.

In some aspects, the NSCLC is metastatic non-squamous NSCLC and the treatment regimen includes alemtuzumab, bevacizumab, paclitaxel, and carboplatin.

In some aspects, the alemtuzumab is administered as an IV infusion at a dose of 1200mg on day 1 of each 21-day cycle; bevacizumab was administered as IV infusion at a dose of 15mg/kg on day 1 of each 21 day cycle; paclitaxel at 200mg/m on day 1 of each 21-day cycle ² Is administered as an IV infusion; and carboplatin was administered at AUC of 6mg/mL/min on day 1 of each 21-day cycle.

In some aspects, the NSCLC is metastatic squamous NSCLC and the treatment regimen comprises alemtuzumab, nab-paclitaxel, and carboplatin.

In some aspects, the alemtuzumab is administered as an IV infusion at a dose of 1200mg on day 1 of each 21-day cycle; nab-paclitaxel at 100mg/m on days 1, 8 and 15 of each 21-day cycle ² Is administered as an IV infusion; and carboplatin was administered at 6mg/mL/min concentration curve area under Area (AUC) on day 1 of each 21 day cycle.

In some aspects, the NSCLC is metastatic squamous NSCLC and the treatment regimen comprises alemtuzumab, paclitaxel, and carboplatin.

In some aspects, the alemtuzumab is administered as an IV infusion at a dose of 1200mg on day 1 of each 21-day cycle; paclitaxel at 175mg/m on days 1, 8 and 15 of each 21-day cycle ² Or 200mg/m ² Is administered as an IV infusion; and carboplatin was administered at AUC of 6mg/mL/min on day 1 of each 21-day cycle.

In some aspects, the method further comprises administering an additional therapeutic agent to the patient.

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

In another aspect, the invention features an article of manufacture for treating NSCLC in a patient in need thereof, comprising a PD-1 axis binding antagonist and instructions for administering the PD-1 axis binding antagonist, the genome of the patient having been determined to comprise at least one copy of HLA-C1.

In another aspect, the invention features an article of manufacture for treating NSCLC in a patient in need thereof, comprising a PD-1 axis binding antagonist and instructions for administering the PD-1 axis binding antagonist, the genome of the patient having been determined to comprise at least one copy of HLA-C1 and at least one copy of KIR2DL 3.

In another aspect, the invention features an article of manufacture for treating NSCLC in a patient in need thereof, comprising a PD-1 axis binding antagonist and instructions for administering the PD-1 axis binding antagonist, the genome of the patient having been determined to comprise at least one copy of HLA-Bw 4.

In another aspect, the invention features an article of manufacture for treating NSCLC in a patient in need thereof, comprising a PD-1 axis binding antagonist and instructions for administering the PD-1 axis binding antagonist, the genome of the patient having been determined to comprise at least one copy of HLA-Bw4 and at least one copy of KIR3DL1.

In another aspect, the invention features an article of manufacture for treating NSCLC in a patient in need thereof, comprising a PD-1 axis binding antagonist and instructions for administering the PD-1 axis binding antagonist, the patient having been determined to have an increased level of Natural Killer (NK) cell infiltration in a tumor sample obtained from the patient relative to a reference level of NK cell infiltration.

In another aspect, the invention features an article of manufacture for treating NSCLC in a patient in need thereof, comprising an NK cell-targeted therapeutic and instructions for administering the NK cell-targeted therapeutic, the genome of the patient having been determined to be deficient in KIR2DL3 or KIR3DL1.

Drawings

FIG. 1A is a graph showing the total survival (OS) risk ratio (HR) of non-small cell lung cancer (NSCLC) patients who were carriers of at least one copy of one of the Human Leukocyte Antigen (HLA) allele HLA-C1 and the killer cell immunoglobulin-like receptor (KIR) gene KIR2DL3 and were treated with a therapy comprising alemtuzumab in an IMpower130, IMpower131 or IMpower150 clinical trial, as compared to a control. Estimates of Treatment Effect (TE), TE standard error (seTE), P-value and weight (fixed and random) are shown. Fixed effect and random effect models are shown.

FIG. 1B is a graph showing Progression Free Survival (PFS) HR of NSCLC patients who are carriers of at least one copy of one of HLA-C1 and KIR2DL3 and who were treated with therapy comprising alemtuzumab in an IMpower130, IMpower131 or IMpower150 clinical trial as compared to control.

FIG. 2A is a graph showing OS HR of NSCLC patients who were carriers of at least one copy of one of HLA alleles HLA-Bw4 and KIR gene KIR3DL1 and were treated with therapies comprising alemtuzumab in an IMpower130, IMpower131 or IMpower150 clinical trial as compared to controls.

Fig. 2B is a graph showing PFS HR of NSCLC patients who were carriers of at least one copy of one of HLA-Bw4 and KIR3DL1 and were treated with therapy comprising alemtuzumab in IMpower130, IMpower131 or IMpower150 clinical trials compared to controls.

FIG. 3A is a graph showing OS HR of NSCLC patients who were carriers of at least one copy of HLA-C1 and were treated with therapy comprising alemtuzumab in an IMpower130, IMpower131 or IMpower150 clinical trial as compared to controls.

FIG. 3B is a graph showing PFS HR of NSCLC patients who were carriers of at least one copy of HLA-C1 and were treated with a therapy comprising alemtuzumab in an IMpower130, IMpower131 or IMpower150 clinical trial as compared to controls.

Fig. 4A is a graph showing OS HR of NSCLC patients who were carriers of at least one copy of HLA-Bw4 and were treated with therapy comprising alemtuzumab in IMpower130, IMpower131 or IMpower150 clinical trials compared to controls.

Fig. 4B is a graph showing PFS HR of NSCLC patients who were carriers of at least one copy of HLA-Bw4 and were treated with therapy comprising atractylizumab in IMpower130, IMpower131 or IMpower150 clinical trials, as compared to controls.

FIG. 5A is a graph showing OS HR of NSCLC and melanoma patients who were carriers of at least one copy of HLA-Bw4 and were treated with a therapy comprising Immune Checkpoint Blockade (ICB) compared to controls in Choshell et al data (see example 1 d) or MSK-IMPACT (see, e.g., zehir et al Nat. Med.23:703-713, 2017).

FIG. 5B is a graph showing OS HR of NSCLC and melanoma patients who were carriers of at least one copy of HLA-C1 and were treated with a therapy comprising Immune Checkpoint Blockade (ICB) compared to controls in Choshell et al data (see example 1 d) or MSK-IMPACT.

Fig. 6A is a graph showing OS HR for NSCLC patients with a Natural Killer (NK) cell score above the median and treated with therapy comprising alemtuzumab compared to controls in IMpower131 or IMpower150 clinical trials.

Fig. 6B is a graph showing OS HR for NSCLC patients with NK cell scores above the median and treated with therapy comprising alemtuzumab compared to controls in IMpower131 or IMpower150 clinical trials.

Fig. 7A is a graph showing OS HR for patients with NK cell scores above the median and in the listed clinical trial, were treated with a therapy comprising alemtuzumab as compared to the control.

Fig. 7B is a graph showing OS HR for patients with CD8A levels above the median and in the listed clinical trial, were treated with a therapy comprising alemtuzumab as compared to the control.

FIG. 8A is a graph showing OS HR of Renal Cell Carcinoma (RCC) patients who were carriers of at least one copy of one of HLA-C1 and KIR2DL3 and were treated with a therapy comprising alemtuzumab in an IMmotion151 clinical trial as compared to a control.

FIG. 8B is a graph showing PFS HR of RCC patients who were carriers of at least one copy of one of HLA-C1 and KIR2DL3 and were treated with a therapy comprising alemtuzumab in an IMmotion151 clinical trial as compared to controls.

FIG. 9A is a graph showing OS HR of RCC patients who were carriers of at least one copy of one of HLA-Bw4 and KIR3DL1 and were treated with a therapy comprising alemtuzumab in an IMmotion151 clinical trial as compared to controls.

FIG. 9B is a graph showing PFS HR of RCC patients who were carriers of at least one copy of one of HLA-Bw4 and KIR3DL1 and were treated with a therapy comprising alemtuzumab in an IMmotion151 clinical trial as compared to controls.

FIG. 10A is a graph showing OS HR of RCC patients who were carriers of at least one copy of HLA-C1 and were treated with a therapy comprising alemtuzumab as compared to controls in an IMmotion151 clinical trial.

FIG. 10B is a graph showing PFS HR of RCC patients who were carriers of at least one copy of HLA-C1 and were treated with a therapy comprising alemtuzumab as compared to controls in an IMmotion151 clinical trial.

FIG. 11A is a graph showing OS HR of RCC patients who were carriers of at least one copy of HLA-Bw4 and were treated with a therapy comprising alemtuzumab as compared to controls in an IMmotion151 clinical trial.

FIG. 11B is a graph showing PFS HR of RCC patients who were carriers of at least one copy of HLA-Bw4 and were treated with a therapy comprising alemtuzumab as compared to controls in an IMmotion151 clinical trial.

Fig. 12A is a graph showing OS HR for RCC patients with NK cell scores above the median and treated with therapy comprising alemtuzumab compared to controls in an immoti 150 or immoti 151 clinical trial.

Fig. 12B is a graph showing PFS HR for RCC patients with NK cell scores above the median and treated with therapy comprising alemtuzumab compared to control in either the immoti 150 or immoti 151 clinical trial.

Fig. 13A is a graph showing OS HR for RCC patients with CD8A levels above the median and treated with therapy comprising alemtuzumab in IMmotion150 or IMmotion151 clinical trials compared to controls.

Fig. 13B is a graph showing PFS HR for RCC patients with CD8A levels above the median and treated with therapy comprising alemtuzumab in IMmotion150 or IMmotion151 clinical trials compared to controls.

Fig. 14 is a graph showing the risk of Immune Checkpoint Inhibitor (ICI) -associated pneumonia in patients carrying HLA class II alleles HLA-DRB1 x 15:01 and treated with ICI compared to controls in the indicated cohorts. GNE, genentech; PICI, park cancer immunotherapy institute; PMC, the center of mecanum cancer; OR, odds ratio; CI, confidence interval; w, weight.

FIG. 15 is a graph showing OS HR for a given cohort, which shows HLA class I heterozygosity Loss (LOH) is prognostic independent. The figure shows the comparison of any type I LOH with no LOH for the specified study of the alemtuzumab group.

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

FIG. 17 is a graph showing that class I LOH correlates with lower CD8A expression. The figure shows the comparison of any type I LOH with no LOH for the specified study of the alemtuzumab group.

FIG. 18 is a graph showing OS HR for a given cohort, which shows that HLA class II LOH is associated with poor prognosis. The figure shows the comparison of any class II LOH with no LOH for the specified study of the alemtuzumab group.

Detailed Description

The present invention provides methods and compositions for the treatment and diagnosis of cancer (e.g., lung cancer (e.g., NSCLC (e.g., non-squamous NSCLC or squamous NSCLC)) or renal cancer (e.g., RCC). The present invention is based, at least in part, on the discovery described herein that the presence of specific human leukocyte antigen genes (e.g., HLA-C1 or HLA-Bw 4) and/or killer cell immunoglobulin-like receptor genes (e.g., KIR2DL3 or KIR3DL 1) in a patient's genome correlates with improved therapeutic benefit from a therapeutic regimen comprising a PD-1 axis binding antagonist (e.g., alemtuzumab). The invention is also based, at least in part, on the discovery described herein that an increase in NK cell infiltration in a tumor sample obtained from a patient correlates with improved therapeutic benefit from a treatment regimen comprising a PD-1 axis binding antagonist (e.g., alemtuzumab). The present invention is also based, at least in part, on the discovery described herein that patients with genomic deficiencies in one or more of KIR2DL3 or KIR3DL1 may benefit from treatment regimens that include NK cell-directed therapeutic agents.

I. Definition of the definition

The following abbreviations are used herein:

the terms "human leukocyte antigen C" and "HLA-C" refer to HLA class I heavy chain genes. 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 a mature HLA-C gene product heavy chain and a beta 2-microglobulin light chain. The heavy chain is about 45kDa and its gene contains 8 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. Polymorphisms within exon 2 and exon 3 are generally responsible for the peptide binding specificity of each class I molecule. About 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 under UniProt accession number P10321, for example.

The term "HLA-C1" refers to an HLA-C gene allele group that is generally 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 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, cw 0706 cw_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, e.g., IPD-IMGT/HLA database (ebi.ac.uk/IPD/IMGT/HLA).

The term "HLA-C2" refers to an HLA-C gene allele group that is generally characterized by a lysine (Lys) 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 Cw 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, e.g., IPD-IMGT/HLA database.

The term "HLA-B" refers to HLA class I heavy chain genes. The HLA-B receptor is a heterodimer comprising a mature HLA-B gene product heavy chain and a beta 2-microglobulin light chain. The heavy chain is about 45kDa and its gene contains 8 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. Polymorphisms within exon 2 and exon 3 are generally responsible for the peptide binding specificity of each class I molecule. Additional information about HLA-B can be found under UniProt accession number P01889, for example. 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, -A32:01, and-A23:01).

The term "HLA-Bw4" refers to a class I HLA allele group characterized by Bw4 epitopes within the alpha-1 helix. The Bw4 epitope is typically defined by five residues within the alpha-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-B57:01 or HLA-B15:13) 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 may be different to produce up to eight different Bw4 motifs. As used herein, the term includes HLA-B or HLA-a molecules containing Bw4 epitopes.

Unless otherwise indicated, the terms "killer cell immunoglobulin-like receptor 2DL3" and "KIR2DL3" refer to any native KIR2DL3 from any vertebrate source, including mammals such as primates (e.g., humans) and rodents (e.g., mice and rats). The term encompasses "full length" unprocessed KIR2DL3, as well as any form of KIR2DL3 produced by processing in cells. The term also encompasses naturally occurring variants of KIR2DL3, such as splice variants or allelic variants. KIR2DL3 is an inhibitory KIR gene that recognizes HLA-C molecules (e.g., HLA-C1 molecules) and certain HLA-B molecules (see, e.g., pende et al front. Immunol. Doi: 10.3389/fimmiu. 2019.01779, 2019). KIR2DL3 is also known in the art as CD158 antigen-like family member B2, KIR-023GB, killer inhibitory receptor CL 2-3, NKAT2a, NKAT2B, natural killer-related 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 may be found in NCBI gene ID: 3804. The nucleic acid sequence of exemplary human KIR2DL3 is shown in 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 indicated, the terms "killer cell immunoglobulin-like receptor 3DL1" and "KIR3DL1" refer to any native KIR3DL1 from any vertebrate source, including mammals such as primates (e.g., humans) and rodents (e.g., mice and rats). The term encompasses "full length" unprocessed KIR3DL1 as well as any form of KIR3DL1 produced by processing in cells. The term also encompasses naturally occurring variants of KIR3DL1, such as splice variants or allelic variants. KIR3DL1 is an inhibitory KIR gene that recognizes HLA-B molecules (e.g., HLA-Bw4 molecules) and some of the HLA-a Bw4 with allotypes. KIR3DL1 is also known in the art as CD158 antigen-like family member E, HLA-BW 4-specific inhibitory NK cell receptor, natural killer-related transcript 3 (NKAT-3), p70 natural killer cell receptor clone CL-2/CL-11 and CD158e. Additional information about human KIR3DL1 may be found in NCBI gene ID:3811. the nucleic acid sequence of exemplary human KIR3DL1 is shown in 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 of the innate immune system that can detect and eliminate, for example, cancer cells. NK cells include, for example, CD56 which constitutes the majority of NK cells and is present in bone marrow, secondary lymphoid tissue, liver and skin ^bright (also known as CD56 ^high ) Cells, and CD56, which is mainly present in the peripheral blood system and is characterized by cytotoxic ability ^dim (also known as CD56 ^low ) And (3) cells. CD56 ^dim NK cells are generally CD16 positive and may be referred to as CD56 ^dim CD16 ^bright NK cells; CD56 ^bright Cells can be converted to CD56 by acquisition of CD16 ^dim And (3) cells.

The term "PD-1 axis binding antagonist" refers to a molecule that inhibits interaction of a PD-1 axis binding partner with one or more of its binding partners to eliminate T cell dysfunction resulting from signaling on the PD-1 signaling axis, with the result that T cell function (e.g., proliferation, cytokine production, and/or target cell killing) is restored or enhanced. 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, the PD-1 axis binding antagonist comprises a PD-L1 binding antagonist or a PD-1 binding antagonist. 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 to its binding partner. In a specific aspect, the 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, antigen-binding fragments thereof, immunoadhesins, fusion proteins, oligopeptides, and other molecules that reduce, block, inhibit, eliminate, or interfere with signal transduction resulting from interaction of PD-L1 with one or more of its binding partners (such as PD-1 and/or B7-1). In one case, the PD-L1 binding antagonist reduces a negative co-stimulatory signal mediated by or through signaling by PD-L1 mediated by a cell surface protein expressed on T lymphocytes, thereby rendering dysfunctional T cells less dysfunctional (e.g., enhancing the response of an effector 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 Ab, MDX-1105, MEDI4736 (Devalumab), MSB0010718C (aviumab), SHR-1316, CS1001, en Wo Lishan antibody (envafolimab), TQB2450, ZKAB001, LP-002, CX-072, IMC-001, KL-A167, APL-502, ke Xili monoclonal antibody (cosibelimab), lodaplizumab (lodaplimab), 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 aspects, the anti-PD-L1 antibody is alemtuzumab, MDX-1105, MEDI4736 (Devaluzumab), or MSB0010718C (avermectin). In a specific aspect, the PD-L1 binding antagonist is MDX-1105. In another specific aspect, the PD-L1 binding antagonist is MEDI4736 (devaluzumab). In another specific aspect, the PD-L1 binding antagonist is MSB0010718C (avilamab). In other aspects, the PD-L1 binding antagonist may be a small molecule, e.g., GS-4224, INCB086550, MAX-10181, INCB090244, CA-170, or ABSK041, which in some cases may 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 alemtuzumab.

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 death 1) is also known in the art as "programmed cell death 1", "PDCD1", "CD279" and "SLEB2". An 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 to one or more of its binding partners. In a specific aspect, the 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, antigen-binding fragments thereof, 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 a negative co-stimulatory signal mediated by or through signaling by PD-1 mediated by a cell surface protein expressed on T lymphocytes, thereby rendering dysfunctional T cells less dysfunctional (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 Na Wu Shankang, palbociclizumab, MEDI-0680, PDR001 (Stidazumab), REGN2810 (Simipu Li Shan antibody), BGB-108, paruo Li Shan, carilizumab, xindi Li Shan antibody, tirilizumab, teripu Li Shan antibody, dutarizumab, ralfordin Li Shan antibody, sashan Li Shan antibody, pe An Puli mab, CS1003, HLX10, SCT-I10A, sapalizumab, butelimumab, jenomab, BI 754091, silimumab, YBL-006, BAT1306, HX008, bragg Li Shan antibody, AMG 404, CX-188, JTX-4014, A, sym021, LZM009, F520, SG001, ENUM 244C8, ENUM D4, STI-1110, AK-103 and hAb21. In a specific aspect, the PD-1 binding antagonist is MDX-1106 (Nawuzumab). In another specific aspect, the PD-1 binding antagonist is MK-3475 (pembrolizumab). In another specific aspect, the PD-1 binding antagonist is a PD-L2 fusion protein, e.g., 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 (swabber). In another specific aspect, the PD-1 binding antagonist is REGN2810 (cimipn Li Shan antibody). In another specific aspect, the PD-1 binding antagonist is BGB-108. In another specific aspect, the PD-1 binding antagonist is a palo Li Shan antagonist. In another specific aspect, the PD-1 binding antagonist is a karite Li Zhushan antagonist. In another specific aspect, the PD-1 binding antagonist is a syndesmosidic Li Shan antagonist. In another specific aspect, the PD-1 binding antagonist is tirelizumab. In another specific aspect, the PD-1 binding antagonist is terlipressin Li Shan. 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 death ligand 2) is also known in the art as "programmed cell death 1 ligand 2", "PDCD1LG2", "CD273", "B7-DC", "Btdc" and "PDL2". An exemplary human PD-L2 is shown in UniProtKB/Swiss-Prot accession number Q9BQ 51. In some cases, a PD-L2 binding antagonist is a molecule that inhibits the binding of PD-L2 to one or more of its binding partners. In a specific aspect, the PD-L2 binding antagonist inhibits the binding of PD-L2 to PD-1. Exemplary PD-L2 antagonists include anti-PD-L2 antibodies, antigen-binding fragments thereof, immunoadhesins, fusion proteins, oligopeptides, and other molecules that reduce, block, inhibit, eliminate, or interfere with signaling resulting from 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 a negative co-stimulatory signal mediated by or through signaling by PD-L2 mediated by a cell surface protein expressed on T lymphocytes, thereby rendering dysfunctional T cells less dysfunctional (e.g., enhancing the response of an effector 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 death ligand 1" and "PD-L1" refer herein to the native sequence human PD-L1 polypeptide. The native sequence PD-L1 polypeptide is provided under Uniprot accession number Q9NZQ 7. For example, the native sequence PD-L1 may have an amino acid sequence as described in Uniprot accession number Q9NZQ7-1 (isomer 1). In another example, the native sequence PD-L1 may have an amino acid sequence as described in Uniprot accession No. Q9NZQ7-2 (isomer 2). In yet another example, the native sequence PD-L1 may have an amino acid sequence as described in Uniprot accession number Q9NZQ7-3 (isomer 3). PD-L1 is also known 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 1-113 of the heavy chain), the Kabat numbering system is generally used (e.g., kabat et al, sequences of Immunological Interest. 5 th edition, U.S. department of health and public service, national institutes of health, besseda (1991)). When referring to residues in the immunoglobulin heavy chain constant region, the "EU numbering system" or "EU index" is generally used (e.g., the EU index reported by Kabat et al, supra). The "EU index as set forth in Kabat" refers to the residue numbering of the human IgG1 EU antibody.

For purposes herein, "alemtuzumab" is an Fc-engineered, humanized, non-glycosylated IgG1 kappa immunoglobulin that binds PD-L1 and comprises the heavy chain sequence of SEQ ID No. 1 and the light chain sequence of SEQ ID No. 2. Alemtuzumab comprises a single amino acid substitution (asparagine to alanine) at position 297 on the heavy chain (N297A), using EU numbering of the Fc region amino acid residues, which results in a non-glycosylated antibody that binds minimally to the Fc receptor. Alemtuzumab is also described in the following documents: WHO pharmaceutical information (international pharmaceutical substance non-patent name), proposed INN: listing 112, volume 28, phase 4, 16 days 1 month 2015 (see page 485).

The terms "cancer" and "cancerous" refer to or describe the physiological condition in mammals that is often characterized by uncontrolled cell growth. Aspects of cancer include solid tumor cancer and non-solid tumor cancer. Examples of cancers 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 Cancer (UC), including metastatic UC (mUC), myometrial Invasive Bladder Cancer (MIBC), and non-myometrial invasive bladder cancer (NMIBC)); kidney or renal cancer (e.g., renal Cell Carcinoma (RCC)); lung cancer, including small cell lung cancer, non-small cell lung cancer, lung adenocarcinoma, and lung squamous cell carcinoma; urinary tract cancer; breast cancer (e.g., her2+ breast cancer and Triple Negative Breast Cancer (TNBC), which refers to estrogen receptor (ER-), progestin receptor (PR-) and HER2 (HER 2-) being negative); prostate cancer, such as castration-resistant prostate cancer (CRPC); peritoneal cancer; hepatocellular carcinoma; gastric cancer (gastric/stomach cancer), including gastrointestinal cancer and gastrointestinal stromal cancer; pancreatic cancer (e.g., pancreatic Ductal Adenocarcinoma (PDAC)); glioblastoma; cervical cancer; ovarian cancer; liver cancer (e.g., hepatocellular carcinoma (HCC)); hepatoma; colon cancer; rectal cancer; colorectal cancer; endometrial or uterine cancer; salivary gland cancer; prostate cancer; vulvar cancer; thyroid cancer; liver cancer; anal cancer; penile cancer; melanoma, including superficial diffuse melanoma, lentigo malignant melanoma, peripheral-type malignant melanoma, and nodular melanoma; multiple myeloma and B-cell lymphomas (including low grade/follicular non-hodgkin's lymphoma (NHL), small Lymphocytic (SL) NHL, medium grade/follicular NHL, medium grade diffuse NHL, hyperimmune blast NHL, high grade lymphocytic NHL, high grade small non-lytic cell NHL, giant tumor NHL, mantle cell lymphoma, AIDS-related lymphoma, waldenstrom's macroglobinemia; chronic Lymphocytic Leukemia (CLL); acute Lymphoblastic Leukemia (ALL); acute Myeloid Leukemia (AML); hairy cell leukemia; chronic Myelogenous Leukemia (CML); post-transplant lymphoproliferative disorder (PTLD); and myelodysplastic syndrome (MDS), as well as abnormal vascular hyperplasia associated with mole-related hamartoma, oedema (such as diseases associated with brain tumors), migus' syndrome, brain cancer, head and neck cancer, and related metastases. In one instance, the cancer is lung cancer (e.g., NSCLC, such as non-squamous NSCLC or squamous NSCLC). In another instance, the cancer is renal cancer (e.g., RCC). Cancers may be locally advanced or metastatic. In some cases, the cancer is locally advanced. In other cases, the cancer is metastatic. In some cases, the cancer is stage IV cancer. In some cases, the cancer may be unresectable (e.g., locally advanced or metastatic cancer that is unresectable).

As used herein, the term "tumor" refers to all neoplastic cell growth and proliferation, whether malignant or benign, and all pre-cancerous and cancerous cells and tissues. The terms "cancer," "cancerous," "cell proliferative disorder," "proliferative disorder," and "tumor" are not mutually exclusive herein.

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

The term "B cell proliferative disorder" or "B cell malignancy" refers to disorders associated with some degree of abnormal B cell proliferation, and includes, for example, lymphomas, leukemias, myelomas, and myelodysplastic syndromes. In one embodiment, the B cell proliferative disorder is a lymphoma, such as non-hodgkin lymphoma (NHL), including, for example, DLBCL (e.g., recurrent or refractory DLBCL), FL (e.g., recurrent or refractory FL or transformed FL), or MCL. In another embodiment, the B cell proliferative disorder is leukemia, such as Chronic Lymphocytic Leukemia (CLL). In yet another embodiment, the 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., atuzumab) or NK cell-directed therapeutic agent) or a combination of therapeutic agents (e.g., a PD-1 axis antagonist and one or more additional therapeutic agents, e.g., a taxane (e.g., nab-paclitaxel or paclitaxel), a platinum-based chemotherapeutic agent (e.g., carboplatin), an anti-angiogenic agent (e.g., an anti-VEGF antibody, such as bevacizumab), and/or an NK cell-directed therapeutic agent). Treatment herein includes, inter alia, adjuvant therapy, neoadjuvant therapy, non-metastatic cancer therapy (e.g., locally advanced cancer therapy), and metastatic cancer therapy. The treatment may be a first line treatment (e.g., the patient may have not been previously treated or has not received past systemic therapy), or a second line or subsequent treatment.

Herein, an "effective amount" refers to an amount of a therapeutic agent (e.g., a PD-1 axis binding antagonist (e.g., atuzumab) or NK cell-directed therapeutic agent) or a combination of therapeutic agents (e.g., a PD-1 axis antagonist and one or more additional therapeutic agents, e.g., a taxane (e.g., nab-paclitaxel or paclitaxel), a platinum-based chemotherapeutic agent (e.g., carboplatin), an anti-angiogenic agent (e.g., bevacizumab), and/or an NK cell-directed therapeutic agent) that achieves a therapeutic result. In some examples, an effective amount of a therapeutic agent or combination of therapeutic agents is an amount of an agent or combination of agents that achieves a clinical endpoint of improved survival (e.g., disease Free Survival (DFS), progression Free Survival (PFS), and/or total survival (OS)), improved total remission rate (ORR), complete Remission (CR), pathologically complete remission (pCR), partial Remission (PR), and/or improved duration of remission (DOR). The improvement (e.g., in terms of remission rate (e.g., ORR, CR, and/or PR), survival (e.g., PFS and/or OS), or DOR) may be relative to a suitable reference treatment, e.g., treatment that does not include a PD-1 axis binding antagonist and/or treatment that does not include a taxane (e.g., nab-paclitaxel or paclitaxel), a platinum-based chemotherapeutic agent (e.g., carboplatin), an anti-angiogenic agent (e.g., bevacizumab), and/or an NK cell-directed therapeutic agent. In some aspects, the improvement may be relative to treatment using a treatment regimen that does not include a PD-1 axis binding antagonist.

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

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

As used herein, "total remission rate," "objective remission rate," and "ORR" are interchangeable, referring to the sum of the complete CR rate and PR rate.

As used herein, "progression free survival" and "PFS" refer to the length of time during and after treatment during which the cancer does not worsen. PFS may include the amount of time a patient has experienced CR or PR, as well as the amount of time a patient has experienced disease stabilization. In some examples, PFS may be determined using a solid tumor efficacy evaluation criteria (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 herein, "total survival" and "OS" refer to the length of time that a patient remains alive from the date of diagnosis or beginning treatment of a disease (e.g., cancer). For example, in some cases, the OS is defined as the time between the randomization date and the death date due to any cause.

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

As used herein, the term "chemotherapeutic agent" refers to a compound useful in the treatment of cancer (e.g., NSCLC). Examples of chemotherapeutic agents include EGFR inhibitors (including small molecule inhibitors (e.g., erlotinib @Genentech/osipanm); PD 183805 (CI 1033,2-acrylamide, N- [4- [ (3-chloro-4-fluorophenyl) amino group]-7- [3- (4-morpholinyl) propoxy]-6-quinazolinyl]-dihydrochloride, pfizer inc.); ZD1839, gefitinib +.>4- (3 '-chloro-4' -fluoroanilino) -7-methoxy-6- (3-morpholinopropoxy) quinazoline, 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)]Pyrimidine-2, 8-diamine, boehringer Ingelheim); PKI-166 ((R) -4- [4- [ (1-phenylethyl) amino group]-1H-pyrrolidone [2,3-d ]]Pyrimidin-6-yl]-phenol); (R) -6- (4-hydroxyphenyl) -4- [ (1-phenethyl) 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 group ]-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 (/ -for example>GSK572016 or N- [ 3-chloro-4- [ (3-fluorophenyl) methoxy group]Phenyl group]6[5[ [2 methylsulfonyl ] ethyl group]Amino group]Methyl group]-2-furyl group]-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 kinase (Pfizer and OSI), dual HER inhibitors that preferentially bind EGFR but simultaneously inhibit both HER2 and EGFR cells such as EKB 569 (available from Wyeth); PKI-166 (Novartis), ubiquitin inhibitors such as Kanetinib (CI-1033; pharmacia), raf-1 inhibitors such as antisense ISIS-5132 (ISIS Pharmaceuticals) that inhibits Raf-1 signaling, non-HER targeted tyrosine kinase inhibitors such as imatinib mesylate (>Glaxo SmithKline); multiple targeted tyrosine kinase inhibitors such as sunitinib (/ -for example)>Pfizer); VEGF receptor tyrosine kinase inhibitors such as, for example, varanib (PTK 787/ZK222584, novartis/Schering AG); MAPK extracellular modulation Section kinase I inhibitor CI-1040 (Pharmacia); quinazolines, such as PD 153035, 4- (3-chloroanilino) quinazoline; pyridopyrimidines; pyrimidopyrimidines; pyrrolopyrimidines such as CGP 59326, CGP 60261 and CGP 62706; pyrrolo pyrimidines, 4- (phenylamino) -7H-pyrrolo [2,3-d]Pyrimidine; curcumin (difluoromethane, 4, 5-bis (4-fluoroanilino) phthalimide); tyrosine containing a nitrothiophene moiety; PD-0183805 (Warner-Lamber); antisense molecules (e.g., molecules that bind to HER-encoding nucleic acids); quinoxalines (U.S. patent No. 5,804,396); tyrosine phosphorylation inhibitors (U.S. 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,/-for a patient)>) A) is provided; proteasome inhibitors, e.g. bortezomibMillennium pharm); disulfiram; epigallocatechin gallate; salt spore amide a; carfilzomib; 17-AAG (geldanamycin); radicicol; lactate dehydrogenase A (LDH-A); fulvestrant (+) >AstraZeneca); letrozole (/ -herba Cichorii)>Novartis), phenacetin (++>Novartis); oxaliplatin (+)>Sanofi); 5-FU (5-Fluorourine)Pyrimidine); leucovorin; ronafani (SCH 66336); sorafenib (+)>Bayer Labs); AG1478 alkylating agents, such as thiotepa andcyclophosphamide; alkyl sulfonates such as busulfan, imperoshu and piposhu; aziridines such as benzotepa, carboquinone, rituximab, and uratepa; ethylimines and methylmelamines, including altretamine, triethylenemelamine, triethylenephosphoramide, triethylenethiophosphamide and trimethylol melamine; annonaceous lactones (especially bullatacin and bullatacin ketone); camptothecins (including topotecan and irinotecan); bryostatin; calistatin; CC-1065 (including adoxolone, calzelone and bizelone analogues thereof); nostoc (in particular, nostoc 1 and nostoc 8); corticosteroids (including prednisone and prednisolone); cyproterone acetate; 5α -reductase (including finasteride and dutasteride); vorinostat, romidepsin, ubibetahist, valproic acid, mo Xisi he; aldrigin, talc, du Kamei (including synthetic analogs KW-2189 and CB1-TM 1); eleutherobin; a podophylline; stoloniferol; sponge chalone; nitrogen mustards such as chlorambucil, chlorpheniramine, cyclophosphamide, estramustine, ifosfamide, mechlorethamine hydrochloride, melphalan, mechlorethamine cholesterol, prednisone mustard, qu Luolin amine, uratemustine; nitrosoureas such as carmustine, chlorourea, fotemustine, lomustine, nimustine and ranimustine; antibiotics such as enediyne antibiotics (e.g., calicheamicin, especially calicheamicin γ1 and calicheamicin ω1); daptomycin, including daptomycin a; biphosphate salts such as chlorophosphonate; ai Simi stars; and new carcinostatin chromophores and related chromophores of the chromoproteins enediynes antibiotics), aclacinomycin, actinomycin, anthramycin, azoserine, actinomycin, cartrubicin, ocean Erythromycin, carcinophilin, chromomycin, actinomycin D, dithiin, 6-azido-5-oxo-L-norleucine, morpholino-doxorubicin, cyanomorpholino-doxorubicin, 2-pyrrolin-doxorubicin and deoxydoxorubicin), epirubicin, isofraxine, idarubicin, marcoromycin, mitomycin, such as mitomycin C, mycophenolic acid, norgamycin, olivomycin, pelomycin, methylmitomycin, puromycin, triforine, rodubicin, streptozotocin, tubercidin, ubenimex, clean statin, zorubicin; antimetabolites such as methotrexate and 5-fluorouracil (5-FU); folic acid analogs such as, for example, dimethyl folic acid, methotrexate, pterin, and trimetrexate; purine analogs such as fludarabine, 6-mercaptopurine, thioadenine, thioguanine; pyrimidine analogs such as ambcitabine, azacytidine, 6-azauridine, carmofur, arabinosporine, dideoxyuridine, deoxyfluorouridine, enocitabine, fluorouridine; androgens such as carbosterone, drotasone propionate, cyclothiolane, emasculan, and testosterone; anti-adrenergic agents such as aminoglutethimide, mitotane, qu Luosi; folic acid supplements such as folinic acid; acetoglucurolactone; aldehyde phosphoramide glycosides; aminolevulinic acid; enuracil; amsacrine; multiple Qu Buxi; a specific group; eda traxas; a phosphoramide; colchicine; imine quinone; enonisole; ammonium elegance; epothilones; an ethyleneoxy pyridine; gallium nitrate; hydroxyurea; lentinan; lonidamine; maytansinoids such as maytansine and ansamitocins; mitoguazone; mitoxantrone; mo Pai dar alcohol; diamine nitroacridine; prastatin; egg ammonia nitrogen mustard; pirarubicin; losoxantrone; podophylloic acid); 2-ethyl hydrazine; methyl benzyl hydrazine; A polysaccharide iron complex (JHS Natural Products); carrying out a process of preparing the raw materials; rhizopus extract; schizophyllan; germanium spiroamine; tenuazonic acid; triiminoquinone; 2,2',2 "-trichlorotriethylamine; trichothecene toxins (especially T-2 mycin, verakulin a, plaque fungus a, and serpentine fungus); a urethane; vinblastine; dacarbazine; mannoseAlcohol nitrogen mustard; dibromomannitol; dibromodulcitol; pipobromine; gastrosin; arabinoside ("Ara-C"); cyclophosphamide; thiotepa; chlorambucil;(gemcitabine); 6-thioguanine; mercaptopurine; methotrexate; etoposide (VP-16); ifosfamide; mitoxantrone; nor Wanlong; teniposide; edatrase; daunorubicin; aminopterin; capecitabineIbandronate; CPT-11; topoisomerase inhibitor RFS 2000; difluoromethyl ornithine (DMFO); retinoids such as retinoic acid; and pharmaceutically acceptable salts, acids, prodrugs and derivatives of any of the foregoing.

The chemotherapeutic agent further comprises: (i) Anti-hormonal agents, such as antiestrogens and Selective Estrogen Receptor Modulators (SERMs), including, for example, tamoxifen (including Tamoxifen citrate), raloxifene, droloxifene (droloxifene), iodoxyfene, 4-hydroxy tamoxifen, qu Aoxi-fene (trioxifene), raloxifene hydrochloride (keoxifene), LY117018, onapristone (onapristone) and(tomiphene citrate (toremifine citrate)); (ii) Aromatase inhibitors that inhibit aromatase, which regulates estrogen production of the adrenal glands, such as, for example, 4 (5) -imidazole, aminoglutethimide,/-for example>(megestrol acetate),>(exemestane; pyroxene), formestane (formestanie), method Qu (fadro)zole)、(Fu Luo (vorozole)), -, etc.>(letrozole; north Hua Co.) and(anastrozole; assailant Corp.); (iii) Antiandrogens such as flutamide, nilutamide, bicalutamide, leuprorelin, and goserelin; buserelin (buserelin), triptorelin (tripterlin), medroxyprogesterone acetate, diethylstilbestrol, beclomethasone, fluoxytestosterone, all trans retinoic acid, valatide (fenretinide), and troxacitabine (1, 3-dioxolane nucleoside cytosine analog); (iv) a protein kinase inhibitor; (v) a lipid kinase inhibitor; (vi) Antisense oligonucleotides, particularly 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 inhibitors of VEGF expression (e.g., +. >) And an inhibitor of HER2 expression; (viii) Vaccines, such as gene therapy vaccines, e.g. +.>And(ix) Growth inhibitors, including vinca (e.g., vincristine and vinblastine), and->(vinorelbine), taxanes (e.g., paclitaxel, albumin-bound paclitaxel, and docetaxel), topoisomerase II inhibitors (e.g., doxorubicin, epirubicin, daunomycin)Etoposide and bleomycin) and DNA alkylating agents (e.g., tamoxifen (tamoxigen), prednisone, dacarbazine, dichloromethyl diethylamine, cisplatin, methotrexate, 5-fluorouracil and ara-C); and (x) pharmaceutically acceptable salts, acids, prodrugs and derivatives of any of the foregoing.

As used herein, the term "cytotoxic agent" refers to any agent that is detrimental to a cell (e.g., causes cell death, inhibits proliferation, or otherwise impedes cell function). Cytotoxic agents include, but are not limited to, radioisotopes (e.g., at ²¹¹ 、I ¹³¹ 、I ¹²⁵ 、Y ⁹⁰ 、Re ¹⁸⁶ 、Re ¹⁸⁸ 、Sm ¹⁵³ 、Bi ²¹² 、P ³² 、Pb ²¹² And a radioisotope of Lu); a chemotherapeutic agent; enzymes and fragments thereof, such as nucleolytic enzymes; and toxins, such as small molecule toxins or enzymatically active toxins of bacterial, fungal, plant or animal origin, including fragments and/or variants thereof. Exemplary cytotoxic agents may be selected from the group consisting of anti-microtubule agents, platinum coordination complexes, alkylating agents, antibiotic agents, topoisomerase II inhibitors, antimetabolites, topoisomerase I inhibitors, hormone 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 antagonist of EGFR, e.g., N- (3-ethynylphenyl) -6, 7-bis (2-methoxyethoxy) quinazolin-4-amine (e.g., erlotinib). In one instance, the cytotoxic agent is a RAF inhibitor, e.g., a BRAF and/or CRAF inhibitor. In one instance, the RAF inhibitor is vemurafenib (vemurafenib). In one instance, the cytotoxic agent is a PI3K inhibitor.

As used herein, a "taxane" is an agent (e.g., a diterpene) that can bind to tubulin, thereby promoting microtubule assembly and stabilization and/or preventing microtubule depolymerization. Exemplary taxanes include, but are not limited to, paclitaxel (i.e.,CAS# 33069-62-4), docetaxel (i.e., +.>CAS# 114977-28-5), ralostazol, cabazitaxel, melatazitaxel, telmisaxel, and/or ortataxel. The taxane compounds included herein also include the taxane class (taxoid) 10-deacetylbaccatin III and/or derivatives thereof. In some embodiments, the taxane is albumin coated nanoparticle (e.g., nanoalbumin binding (nab) -paclitaxel (i.e.,/->) And/or nab-docetaxel (ABI-008)). In some embodiments, the taxane is nab-paclitaxel +.>In some embodiments, the taxane is formulated at +.>(e.g.)>) Neutralization/or +.>(such as polysorbate 80 (e.g.,) A) is provided. In some embodiments, the taxane is a liposome-encapsulated taxane. In some embodiments, the taxane is a prodrug form and/or conjugated form of the taxane (e.g., DHA is covalently conjugated to paclitaxel, polyglutamate paclitaxel, and/or an linoleyl carbonate-paclitaxel). In some embodiments, the paclitaxel is formulated to be substantially free of surfactant (e.g., in the absence +. >And/or +.>(such as->) In the case of paclitaxel).

Chemotherapeutic agents also include "platinum-based" chemotherapeutic agents that comprise an organic compound containing platinum as part of the molecule. Typically, the platinum-based chemotherapeutic agent is a coordination complex of platinum. Platinum-based chemotherapeutic agents are sometimes referred to in the art as "platinum-based agents". Examples of platinum-based chemotherapeutic agents include, but are not limited to, cisplatin, carboplatin, oxaliplatin, nedaplatin, triplatinum tetranitrate, phenanthriplatin, picoplatin, lipoplatin, and satraplatin. The platinum-based chemotherapeutic agent (e.g., cisplatin or carboplatin) may be administered in combination with one or more additional chemotherapeutic agents (e.g., nucleoside analogs (e.g., gemcitabine)).

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

An "anti-angiogenic agent" or "angiogenesis inhibitor" refers to a small molecular weight substance, polynucleotide, polypeptide, isolated protein, recombinant protein, antibody, or conjugate or fusion protein thereof that directly or indirectly inhibits angiogenesis, vasculogenesis, or poor vascular permeability. It is understood that anti-angiogenic agents include those agents that bind to and block the angiogenic activity of angiogenic factors or their receptors. For example, anti-angiogenic and anti-PDGFR inhibitors such as GLEEVEC are antibodies or other antagonists to the agents defined above, e.g. VEGF-Sub>A or VEGF-Sub>A receptor (e.g. KDR receptor or Flt-1 receptor) ^TM (imatinib mesylate). Anti-angiogenic agents also include natural angiogenesis inhibitors, e.g., angiostatin, endostatin, and the like. See, e.g., klagsbrun and D' Amore, annu.Physiol, 53:217-39 (1991); streit and Detmar, oncogene,22:3172-3179 (2003) (e.g., table 3 lists anti-angiogenic therapies for malignant melanoma); ferrara and Alitalo, nature Medicine 5 (12): 1359-1364 (1999); tonni et al, oncogene,22:6549-6556 (2003) and Sato Int.J. Clin. Oncol.,8:200-206 (2003).

An "anti-VEGF antibody" is an antibody that binds VEGF with sufficient affinity and specificity. In certain embodiments, the antibody will have a sufficiently high binding affinity for VEGF, e.g., the antibody can bind hVEGF with a Kd value between 100nM and 1 pM. Antibody affinity may be determined, for example, by an assay based on surface plasmon resonance (such as described in PCT application publication No. WO2005/012359Assays), enzyme-linked immunosorbent assays (ELISA) and competition assays (e.g., radioimmunoassays (RIA)).

In certain embodiments, anti-VEGF antibodies may be used as therapeutic agents that target and interfere with diseases or conditions in which VEGF activity is involved. Moreover, other biological activity 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 antibody. Examples include HUVEC inhibition assays; tumor cell growth inhibition assays (e.g., as described in WO 89/06692); antibody-dependent cellular cytotoxicity (ADCC) and complement-mediated cytotoxicity (CDC) assays (U.S. Pat. No. 5,500,362); an agonist activity or haematopoietic assay (see WO 95/27062). anti-VEGF antibodies typically do not bind to other VEGF homologs (such as VEGF-B or VEGF-C) nor to other growth factors (such as PlGF, 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 produced by 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, a monoclonal antibody known as bevacizumab (BV; ) Is a human antibody.

anti-VEGF antibodies "bevacizumab" are also known as "rhuMAb VEGF", "BV" orIs a recombinant humanized anti-VEGF monoclonal antibody produced according to Presta et al (Cancer Res.57:4593-4599, 1997). It comprises a mutated human IgG1 framework region and an antigen-binding complementarity determining region from murine anti-hVEGF monoclonal antibody a.4.6.1 that blocks binding of human VEGF to its receptor. About 93% of the amino acid sequence of bevacizumab, including the majority of the framework regions, was derived from human IgG1, and about 7% of the sequence was derived from murine antibody a4.6.1. Bevacizumab has a molecular mass of about 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 26, 2.2005, the entire disclosure of which is expressly incorporated herein by reference. Other preferred antibodies include antibodies of the G6 or B20 series (e.g., G6-31, B20-4.1) as described in PCT application publication No. WO 2005/012359. For additional preferred antibodies, see U.S. patent nos. 7,060,269, 6,582,959, 6,703,020, 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; popkov et al (Journal of Immunological Methods288:149-164, 2004). Other preferred antibodies include antibodies that bind to a functional epitope on human VEGF that comprises residues F17, M18, D19, Y21, Y25, Q89, 191, K101, E103, and C104, or alternatively, residues F17, Y21, Q22, Y25, D63, 183, and Q89.

The term "NK cell-directed therapeutic agent" is meant to include NK cells or agents that modulate the number, activity or function of NK cells. In some cases, NK cell-targeted therapeutics include adoptive cell transfer (e.g., using allogeneic NK cells, autologous NK cells, ready NK cells, or Chimeric Antigen Receptor (CAR) -NK cells), cytokine therapy, NK cell cement (e.g., bispecific killer cell cement (BiKE), trispecific killer cell cement (tripe), or tetraspecific killer cell cement (TetraKE)), NK cell checkpoint receptor antagonists, or oncolytic viruses. Exemplary NK cell directed therapeutic agents are described, for example, in Hodgins et al J.Clin.Invest.129 (9): 3499-3510, 2019.

The term "NK cell cement" refers to a molecule that brings NK cells and tumor cells together, for example, by binding to one or more targets (e.g., proteins, e.g., receptors) on the surface of NK cells (e.g., CD16, NKG2D, SLAM family proteins, NKp30, NKp44, or NKp 46) and one or more targets (e.g., proteins, e.g., receptors) on the surface of tumor cells (e.g., tumor antigens, including any of the tumor antigens described in CD30, CD33, EGFR, BCMA, or table C). NK cell cements can be multispecific, e.g., bispecific, trispecific, or tetraspecific. For a particular target, the NK cell binding agent may be multivalent, e.g., bivalent, trivalent, tetravalent, pentavalent, or hexavalent. For example, the NK cell cement may be at least bivalent for CD16A, i.e. comprise at least two CD16A antigen binding portions. In some examples, the NK cell cement comprises at least a first targeting domain that binds to an epitope on an NK cell and at least a second targeting domain that binds to a different target (e.g., a tumor antigen (e.g., any of the tumor antigens described in table C)). Exemplary NK cell cements 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 (15 suppl), 2016; and Ellwanger et al JImmunother Cancer,3 (Suppl 2): 219,2015. In some embodiments, the NK-cell cement is a nanoparticle-based NK-cell cement, such as a nanoparticle-based trispecific NK-cell cement (nano-TriNKE); see, e.g., au et al Science Advances6 (27): eaba8564,2020. Exemplary NK cell cements include, for example, IPH6101 (Innate Pharma/Sanofi).

The term "patient" refers to a human patient. For example, the patient may be adult.

The term "antibody" herein specifically covers monoclonal antibodies (including full length monoclonal antibodies), polyclonal antibodies, multispecific antibodies (e.g., bispecific antibodies), and antibody fragments so long as they exhibit the desired biological activity. In one instance, the antibody is a full length monoclonal antibody.

As used herein, the term IgG "isotype" or "subclass" refers to any subclass of immunoglobulin defined by the chemistry and antigenic characteristics of the immunoglobulin constant region.

Antibodies (immunoglobulins) may be assigned to different classes based on the amino acid sequence of their heavy chain constant domains. Immunoglobulins are largely divided into five classes: igA, igD, igE, igG and IgM, and some of them can be further divided into subclasses (isotypes), for example, igG1, igG2, igG3, igG4, igA1 and IgA2. The heavy chain constant domains corresponding to the different classes of immunoglobulins are called α, γ, ε, γ and μ, respectively. The subunit structure and three-dimensional configuration of different classes of immunoglobulins are well known and are generally described, for example, in the following documents: abbas et al Cellular and mol.immunology, 4 th edition (W.B.Saundrs, co., 2000). An antibody may be part of a larger fusion molecule formed by covalent or non-covalent association of the antibody with one or more other proteins or peptides.

The terms "full length antibody", "whole antibody" and "whole antibody" are used interchangeably herein to refer to an antibody in its substantially intact form rather than an antibody fragment as defined below. The term refers to antibodies comprising an Fc region.

The term "Fc region" is used herein to define the C-terminal region of an immunoglobulin heavy chain, which comprises at least a portion of a constant region. The term includes native sequence Fc regions and variant Fc regions. In one aspect, the human IgG heavy chain Fc region extends from Cys226 or from Pro230 to the carboxy terminus of the heavy chain. However, antibodies produced by the host cell may undergo post-translational cleavage of one or more (particularly one or two) amino acids from the C-terminus of the heavy chain. Thus, an antibody produced by a host cell by expression of a particular nucleic acid molecule encoding a full-length heavy chain may comprise a full-length heavy chain, or the antibody may comprise a cleaved variant of a full-length heavy chain. This may be the case where the last two C-terminal amino acids of the heavy chain are glycine (G446) and lysine (K447). Thus, the C-terminal lysine (Lys 447) or C-terminal glycine (Gly 446) and lysine (Lys 447) of the Fc region may or may not be present. If not otherwise indicated, the amino acid sequence of the heavy chain comprising the Fc region is herein denoted without the C-terminal lysine (Lys 447). In one aspect, a heavy chain comprising an Fc region as specified herein is included in an antibody according to the disclosure, the heavy chain comprising an additional C-terminal glycine-lysine dipeptide (G446 and K447). In one aspect, a heavy chain comprising an Fc region as specified herein, comprising an additional C-terminal glycine residue (G446), is included in an antibody according to the disclosure herein. In one aspect, a heavy chain comprising an Fc region as specified herein, comprising an additional C-terminal lysine residue (K447), is included in an antibody according to the disclosure herein. In one embodiment, the Fc region contains the single amino acid substitution N297A of the heavy chain. Unless otherwise specified herein, numbering of amino acid residues in the Fc region or constant region is according to the EU numbering system, also known as the EU index, as described in Kabat et al, sequences of Proteins of Immunological Interest, 5 th 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 radiolabeled. The naked antibody may be present in a pharmaceutical composition.

An "antibody fragment" comprises a portion of an intact antibody, preferably comprising an antigen binding region thereof. 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; a diabody antibody; a linear antibody; single chain antibody molecules (e.g., scFv); and multispecific antibodies formed from antibody fragments.

The term "monoclonal antibody" as used herein refers to an antibody obtained from a substantially homogeneous population of antibodies, i.e., individual antibodies comprising the population have identity and/or bind to the same epitope, except possibly variant antibodies (e.g., containing naturally occurring mutations or produced during production of a monoclonal antibody preparation, such variants typically being present in minor amounts). In contrast to polyclonal antibody preparations, which typically include different antibodies directed against different determinants (epitopes), each monoclonal antibody in a monoclonal antibody preparation is directed against a single determinant on the antigen. Thus, the modifier "monoclonal" indicates the character of the antibody as being obtained from a substantially homogeneous population of antibodies, and is not to be construed as requiring production of the antibody by any particular method. For example, 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 comprising all or part of the human immunoglobulin loci.

The term "hypervariable region" or "HVR" as used herein refers to the individual regions of an antibody variable domain that are hypervariable in sequence and determine antigen binding specificity, e.g., the "complementarity determining regions" ("CDRs").

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

(a) A highly variable loop present 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, 5 th edition, public Health Service, national Institutes of Health, bethesda, MD (1991)); and

(c) Antigen contact points occur 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)). The CDRs are determined according to the method described by Kabat et al, supra, unless otherwise indicated. Those skilled in the art will appreciate that CDR names may also be determined according to the method described by Chothia, supra, mccallium, supra, or any other scientifically accepted naming system.

"framework" or "FR" refers to the variable domain residues other than the Complementarity Determining Regions (CDRs). The FR of the variable domain typically consists of four FR domains: FR1, FR2, FR3 and FR4. Thus, CDR and FR sequences typically occur in VH (or VL) with the following sequences: FR1-CDR-H1 (CDR-L1) -FR2-CDR-H2 (CDR-L2) -FR3-CDR-H3 (CDR-L3) -FR4.

The term "Kabat-described variable domain residue number" or "Kabat-described amino acid position number" and variants thereof refer to the numbering system for heavy chain variable domains or light chain variable domains set forth in the above-mentioned Kabat et al literature. Using this numbering system, the actual linear amino acid sequence may contain fewer or additional amino acids, which correspond to shortening or insertion of FR or HVR of the variable domain. For example, the heavy chain variable domain may include a single amino acid insert (residue 52a according to Kabat numbering) following residue 52 of H2 and an insert residue (e.g., residues 82a, 82b, 82c, etc. according to Kabat numbering) following heavy chain FR residue 82. The Kabat numbering of residues of a given antibody can be determined by aligning the antibody sequences with regions of homology of the "standard" Kabat numbering sequences.

The term "package insert" is used to refer to instructions typically included in commercial packages of therapeutic products that contain information concerning the indication, usage, dosage, administration, combination therapy, contraindications and/or warnings concerning the use of such therapeutic products.

As used herein, "in combination with … …" refers to a treatment regimen that includes administration of a PD-1 axis binding antagonist (e.g., alemtuzumab) and a taxane (e.g., nab-paclitaxel or paclitaxel), a platinum-based chemotherapeutic agent (e.g., carboplatin), an anti-angiogenic agent (e.g., an anti-VEGF antibody, such as bevacizumab), and/or an NK cell-directed therapeutic agent, in addition to another treatment regimen. Thus, "in combination with … …" refers to the administration of one treatment modality prior to, during, or after the administration of another treatment modality to a patient.

A drug administered "concurrently" with one or more other drugs is administered on the same day of treatment with the one or more other drugs, and optionally concurrently with the one or more other drugs, within the same treatment cycle. For example, for 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 means of detection, including direct detection 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, e.g., an HLA gene (e.g., HLA-C1 or HLA-Bw 4), a KIR gene (e.g., KIR2DL3 or KIR3DL 1), NK cell infiltration, or NK cell characteristics (e.g., NK cell characteristics including one or more of the following genes: CD160, CD244, CTSW, FASLG, GZMA, GZMB, GZMH, IL RAP, IL2RB, KIR2DL4, KLRB1, KLRC3, KLRD1, KRLF1, KLRK1, NCR1, NKG7, PRF1, XCL1, and XCL 2). Biomarkers can be used as indicators of specific subtypes of a disease or disorder (e.g., cancer) characterized by certain characteristics, molecular characteristics, pathological characteristics, histological characteristics, and/or clinical characteristics. 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), polypeptides, and polynucleotide modifications (e.g., post-translational modifications), carbohydrates, and/or glycolipid-based molecular markers.

The term "CD160" as used herein refers to any natural CD160 (cluster of differentiation 160; also known as NK1; BY55; and NK 28) from any vertebrate source, including mammals such as primates (e.g., humans) and rodents (e.g., mice and rats), unless otherwise indicated. The term encompasses "full length" unprocessed CD160, as well as any form of CD160 produced by processing in a cell. The term also encompasses naturally occurring variants of CD160, such as splice variants or allelic variants. The nucleic acid sequence of exemplary human CD160 is shown in NCBI reference sequence: nm_ 007053.4. The amino acid sequence of an exemplary protein encoded by human CD160 is shown under UniProt accession No. Q6FH 89.

The term "CD244" as used herein refers to any natural CD244 (cluster 244; also known as natural killer cell receptor 2b4; nail; nkr2b4; nmrk; and SLAMF 4) from any vertebrate source, including mammals such as primates (e.g., humans) and rodents (e.g., mice and rats), unless otherwise indicated. The term encompasses "full length" unprocessed CD244, as well as any form of CD244 produced by processing in a cell. The term also encompasses naturally occurring variants of CD244, such as splice variants or allelic variants. The nucleic acid sequence of exemplary human CD244 is shown in NCBI reference sequence: nm_ 016382.4. The amino acid sequence of an exemplary protein encoded by human CD244 is shown under UniProt accession No. Q07763.

The term "CTSW" as used herein refers to any native CTSW (cathepsin W; also referred to as LYPN) from any vertebrate source, including mammals such as primates (e.g., humans) and rodents (e.g., mice and rats), unless otherwise indicated. The term encompasses "full length" unprocessed CTSW, as well as any form of CTSW produced by processing in a cell. The term also encompasses naturally occurring variants of CTSW, such as splice variants or allelic variants. The nucleic acid sequence of an exemplary human CTSW is shown in NCBI reference sequence: nm_ 001335.4. The amino acid sequence of an exemplary protein encoded by human CTSW is shown under UniProt accession No. P56202.

The term "FASLG" as used herein refers to any natural FASLG (Fas ligand; also known as Fas; CD95L; and CD 178) from any vertebrate source, including mammals such as primates (e.g., humans) and rodents (e.g., mice and rats), unless otherwise indicated. The term encompasses "full length" unprocessed FASLG, as well as any form of FASLG produced by processing in a cell. The term also encompasses naturally occurring variants of FASLG, such as splice variants or allelic variants. The nucleic acid sequence of an exemplary human FASLG is shown in NCBI reference sequence: nm_ 000639.3. The amino acid sequence of an exemplary protein encoded by human FASLG is shown under UniProt accession number P48023.

The term "GZMA" as used herein refers to any native 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), unless otherwise indicated. The term encompasses "full length" unprocessed GZMA, as well as any form of GZMA produced by processing in a cell. The term also encompasses naturally occurring variants of GZMA, such as splice variants or allelic variants. The nucleic acid sequence of an exemplary human GZMA is shown in NCBI reference sequence: nm_ 006144.4. The amino acid sequence of an exemplary protein encoded by human GZMA is shown under UniProt accession No. P12544.

The term "GZMB" as used herein refers to any native 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), unless otherwise indicated. The term encompasses "full length" unprocessed GZMB, as well as any form of GZMB produced by processing in a cell. The term also encompasses naturally occurring variants of GZMB, such as splice variants or allelic variants. The nucleic acid sequence of an exemplary human GZMB is shown in NCBI reference sequence: nm_ 004131.6. The amino acid sequence of an exemplary protein encoded by human GZMB is shown under UniProt accession No. P10144.

The term "GZMH" as used herein refers to any native 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), unless otherwise indicated. The term encompasses "full-length" unprocessed GZMH, as well as any form of GZMH produced by processing in cells. The term also encompasses naturally occurring variants of GZMH, such as splice variants or allelic variants. The nucleic acid sequence of an exemplary human GZMH is shown in NCBI reference sequence: nm_ 033423.5. The amino acid sequence of an exemplary protein encoded by human GZMH is shown under UniProt accession No. P20718.

The term "IL18RAP" as used herein refers to any native IL18RAP (interleukin 18 receptor accessory protein; also referred to as CDw218 b) from any vertebrate source, including mammals such as primates (e.g., humans) and rodents (e.g., mice and rats), unless otherwise indicated. The term encompasses "full length" unprocessed IL18RAP, as well as any form of IL18RAP produced by processing in a cell. The term also encompasses naturally occurring variants of IL18RAP, such as splice variants or allelic variants. The nucleic acid sequence of exemplary human IL18RAP is shown in NCBI reference sequence: nm_ 003853.4. The amino acid sequence of an exemplary protein encoded by human IL18RAP is shown under UniProt accession No. O95256.

The term "IL2RB" as used herein refers to any native IL2RB (interleukin-2 receptor subunit beta; 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), unless otherwise indicated. The term encompasses "full length" unprocessed IL2 RBs, as well as any form of IL2RB produced by processing in a cell. The term also encompasses naturally occurring variants of IL2RB, such as splice variants or allelic variants. The nucleic acid sequence of an exemplary human IL2RB is shown in 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.

The term "KIR2DL4" AS used herein refers to any native KIR2DL4 (killer cell immunoglobulin-like receptor 2DL4; also referred to AS CD158D and KIR103 AS) from any vertebrate source, including mammals such AS primates (e.g., humans) and rodents (e.g., mice and rats), unless otherwise indicated. The term encompasses "full length" unprocessed KIR2DL4, as well as any form of KIR2DL4 produced by processing in a cell. The term also encompasses naturally occurring variants of KIR2DL4, such as splice variants or allelic variants. The nucleic acid sequence of exemplary human KIR2DL4 is shown in NCBI reference sequence: nm_ 002255.6. The amino acid sequence of an exemplary protein encoded by human KIR2DL4 is shown under UniProt accession No. Q99706.

The term "KLRB1" as used herein refers to any native KLRB1 (killer lectin-like receptor subfamily B member 1; also referred to as NKR-P1A and CD 161) from any vertebrate source, including mammals such as primates (e.g., humans) and rodents (e.g., mice and rats), unless otherwise indicated. The term encompasses "full length" unprocessed KLRB1, as well as any form of KLRB1 produced by processing in a cell. The term also encompasses naturally occurring variants of KLRB1, such as splice variants or allelic variants. The nucleic acid sequence of exemplary human KLRB1 is shown in NCBI reference sequence: nm_ 002258.3. The amino acid sequence of an exemplary protein encoded by human KLRB1 is shown under UniProt accession No. Q12918.

The term "KLRC3" as used herein refers to any native KLRC3 (killer cell lectin-like receptor C3; also known as NKG 2E) from any vertebrate source, including mammals such as primates (e.g., humans) and rodents (e.g., mice and rats), unless otherwise indicated. The term encompasses "full length" unprocessed KLRC3, as well as any form of KLRC3 produced by processing in a cell. The term also encompasses naturally occurring variants of KLRC3, such as splice variants or allelic variants. The nucleic acid sequence of exemplary human KLRC3 is shown in NCBI reference sequence: nm_ 002261.3. The amino acid sequence of an exemplary protein encoded by human KLRC3 is shown under UniProt accession No. Q07444.

The term "KLRD1" as used herein refers to any native KLRD1 (killer cell lectin-like receptor D1; also referred to as CD 94) from any vertebrate source, including mammals such as primates (e.g., humans) and rodents (e.g., mice and rats), unless otherwise indicated. The term encompasses "full length" unprocessed KLRD1, as well as any form of KLRD1 resulting from processing in a cell. The term also encompasses naturally occurring variants of KLRD1, such as splice variants or allelic variants. The nucleic acid sequence of exemplary human KLRD1 is shown in NCBI reference sequence: nm_ 002262.5. The amino acid sequence of an exemplary protein encoded by human KLRD1 is shown under UniProt accession number Q13241.

The term "KLRF1" as used herein refers to any native KLRF1 (killer lectin-like receptor subfamily F member 1; also referred to as CLEC 5C) from any vertebrate source, including mammals such as primates (e.g., humans) and rodents (e.g., mice and rats), unless otherwise indicated. The term encompasses "full length" unprocessed KLRF1, as well as any form of KLRF1 produced by processing in a cell. The term also encompasses naturally occurring variants of KLRF1, such as splice variants or allelic variants. The nucleic acid sequence of exemplary human KLRF1 is shown in NCBI reference sequence: nm_ 016523.3. The amino acid sequence of an exemplary protein encoded by human KLRF1 is shown under UniProt accession No. Q9NZS 2.

The term "KLRK1" as used herein refers to any native KLRK1 (killer lectin-like receptor subfamily K member 1; also referred to as NKG 2D) from any vertebrate source, including mammals such as primates (e.g., humans) and rodents (e.g., mice and rats), unless otherwise indicated. The term encompasses "full length" unprocessed KLRK1, as well as any form of KLRK1 produced by processing in cells. The term also encompasses naturally occurring variants of KLRK1, such as splice variants or allelic variants. The nucleic acid sequence of exemplary human KLRK1 is shown in NCBI reference sequence: nm_ 007360.4. The amino acid sequence of an exemplary protein encoded by human KLRK1 is shown under UniProt accession number P26718.

The term "NCR1" as used herein refers to any native NCR1 (native cytotoxicity trigger receptor 1; also known as CD335; NKP46; and LY 94) from any vertebrate source, including mammals such as primates (e.g., humans) and rodents (e.g., mice and rats), unless otherwise indicated. The term encompasses "full length" unprocessed NCR1, as well as any form of NCR1 resulting from processing in a cell. The term also encompasses naturally occurring variants of NCR1, such as splice variants or allelic variants. The nucleic acid sequence of exemplary human NCR1 is shown in NCBI reference sequence: nm_ 004829.7. The amino acid sequence of an exemplary protein encoded by human NCR1 is shown under UniProt accession No. O76036.

The term "NKG7" as used herein refers to any natural NKG7 (natural killer cell granule protein 7; also known as GIG1; GMP-17; and p 15-TIA-1) from any vertebrate source, including mammals such as primates (e.g., humans) and rodents (e.g., mice and rats), unless otherwise indicated. The term encompasses "full length" unprocessed NKG7, as well as any form of NKG7 resulting from processing in a cell. The term also encompasses naturally occurring variants of NKG7, such as splice variants or allelic variants. The nucleic acid sequence of exemplary human NKG7 is shown in NCBI reference sequence: nm_ 005601.4. The amino acid sequence of an exemplary protein encoded by human NKG7 is shown under UniProt accession No. Q16617.

The term "PRF1" as used herein refers to any natural PRF1 (perforin-1; also referred to as PFP) from any vertebrate source, including mammals such as primates (e.g., humans) and rodents (e.g., mice and rats), unless otherwise indicated. The term encompasses "full length" unprocessed PRF1, as well as any form of PRF1 produced by processing in a cell. The term also encompasses naturally occurring variants of PRF1, such as splice variants or allelic variants. The nucleic acid sequence of an exemplary human PRF1 is shown in NCBI reference sequence: nm_ 005041.6. The amino acid sequence of an exemplary protein encoded by human PRF1 is shown under UniProt accession No. P14222.

The term "XCL1" as used herein refers to any natural XCL1 (chemokine (C motif) ligand; also known as LTN and SCYC 1) from any vertebrate source, including mammals such as primates (e.g., humans) and rodents (e.g., mice and rats), unless otherwise indicated. The term encompasses "full length" unprocessed XCL1, as well as any form of XCL1 resulting from processing in a cell. The term also encompasses naturally occurring variants of XCL1, such as splice variants or allelic variants. The nucleic acid sequence of exemplary human XCL1 is shown in NCBI reference sequence: nm_ 002995.3. The amino acid sequence of an exemplary protein encoded by human XCL1 is shown under UniProt accession number P47992.

The term "XCL2" as used herein refers to any native XCL2 (chemokine (C motif) ligand 2; also referred to as SCM1B and SCYC 2) from any vertebrate source, including mammals such as primates (e.g., humans) and rodents (e.g., mice and rats), unless otherwise indicated. The term encompasses "full length" unprocessed XCL2, as well as any form of XCL2 resulting from processing in a cell. The term also encompasses naturally occurring variants of XCL2, such as splice variants or allelic variants. The nucleic acid sequence of exemplary human XCL2 is shown in NCBI reference sequence: nm_ 003175.4. The amino acid sequence of an exemplary protein encoded by human XCL2 is shown under UniProt accession No. Q9UBD 3.

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

In general, the terms "level of expression" or "expression level" are used interchangeably and generally refer to the amount of a biomarker in a biological sample. "expression" generally refers to the process of converting information (e.g., genetic code and/or epigenetic information) into structures that are present and run in a cell. Thus, as used herein, "expression" may 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). Transcribed polynucleotides, translated polypeptides, or fragments of a polynucleotide and/or polypeptide modification (e.g., post-translational modification of a polypeptide) are also considered to have been expressed, whether they originate from transcripts generated by alternatively spliced or degraded transcripts, or from post-translational processing of the polypeptide (e.g., by proteolysis). "expressed genes" include those transcribed into polynucleotides such as mRNA and then translated into polypeptides, and also 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 level," or "elevated level" refers to an increased expression or increased level of a biomarker in an individual relative to a control, such as one or more individuals not suffering from a disease or disorder (e.g., cancer) or an internal control (e.g., a housekeeping biomarker).

"reduced expression," "reduced expression level," "reduced expression level," or "reduced level" refers to an increased or reduced level of expression of a biomarker in an individual relative to one or more individuals or internal controls (e.g., housekeeping biomarkers) that do not have a disease or disorder (e.g., cancer) relative to the control. In some embodiments, reduced expression is little or no expression.

The term "housekeeping biomarker" refers to a biomarker or a set of biomarkers (e.g., polynucleotides and/or polypeptides) that are typically similarly present in all cell types. In some embodiments, the housekeeping biomarker is a "housekeeping gene". "housekeeping gene" refers herein to a gene or set of genes encoding proteins whose activity is essential for maintaining cellular function, and housekeeping genes are typically found similarly in all cell types.

The term "diagnosis" as used herein refers to the identification or classification of a molecular or pathological state, disease or condition (e.g., cancer (e.g., NSCLC)). For example, "diagnosis" may refer to the identification of a particular type of cancer. "diagnosis" may also refer to the classification of a particular subtype of cancer, e.g., by histopathological criteria or molecular characteristics (e.g., a subtype characterized by expression of one biomarker or combination of biomarkers (e.g., a particular gene or protein encoded by the gene)).

As used herein, the term "sample" refers to a composition obtained or derived from a subject and/or individual of interest that contains cells and/or other molecular entities to be characterized and/or identified, e.g., based on physical, biochemical, chemical, and/or physiological characteristics. For example, the phrase "disease sample" and variations thereof refers to any sample obtained from a target subject that is expected or known to contain the cellular 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 humor, lymph, synovial fluid, follicular fluid, semen, amniotic fluid, milk, whole blood, blood derived cells, urine, cerebrospinal fluid, saliva, sputum, tears, sweat, mucus, tumor lysate and tissue culture media, tissue extracts such as homogenized tissue, tumor tissue, cell extracts, and combinations thereof.

"tissue sample" or "cell sample" refers to a collection of similar cells obtained from the tissue of a subject or individual. The source of the tissue or cell sample may 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; cells at any time during gestation or development in a subject. The tissue sample may also be a primary or cultured cell or cell line. Optionally, the tissue or cell sample is obtained from a 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. The tissue sample may comprise a mixed population of cell types (e.g., tumor cells and non-tumor cells, cancer cells and non-cancer cells). The tissue sample may comprise compounds that are not naturally mixed with the tissue in the natural environment, such as preservatives, anticoagulants, buffers, fixatives, nutrients, antibiotics, or the like.

As used herein, "tumor-infiltrating immune cells" refers to any immune cells present in a tumor or sample thereof. 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 myeloid lineage cells, including granulocytes (e.g., neutrophils, eosinophils, and basophils), monocytes, macrophages, dendritic cells (e.g., finger dendritic cells), tissue cells, and natural killer cells.

As used herein, "tumor cells" refers to any tumor cells present in a tumor or sample thereof. Using methods known in the art and/or 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 for comparison 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 non-diseased 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 can be healthy and/or non-diseased cells or tissues adjacent to diseased cells or tissues (e.g., cells or tissues 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 non-diseased body part (e.g., tissue or cell) of an individual that is not the subject or subject. In 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 that is not the subject or subject.

For purposes herein, a "slice" of a tissue sample refers to a single portion or piece of the tissue sample, e.g., a slice of tissue or cells excised from the tissue sample (e.g., a tumor sample). It is to be understood that multiple portions of a tissue sample may be obtained and analyzed, provided that it is understood that the same portion of the tissue sample may be analyzed at the morphological and molecular level, or may be analyzed for polypeptides (e.g., by immunohistochemistry) and/or polynucleotides (e.g., by in situ hybridization).

"correlating" or "correlating" refers to 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 manner. For example, the results of the first analysis or scheme may be used when performing the second scheme and/or the results of the first analysis or scheme may be used to determine whether the second analysis or scheme should be performed. With respect to embodiments of polypeptide assays or protocols, the results of polypeptide expression assays or protocols can be used to determine whether a particular therapeutic protocol should be administered. With respect to embodiments of polynucleotide assays or protocols, the results of polynucleotide expression assays or protocols can be used to determine whether a particular therapeutic protocol should be administered.

The phrase "based on" as used herein refers to information about one or more biomarkers used to inform information provided on a treatment decision, package insert, or marketing/promotion guide, etc.

As used herein, the term "adverse event" or "AE" refers to any sign of inconvenience and accident (including abnormal laboratory findings), symptom, or disease that is temporally related to the use of a medical treatment or procedure, which may or may not be considered to be related to the medical treatment or procedure. Adverse events may be classified by "grade" as defined by the national cancer institute adverse event common term standard v5.0 (NIH CTCAE). In some aspects, the AE is a low level AE, such as a level 1 or level 2 AE. Grade 1 includes an asymptomatic or slightly symptomatic AE. Grade 2 includes AEs that are medium and limit auxiliary activities of daily living for the appropriate age (e.g., preparing meals, purchasing groceries or clothing) and indicate local or non-invasive intervention. In other cases, the AE is a high level AE, such as a level 3, level 4, or level 5 AE. Grade 3 includes severe 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 indicating the need for emergency intervention. Grade 5 includes AEs leading to or associated with death.

As used herein, the term "immune-mediated adverse event" or "imAE" refers to an adverse event classified by NIH CTCAE with a putative immune-related etiology or an "adverse event of particular interest" ("AESI"). In some aspects, imAE is AESI that occurs as a result of immune checkpoint inhibitor therapy. In some aspects, the imAE affects the respiratory tract, the endocrine system ("endocrine imAE"), the skin ("dermatological imAE" or "dermatological imAE"), or the gastrointestinal tract ("GI imAE"). In some aspects, the 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 modulation of an immune response, e.g., down-regulate, inhibit, up-regulate, or activate an immune response. The term "immune checkpoint blockade" may be used to refer to therapies comprising 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), T cell activated V domain Ig inhibitor (VISTA), B7-H2, B7-H3, B7-H4, B7-H6, 2B4, ICOS, HVEM, CD, gp49B, PIR-B, KIR family receptors, TIM-1, TIM-3, TIM-4, LAG-3, BTLA, SIRP alpha (CD 47), CD48, 2B4 (CD 244), B7.1, B7.2, ILT-2, ILT-4, LAG-3, BTLA, IDO, OX40 and A2aR. In some aspects, the immune checkpoint protein can be expressed on the surface of activated T cells. Therapeutic agents that may be used as immune checkpoint inhibitors for the methods of the invention include, but are not limited to, agents that target 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, SIRPalpha (CD 47), CD48, 2B4 (CD 244), B7.1, B7.2, ILT-2, ILT-4, LAG-3, BTLA, IDO, OX40, and A2aR. In some aspects, the immune checkpoint inhibitor enhances or inhibits the function of one or more targeted immune checkpoint proteins. In some aspects, the immune checkpoint inhibitor is a PD-1 axis binding antagonist, such as alemtuzumab, as described herein.

Methods and compositions for the treatment and diagnosis of lung cancer

Provided herein are therapeutic and diagnostic methods for cancer (e.g., NSCLC), wherein a patient can be identified, selected, and/or administered a treatment regimen comprising a PD-1 axis binding antagonist (e.g., alemtuzumab) based on the patient's genotype comprising an HLA or KIR gene or HLA/KIR pair associated with improved NK cell education, e.g., 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 KIR3DL 1. For example, in some examples, provided herein are therapeutic and diagnostic methods for cancer (e.g., NSCLC), wherein a patient can be identified, selected, and/or administered a treatment regimen comprising a PD-1 axis binding antagonist (e.g., alemtuzumab) based on the patient's genotype, which comprises at least one copy of HLA-C1 and/or at least one copy of KIR2DL 3. In another example, provided herein are therapeutic and diagnostic methods for cancer (e.g., NSCLC), wherein a patient can be identified, selected, and/or administered a treatment regimen comprising a PD-1 axis binding antagonist (e.g., alemtuzumab) based on the patient's genotype, which comprises at least one copy of HLA-Bw4 and/or at least one copy of KIR3DL 1. Without wishing to be bound by theory, such patients may have increased NK cell activity or function, for example, due to improved NK cell education. Thus, such patients may also benefit from NK cell-directed therapeutic agents, either alone or in combination with PD-1 axis binding antagonists (e.g., alemtuzumab).

Also provided herein are therapeutic and diagnostic methods for cancer, wherein patients can be identified, selected, and/or administered a treatment regimen comprising a PD-1 axis binding antagonist (e.g., alemtuzumab) based on an increase in NK cell infiltration level in a tumor sample relative to a reference level of NK cell infiltration. Without wishing to be bound by theory, such patients may have increased NK cell activity or function, for example, due to improved NK cell education. Thus, such patients may also benefit from NK cell-directed therapeutic agents, either alone or in combination with PD-1 axis binding antagonists.

Also provided are in vitro methods for NK cell education, e.g., wherein NK cells expressing KIR2DL3 or KIR3DL1, respectively, can be contacted with cells expressing HLA-C1 or HLA-Bw 4. The resulting NK cells may be used, for example, for adoptive cell therapy for patients with, for example, an HLA loss phenotype.

In one example, provided herein is a method of treating cancer (e.g., NSCLC) in a patient in need thereof whose genome has been determined to contain at least one copy of HLA-C1, comprising administering to the patient an effective amount of a treatment regimen comprising a PD-1 axis binding antagonist (e.g., atuzumab). In some cases, the patient's genome further comprises at least one copy of KIR2DL 3.

In another example, provided herein is a PD-1 axis binding antagonist (e.g., alemtuzumab) for treating cancer (e.g., NSCLC) in a patient in need thereof whose genome has been determined to comprise at least one copy of HLA-C1. In some cases, the patient's genome further comprises at least one copy of KIR2DL 3.

In another example, provided herein is a method of treating cancer (e.g., NSCLC) in a patient in need thereof whose genome has been determined to comprise at least one copy of HLA-C1 and at least one copy of KIR2DL3, comprising administering to the patient an effective amount of a therapeutic regimen comprising a PD-1 axis binding antagonist (e.g., alemtuzumab).

In another example, provided herein is a PD-1 axis binding antagonist (e.g., alemtuzumab) for treating cancer (e.g., NSCLC) in a patient in need thereof whose genome has been determined to comprise at least one copy of HLA-C1 and at least one copy of KIR2DL 3.

In another example, provided herein is a method of treating cancer (e.g., NSCLC) in a patient in need thereof whose genome has been determined to contain at least one copy of HLA-Bw4, comprising administering to the patient an effective amount of a treatment regimen comprising a PD-1 axis binding antagonist (e.g., atuzumab). In some cases, the patient's genome further comprises at least one copy of KIR3DL 1.

In another example, provided herein is a PD-1 axis binding antagonist (e.g., alemtuzumab) for treating cancer (e.g., NSCLC) in a patient in need thereof whose genome has been determined to comprise at least one copy of HLA-Bw 4. In some cases, the patient's genome further comprises at least one copy of KIR3DL 1.

In another example, provided herein is a method of treating cancer (e.g., NSCLC) in a patient in need thereof whose genome has been determined to comprise at least one copy of HLA-Bw4 and at least one copy of KIR3DL1, comprising administering to the patient an effective amount of a therapeutic regimen comprising a PD-1 axis binding antagonist (e.g., atuzumab).

In another example, provided herein is a PD-1 axis binding antagonist (e.g., alemtuzumab) for treating cancer (e.g., NSCLC) in a patient in need thereof whose genome has been determined to comprise at least one copy of HLA-Bw4 and at least one copy of KIR3DL 1.

In another example, provided herein is a method of treating cancer (e.g., NSCLC) in a patient in need thereof, the method comprising: (a) Determining whether the patient's genome comprises 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 is likely to benefit from a treatment regimen comprising a PD-1 axis binding antagonist (e.g., atuzumab); 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 genome of the patient. In some cases, step (a) further comprises determining whether the patient's genome comprises at least one copy of KIR2DL 3.

In another example, provided herein is a PD-1 axis binding antagonist (e.g., alemtuzumab) for use in a method of treating cancer (e.g., NSCLC) in a patient in need thereof, the method comprising: (a) Determining whether the patient's genome comprises 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 is likely to 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 genome of the patient. In some cases, step (a) further comprises determining whether the patient's genome comprises at least one copy of KIR2DL 3.

In another example, provided herein is a method of treating cancer (e.g., NSCLC) in a patient in need thereof, the method comprising: (a) Determining whether the patient's genome comprises 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 (e.g., alemtuzumab); 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 and at least one copy of KIR2DL3 in the genome of the patient.

In another example, provided herein is a PD-1 axis binding antagonist (e.g., alemtuzumab) for treating cancer (e.g., NSCLC) in a patient in need thereof, comprising: (a) Determining whether the patient's genome comprises 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 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 and at least one copy of KIR2DL3 in the genome of the patient.

In another example, provided herein is a method of treating cancer (e.g., NSCLC) in a patient in need thereof, the method comprising: (a) Determining whether the patient's genome comprises 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 is likely to benefit from a treatment regimen comprising a PD-1 axis binding antagonist (e.g., atuzumab); 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 genome of the patient. In some cases, step (a) further comprises determining whether the patient's genome comprises at least one copy of KIR3DL 1.

In another example, provided herein is a PD-1 axis binding antagonist (e.g., alemtuzumab) for treating cancer (e.g., NSCLC) in a patient in need thereof, comprising: (a) Determining whether the patient's genome comprises 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 genome of the patient. In some cases, step (a) further comprises determining whether the patient's genome comprises at least one copy of KIR3DL 1.

In another example, provided herein is a method of treating cancer (e.g., NSCLC) in a patient in need thereof, the method comprising: (a) Determining whether the patient's genome comprises 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 (e.g., alemtuzumab); 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 genome of the patient.

In another example, provided herein is a PD-1 axis binding antagonist (e.g., alemtuzumab) for treating cancer (e.g., NSCLC) in a patient in need thereof, comprising: (a) Determining whether the patient's genome comprises 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 genome of the patient.

In another example, provided herein is a method of identifying a patient having cancer (e.g., NSCLC) who may benefit from a treatment regimen comprising a PD-1 axis binding antagonist (e.g., atuzumab), the method comprising determining whether the patient's genome comprises 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 comprising a PD-1 axis binding antagonist. In some cases, the method further comprises determining whether the patient's genome comprises at least one copy of KIR2DL 3.

In another example, provided herein is a method of identifying a patient having cancer (e.g., NSCLC) who may benefit from a treatment regimen comprising a PD-1 axis binding antagonist (e.g., atuzumab), the method comprising: (a) Germline Whole Genome Sequencing (WGS) or Whole Exome Sequencing (WES) by fragmenting a DNA sample obtained from the patient to produce fragmented DNA, adding adaptors 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 comprising a PD-1 axis binding antagonist by determining whether the patient's genome comprises 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 comprising a PD-1 axis binding antagonist. In some cases, the method further comprises determining whether the patient's genome comprises at least one copy of KIR2DL 3.

In another example, provided herein is a method of identifying a patient having cancer (e.g., NSCLC) who may benefit from a treatment regimen comprising a PD-1 axis binding antagonist (e.g., atuzumab), the method comprising determining whether the patient's genome comprises 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 comprising a PD-1 axis binding antagonist.

In another example, provided herein is a method of identifying a patient having cancer (e.g., NSCLC) who may benefit from a treatment regimen comprising a PD-1 axis binding antagonist (e.g., atuzumab), the method comprising: (a) Germline WGS or WES is performed by fragmenting a DNA sample obtained from the patient to produce fragmented DNA, adding adaptors 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 comprising a PD-1 axis binding antagonist by determining whether the patient's genome comprises 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 comprising a PD-1 axis binding antagonist.

In another example, provided herein is a method of identifying a patient having cancer (e.g., NSCLC) who may benefit from a treatment regimen comprising a PD-1 axis binding antagonist (e.g., atuzumab), the method comprising determining whether the patient's genome comprises 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 comprising a PD-1 axis binding antagonist. In some cases, the method further comprises determining whether the patient's genome comprises at least one copy of KIR3DL 1.

In another example, provided herein is a method of identifying a patient having cancer (e.g., NSCLC) who may benefit from a treatment regimen comprising a PD-1 axis binding antagonist (e.g., atuzumab), the method comprising: (a) Germline WGS or WES is performed by fragmenting a DNA sample obtained from the patient to produce fragmented DNA, adding adaptors 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 comprising a PD-1 axis binding antagonist by determining whether the patient's genome comprises 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 comprising a PD-1 axis binding antagonist. In some cases, the method further comprises determining whether the patient's genome comprises at least one copy of KIR3DL 1.

In another example, provided herein is a method of identifying a patient having cancer (e.g., NSCLC) who may benefit from a treatment regimen comprising a PD-1 axis binding antagonist (e.g., atuzumab), the method comprising determining whether the patient's genome comprises 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 with a treatment regimen comprising a PD-1 axis binding antagonist.

In another example, provided herein is a method of identifying a patient having cancer (e.g., NSCLC) who may benefit from a treatment regimen comprising a PD-1 axis binding antagonist (e.g., atuzumab), the method comprising: (a) Germline WGS or WES is performed by fragmenting a DNA sample obtained from the patient to produce fragmented DNA, adding adaptors 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 comprising a PD-1 axis binding antagonist by determining whether the patient's genome comprises 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 comprising a PD-1 axis binding antagonist.

In another example, provided herein is a method of selecting a therapy for a patient having cancer (e.g., NSCLC), the method comprising: (a) Determining whether the patient's genome comprises 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 is likely to benefit from a treatment regimen comprising a PD-1 axis binding antagonist (e.g., atuzumab); and (b) selecting a treatment regimen comprising a PD-1 axis binding antagonist based on the presence of at least one copy of HLA-C1 in the genome of the patient. In some cases, the method further comprises determining whether the patient's genome comprises at least one copy of KIR2DL 3.

In another example, provided herein is a method of selecting a therapy for a patient having cancer (e.g., NSCLC), the method comprising: (a) Determining whether the patient's genome comprises 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 (e.g., alemtuzumab); and (b) selecting a treatment regimen comprising 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 genome of the patient.

In another example, provided herein is a method of selecting a therapy for a patient having cancer (e.g., NSCLC), the method comprising: (a) Determining whether the patient's genome comprises 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 is likely to benefit from a treatment regimen comprising a PD-1 axis binding antagonist (e.g., atuzumab); and (b) selecting a treatment regimen comprising a PD-1 axis binding antagonist based on the presence of at least one copy of HLA-Bw4 in the genome of the patient. In some cases, the method further comprises determining whether the patient's genome comprises at least one copy of KIR3DL 1.

In another example, provided herein is a method of selecting a therapy for a patient having cancer (e.g., NSCLC), the method comprising: (a) Determining whether the patient's genome comprises 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 (e.g., alemtuzumab); and (b) selecting 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 genome of the patient.

Any of the foregoing examples can further comprise administering to the patient an effective amount of a therapeutic regimen comprising a PD-1 axis binding antagonist (e.g., atrazumab).

In any of the examples described herein, the presence of HLA-C1, HLA-Bw4, KIR2DL3, and/or KIR3DL1 in the patient's genome can be determined using any suitable method. For example, in some cases, the presence of HLA-C1, HLA-Bw4, KIR2DL3, and/or KIR3DL1 in the patient's genome is determined using next generation sequencing, sanger sequencing, polymerase Chain Reaction (PCR) based assays, or Single Nucleotide Polymorphism (SNP) arrays. In some cases, the next generation sequencing includes germline whole genome sequencing or germline whole exome sequencing. In some cases, PCR-based assays include quantitative PCR (qPCR), typing using sequence-specific primers (SSP), or typing using sequence-specific oligonucleotide probes (SSO).

In another example, provided herein is a method of treating cancer (e.g., NSCLC) in a patient in need thereof, the patient having been determined to have an increased level of Natural Killer (NK) cell infiltration relative to a reference level of NK cell infiltration in a tumor sample obtained from the patient, the method comprising administering to the patient an effective amount of a therapeutic regimen comprising a PD-1 axis binding antagonist (e.g., atuzumab).

In another example, provided herein is a PD-1 axis binding antagonist for use in treating cancer (e.g., NSCLC) in a patient in need thereof who has been determined to have an increased NK cell infiltration level relative to a reference level of NK cell infiltration in a tumor sample obtained from the patient.

In another example, provided herein is a method of treating cancer (e.g., NSCLC) in a patient in need thereof, the method comprising: (a) Determining whether a tumor sample obtained from the patient has an increased NK cell infiltration level relative to a reference level of NK cell infiltration, wherein an increase in NK cell infiltration level relative to the reference level of NK cell infiltration in the tumor sample obtained from the patient indicates that the patient is likely to benefit from a treatment regimen comprising a PD-1 axis binding antagonist (e.g., alemtuzumab); and (b) administering to the patient an effective amount of a treatment regimen comprising a PD-1 axis binding antagonist based on an increase in NK cell infiltration level relative to a reference level of NK cell infiltration in a tumor sample obtained from the patient.

In another example, provided herein is a PD-1 axis binding antagonist (e.g., alemtuzumab) for use in a method of treating cancer (e.g., NSCLC) in a patient in need thereof, the method comprising: (a) Determining whether a tumor sample obtained from the patient has an increased NK cell infiltration level relative to a reference level of NK cell infiltration, wherein an increase in NK cell infiltration level relative to the reference level of NK cell infiltration in the tumor sample obtained from the patient indicates that the patient is likely to 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 an increase in NK cell infiltration level relative to a reference level of NK cell infiltration in a tumor sample obtained from the patient.

In another example, provided herein is a method of identifying a patient having cancer (e.g., NSCLC) who may benefit from a treatment regimen comprising a PD-1 axis binding antagonist (e.g., atuzumab), the method comprising determining whether a tumor sample obtained from the patient has an increased NK cell infiltration level relative to a reference level of NK cell infiltration, wherein an increase in NK cell infiltration level 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 comprising a PD-1 axis binding antagonist.

In another example, provided herein is a method of identifying a patient having cancer (e.g., NSCLC) who may benefit from a treatment regimen comprising a PD-1 axis binding antagonist (e.g., atuzumab), the method comprising: (a) Contacting a tumor sample obtained from the patient with one or more antibodies or nucleotide probes that bind 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 NK cell infiltration level relative to a reference level of NK cell infiltration, wherein an increase in NK cell infiltration level relative to the reference level of NK cell infiltration in the tumor sample obtained from the patient indicates that the patient is likely to benefit from a treatment regimen comprising a PD-1 axis binding antagonist. Any suitable antibody or nucleotide probe may 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 (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or all 20) of the following genes: CD160, CD244, CTSW, FASLG, GZMA, GZMB, GZMH, IL18RAP, IL2RB, KIR2DL4, KLRB1, KLRC3, KLRD1, KRRF 1, KLRK1, NCR1, NKG7, PRF1, XCL1 and XCL2.

In another example, provided herein is a method of selecting a therapy for a patient having cancer (e.g., NSCLC), the method comprising: (a) Determining whether a tumor sample obtained from the patient has an increased NK cell infiltration level relative to a reference level of NK cell infiltration, wherein an increase in NK cell infiltration level relative to the reference level of NK cell infiltration in the tumor sample obtained from the patient indicates that the patient is likely to benefit from a treatment regimen comprising a PD-1 axis binding antagonist (e.g., alemtuzumab); and (b) selecting a treatment regimen comprising a PD-1 axis binding antagonist based on an increase in NK cell infiltration level relative to a reference level of NK cell infiltration in a tumor sample obtained from the patient.

Any of the examples described herein can include administering to a patient an effective amount of a therapeutic regimen that includes a PD-1 axis binding antagonist (e.g., atrazumab).

In any of the examples 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 is determined by determining the expression level of the NK cell gene signature, 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, e.g., by immunofluorescence, immunohistochemistry, western blotting, flow cytometry, or any other suitable method. Any suitable NK cell marker or combination of NK cell markers may be used. In some aspects, the NK cell marker is a co-stimulatory receptor such as TRAIL, CD16a, CD16B, NKG2D, NKG C, 4-1BB, OX40, CD27, 2B4, DNAM-1, NKp30, NKp46, NKp44, NKp80, KIR2DS1 and KIR2DS2. In some aspects, the NK cell receptor is a co-stimulatory receptor. In some aspects, the co-inhibitory receptor is NKG2A or KIR, e.g., KIR3DL1, KIR2DL2, or KIR2DL3.

In any of the examples described herein, the NK cell gene signature can 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, KRRF 1, KLRK1, NCR1, NKG7, PRF1, XCL1 and XCL2. In some cases, the NK cell gene signature comprises 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 cases, the reference level of NK cell infiltration is a median level. In some cases, the median level is a median level in a population of patients with cancer (e.g., NSCLC).

In some examples, the genome of the patient comprises at least one copy (e.g., 1 or 2 copies) of HLA-C1 or at least one copy (e.g., 1 or 2 copies) of HLA-Bw 4. In some cases, the patient's genome comprises at least one copy (e.g., 1 or 2 copies) of HLA-C1. In some cases, the patient's genome comprises at least one copy (e.g., 1 or 2 copies) of HLA-Bw 4.

In some examples, the genome of the patient comprises at least one copy (e.g., 1 or 2 copies) of KIR2DL3 or at least one copy (e.g., 1 or 2 copies) of KIR3DL 1. In some cases, the patient's genome comprises at least one copy (e.g., 1 or 2 copies) of KIR2DL 3. In some cases, the patient's genome comprises at least one copy (e.g., 1 or 2 copies) of KIR3DL 1.

Any of the examples disclosed herein, including any of the preceding examples, can further comprise administering to the patient an effective amount of a treatment regimen comprising an NK cell-directed therapeutic agent (e.g., NK cell cement). Any suitable NK cell-directed therapeutic agent may be used, such as any of the NK cell-directed therapeutic agents described in section V below. In some examples, any NK cell directed therapy described in Hodgins et al J.Clin. Invest.129 (9): 3499-3510,2019 may be used. In some cases, the NK cell-targeted therapeutic includes allogeneic NK cells, autologous NK cells, ready NK cells, chimeric Antigen Receptor (CAR) -NK cells, cytokine therapy, NK cell cement (e.g., bispecific killer cell cement (BiKE), trispecific killer cell cement (tripe), or tetraspecific killer cell cement (TetraKE)), NK cell checkpoint receptor antagonists, or oncolytic viruses.

In another example, provided herein is a method of treating cancer (e.g., NSCLC) in a patient in need thereof whose genome has been determined to contain at least one copy of HLA-C1, comprising administering to the patient an effective amount of a treatment regimen comprising an NK cell-directed therapeutic agent (e.g., NK cell cement). In some cases, the patient's genome further comprises at least one copy of KIR2DL 3.

In another example, provided herein is an NK cell-targeted therapeutic (e.g., NK cell cement) for treating cancer (e.g., NSCLC) in a patient in need thereof whose genome has been determined to contain at least one copy of HLA-C1. In some cases, the patient's genome further comprises at least one copy of KIR2DL 3.

In another example, provided herein is a method of treating cancer (e.g., NSCLC) in a patient in need thereof whose genome has been determined to comprise at least one copy of HLA-C1 and at least one copy of KIR2DL3, comprising administering to the patient an effective amount of a treatment regimen comprising an NK cell-directed therapeutic agent (e.g., NK cell cement).

In another example, provided herein is an NK cell-targeted therapeutic (e.g., NK cell cement) for treating cancer (e.g., NSCLC) in a patient in need thereof whose genome has been determined to contain at least one copy of HLA-C1 and at least one copy of KIR2DL 3.

In another example, provided herein is a method of treating cancer (e.g., NSCLC) in a patient in need thereof whose genome has been determined to contain at least one copy of HLA-Bw4, comprising administering to the patient an effective amount of a treatment regimen comprising an NK cell-directed therapeutic agent (e.g., NK cell cement). In some cases, the patient's genome further comprises at least one copy of KIR3DL 1.

In another example, provided herein is an NK cell-targeted therapeutic (e.g., NK cell cement) for treating cancer (e.g., NSCLC) in a patient in need thereof whose genome has been determined to contain at least one copy of HLA-Bw 4. In some cases, the patient's genome further comprises at least one copy of KIR3DL 1.

In another example, provided herein is a method of treating cancer (e.g., NSCLC) in a patient in need thereof whose genome has been determined to comprise at least one copy of HLA-Bw4 and at least one copy of KIR3DL1, comprising administering to the patient an effective amount of a treatment regimen comprising an NK cell-directed therapeutic agent (e.g., NK cell cement).

In another example, provided herein is an NK cell-targeted therapeutic (e.g., NK cell cement) for treating cancer (e.g., NSCLC) in a patient in need thereof whose genome has been determined to contain at least one copy of HLA-Bw4 and at least one copy of KIR3DL 1.

In another example, provided herein is a method of treating cancer (e.g., NSCLC) in a patient in need thereof, the method comprising: (a) Determining whether the patient's genome comprises 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 is likely to benefit from a treatment regimen comprising an NK cell-directed therapeutic (e.g., NK cell cement); and (b) administering to the patient an effective amount of a treatment regimen comprising an NK cell-directed therapeutic agent based on the presence of at least one copy of HLA-C1 in the genome of the patient. In some cases, step (a) further comprises determining whether the patient's genome comprises at least one copy of KIR2DL 3.

In another example, provided herein is a NK cell-targeted therapeutic (e.g., NK cell cement) for use in a method of treating cancer (e.g., NSCLC) in a patient in need thereof, the method comprising: (a) Determining whether the patient's genome comprises 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 is likely to benefit from a treatment regimen comprising an NK cell-directed therapeutic; and (b) administering to the patient an effective amount of a treatment regimen comprising an NK cell-directed therapeutic agent based on the presence of at least one copy of HLA-C1 in the genome of the patient. In some cases, step (a) further comprises determining whether the patient's genome comprises at least one copy of KIR2DL 3.

In another example, provided herein is a method of treating cancer (e.g., NSCLC) in a patient in need thereof, the method comprising: (a) Determining whether the patient's genome comprises 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 an NK cell-directed therapeutic agent (e.g., NK cell cement); and (b) administering to the patient an effective amount of a treatment regimen comprising an NK cell-directed therapeutic agent based on the presence of at least one copy of HLA-C1 and at least one copy of KIR2DL3 in the genome of the patient.

In another example, provided herein is an NK cell-targeted therapeutic (e.g., NK cell cement) for treating cancer (e.g., NSCLC) in a patient in need thereof, the method comprising: (a) Determining whether the patient's genome comprises 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 an NK cell-directed therapeutic; and (b) administering to the patient an effective amount of a treatment regimen comprising an NK cell-directed therapeutic agent based on the presence of at least one copy of HLA-C1 and at least one copy of KIR2DL3 in the genome of the patient.

In another example, provided herein is a method of treating cancer (e.g., NSCLC) in a patient in need thereof, the method comprising: (a) Determining whether the patient's genome comprises 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 (e.g., NK cell cement); and (b) administering to the patient an effective amount of a treatment regimen comprising an NK cell-directed therapeutic agent based on the presence of at least one copy of HLA-Bw4 in the genome of the patient. In some cases, step (a) further comprises determining whether the patient's genome comprises at least one copy of KIR3DL 1.

In another example, provided herein is an NK cell-targeted therapeutic (e.g., NK cell cement) for treating cancer (e.g., NSCLC) in a patient in need thereof, the method comprising: (a) Determining whether the patient's genome comprises 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; and (b) administering to the patient an effective amount of a treatment regimen comprising an NK cell-directed therapeutic agent based on the presence of at least one copy of HLA-Bw4 in the genome of the patient. In some cases, step (a) further comprises determining whether the patient's genome comprises at least one copy of KIR3DL 1.

In another example, provided herein is a method of treating cancer (e.g., NSCLC) in a patient in need thereof, the method comprising: (a) Determining whether the patient's genome comprises 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 an NK cell-directed therapeutic (e.g., NK cell cement); and (b) administering to the patient an effective amount of a treatment regimen comprising an NK cell-directed therapeutic agent based on the presence of at least one copy of HLA-Bw4 and at least one copy of KIR3DL1 in the genome of the patient.

In another example, provided herein is an NK cell-targeted therapeutic (e.g., NK cell cement) for treating cancer (e.g., NSCLC) in a patient in need thereof, the method comprising: (a) Determining whether the patient's genome comprises 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 is likely to benefit from a treatment regimen comprising an NK cell-directed therapeutic; and (b) administering to the patient an effective amount of a treatment regimen comprising an NK cell-directed therapeutic agent based on the presence of at least one copy of HLA-Bw4 and at least one copy of KIR3DL1 in the genome of the patient.

In another example, provided herein is a method of identifying a patient having cancer (e.g., NSCLC) who may benefit from a treatment regimen comprising an NK cell-directed therapeutic agent (e.g., NK cell cement), the method comprising determining whether the patient's genome comprises 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 comprising an NK cell-directed therapeutic agent. In some cases, the method further comprises determining whether the patient's genome comprises at least one copy of KIR2DL 3.

In another example, provided herein is a method of identifying a patient having cancer (e.g., NSCLC) who may benefit from a treatment regimen comprising an NK cell-directed therapeutic agent (e.g., NK cell cement), the method comprising: (a) Germline Whole Genome Sequencing (WGS) or Whole Exome Sequencing (WES) by fragmenting a DNA sample obtained from the patient to produce fragmented DNA, adding adaptors 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 comprising an NK cell directed therapeutic by determining whether the patient's genome comprises 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 comprising an NK cell directed therapeutic. In some cases, the method further comprises determining whether the patient's genome comprises at least one copy of KIR2DL 3.

In another example, provided herein is a method of identifying a patient having cancer (e.g., NSCLC) who may benefit from a treatment regimen comprising an NK cell-directed therapeutic agent (e.g., NK cell cement), the method comprising determining whether the patient's genome comprises 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 comprising an NK cell-directed therapeutic agent.

In another example, provided herein is a method of identifying a patient having cancer (e.g., NSCLC) who may benefit from a treatment regimen comprising an NK cell-directed therapeutic agent (e.g., NK cell cement), the method comprising: (a) Germline WGS or WES is performed by fragmenting a DNA sample obtained from the patient to produce fragmented DNA, adding adaptors 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 comprising an NK cell directed therapeutic by determining whether the patient's genome comprises 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 comprising an NK cell directed therapeutic.

In another example, provided herein is a method of identifying a patient having cancer (e.g., NSCLC) who may benefit from a treatment regimen comprising an NK cell-directed therapeutic agent (e.g., NK cell cement), the method comprising determining whether the patient's genome comprises 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 comprising an NK cell-directed therapeutic agent. In some cases, the method further comprises determining whether the patient's genome comprises at least one copy of KIR3DL 1.

In another example, provided herein is a method of identifying a patient having cancer (e.g., NSCLC) who may benefit from a treatment regimen comprising an NK cell-directed therapeutic agent (e.g., NK cell cement), the method comprising: (a) Germline WGS or WES is performed by fragmenting a DNA sample obtained from the patient to produce fragmented DNA, adding adaptors 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 comprising an NK cell-directed therapeutic agent by determining whether the patient's genome comprises 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 comprising an NK cell-directed therapeutic agent. In some cases, the method further comprises determining whether the patient's genome comprises at least one copy of KIR3DL 1.

In another example, provided herein is a method of identifying a patient having cancer (e.g., NSCLC) who may benefit from a treatment regimen comprising an NK cell-directed therapeutic agent (e.g., NK cell cement), the method comprising determining whether the patient's genome comprises 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 comprising an NK cell-directed therapeutic agent.

In another example, provided herein is a method of identifying a patient having cancer (e.g., NSCLC) who may benefit from a treatment regimen comprising an NK cell-directed therapeutic agent (e.g., NK cell cement), the method comprising: (a) Germline WGS or WES is performed by fragmenting a DNA sample obtained from the patient to produce fragmented DNA, adding adaptors 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 comprising an NK cell directed therapeutic by determining whether the patient's genome comprises 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 comprising an NK cell directed therapeutic.

In another example, provided herein is a method of selecting a therapy for a patient having cancer (e.g., NSCLC), the method comprising: (a) Determining whether the patient's genome comprises 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 is likely to benefit from a treatment regimen comprising an NK cell-directed therapeutic (e.g., NK cell cement); and (b) selecting a treatment regimen comprising an NK cell-directed therapeutic agent based on the presence of at least one copy of HLA-C1 in the genome of the patient. In some cases, the method further comprises determining whether the patient's genome comprises at least one copy of KIR2DL 3.

In another example, provided herein is a method of selecting a therapy for a patient having cancer (e.g., NSCLC), the method comprising: (a) Determining whether the patient's genome comprises 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 an NK cell-directed therapeutic agent (e.g., NK cell cement); and (b) selecting a treatment regimen comprising an NK cell-directed therapeutic agent based on the presence of at least one copy of HLA-C1 and at least one copy of KIR2DL3 in the genome of the patient.

In another example, provided herein is a method of selecting a therapy for a patient having cancer (e.g., NSCLC), the method comprising: (a) Determining whether the patient's genome comprises 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 (e.g., NK cell cement); and (b) selecting a treatment regimen comprising an NK cell-directed therapeutic agent based on the presence of at least one copy of HLA-Bw4 in the genome of the patient. In some cases, the method further comprises determining whether the patient's genome comprises at least one copy of KIR3DL 1.

In another example, provided herein is a method of selecting a therapy for a patient having cancer (e.g., NSCLC), the method comprising: (a) Determining whether the patient's genome comprises 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 an NK cell-directed therapeutic (e.g., NK cell cement); and (b) selecting a treatment regimen comprising an NK cell-directed therapeutic agent based on the presence of at least one copy of HLA-Bw4 and at least one copy of KIR3DL1 in the genome of the patient.

Any of the examples described herein can include administering to a patient an effective amount of a treatment regimen including an NK cell-directed therapeutic agent (e.g., NK cell cement).

In another example, provided herein is a method of treating cancer (e.g., NSCLC) in a patient in need thereof, the patient having been determined to have an increased level of Natural Killer (NK) cell infiltration relative to a reference level of 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-directing therapeutic agent (e.g., NK cell cement).

In another example, provided herein is an NK cell-targeted therapeutic (e.g., NK cell cement) for treating cancer (e.g., NSCLC) in a patient in need thereof who has been determined to have an increased NK cell infiltration level relative to a reference level of NK cell infiltration in a tumor sample obtained from the patient.

In another example, provided herein is a method of treating cancer (e.g., NSCLC) in a patient in need thereof, the method comprising: (a) Determining whether a tumor sample obtained from the patient has an increased NK cell infiltration level relative to a reference level of NK cell infiltration, wherein an increase in NK cell infiltration level relative to the reference level of NK cell infiltration in the tumor sample obtained from the patient indicates that the patient is likely to benefit from a treatment regimen comprising an NK cell-directed therapeutic agent (e.g., NK cell cement); and (b) administering to the patient an effective amount of a treatment regimen comprising an NK cell-directed therapeutic agent based on an increase in NK cell infiltration level relative to a reference level of NK cell infiltration in a tumor sample obtained from the patient.

In another example, provided herein is a NK cell-targeted therapeutic (e.g., NK cell cement) for use in a method of treating cancer (e.g., NSCLC) in a patient in need thereof, the method comprising: (a) Determining whether a tumor sample obtained from the patient has an increased NK cell infiltration level relative to a reference level of NK cell infiltration, wherein an increase in NK cell infiltration level relative to the reference level of NK cell infiltration in the tumor sample obtained from the patient indicates that the patient is likely to benefit from a treatment regimen comprising an NK cell-directed therapeutic; and (b) administering to the patient an effective amount of a treatment regimen comprising an NK cell-directed therapeutic agent based on an increase in NK cell infiltration level relative to a reference level of NK cell infiltration in a tumor sample obtained from the patient.

In another example, provided herein is a method of identifying a patient having cancer (e.g., NSCLC) who may benefit from a treatment regimen comprising an NK cell-directed therapeutic agent (e.g., NK cell cement), the method comprising determining whether a tumor sample obtained from the patient has an increased NK cell infiltration level relative to a reference level of NK cell infiltration, wherein an increase in NK cell infiltration level 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 comprising an NK cell-directed therapeutic agent.

In another example, provided herein is a method of identifying a patient having cancer (e.g., NSCLC) who may benefit from a treatment regimen comprising an NK cell-directed therapeutic agent (e.g., NK cell cement), the method comprising: (a) Contacting a tumor sample obtained from the patient with one or more antibodies or nucleotide probes that bind 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 increase in the level of NK cell infiltration relative to the reference level of NK cell infiltration in the tumor sample obtained from the patient indicates that the patient is likely to benefit from a treatment regimen comprising an NK cell-directed therapeutic.

Any suitable antibody or nucleotide probe may 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 (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or all 20) of the following genes: CD160, CD244, CTSW, FASLG, GZMA, GZMB, GZMH, IL18RAP, IL2RB, KIR2DL4, KLRB1, KLRC3, KLRD1, KRRF 1, KLRK1, NCR1, NKG7, PRF1, XCL1 and XCL2.

In another example, provided herein is a method of selecting a therapy for a patient having cancer (e.g., NSCLC), the method comprising: (a) Determining whether a tumor sample obtained from the patient has an increased NK cell infiltration level relative to a reference level of NK cell infiltration, wherein an increase in NK cell infiltration level relative to the reference level of NK cell infiltration in the tumor sample obtained from the patient indicates that the patient is likely to benefit from a treatment regimen comprising an NK cell-directed therapeutic agent (e.g., NK cell cement); and (b) selecting a treatment regimen comprising an NK cell-targeted therapeutic based on an increase in NK cell infiltration level relative to a reference level of NK cell infiltration in a tumor sample obtained from the patient.

Any suitable NK cell-directed therapeutic agent may be used, such as any of the NK cell-directed therapeutic agents described in section V below. Any suitable NK cell-directed therapy may be used, including any of the NK cell-directed therapies described herein (see section V below). In some examples, any NK cell directed therapy described in Hodgins et al J.Clin. Invest.129 (9): 3499-3510,2019 may be used. In some cases, the NK cell-targeted therapeutic includes allogeneic NK cells, autologous NK cells, ready NK cells, chimeric Antigen Receptor (CAR) -NK cells, cytokine therapy, NK cell cement (e.g., bispecific killer cell cement (BiKE), trispecific killer cell cement (tripe), or tetraspecific killer cell cement (TetraKE)), NK cell checkpoint receptor antagonists, or oncolytic viruses.

Any of the foregoing examples wherein administering an NK cell-directed therapeutic to a patient may further comprise administering a PD-1 axis binding antagonist (e.g., alemtuzumab) to the patient.

Also provided herein are in vitro methods for NK cell education. For example, such methods can include contacting NK cells expressing KIR2DL3 or KIR3DL1 with cells expressing HLA-C1 or HLA-Bw4, e.g., under conditions and for a time sufficient to provide NK cell education. Such educational NK cells can be used for adoptive cell therapy for patients with, for example, HLA loss phenotypes.

For example, provided herein is an in vitro method of NK cell education comprising contacting NK cells expressing KIR2DL3 with cells expressing HLA-C1, e.g., under conditions and for a time sufficient to provide NK cell education.

In another example, provided herein is an in vitro method of NK cell education comprising contacting NK cells expressing KIR3DL1 with cells expressing HLA-Bw4, e.g., under conditions and for a time sufficient to provide NK cell education.

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

In some examples, NK cells for in vitro education as described herein may be used for adoptive cell therapy. For example, in some examples, in vitro educated NK cells as described herein can be used to treat patients with HLA loss phenotypes (e.g., NSCLC patients). In some examples, the in vitro educational NK cells as described herein can be used to treat a patient with cancer (e.g., NSCLC) whose genome lacks HLA-C1, HLA-Bw4, KIR2DL3, and/or KIR3DL1. In some examples, the genome of the patient lacks HLA-C1. In some examples, the genome of the patient lacks HLA-Bw4. In some examples, the genome of the patient lacks KIR2DL3. In some examples, the genome of the patient lacks KIR3DL1.

In another example, provided herein is a method of treating cancer (e.g., NSCLC) in a patient in need thereof whose genome has been determined to be deficient in KIR2DL3 or KIR3DL1, comprising administering to the patient an effective amount of a treatment regimen comprising an NK cell-directed therapeutic agent.

In another example, provided herein is an NK cell-targeted therapeutic for treating cancer (e.g., NSCLC) in a patient in need thereof whose genome has been determined to be deficient in KIR2DL3 or KIR3DL1.

In another example, provided herein is a method of treating cancer (e.g., NSCLC) in a patient in need thereof, the method comprising: (a) Determining whether the patient's genome lacks KIR2DL3 or KIR3DL1, wherein the absence of KIR2DL3 or KIR3DL1 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 to the patient an effective amount of a treatment regimen comprising an NK cell-directed therapeutic agent based on the lack of KIR2DL3 or KIR3DL1 in the patient's genome.

In another example, provided herein is a NK cell-directed therapeutic agent for use in a method of treating cancer (e.g., NSCLC) in a patient in need thereof, the method comprising: (a) Determining whether the patient's genome lacks KIR2DL3 or KIR3DL1, wherein the absence of KIR2DL3 or KIR3DL1 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 to the patient an effective amount of a treatment regimen comprising an NK cell-directed therapeutic agent based on the lack of KIR2DL3 or KIR3DL1 in the patient's genome.

In another example, provided herein is a method of identifying a patient having cancer (e.g., NSCLC) who may benefit from a treatment regimen comprising an NK cell-directed therapeutic agent, the method comprising determining whether the genome of the patient lacks KIR2DL3 or KIR3DL1, wherein the lack of KIR2DL3 or KIR3DL1 in the genome of the patient identifies the patient as a patient who may benefit from treatment using a treatment regimen comprising an NK cell-directed therapeutic agent.

In another example, provided herein is a method of identifying a patient having cancer (e.g., NSCLC) who may benefit from a treatment regimen comprising an NK cell-directed therapeutic agent, the method comprising: (a) Germline WGS or WES is performed by fragmenting a DNA sample obtained from the patient to produce fragmented DNA, adding adaptors 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 comprising an NK cell directed therapeutic by determining whether the patient's genome lacks KIR2DL3 or KIR3DL1, wherein the patient is identified as a patient who may benefit from treatment using a treatment regimen comprising an NK cell directed therapeutic in the patient's genome in the absence of KIR2DL3 or KIR3DL 1.

In another example, provided herein is a method of selecting a therapy for a patient having cancer (e.g., NSCLC), the method comprising: (a) Determining whether the patient's genome lacks KIR2DL3 or KIR3DL1, wherein the absence of KIR2DL3 or KIR3DL1 in the patient's genome identifies the patient as likely to benefit from treatment using a treatment regimen comprising an NK cell-directed therapeutic agent; and (b) selecting a treatment regimen comprising an NK cell-directed therapeutic agent based on the lack of KIR2DL3 or KIR3DL1 in the patient's genome.

Any suitable NK cell-directed therapy may be used, including any of the NK cell-directed therapies described herein (see section V below). In some examples, any NK cell directed therapy described in Hodgins et al J.Clin. Invest.129 (9): 3499-3510,2019 may be used. In some cases, the NK cell-targeted therapeutic includes allogeneic NK cells, autologous NK cells, ready NK cells, chimeric Antigen Receptor (CAR) -NK cells, cytokine therapy, NK cell cement (e.g., bispecific killer cell cement (BiKE), trispecific killer cell cement (tripe), or tetraspecific killer cell cement (TetraKE)), NK cell checkpoint receptor antagonists, or oncolytic viruses.

In some examples, the NK cell-targeted therapeutic includes allogeneic NK cells, autologous NK cells, ready NK cells, or a combination thereof. In some cases, the NK cell-directed therapeutic agent comprises allogeneic NK cells. In other cases, the NK cell-directed therapeutic agent comprises autologous NK cells. In still other cases, the NK cell-directed therapeutic agent comprises an off-the-shelf NK cell.

In some examples, 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 ready NK cells are engineered to express KIR2DL3. For example, in other cases, allogeneic NK cells, autologous NK cells, or ready NK cells are engineered to express KIR3DL1.

In some examples, treatment with allogeneic NK cells, autologous NK cells, or off-the-shelf NK cells engineered to express KIR2DL3 or KIR3DL1 makes patients a patient who may benefit from treatment with a treatment regimen that includes a PD-1 axis binding antagonist (e.g., alemtuzumab).

Any of the foregoing examples can further include, for example, administering to the patient a treatment regimen comprising a PD-1 axis binding antagonist (e.g., alemtuzumab) prior to, concurrently with, or after treatment with a treatment regimen comprising an NK cell-directed therapeutic agent.

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 using a treatment regimen that does not include a PD-1 axis binding antagonist (e.g., alemtuzumab).

The cancer may be any suitable cancer. For example, in some examples, the cancer is lung cancer (e.g., NSCLC), renal cancer (e.g., renal cell carcinoma), or melanoma.

In some examples, 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 example, provided herein is a method of treating NSCLC in a patient in need thereof whose genome has been determined to contain at least one copy of HLA-C1, comprising administering to the patient an effective amount of a treatment regimen comprising a PD-1 axis binding antagonist (e.g., alemtuzumab). In some cases, the patient's genome further comprises at least one copy of KIR2DL 3.

In another example, provided herein is a PD-1 axis binding antagonist (e.g., alemtuzumab) for treating NSCLC in a patient in need thereof whose genome has been determined to comprise at least one copy of HLA-C1. In some cases, the patient's genome further comprises at least one copy of KIR2DL 3.

In another example, provided herein is a method of treating NSCLC in a patient in need thereof whose genome has been determined to comprise at least one copy of HLA-C1 and at least one copy of KIR2DL3, comprising administering to the patient an effective amount of a therapeutic regimen comprising a PD-1 axis binding antagonist (e.g., alemtuzumab).

In another example, provided herein is a PD-1 axis binding antagonist (e.g., alemtuzumab) for treating NSCLC in a patient in need thereof whose genome has been determined to comprise at least one copy of HLA-C1 and at least one copy of KIR2DL 3.

In another example, provided herein is a method of treating NSCLC in a patient in need thereof whose genome has been determined to contain at least one copy of HLA-Bw4, comprising administering to the patient an effective amount of a treatment regimen comprising a PD-1 axis binding antagonist (e.g., atuzumab). In some cases, the patient's genome further comprises at least one copy of KIR3DL 1.

In another example, provided herein is a PD-1 axis binding antagonist (e.g., alemtuzumab) for treating NSCLC in a patient in need thereof whose genome has been determined to comprise at least one copy of HLA-Bw 4. In some cases, the patient's genome further comprises at least one copy of KIR3DL 1.

In another example, provided herein is a method of treating NSCLC in a patient in need thereof whose genome has been determined to comprise at least one copy of HLA-Bw4 and at least one copy of KIR3DL1, comprising administering to the patient an effective amount of a treatment regimen comprising a PD-1 axis binding antagonist (e.g., alemtuzumab).

In another example, provided herein is a PD-1 axis binding antagonist (e.g., alemtuzumab) for treating NSCLC in a patient in need thereof whose genome has been determined to comprise at least one copy of HLA-Bw4 and at least one copy of KIR3DL 1.

In another example, provided herein is a method of treating NSCLC in a patient in need thereof, the method comprising: (a) Determining whether the patient's genome comprises 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 is likely to benefit from a treatment regimen comprising a PD-1 axis binding antagonist (e.g., atuzumab); 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 genome of the patient. In some cases, step (a) further comprises determining whether the patient's genome comprises at least one copy of KIR2DL 3.

In another example, provided herein is a PD-1 axis binding antagonist (e.g., alemtuzumab) for use in a method of treating NSCLC in a patient in need thereof, comprising: (a) Determining whether the patient's genome comprises 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 is likely to 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 genome of the patient. In some cases, step (a) further comprises determining whether the patient's genome comprises at least one copy of KIR2DL 3.

In another example, provided herein is a method of treating NSCLC in a patient in need thereof, the method comprising: (a) Determining whether the patient's genome comprises 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 (e.g., alemtuzumab); 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 and at least one copy of KIR2DL3 in the genome of the patient.

In another example, provided herein is a PD-1 axis binding antagonist (e.g., alemtuzumab) for treating NSCLC in a patient in need thereof, comprising: (a) Determining whether the patient's genome comprises 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 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 and at least one copy of KIR2DL3 in the genome of the patient.

In another example, provided herein is a method of treating NSCLC in a patient in need thereof, the method comprising: (a) Determining whether the patient's genome comprises 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 is likely to benefit from a treatment regimen comprising a PD-1 axis binding antagonist (e.g., atuzumab); 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 genome of the patient. In some cases, step (a) further comprises determining whether the patient's genome comprises at least one copy of KIR3DL 1.

In another example, provided herein is a PD-1 axis binding antagonist (e.g., alemtuzumab) for treating NSCLC in a patient in need thereof, comprising: (a) Determining whether the patient's genome comprises 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 genome of the patient. In some cases, step (a) further comprises determining whether the patient's genome comprises at least one copy of KIR3DL 1.

In another example, provided herein is a method of treating NSCLC in a patient in need thereof, the method comprising: (a) Determining whether the patient's genome comprises 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 (e.g., alemtuzumab); 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 genome of the patient.

In another example, provided herein is a PD-1 axis binding antagonist for use in treating NSCLC in a patient in need thereof, the method comprising: (a) Determining whether the patient's genome comprises 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 (e.g., alemtuzumab); 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 genome of the patient.

In another example, provided herein is a method of identifying a patient having NSCLC who may benefit from a treatment regimen comprising a PD-1 axis binding antagonist (e.g., atuzumab), the method comprising determining whether the patient's genome comprises 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 comprising a PD-1 axis binding antagonist. In some cases, the method further comprises determining whether the patient's genome comprises at least one copy of KIR2DL 3.

In another example, provided herein is a method of identifying a patient having NSCLC who may benefit from a treatment regimen comprising a PD-1 axis binding antagonist (e.g., atuzumab), the method comprising: (a) Germline WGS or WES is performed by fragmenting a DNA sample obtained from the patient to produce fragmented DNA, adding adaptors 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 comprising a PD-1 axis binding antagonist by determining whether the patient's genome comprises 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 comprising a PD-1 axis binding antagonist. In some cases, the method further comprises determining whether the patient's genome comprises at least one copy of KIR2DL 3.

In another example, provided herein is a method of identifying a patient having NSCLC who may benefit from a treatment regimen comprising a PD-1 axis binding antagonist (e.g., atuzumab), the method comprising determining whether the patient's genome comprises 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 comprising a PD-1 axis binding antagonist.

In another example, provided herein is a method of identifying a patient having NSCLC who may benefit from a treatment regimen comprising a PD-1 axis binding antagonist (e.g., atuzumab), the method comprising: (a) Germline WGS or WES is performed by fragmenting a DNA sample obtained from the patient to produce fragmented DNA, adding adaptors 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 comprising a PD-1 axis binding antagonist by determining whether the patient's genome comprises 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 comprising a PD-1 axis binding antagonist.

In another example, provided herein is a method of identifying a patient having NSCLC who may benefit from a treatment regimen comprising a PD-1 axis binding antagonist (e.g., atuzumab), the method comprising determining whether the patient's genome comprises 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 comprising a PD-1 axis binding antagonist. In some cases, the method further comprises determining whether the patient's genome comprises at least one copy of KIR3DL 1.

In another example, provided herein is a method of identifying a patient having NSCLC who may benefit from a treatment regimen comprising a PD-1 axis binding antagonist (e.g., atuzumab), the method comprising: (a) Germline WGS or WES is performed by fragmenting a DNA sample obtained from the patient to produce fragmented DNA, adding adaptors 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 comprising a PD-1 axis binding antagonist by determining whether the patient's genome comprises 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 comprising a PD-1 axis binding antagonist. In some cases, the method further comprises determining whether the patient's genome comprises at least one copy of KIR3DL 1.

In another example, provided herein is a method of identifying a patient having NSCLC who may benefit from a treatment regimen comprising a PD-1 axis binding antagonist (e.g., atuzumab), the method comprising determining whether the patient's genome comprises 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 with a treatment regimen comprising a PD-1 axis binding antagonist.

In another example, provided herein is a method of identifying a patient having NSCLC who may benefit from a treatment regimen comprising a PD-1 axis binding antagonist (e.g., atuzumab), the method comprising: (a) Germline WGS or WES is performed by fragmenting a DNA sample obtained from the patient to produce fragmented DNA, adding adaptors 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 comprising a PD-1 axis binding antagonist by determining whether the patient's genome comprises 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 comprising a PD-1 axis binding antagonist.

In another example, provided herein is a method of selecting a therapy for a patient having NSCLC, the method comprising: (a) Determining whether the patient's genome comprises 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 is likely to benefit from a treatment regimen comprising a PD-1 axis binding antagonist (e.g., atuzumab); and (b) selecting a treatment regimen comprising a PD-1 axis binding antagonist based on the presence of at least one copy of HLA-C1 in the genome of the patient. In some cases, the method further comprises determining whether the patient's genome comprises at least one copy of KIR2DL 3.

In another example, provided herein is a method of selecting a therapy for a patient having NSCLC, the method comprising: (a) Determining whether the patient's genome comprises 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 (e.g., alemtuzumab); and (b) selecting a treatment regimen comprising 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 genome of the patient.

In another example, provided herein is a method of selecting a therapy for a patient having NSCLC, the method comprising: (a) Determining whether the patient's genome comprises 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 is likely to benefit from a treatment regimen comprising a PD-1 axis binding antagonist (e.g., atuzumab); and (b) selecting a treatment regimen comprising a PD-1 axis binding antagonist based on the presence of at least one copy of HLA-Bw4 in the genome of the patient. In some cases, the method further comprises determining whether the patient's genome comprises at least one copy of KIR3DL 1.

In another example, provided herein is a method of selecting a therapy for a patient having NSCLC, the method comprising: (a) Determining whether the patient's genome comprises 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 (e.g., alemtuzumab); and (b) selecting 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 genome of the patient.

Any of the foregoing examples can further comprise administering to the patient an effective amount of a therapeutic regimen comprising a PD-1 axis binding antagonist.

In another example, provided herein is a method of treating NSCLC in a patient in need thereof, the patient having been determined to have an increased NK cell infiltration level relative to a reference level of NK cell infiltration in a tumor sample obtained from the patient, the method comprising administering to the patient an effective amount of a therapeutic regimen comprising a PD-1 axis binding antagonist (e.g., alemtuzumab).

In another example, provided herein is a PD-1 axis binding antagonist (e.g., alemtuzumab) for treating NSCLC in a patient in need thereof who has been determined to have an increased NK cell infiltration level relative to a reference level of NK cell infiltration in a tumor sample obtained from the patient.

In another example, provided herein is a method of treating NSCLC in a patient in need thereof, the method comprising: (a) Determining whether a tumor sample obtained from the patient has an increased NK cell infiltration level relative to a reference level of NK cell infiltration, wherein an increase in NK cell infiltration level relative to the reference level of NK cell infiltration in the tumor sample obtained from the patient indicates that the patient is likely to benefit from a treatment regimen comprising a PD-1 axis binding antagonist (e.g., alemtuzumab); and (b) administering to the patient an effective amount of a treatment regimen comprising a PD-1 axis binding antagonist based on an increase in NK cell infiltration level relative to a reference level of NK cell infiltration in a tumor sample obtained from the patient.

In another example, provided herein is a PD-1 axis binding antagonist (e.g., alemtuzumab) for use in a method of treating NSCLC in a patient in need thereof, comprising: (a) Determining whether a tumor sample obtained from the patient has an increased NK cell infiltration level relative to a reference level of NK cell infiltration, wherein an increase in NK cell infiltration level relative to the reference level of NK cell infiltration in the tumor sample obtained from the patient indicates that the patient is likely to 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 an increase in NK cell infiltration level relative to a reference level of NK cell infiltration in a tumor sample obtained from the patient.

In another example, provided herein is a method of identifying a patient having NSCLC who may benefit from a treatment regimen comprising a PD-1 axis binding antagonist (e.g., atuzumab), the method comprising determining whether a tumor sample obtained from the patient has an increased NK cell infiltration level relative to a reference level of NK cell infiltration, wherein an increase in NK cell infiltration level 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 comprising a PD-1 axis binding antagonist.

In another example, provided herein is a method of identifying a patient having NSCLC who may benefit from a treatment regimen comprising a PD-1 axis binding antagonist (e.g., atuzumab), the method comprising: (a) Contacting a tumor sample obtained from the patient with one or more antibodies or nucleotide probes that bind 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 NK cell infiltration level relative to a reference level of NK cell infiltration, wherein an increase in NK cell infiltration level relative to the reference level of NK cell infiltration in the tumor sample obtained from the patient indicates that the patient is likely to benefit from a treatment regimen comprising a PD-1 axis binding antagonist.

In another example, provided herein is a method of selecting a therapy for a patient having NSCLC, the method comprising: (a) Determining whether a tumor sample obtained from the patient has an increased NK cell infiltration level relative to a reference level of NK cell infiltration, wherein an increase in NK cell infiltration level relative to the reference level of NK cell infiltration in the tumor sample obtained from the patient indicates that the patient is likely to benefit from a treatment regimen comprising a PD-1 axis binding antagonist (e.g., alemtuzumab); and (b) selecting a treatment regimen comprising a PD-1 axis binding antagonist based on an increase in NK cell infiltration level relative to a reference level of NK cell infiltration in a tumor sample obtained from the patient.

In any of the examples 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 is determined by determining the expression level of the NK cell gene signature, 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, e.g., by immunofluorescence, immunohistochemistry, western blotting, flow cytometry, or any other suitable method.

In any of the examples described herein, the NK cell gene signature can 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, KRRF 1, KLRK1, NCR1, NKG7, PRF1, XCL1 and XCL2. In some cases, the NK cell gene signature comprises 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 cases, the reference level of NK cell infiltration is a median level. In some cases, the median level is a median level in a population of NSCLC patients.

In another example, provided herein is a method of treating NSCLC in a patient in need thereof whose genome has been determined to be deficient in KIR2DL3 or KIR3DL1, comprising administering to the patient an effective amount of a treatment regimen comprising an NK cell-directed therapeutic agent.

In another example, provided herein is an NK cell-targeted therapeutic for treating NSCLC in a patient in need thereof whose genome has been determined to be deficient in KIR2DL3 or KIR3DL1.

In another example, provided herein is a method of treating NSCLC in a patient in need thereof, the method comprising: (a) Determining whether the patient's genome lacks KIR2DL3 or KIR3DL1, wherein the absence of KIR2DL3 or KIR3DL1 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 to the patient an effective amount of a treatment regimen comprising an NK cell-directed therapeutic agent based on the lack of KIR2DL3 or KIR3DL1 in the patient's genome.

In another example, provided herein is a NK cell-directed therapeutic agent for use in a method of treating NSCLC in a patient in need thereof, the method comprising: (a) Determining whether the patient's genome lacks KIR2DL3 or KIR3DL1, wherein the absence of KIR2DL3 or KIR3DL1 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 to the patient an effective amount of a treatment regimen comprising an NK cell-directed therapeutic agent based on the lack of KIR2DL3 or KIR3DL1 in the patient's genome.

In another example, provided herein is a method of identifying a patient having NSCLC who may benefit from a treatment regimen comprising an NK cell-directed therapeutic agent, the method comprising determining whether the patient's genome lacks KIR2DL3 or KIR3DL1, wherein the absence of KIR2DL3 or KIR3DL1 in the patient's genome identifies the patient as a patient who may benefit from treatment using a treatment regimen comprising an NK cell-directed therapeutic agent.

In another example, provided herein is a method of identifying a patient having NSCLC who may benefit from a treatment regimen comprising an NK cell-directed therapeutic agent, the method comprising: (a) Germline WGS or WES is performed by fragmenting a DNA sample obtained from the patient to produce fragmented DNA, adding adaptors 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 comprising an NK cell directed therapeutic by determining whether the patient's genome lacks KIR2DL3 or KIR3DL1, wherein the patient is identified as a patient who may benefit from treatment using a treatment regimen comprising an NK cell directed therapeutic in the patient's genome in the absence of KIR2DL3 or KIR3DL 1.

In some examples, the cancer is renal cancer. . In some cases, the renal cancer is RCC. In some cases, the RCC is a locally advanced or metastatic RCC.

For example, provided herein is a method of treating renal cancer (e.g., RCC) in a patient in need thereof whose genome has been determined to contain at least one copy of HLA-C1, comprising administering to the patient an effective amount of a therapeutic regimen comprising a PD-1 axis binding antagonist (e.g., atuzumab). In some cases, the patient's genome further comprises at least one copy of KIR2DL 3.

In another example, provided herein is a PD-1 axis binding antagonist (e.g., alemtuzumab) for treating renal cancer (e.g., RCC) in a patient in need thereof whose genome has been determined to comprise at least one copy of HLA-C1. In some cases, the patient's genome further comprises at least one copy of KIR2DL 3.

In another example, provided herein is a method of treating renal cancer (e.g., RCC) in a patient in need thereof whose genome has been determined to comprise at least one copy of HLA-C1 and at least one copy of KIR2DL3, comprising administering to the patient an effective amount of a therapeutic regimen comprising a PD-1 axis binding antagonist (e.g., alemtuzumab).

In another example, provided herein is a PD-1 axis binding antagonist (e.g., alemtuzumab) for treating renal cancer (e.g., RCC) in a patient in need thereof whose genome has been determined to comprise at least one copy of HLA-C1 and at least one copy of KIR2DL 3.

In another example, provided herein is a method of treating renal cancer (e.g., RCC) in a patient in need thereof whose genome has been determined to contain at least one copy of HLA-Bw4, comprising administering to the patient an effective amount of a treatment regimen comprising a PD-1 axis binding antagonist (e.g., alemtuzumab). In some cases, the patient's genome further comprises at least one copy of KIR3DL 1.

In another example, provided herein is a PD-1 axis binding antagonist (e.g., alemtuzumab) for treating renal cancer (e.g., RCC) in a patient in need thereof whose genome has been determined to comprise at least one copy of HLA-Bw 4. In some cases, the patient's genome further comprises at least one copy of KIR3DL 1.

In another example, provided herein is a method of treating renal cancer (e.g., RCC) in a patient in need thereof whose genome has been determined to comprise at least one copy of HLA-Bw4 and at least one copy of KIR3DL1, comprising administering to the patient an effective amount of a therapeutic regimen comprising a PD-1 axis binding antagonist (e.g., alemtuzumab).

In another example, provided herein is a PD-1 axis binding antagonist (e.g., alemtuzumab) for treating renal cancer (e.g., RCC) in a patient in need thereof whose genome has been determined to comprise at least one copy of HLA-Bw4 and at least one copy of KIR3DL 1.

In another example, provided herein is a method of treating renal cancer (e.g., RCC) in a patient in need thereof, the method comprising: (a) Determining whether the patient's genome comprises 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 is likely to benefit from a treatment regimen comprising a PD-1 axis binding antagonist (e.g., atuzumab); 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 genome of the patient. In some cases, step (a) further comprises determining whether the patient's genome comprises at least one copy of KIR2DL 3.

In another example, provided herein is a PD-1 axis binding antagonist (e.g., alemtuzumab) for use in a method of treating renal cancer (e.g., RCC) in a patient in need thereof, the method comprising: (a) Determining whether the patient's genome comprises 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 is likely to 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 genome of the patient. In some cases, step (a) further comprises determining whether the patient's genome comprises at least one copy of KIR2DL 3.

In another example, provided herein is a method of treating renal cancer (e.g., RCC) in a patient in need thereof, the method comprising: (a) Determining whether the patient's genome comprises 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 (e.g., alemtuzumab); 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 and at least one copy of KIR2DL3 in the genome of the patient.

In another example, provided herein is a PD-1 axis binding antagonist (e.g., alemtuzumab) for treating renal cancer (e.g., RCC) in a patient in need thereof, comprising: (a) Determining whether the patient's genome comprises 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 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 and at least one copy of KIR2DL3 in the genome of the patient.

In another example, provided herein is a method of treating renal cancer (e.g., RCC) in a patient in need thereof, the method comprising: (a) Determining whether the patient's genome comprises 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 is likely to benefit from a treatment regimen comprising a PD-1 axis binding antagonist (e.g., atuzumab); 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 genome of the patient. In some cases, step (a) further comprises determining whether the patient's genome comprises at least one copy of KIR3DL 1.

In another example, provided herein is a PD-1 axis binding antagonist (e.g., alemtuzumab) for treating renal cancer (e.g., RCC) in a patient in need thereof, comprising: (a) Determining whether the patient's genome comprises 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 genome of the patient. In some cases, step (a) further comprises determining whether the patient's genome comprises at least one copy of KIR3DL 1.

In another example, provided herein is a method of treating renal cancer (e.g., RCC) in a patient in need thereof, the method comprising: (a) Determining whether the patient's genome comprises 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 (e.g., alemtuzumab); 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 genome of the patient.

In another example, provided herein is a PD-1 axis binding antagonist (e.g., alemtuzumab) for treating renal cancer (e.g., RCC) in a patient in need thereof, comprising: (a) Determining whether the patient's genome comprises 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 genome of the patient.

In another example, provided herein is a method of identifying a patient having renal cancer (e.g., RCC) who may benefit from a treatment regimen comprising a PD-1 axis binding antagonist (e.g., atuzumab), the method comprising determining whether the patient's genome comprises 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 comprising a PD-1 axis binding antagonist. In some cases, the method further comprises determining whether the patient's genome comprises at least one copy of KIR2DL 3.

In another example, provided herein is a method of identifying a patient having renal cancer (e.g., RCC) who may benefit from a treatment regimen comprising a PD-1 axis binding antagonist (e.g., atuzumab), the method comprising: (a) Germline WGS or WES is performed by fragmenting a DNA sample obtained from the patient to produce fragmented DNA, adding adaptors 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 comprising a PD-1 axis binding antagonist by determining whether the patient's genome comprises 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 comprising a PD-1 axis binding antagonist. In some cases, the method further comprises determining whether the patient's genome comprises at least one copy of KIR2DL 3.

In another example, provided herein is a method of identifying a patient having renal cancer (e.g., RCC) who may benefit from a treatment regimen comprising a PD-1 axis binding antagonist (e.g., atuzumab), the method comprising determining whether the patient's genome comprises 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 comprising a PD-1 axis binding antagonist.

In another example, provided herein is a method of identifying a patient having renal cancer (e.g., RCC) who may benefit from a treatment regimen comprising a PD-1 axis binding antagonist (e.g., atuzumab), the method comprising: (a) Germline WGS or WES is performed by fragmenting a DNA sample obtained from the patient to produce fragmented DNA, adding adaptors 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 comprising a PD-1 axis binding antagonist by determining whether the patient's genome comprises 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 comprising a PD-1 axis binding antagonist.

In another example, provided herein is a method of identifying a patient having renal cancer (e.g., RCC) who may benefit from a treatment regimen comprising a PD-1 axis binding antagonist (e.g., atuzumab), the method comprising determining whether the patient's genome comprises 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 comprising a PD-1 axis binding antagonist. In some cases, the method further comprises determining whether the patient's genome comprises at least one copy of KIR3DL 1.

In another example, provided herein is a method of identifying a patient having renal cancer (e.g., RCC) who may benefit from a treatment regimen comprising a PD-1 axis binding antagonist (e.g., atuzumab), the method comprising: (a) Germline WGS or WES is performed by fragmenting a DNA sample obtained from the patient to produce fragmented DNA, adding adaptors 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 comprising a PD-1 axis binding antagonist by determining whether the patient's genome comprises 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 comprising a PD-1 axis binding antagonist. In some cases, the method further comprises determining whether the patient's genome comprises at least one copy of KIR3DL 1.

In another example, provided herein is a method of identifying a patient having renal cancer (e.g., RCC) who may benefit from a treatment regimen comprising a PD-1 axis binding antagonist (e.g., atuzumab), the method comprising determining whether the patient's genome comprises 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 with a treatment regimen comprising a PD-1 axis binding antagonist.

In another example, provided herein is a method of identifying a patient having renal cancer (e.g., RCC) who may benefit from a treatment regimen comprising a PD-1 axis binding antagonist (e.g., atuzumab), the method comprising: (a) Germline WGS or WES is performed by fragmenting a DNA sample obtained from the patient to produce fragmented DNA, adding adaptors 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 comprising a PD-1 axis binding antagonist by determining whether the patient's genome comprises 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 comprising a PD-1 axis binding antagonist.

In another example, provided herein is a method of selecting a therapy for a patient having renal cancer (e.g., RCC), the method comprising: (a) Determining whether the patient's genome comprises 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 is likely to benefit from a treatment regimen comprising a PD-1 axis binding antagonist (e.g., atuzumab); and (b) selecting a treatment regimen comprising a PD-1 axis binding antagonist based on the presence of at least one copy of HLA-C1 in the genome of the patient. In some cases, the method further comprises determining whether the patient's genome comprises at least one copy of KIR2DL 3.

In another example, provided herein is a method of selecting a therapy for a patient having renal cancer (e.g., RCC), the method comprising: (a) Determining whether the patient's genome comprises 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 (e.g., alemtuzumab); and (b) selecting a treatment regimen comprising 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 genome of the patient.

In another example, provided herein is a method of selecting a therapy for a patient having renal cancer (e.g., RCC), the method comprising: (a) Determining whether the patient's genome comprises 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 is likely to benefit from a treatment regimen comprising a PD-1 axis binding antagonist (e.g., atuzumab); and (b) selecting a treatment regimen comprising a PD-1 axis binding antagonist based on the presence of at least one copy of HLA-Bw4 in the genome of the patient. In some cases, the method further comprises determining whether the patient's genome comprises at least one copy of KIR3DL 1.

In another example, provided herein is a method of selecting a therapy for a patient having renal cancer (e.g., RCC), the method comprising: (a) Determining whether the patient's genome comprises 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 (e.g., alemtuzumab); and (b) selecting 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 genome of the patient.

In another example, provided herein is a method of treating renal cancer (e.g., RCC) in a patient in need thereof, the patient having been determined to have an increased level of Natural Killer (NK) cell infiltration relative to a reference level of 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 (e.g., atrazumab).

In another example, provided herein is a PD-1 axis binding antagonist (e.g., alemtuzumab) for use in treating renal cancer (e.g., RCC) in a patient in need thereof who has been determined to have an increased NK cell infiltration level relative to a reference level of NK cell infiltration in a tumor sample obtained from the patient.

In another example, provided herein is a method of treating renal cancer (e.g., RCC) in a patient in need thereof, the method comprising: (a) Determining whether a tumor sample obtained from the patient has an increased NK cell infiltration level relative to a reference level of NK cell infiltration, wherein an increase in NK cell infiltration level relative to the reference level of NK cell infiltration in the tumor sample obtained from the patient indicates that the patient is likely to benefit from a treatment regimen comprising a PD-1 axis binding antagonist (e.g., alemtuzumab); and (b) administering to the patient an effective amount of a treatment regimen comprising a PD-1 axis binding antagonist based on an increase in NK cell infiltration level relative to a reference level of NK cell infiltration in a tumor sample obtained from the patient.

In another example, provided herein is a PD-1 axis binding antagonist (e.g., alemtuzumab) for use in a method of treating renal cancer (e.g., RCC) in a patient in need thereof, the method comprising: (a) Determining whether a tumor sample obtained from the patient has an increased NK cell infiltration level relative to a reference level of NK cell infiltration, wherein an increase in NK cell infiltration level relative to the reference level of NK cell infiltration in the tumor sample obtained from the patient indicates that the patient is likely to 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 an increase in NK cell infiltration level relative to a reference level of NK cell infiltration in a tumor sample obtained from the patient.

In another example, provided herein is a method of identifying a patient having renal cancer (e.g., RCC) who may benefit from a treatment regimen comprising a PD-1 axis binding antagonist (e.g., atuzumab), the method comprising determining whether a tumor sample obtained from the patient has an increased NK cell infiltration level relative to a reference level of NK cell infiltration, wherein an increase in NK cell infiltration level 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 comprising a PD-1 axis binding antagonist.

In another example, provided herein is a method of identifying a patient having renal cancer (e.g., RCC) who may benefit from a treatment regimen comprising a PD-1 axis binding antagonist (e.g., atuzumab), the method comprising: (a) Contacting a tumor sample obtained from the patient with one or more antibodies or nucleotide probes that bind 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 NK cell infiltration level relative to a reference level of NK cell infiltration, wherein an increase in NK cell infiltration level relative to the reference level of NK cell infiltration in the tumor sample obtained from the patient indicates that the patient is likely to benefit from a treatment regimen comprising a PD-1 axis binding antagonist.

In another example, provided herein is a method of selecting a therapy for a patient having renal cancer (e.g., RCC), the method comprising: (a) Determining whether a tumor sample obtained from the patient has an increased NK cell infiltration level relative to a reference level of NK cell infiltration, wherein an increase in NK cell infiltration level relative to the reference level of NK cell infiltration in the tumor sample obtained from the patient indicates that the patient is likely to benefit from a treatment regimen comprising a PD-1 axis binding antagonist (e.g., alemtuzumab); and (b) selecting a treatment regimen comprising a PD-1 axis binding antagonist based on an increase in NK cell infiltration level relative to a reference level of NK cell infiltration in a tumor sample obtained from the patient.

In any of the examples described herein, the NK cell gene signature can 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, KRRF 1, KLRK1, NCR1, NKG7, PRF1, XCL1 and XCL2. In some cases, the NK cell gene signature comprises 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 cases, the reference level of NK cell infiltration is a median level. In some cases, the median level is a median level in a population of patients with renal cancer (e.g., RCC).

In another example, provided herein is a method of treating renal cancer (e.g., RCC) in a patient in need thereof whose genome has been determined to be deficient in KIR2DL3 or KIR3DL1, comprising administering to the patient an effective amount of a treatment regimen comprising an NK cell-directed therapeutic agent.

In another example, provided herein is an NK cell-targeted therapeutic for treating renal cancer (e.g., RCC) in a patient in need thereof whose genome has been determined to be deficient in KIR2DL3 or KIR3DL1.

In another example, provided herein is a method of treating renal cancer (e.g., RCC) in a patient in need thereof, the method comprising: (a) Determining whether the patient's genome lacks KIR2DL3 or KIR3DL1, wherein the absence of KIR2DL3 or KIR3DL1 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 to the patient an effective amount of a treatment regimen comprising an NK cell-directed therapeutic agent based on the lack of KIR2DL3 or KIR3DL1 in the patient's genome.

In another example, provided herein is a NK cell-directed therapeutic agent for use in a method of treating renal cancer (e.g., RCC) in a patient in need thereof, the method comprising: (a) Determining whether the patient's genome lacks KIR2DL3 or KIR3DL1, wherein the absence of KIR2DL3 or KIR3DL1 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 to the patient an effective amount of a treatment regimen comprising an NK cell-directed therapeutic agent based on the lack of KIR2DL3 or KIR3DL1 in the patient's genome.

In another example, provided herein is a method of identifying a patient having renal cancer (e.g., RCC) who may benefit from a treatment regimen comprising an NK cell-directed therapeutic agent, 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 comprising an NK cell-directed therapeutic agent.

In another example, provided herein is a method of identifying a patient having renal cancer (e.g., RCC) who may benefit from a treatment regimen comprising an NK cell-directed therapeutic agent, the method comprising: (a) Germline WGS or WES is performed by fragmenting a DNA sample obtained from the patient to produce fragmented DNA, adding adaptors 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 comprising an NK cell directed therapeutic by determining whether the patient's genome lacks KIR2DL3 or KIR3DL1, wherein the patient is identified as a patient who may benefit from treatment using a treatment regimen comprising an NK cell directed therapeutic in the patient's genome in the absence of KIR2DL3 or KIR3DL 1.

In another example, provided herein is a method of selecting a therapy for a patient having renal cancer (e.g., RCC), the method comprising: (a) Determining whether the patient's genome lacks KIR2DL3 or KIR3DL1, wherein the absence of KIR2DL3 or KIR3DL1 in the patient's genome identifies the patient as likely to benefit from treatment using a treatment regimen comprising an NK cell-directed therapeutic agent; and (b) selecting a treatment regimen comprising an NK cell-directed therapeutic agent based on the lack of KIR2DL3 or KIR3DL1 in the patient's genome.

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 using a treatment regimen that does not include a PD-1 axis binding antagonist.

In any of the examples described herein, the patient may be a primary chemotherapeutic treatment.

In any of the examples described herein, the treatment regimen may be a first-line treatment regimen.

Any suitable PD-1 axis binding antagonist may be used, including any of the PD-1 axis binding antagonists described herein (see section IV below). In some examples, 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 examples, 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 (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). In some cases, the anti-PD-L1 antibody comprises (a) a VH comprising the amino acid sequence of SEQ ID NO:9, and (b) a VL comprising the amino acid sequence of SEQ ID NO: 10. In some cases, the anti-PD-L1 antibody is alemtuzumab, devaluzumab, avilamab, or MDX-1105. In some cases, the anti-PD-L1 antibody is alemtuzumab. In some cases, the anti-PD-L1 antibody is administered intravenously or subcutaneously. In some cases, the alemtuzumab is administered intravenously at a dose of 840mg every two weeks. In some cases, the alemtuzumab is administered intravenously at a dose of 1200mg every three weeks. In some cases, the alemtuzumab is administered intravenously at a dose of 1680mg every four weeks.

In other examples, 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 na Wu Shankang, pamil mab, MEDI-0680, swamp mab, cimetidine Li Shan antibody, karilimab, singdi Li Shan antibody, tirelimab, terlipressin Li Shan antibody, or multi-tarolimab.

In some examples, the 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 a taxane (e.g., nab-paclitaxel or paclitaxel), a platinum-based chemotherapeutic agent (e.g., carboplatin), an anti-angiogenic agent (e.g., an anti-VEGF antibody, such as atrazumab), NK cell-directed therapy (e.g., NK cell cement), or a combination thereof.

In some examples, the treatment regimen further comprises a taxane (e.g., nab-paclitaxel or paclitaxel). In some cases, the taxane is nab-paclitaxel. In some cases, the taxane is paclitaxel.

In some examples, the treatment regimen further comprises a platinum-based chemotherapeutic agent. In some cases, the platinum-based chemotherapeutic agent is carboplatin.

In some examples, the treatment regimen further comprises 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 of the examples described herein can further comprise administering an additional therapeutic agent to the patient. In some cases, the additional therapeutic agent is selected from the group consisting of: immunotherapeutic agents, cytotoxic agents, growth inhibitory agents, radiotherapeutic agents, anti-angiogenic agents, and combinations thereof. In some cases, the immunotherapeutic agent is an NK cell directing agent, including any of the NK cell directing agents described herein.

In any of the foregoing examples, each dosing cycle may have any suitable length, for example, about 7 days, about 14 days, about 21 days, about 28 days, or longer. In some cases, each dosing cycle was about 21 days.

The patient is preferably a human.

As a general proposal, a therapeutically effective amount of a PD-1 axis binding antagonist (e.g., alemtuzumab) administered to a human will be in the range of about 0.01 to about 50mg/kg patient body weight, whether by one or more administrations.

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

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

In some cases, a total of 1 to 50 doses of the PD-1 axis binding antagonist are administered to a patient, e.g., 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, 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, 20 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 50 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 dose may be administered intravenously.

In some cases, the alemtuzumab is administered intravenously to the patient at a dose of about 840mg every 2 weeks, at a dose of about 1200mg every 3 weeks, or at a dose of about 1680mg every 4 weeks. In some cases, the alemtuzumab is administered intravenously to the patient at a dose of 1200mg every 3 weeks.

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

The PD-1 axis binding antagonist and any additional therapeutic agent may be administered by the same route of administration or by different routes of administration. In some cases, the PD-1 axis binding antagonist is administered intravenously, intramuscularly, subcutaneously, topically, orally, transdermally, intraperitoneally, intraorbitally, by implantation, by inhalation, intrathecally, intraventricularly, or intranasally. In some cases, the additional therapeutic agent is administered intravenously, intramuscularly, subcutaneously, topically, orally, transdermally, intraperitoneally, intraorbitally, by implantation, by inhalation, intrathecally, intraventricularly, or intranasally.

In preferred embodiments, the PD-1 axis binding antagonist is administered intravenously. In one example, the alemtuzumab can be administered intravenously over 60 minutes; if the first infusion can be tolerated, all subsequent infusions can be delivered over 30 minutes. In some examples, the PD-1 axis binding antagonist is not administered as an intravenous bolus or bolus injection. In some examples, a taxane (e.g., nab-paclitaxel or paclitaxel), a platinum-based chemotherapeutic agent (e.g., carboplatin), an anti-angiogenic agent (e.g., an anti-VEGF antibody, such as bevacizumab), and/or NK cell-directed therapy (e.g., NK cell cement) is administered intravenously.

In some examples, the NSCLC is metastatic non-squamous NSCLC and the treatment regimen includes alemtuzumab, nab-paclitaxel, and carboplatin. In some cases, the alemtuzumab is administered as an Intravenous (IV) infusion at a dose of 1200mg on day 1 of each 21-day cycle; nab-paclitaxel at 100mg/m on days 1, 8 and 15 of each 21-day cycle ² Is administered as an IV infusion; and carboplatin was administered at 6mg/mL/min concentration curve area under Area (AUC) on day 1 of each 21 day cycle.

In some examples, the NSCLC is metastatic non-squamous NSCLC and the treatment regimen includes alemtuzumab, paclitaxel, and carboplatin. In some cases, the alemtuzumab was administered as an IV infusion at a dose of 1200mg on day 1 of each 21-day cycle; paclitaxel at 200mg/m on day 1 of each 21-day cycle ² Is administered as an IV infusion; and carboplatin was administered at AUC of 6mg/mL/min on day 1 of each 21-day cycle.

In some examples, the NSCLC is metastatic non-squamous NSCLC and the treatment regimen includes alemtuzumab, bevacizumab, paclitaxel, and carboplatin. In some cases, the alemtuzumab was administered as an IV infusion at a dose of 1200mg on day 1 of each 21-day cycle; bevacizumab was administered as IV infusion at a dose of 15mg/kg on day 1 of each 21 day cycle; paclitaxel at 200mg/m on day 1 of each 21-day cycle ² Is administered as an IV infusion; and carboplatin was administered at AUC of 6mg/mL/min on day 1 of each 21-day cycle.

In some examples, the NSCLC is metastatic squamous NSCLC and the treatment regimen includes alemtuzumab, nab-paclitaxel, and carboplatin. In some cases, the alemtuzumab was administered as an IV infusion at a dose of 1200mg on day 1 of each 21-day cycle; nab-paclitaxel at 100mg/m on days 1, 8 and 15 of each 21-day cycle ² Is administered as an IV infusion; and carboplatin was administered at 6mg/mL/min concentration curve area under Area (AUC) on day 1 of each 21 day cycle.

In some examples, the NSCLC is metastatic squamous NSCLC and the treatment regimen includes alemtuzumab, paclitaxel, and carboplatin. In some cases, the alemtuzumab was administered as an IV infusion at a dose of 1200mg on day 1 of each 21-day cycle; paclitaxel at 175mg/m on days 1, 8 and 15 of each 21-day cycle ² Or 200mg/m ² Is administered as an IV infusion; and carboplatin was administered at AUC of 6mg/mL/min on day 1 of each 21-day cycle.

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

Also provided herein are methods for treating cancer (e.g., NSCLC) in a patient, the methods comprising administering to the patient a treatment regimen comprising an effective amount of a PD-1 axis binding antagonist (e.g., atuzumab) and/or a taxane (e.g., nab-paclitaxel or paclitaxel), a platinum-based chemotherapeutic agent (e.g., carboplatin), an anti-angiogenic agent (e.g., an anti-VEGF antibody, such as bevacizumab), and/or a combination of NK cell-directed therapy (e.g., NK cell cement) with another anticancer agent or cancer therapy. For example, a PD-1 axis binding antagonist may be administered in combination with: additional chemotherapeutics or chemotherapeutics (see definition above); targeted therapies or targeted therapeutic agents; immunotherapy or immunotherapeutic agents, e.g., monoclonal antibodies; one or more cytotoxic agents (see definition above); or a combination thereof. For example, the PD-1 axis binding antagonist may be administered in combination with bevacizumab, paclitaxel, protein-bound paclitaxel (e.g., albumin-bound paclitaxel), carboplatin, cisplatin, pemetrexed, gemcitabine, etoposide, cobicitinib (cobimeinib), vemurafenib, or a combination thereof. The PD-1 axis binding antagonist is an anti-PD-L1 antibody (e.g., alemtuzumab) or an anti-PD-1 antibody.

For example, when administered with chemotherapy with or without bevacizumab, alemtuzumab may be administered prior to chemotherapy and bevacizumab at a dose of 1200mg every 3 weeks. In another example, after completion of 4 to 6 cycles of chemotherapy, and if bevacizumab is discontinued, atrazumab may be administered at a dose of 840mg every 2 weeks, 1200mg every 3 weeks, or 1680mg every four weeks. In another example, alemtuzumab can be administered at a dose of 840mg followed by 100mg/m ² Protein-bound paclitaxel (e.g., albumin-bound paclitaxel); for each 28 day cycle, alemtuzumab was administered on days 1 and 15, and protein-bound paclitaxel was administered on days 1, 8, and 15. In another example, when administered with carboplatin and etoposide, atraumatin may be administered at a dose of 1200mg every 3 weeks prior to chemotherapy. In yet another example, after completion of 4 cycles of carboplatin and etoposide, atraumatic bead mab may be administered at a dose of 840mg every 2 weeks, 1200mg every 3 weeks, or 1680mg every 4 weeks. In another example, after a 28 day period of cobicitinib and vemurafenib is completed, the alemtuzumab may be orally administered once daily at a dose of 840mg every 2 weeks with cobicitinib (taken for 21 days, 7 days off) at a dose of 60mg and vemurafenib twice daily at a dose of 720mg The feenix is administered together.

In some cases, the treatment may further include additional therapies. Any suitable additional therapy known in the art or described herein may be used. The additional therapy may be 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, the additional therapy is administration of side-effect limiting agents (e.g., agents intended to reduce the occurrence and/or severity of therapeutic side-effects, e.g., anti-nausea agents, corticosteroids (e.g., prednisone or equivalent, e.g., at a dose of 1 to 2 mg/kg/day), hormone replacement drugs, etc.).

Evaluation of PD-L1 expression

The expression of PD-L1 in a patient treated according to any of the methods and compositions described herein for use can be assessed. The methods and compositions for use may include determining the expression level of PD-L1 in a biological sample (e.g., a tumor sample) obtained from a patient. In other examples, the PD-L1 expression level in a biological sample (e.g., a tumor sample) obtained from the patient has been determined prior to initiation of the treatment or after initiation of the treatment. PD-L1 expression may be determined using any suitable method. For example, PD-L1 expression may be determined as described in U.S. patent application publication nos. US2018/0030138 and US 2018/0037655, which are incorporated herein by reference in their entirety. Any suitable tumor sample may be used, for example, 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 from the percentage of tumor samples occupied by tumor-infiltrating immune cells expressing detectable levels of PD-L1 expression, as the percentage of tumor-infiltrating immune cells expressing detectable levels of PD-L1 expression in a tumor sample, and/or as the percentage of tumor cells expressing detectable levels of PD-L1 expression in a tumor sample. It will be appreciated that in any of the foregoing examples, the percentage of tumor sample occupied by tumor-infiltrating immune cells can be the percentage of tumor area covered by tumor-infiltrating immune cells in a section of tumor sample obtained from a patient, e.g., as assessed by IHC using an anti-PD-L1 antibody (e.g., SP142 antibody). Any suitable anti-PD-L1 antibody may be used, including, for example, SP142 (Ventana), SP263 (Ventana), 22C3 (Dako), 28-8 (Dako), E1L3N (Cell Signaling 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, a tumor sample obtained from a patient has a detectable level of PD-L1 expression in less than 1% of tumor cells in the tumor sample, in 1% or more of tumor cells in the tumor sample, in 1% to less than 5% of tumor cells in the tumor sample, in 5% or more of tumor cells in the tumor sample, in 5% to less than 50% of tumor cells in the tumor sample, or in 50% or more of tumor cells in the tumor sample.

In some examples, a tumor sample obtained from a patient has a detectable level of PD-L1 expression in tumor-infiltrating immune cells that occupy less than 1% of the tumor sample, greater than 1% of the tumor sample, 1% to less than 5% of the tumor sample, greater than 5% of the tumor sample, 5% to less than 10% of the tumor sample, or greater than 10% of the tumor sample.

In some embodiments, tumor samples may be scored for PD-L1 positives 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 tumor infiltrating Immune Cell (IC) IHC diagnostic criteria

TABLE 2 IHC diagnostic criteria for Tumor Cells (TC)

PD-1 axis 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 may be used.

PD-L1 binding antagonists

In some cases, the PD-L1 binding antagonist inhibits the binding of PD-L1 to one or more of its ligand binding partners. In other cases, the PD-L1 binding antagonist inhibits the binding of PD-L1 to PD-1. In still other cases, the PD-L1 binding antagonist inhibits the binding of PD-L1 to B7-1. In some cases, the PD-L1 binding antagonist inhibits the binding of PD-L1 to both PD-1 and B7-1. The PD-L1 binding antagonist may be, but is not limited to, an antibody, antigen binding fragment thereof, immunoadhesin, fusion protein, oligopeptide or small molecule. In some cases, the PD-L1 binding antagonist is a small molecule that inhibits PD-L1 (e.g., GS-4224, INCB086550, MAX-10181, INCB090244, CA-170, or ABSK 041). In some cases, the PD-L1 binding antagonist is a small molecule that inhibits 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 PD-L1 and TIM 3. In some cases, the small molecule is a compound described in WO 2015/033301 and WO 2015/033299.

In some cases, the PD-L1 binding antagonist is an anti-PD-L1 antibody. Various anti-PD-L1 antibodies are contemplated and described herein. In any case herein, the isolated anti-PD-L1 antibody can bind to human PD-L1 (e.g., human PD-L1 shown in UniProtKB/Swiss-Prot accession No. Q9NZQ7-1, or a variant thereof). In some cases, the anti-PD-L1 antibody is capable of inhibiting binding between PD-L1 and PD-1 and/or between PD-L1 and B7-1. In some cases, the anti-PD-L1 antibody is a monoclonal antibody. In some cases, the anti-PD-L1 antibody is an antibody fragment selected from the group consisting of Fab, fab '-SH, fv, scFv, and (Fab') 2 fragments. In some cases, the anti-PD-L1 antibody is a humanized antibody. In some cases, the anti-PD-L1 antibody is a human antibody. Exemplary anti-PD-L1 antibodies include alemtuzumab, MDX-1105, MEDI4736 (Devaluzumab), MSB0010718C (Avmumab), SHR-1316, CS1001, en Wo Lishan antibody, TQB2450, ZKAB001, LP-002, CX-072, IMC-001, KL-A167, APL-502, ke Xili mab, lodendmab, 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 and methods for their preparation that can be used in the methods of the invention are described in international patent application publication No. WO 2010/077634 and U.S. patent No. 8,217,149, each of which is incorporated herein by reference in its entirety.

In some cases, the anti-PD-L1 antibody comprises:

(a) Sequences of HVR-H1, HVR-H2 and HVR-H3 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) A heavy chain variable region (VH) comprising the amino acid sequence:

EVQLVESGGGLVQPGGSLRLSCAASGFTFSDSWIHWVRQAPGKGLEWVAWISPYGGSTYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARRHWPGGFDYWGQGTLVTVSS (SEQ ID NO: 9) and

(b) A light chain variable region (VL) comprising the amino acid sequence:

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

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

(a) The following heavy chain amino acid sequences:

EVQLVESGGGLVQPGGSLRLSCAASGFTFSDSWIHWVRQAPGKGLEWVAWISPYGGSTYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARRHWPGGFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYASTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPG (SEQ ID NO: 1) and

(b) The following light chain amino acid sequences:

DIQMTQSPSSLSASVGDRVTITCRASQDVSTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQYLYHPATFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC(SEQ ID NO:2)。

in some cases, the anti-PD-L1 antibody is avilamab (CAS registry number 1537032-82-8). Avermectin, also known as MSB0010718C, is a human monoclonal IgG1 anti-PD-L1 antibody (Merck KGaA), a pyroxene company.

In some cases, the anti-PD-L1 antibody is Dewaruzumab (CAS registry number 1428935-60-7). Dewaruzumab, also known as MEDI4736, is an Fc-optimized human monoclonal IgG1 kappa anti-PD-L1 antibody (MedImmune, african) described in WO 2011/066389 and US 2013/034559.

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

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

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

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

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

In some cases, the anti-PD-L1 antibody comprises six HVR sequences (e.g., three heavy chain HVRs and three light chain HVRs) and/or a heavy chain variable domain and a light chain variable domain 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 further specific aspect, the anti-PD-L1 antibody has reduced or minimal effector function. In a still further specific aspect, minimal effector function results from an "Fc mutation of a null effector" or a glycosylation free mutation. In a further aspect, the null effector Fc mutation is an N297A or D265A/N297A substitution in the constant region. In a further aspect, the null effector Fc mutation is an N297A substitution in the constant region. In some cases, the isolated anti-PD-L1 antibody is aglycosylated. Glycosylation of antibodies is typically N-linked or O-linked. N-linked refers to the attachment of the carbohydrate moiety to the side chain of an asparagine residue. Tripeptide sequences asparagine-X-serine and asparagine-X-threonine (where X is any amino acid other than proline) are recognition sequences for enzymatic attachment of a carbohydrate moiety to an asparagine side chain. Thus, the presence of any of these tripeptide sequences in a polypeptide creates a potential glycosylation site. O-linked glycosylation refers to the attachment of one of the sugars N-acetylgalactosamine, galactose or xylose to a hydroxyamino acid (most typically serine or threonine, although 5-hydroxyproline or 5-hydroxylysine may also be used). Glycosylation sites can be conveniently removed from antibodies by altering the amino acid sequence to remove one of the tripeptide sequences described above (for an N-linked glycosylation site). Variations may be made by substitution of an asparagine, serine or threonine residue within a glycosylation site to another amino acid residue (e.g., glycine, alanine or conservative substitutions).

PD-1 binding antagonists

In some cases, the PD-1 axis binding antagonist is a PD-1 binding antagonist. For example, in some cases, a PD-1 binding antagonist inhibits the binding of PD-1 to one or more of its ligand binding partners. In some cases, the PD-1 binding antagonist inhibits the binding of PD-1 to PD-L1. In other cases, the PD-1 binding antagonist inhibits the binding of PD-1 to PD-L2. In still other cases, the PD-1 binding antagonist inhibits the binding of PD-1 to both PD-L1 and PD-L2. The PD-1 binding antagonist may be, but is not limited to, an antibody, antigen binding fragment thereof, immunoadhesin, fusion protein, oligopeptide or small molecule. In some cases, the PD-1 binding antagonist is an immunoadhesin (e.g., an immunoadhesin comprising an extracellular or PD-1 binding portion of PD-L1 or PD-L2 fused to a constant region (e.g., an Fc region of an immunoglobulin sequence)). For example, in some cases, the PD-1 binding antagonist is an Fc fusion protein. In some cases, the PD-1 binding antagonist is AMP-224.AMP-224, also known as B7-DCIg, is a PD-L2-Fc fusion soluble receptor as 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, the PD-1 binding antagonist is a small molecule that inhibits PD-1.

In some cases, the PD-1 binding antagonist is an anti-PD-1 antibody. A variety of anti-PD-1 antibodies may be utilized in the methods and uses disclosed herein. In any case hereinThe PD-1 antibody may 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 '-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 Na Wu Shankang, palbociclizumab, MEDI-0680, PDR001 (Stidazumab), REGN2810 (Simipu Li Shan antibody), BGB-108, paruo Li Shan, carilizumab, xindi Li Shan antibody, tirilizumab, teripu Li Shan antibody, dutarizumab, ralfordin Li Shan antibody, sashan Li Shan antibody, pe An Puli mab, CS1003, HLX10, SCT-I10A, sapalizumab, butelimumab, jenomab, BI 754091, silimumab, YBL-006, BAT1306, HX008, bragg Li Shan antibody, AMG 404, CX-188, JTX-4014, A, sym021, LZM009, F520, SG001, ENUM 244C8, ENUM D4, STI-1110, AK-103 and hAb21.

In some cases, the anti-PD-1 antibody is nivolumab (CAS registry number 946414-94-4). Nawuzumab (Bai Shi Gui Bao/Daye pharmaceutical (Ono)), also known as MDX-1106-04, MDX-1106, ONO-4538, BMS-936558 andis an anti-PD-1 antibody as described in WO 2006/121168.

In some cases, the anti-PD-1 antibody is palbociclizumab (CAS registry number 1374853-91-4). Parbolizumab (Merck), also known as MK-3475, merck3475, pembrolizumab, SCH-900475 andis an anti-PD-1 antibody described in WO 2009/114335.

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

In some cases, the anti-PD-1 antibody is PDR001 (CAS registry number 1859072-53-9; north). 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 (Baiji Shenzhou).

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

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

In some cases, the anti-PD-1 antibody is STI-A1110 (Soronto Corp.). 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 (gabbro).

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 the function of PD-1 without preventing the binding of PD-L1 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, the anti-PD-1 antibody comprises six HVR sequences (e.g., three heavy chain HVRs and three light chain HVRs) and/or a heavy chain variable domain and a light chain variable domain from the anti-PD-1 antibodies described in the following patents: WO 2015/112800, WO 2015/112805, WO 2015/112900, US20150210769, WO2016/089873, WO 2015/035606, WO 2015/085847, WO 2014/206107, WO 2012/145493, US 9,205,148, WO 2015/119930, WO 2015/119923, WO 2016/032927, WO 2014/179664, WO 2016/106160 and WO 2014/194302.

In a further specific aspect, the anti-PD-1 antibody has reduced or minimal effector function. In a still further specific aspect, minimal effector function results from an "Fc mutation of a null effector" or a glycosylation free mutation. In a further aspect, the null effector Fc mutation is an N297A or D265A/N297A substitution in the constant region. In some cases, the isolated anti-PD-1 antibody is aglycosylated.

PD-L2 binding antagonists

In some cases, the PD-1 axis binding antagonist is a PD-L2 binding antagonist. In some cases, a PD-L2 binding antagonist is a molecule that inhibits the binding of PD-L2 to its ligand binding partner. In a specific aspect, the PD-L2 binding ligand partner is PD-1. The PD-L2 binding antagonist may be, but is not limited to, an antibody, antigen binding fragment thereof, immunoadhesin, fusion protein, oligopeptide or small molecule.

In some cases, the PD-L2 binding antagonist is an anti-PD-L2 antibody. In any of the cases herein, the anti-PD-L2 antibody can 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 '-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 further specific aspect, the anti-PD-L2 antibody has reduced or minimal effector function. In a still further specific aspect, minimal effector function results from an "Fc mutation of a null effector" or a glycosylation free mutation. In a further aspect, the null effector Fc mutation is an N297A or D265A/N297A substitution in the constant region. In some cases, the isolated anti-PD-L2 antibody is aglycosylated.

NK cell directed therapy

Provided herein are methods for treating cancer (e.g., NSCLC) in a patient, the methods comprising administering to the patient a treatment regimen comprising an NK cell-directed therapeutic agent. Related compositions (e.g., pharmaceutical compositions), kits, and articles of manufacture for use are also provided. Any of the methods, compositions for use, kits, or articles of manufacture described herein may include or relate to any of the agents described below.

Any suitable NK cell-directed therapeutic agent may be used. In some examples, any NK cell directed therapy described in Hodgins et al J.Clin. Invest.129 (9): 3499-3510,2019 may be used. In some cases, the NK cell-targeted therapeutic includes allogeneic NK cells, autologous NK cells, ready NK cells, chimeric Antigen Receptor (CAR) -NK cells, cytokine therapy, NK cell cement (e.g., bispecific killer cell cement (BiKE), trispecific killer cell cement (tripe), or tetraspecific killer cell cement (TetraKE)), an NK cell checkpoint receptor antagonist, or an oncolytic virus. In some cases, the NK cell-directed therapeutic agent includes adoptive cell transfer (e.g., using allogeneic NK cells, autologous NK cells, ready NK cells, or Chimeric Antigen Receptor (CAR) -NK cells).

Exemplary NK cells that may be used include, but are not limited to, FT500 from Fate Therapeutics (general ready NK cell Cancer immunotherapy derived from the cloned master iPSC line; see, e.g., cichocki et al Sci.Trans.Med.12 (568): eaaz5618,2020), FT516 (a common off-the-shelf NK cell Cancer immunotherapy derived from the cloned main iPSC line, engineered to express the high affinity 158V, non-cleavable CD16 (hnCD 16) Fc receptor that has been modified to prevent its down-regulation and enhance its binding to tumor targeting antibodies; see, e.g., zhu et al Blood135 (6): 399-410,2020), FT536 (universal off-the-shelf NK cell Cancer immunotherapy derived from the clone-master engineered iPSC line, which includes four functional modifications of MICA and MICB alpha 3 domain-targeting CAR, ADCC-enhancing high affinity 158V, non-cleavable CD16 (hnCD 16) Fc receptor, IL-15 receptor fusion (IL-15 RF) that promotes NK cell activity, and CD38 expression abrogating that enhances NK cell metabolic adaptability, persistence and antitumor function, see, e.g., de Andrade et al Cancer immunol. Res.8:769-80,2020), FT596 (engineered universal off-the-shelf NK cell Cancer immunotherapy derived from the clone-master iPSC line, which has three modes of antitumor function: CD 19-targeting CAR 158V, non-cleavable CD16 (hnCD 16) Fc receptor that has been modified to prevent down-regulation and its binding to its tumor antigen, IL-enhancement of the receptor fusion (IL-15, see, e.g., de-gastric 4. Gamma.: 10,2020), and IL-382. Alpha. Gamma. Directed to the human NK cell antigen, e.g., IL-binding to the human tumor cell receptor (e.g., IL-15, J-15) FT538 (universal off-the-shelf NK cell cancer immunotherapy derived from a cloned master iPSC line incorporating three functional modifications of high affinity 158V, uncleaved CD16 (hnCD 16) Fc receptor that has been modified to enhance ADCC, IL-15 receptor fusion (IL-15 RF) that enhances NK cell activity, and elimination of CD38 expression that alleviates the possibility of NK cell self-killing), FT573 (universal off-the-shelf NK cell cancer immunotherapy derived from a cloned master engineered iPSC line incorporating four functional modifications of a CAR targeting B7H3, high affinity 158V, uncleaved CD16 (hnCD 16) Fc receptor that enhances ADCC, IL-15 receptor fusion (IL-15 RF) that enhances NK cell activity, elimination of CD38 expression that enhances NK cell metabolic adaptation, persistence and antitumor function) and FT576 (universal off-the-shelf NK cell cancer immunotherapy derived from a cloned master iPSC line) incorporating four functional modifications of a CAR targeting BCMA, high affinity 158V, uncleaved CD16 (hnCD 16) Fc receptor fusion that enhances NK cell activity and elimination of IL-15 receptor (IL-15 RF).

In some examples, NK cells (e.g., allogeneic NK cells, autologous NK cells, or ready NK cells) are engineered to express KIR2DL3 or KIR3DL1. For example, in some cases, allogeneic NK cells, autologous NK cells, or ready NK cells are engineered to express KIR2DL3. For example, in other cases, allogeneic NK cells, autologous NK cells, or ready NK cells are engineered to express KIR3DL1. NK cells (e.g., allogeneic NK cells, autologous NK cells, or ready NK cells) can be engineered to express KIR2DL3 or KIR3DL1 using any suitable method, including gene editing or transduction (e.g., lentiviral transduction).

In some examples, the allogeneic NK cells are derived from a cell line, such as NK92 or KyHG1. In other examples, the allogeneic NK cells may be derived from umbilical cord blood or iPSC.

In some examples, the NK cell targeted therapeutic is a natural killer cell transduced with a chimeric antigen receptor (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., a tumor antigen of table 3), a transmembrane domain, and one or more intracellular signaling domains, such as a primary signaling domain (e.g., CD3 ζ) and/or a costimulatory signaling domain (e.g., CD28,4-1 BB) (WO 2017-114497; hartmann et al EMBO Molecular Medicine,9 (9), 2017). The intracellular signaling domain may act to activate cytotoxicity.

In some examples, the CAR is introduced into the NK cell population. As described in WO 2017/117112, NK cell populations can be prepared for CARs, for example, by using a flow-through module. NK cells may be autologous, e.g. derived from the patient, or allogeneic, e.g. derived from the donor. In some aspects, the CAR-NK cells are introduced into the patient intravenously or intratumorally.

Table 3: exemplary tumor antigens

In some examples, the NK cell-targeted therapeutic is an NK cell cement (e.g., bispecific killer cell cement (BiKE), trispecific killer cell cement (tripe), or tetraspecific killer cell cement (TetraKE)). In some cases, the NK cell cement binds to one or more targets (e.g., proteins, e.g., receptors) on the surface of NK cells (e.g., CD16, NKG2D, SLAM family proteins, NKp30, NKp44, or NKp 46) and one or more targets (e.g., proteins, e.g., receptors) on the surface of tumor cells (e.g., tumor antigens, including CD30, CD33, EGFR, BCMA, or any of the tumor antigens described in table 3). Exemplary NK cell cements 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 (15 suppl), 2016; and Ellwanger et al J Immunother Cancer,3 (Suppl 2): 219,2015. In some embodiments, the NK-cell cement is a nanoparticle-based NK-cell cement, such as a nanoparticle-based trispecific NK-cell cement (nano-TriNKE) (see, e.g., au et al Science Advances 6 (27): eaba8564,2020 exemplary NK-cell cements include, e.g., IPH6101 (Innate Pharma/Sanofi).

NK cell cements can be multispecific, e.g., bispecific, trispecific, or tetraspecific.

For a particular target, the NK cell binding agent may be multivalent, e.g., bivalent, trivalent, tetravalent, pentavalent, or hexavalent.

In some examples, the NK cell cement is a bispecific NK cell cement comprising a first targeting domain that binds to an epitope on an NK cell and a second targeting domain that binds to a different target, e.g., a tumor antigen. In some aspects, the bispecific NK cell cement comprises a first targeting domain that binds CD16a (a protein expressed on the surface of NK cells) and a second targeting domain that binds the tumor marker CD 30. In some aspects, the bispecific NK cell cement comprises a first targeting domain that binds CD16a and a second targeting domain that binds Epidermal Growth Factor Receptor (EGFR) or egfrvlll. In some aspects, the bispecific NK cell cement comprises a first targeting domain that binds NKp46 and a second targeting domain that binds a tumor antigen (e.g., a tumor antigen listed in table 3).

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

Any suitable NK cell checkpoint receptor antagonist may be used. Illustrative non-limiting examples of NK cell checkpoint receptor antagonists include, for example, KIR antagonists (e.g., anti-KIR antibodies, such as Li Ruilu mab (IPH 2102) targeting KIR2DL1-3 and KIR2DS 1-2), CD94/NKG2A antagonists (e.g., anti-CD 94 antibodies or Protein Expression Blockers (PEBL) or anti-NKG 2A antibodies (e.g., mo Nali bead mab (IPH 2201) or PEBL)), CTLA-4 antagonists (e.g., anti-CTLA-4 antibodies), PD-1 axis binding antagonists, LAG3 antagonists (e.g., anti-LAG 3 antibodies), or TIM-3 antagonists (e.g., anti-TIM-3 antibodies).

Any suitable cytokine therapy may be used. For example, cytokine therapies may include type 1 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 may be used, such as any of the oncolytic viruses described in Hodgins et al, supra.

VII pharmaceutical composition and formulation

Also provided herein are pharmaceutical compositions and formulations comprising a PD-1 axis binding antagonist (e.g., alemtuzumab) and optionally a pharmaceutically acceptable carrier. The present disclosure also provides pharmaceutical compositions and formulations comprising a taxane (e.g., nab-paclitaxel or paclitaxel), a platinum-based chemotherapeutic agent (e.g., carboplatin), an anti-angiogenic agent (e.g., bevacizumab), and/or an NK cell-targeted therapeutic agent (e.g., NK cell cement), and optionally a pharmaceutically acceptable carrier.

The pharmaceutical compositions and formulations described herein may be prepared in the form of lyophilized formulations or aqueous solutions by mixing an active ingredient (e.g., a PD-1 axis binding antagonist) of the desired purity with one or more optional pharmaceutically acceptable carriers (see, e.g., remington's Pharmaceutical Sciences, 16 th edition, osol, a. Code (1980)).

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

Products or kits

In another aspect, provided herein are articles of manufacture or kits comprising a PD-1 axis binding antagonist (e.g., atuzumab) and/or a taxane (e.g., nab-paclitaxel or paclitaxel), a platinum-based chemotherapeutic agent (e.g., carboplatin), an anti-angiogenic agent (e.g., bevacizumab), and/or an NK cell-directed therapeutic agent (e.g., NK cell cement). In some cases, the article of manufacture or kit further comprises a package insert comprising instructions for using the PD-1 axis binding antagonist to treat or delay progression of cancer (e.g., NSCLC) in a patient. In some cases, the article of manufacture or kit further comprises a package insert comprising instructions for using a PD-1 axis binding antagonist in combination with a taxane (e.g., nab-paclitaxel or paclitaxel), a platinum-based chemotherapeutic agent (e.g., carboplatin), an anti-angiogenic agent (e.g., bevacizumab), and/or an NK cell-directed therapeutic agent (e.g., NK cell cement) to treat or delay progression of cancer in a patient. Any of the PD-1 axis binding antagonists and/or taxanes, platinum-based chemotherapeutic agents, anti-angiogenic agents, and/or NK cell-directed therapeutic agents described herein may be included in the article of manufacture or kit.

In another aspect, provided herein are articles of manufacture or kits comprising NK cell-targeted therapeutic agents (e.g., NK cell cement). In some cases, the article of manufacture or kit further comprises a package insert comprising instructions for using the NK cell-directed therapeutic agent to treat or delay progression of cancer (e.g., NSCLC) in a patient.

In some cases, the PD-1 axis binding antagonist and the additional therapeutic agent (e.g., a taxane (e.g., nab-paclitaxel or paclitaxel), a platinum-based chemotherapeutic agent (e.g., carboplatin), an anti-angiogenic agent (e.g., bevacizumab), and/or an NK cell-directed therapeutic agent (e.g., NK cell cement)) are in the same container or separate containers. Suitable containers include, for example, bottles, vials, bags, and syringes. The container may be formed from a variety of materials, for example glass, plastic (such as polyvinyl chloride or polyolefin) or metal alloys (such as 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 article of manufacture or kit may also include other materials desirable from a commercial and user standpoint, including other buffers, diluents, filters, needles, syringes, and package inserts with instructions for use. In some cases, the article of manufacture further comprises one or more other agents (e.g., additional chemotherapeutic agents and antineoplastic agents). Suitable containers for one or more reagents include, for example, bottles, vials, bags, and syringes.

Any article of manufacture or kit may include instructions for administering a PD-1 axis binding antagonist and/or taxane (e.g., nab-paclitaxel or paclitaxel), a platinum-based chemotherapeutic agent (e.g., carboplatin), an anti-angiogenic agent (e.g., bevacizumab), and/or an NK cell-directed therapeutic agent (e.g., NK cell cement) 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 example, provided herein is an article of manufacture for treating cancer (e.g., NSCLC) in a patient in need thereof, comprising a PD-1 axis binding antagonist and instructions for administering the PD-1 axis binding antagonist, the genome of the patient having been determined to comprise at least one copy of HLA-C1. In some cases, the patient's genome further comprises at least one copy of KIR2DL 3.

In another example, provided herein is an article of manufacture for treating cancer (e.g., NSCLC) in a patient in need thereof, comprising a PD-1 axis binding antagonist and instructions for administering the PD-1 axis binding antagonist, the genome of the patient having been determined to comprise at least one copy of HLA-C1 and at least one copy of KIR2DL 3.

In another example, provided herein is an article of manufacture for treating cancer (e.g., NSCLC) in a patient in need thereof, comprising a PD-1 axis binding antagonist and instructions for administering the PD-1 axis binding antagonist, the genome of the patient having been determined to comprise at least one copy of HLA-Bw 4. In some cases, the patient's genome further comprises at least one copy of KIR3DL 1.

In another example, provided herein is an article of manufacture for treating cancer (e.g., NSCLC) in a patient in need thereof, comprising a PD-1 axis binding antagonist and instructions for administering the PD-1 axis binding antagonist, the genome of the patient having been determined to comprise at least one copy of HLA-Bw4 and at least one copy of KIR3DL1.

In another example, provided herein is an article of manufacture for treating cancer (e.g., NSCLC) in a patient in need thereof, comprising a PD-1 axis binding antagonist and instructions for administering the PD-1 axis binding antagonist, the patient having been determined to have an increased NK cell infiltration level relative to a reference level of NK cell infiltration in a tumor sample obtained from the patient.

In another example, provided herein is an article of manufacture for treating cancer (e.g., NSCLC) in a patient in need thereof, comprising an NK cell-targeted therapeutic and instructions for administering the NK cell-targeted therapeutic, the genome of the patient having been determined to be deficient in KIR2DL3 or KIR3DL1.

Examples

EXAMPLE 1 immune genetic variation involved in NK cell education and NK cell infiltration is correlated with prognosis of non-small cell lung cancer patients treated with immune checkpoint blockade

a. Introduction to the invention

Natural Killer (NK) cells are an important contributor to the anti-tumor immune response. In addition to NK cell abundance in tumors, multiple tumor immune evasion strategies targeting NK cells, and differential distribution of NK cell subsets among different tissue types, the immune genetic composition of the patient genome is considered an important determinant of NK cell effectiveness.

In particular, genetic variation of Human Leukocyte Antigen (HLA) and killer cell immunoglobulin-like receptor (KIR) genes can affect NK cell education and function. NK cell education is a dynamic process that achieves functional maturation and self-tolerance, and better NK cell education leads to a stronger response to the "lost self" phenotype. Allele-specific interactions of inhibitory 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 to MHC deficient tumors (IFNy production) (Kim et al, PNAS,105 (8): 3053-3058, 2008). KIR2DL3 and KIR3DL1 occur predominantly on KIR a haplotypes, which are generally associated with improved responses to pathogens (Jamil and Khakoo, J Biomed Biotechnol,2011:Article ID 298348,2011).

b. Method of

Variation of HLA alleles and presence of KIR genes was deduced using germline whole genome sequencing data from 1,395 patients in three atrazumab (anti-PD-L1) clinical trials (IMpower 130, IMpower131, IMpower 150) from non-small cell lung cancer (NSCLC). IMpower130 (NCT 02367781) investigated the safety and efficacy of treatment regimens comprising alemtuzumab, nab-paclitaxel and carboplatin in metastatic non-squamous NSCLC compared to control treatment without alemtuzumab. IMpower131 (NCT 02367794) investigated the safety and efficacy of treatment regimens comprising alemtuzumab, paclitaxel and carboplatin or alemtuzumab, nab-paclitaxel and carboplatin in metastatic squamous NSCLC compared to control treatment without alemtuzumab. IMpower150 (NCT 02367794) investigated the safety and efficacy of treatment regimens comprising alemtuzumab, paclitaxel and carboplatin or alemtuzumab, bevacizumab, paclitaxel and carboplatin in metastatic non-squamous NSCLC compared to control treatment without alemtuzumab. The number of patients included in the germ line genetic analysis for atezo (atezo) and control are shown in table 4.

TABLE 4 patient population for germ line genetic analysis

Study of	Atezo group	Control group
			IMpower150	433	182
IMpower130	202	102
			IMpower131	320	156

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

The presence of the KIR gene was computationally inferred from germline whole genome sequencing data (30 x coverage) using software KPI (Roe et al front.immunol.,11:583013, 2020). The KIR gene is variable in terms of copy number, and an individual may carry the KIR gene on its 0, 1 or both chromosomes. The software method used identifies the presence or absence of a certain KIR gene (0 vs. 1/2) in an individual.

Correlation analysis is first performed at the research level. The Cox proportional hazards model was used to study the association of genotype or genetic score (high/low defined median cut) with overall or progression free survival.

The meta function in the meta-package of R is used for meta-analysis (e.g., fixed effect and random effect meta-analysis based on the estimates and their standard errors). The combination is performed using the inverse variance method.

As detailed in sections c-f below, the results indicate that both NK cell genotype and NK cell infiltration degree play an important role in patient response to immunotherapy against PD-L1 cancers.

c. HLA-KIR interactions in NSCLC are correlated with prognosis of treatment with alemtuzumab

The total survival (OS) and Progression Free Survival (PFS) of patients carrying KIR2DL3 and at least one copy of its ligand HLA-C1 were longer (n=955, hr=0.71, p=0.0002) with alemtuzumab compared to patients without such NK cell educational interactions (fig. 1A and 1B). No correlation was observed in the control group tested.

Also, patients treated with atractylizumab carried at least one copy of KIR3DL1 and its ligand HLA-Bw4 had longer OS and PFS (hr=0.84, p=0.04) compared to patients without this interaction (fig. 2A and 2B). No significant association was found in the experimental chemotherapy control group (n=440).

HLA-C1 carrier status and prognosis for treatment with alemtuzumab

Likewise, regardless of patient KIR genotype, HLA ligand sets defined according to KIR interactions (HLA-C1 carrier status and HLA-Bw4 carrier status) were also found to correlate with prognosis (PFS and OS) of patients treated with alemtuzumab (fig. 3A, 3B, 4A and 4B).

Furthermore, in the analysis of recently released melanoma and NSCLC patient datasets, HLA-C1 carrier status was found to be beneficial for prognosis of immune checkpoint blocking treatment (n=1.55, hr=0.74, p=0.01, data from choicell et al, science,359 (6375): 582-587, 2018) (fig. 5A and 5B).

NK cell infiltration and Abutilizumab treatment prognosis correlation

High (above median) NK cell infiltration was found to correlate with longer OS in patients treated with alemtuzumab (n=619, hr=0.75, p=0.01) using gene signatures derived from RNA sequencing data (NK cell score; cursons et al, cancer Immunology Research,7 (7): 1162-1174, 2019) (fig. 6A). The gene signature contains 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. Gene signatures are measured as described in Cursons et al Cancer Immunology Research,7 (7): 1162-1174, 2019. The correlation analysis was performed as described in example 1b above. Likewise, no significant association was found in the control group (n=288) (fig. 6B).

Notably, T cell and NK cell infiltration was relevant (fig. 7A and 7B).

The number of patients in the alemtuzumab and control groups included in the NK scoring RNAseq analysis is shown in table 5.

TABLE 5 patient population for RNAseq analysis

Study of	Atezo group	Control group
			IMpower150	360	151
IMpower131	259	137

Example 2 evaluation of the immunogenetic variation involved in NK cell education and NK cell infiltration and prognosis of renal cancer patients treated with immune checkpoint blocking

a. Method of

HLA allelic variation and presence of KIR genes were deduced using germline whole genome sequencing data from the atuzumab (anti-PD-L1) clinical trial immoti 151, as described in example 1. IMmotion151 (NCT 02420821) investigated the safety and efficacy of treatment regimens including alemtuzumab and bevacizumab in participants with inoperable, locally advanced, or metastatic Renal Cell Carcinoma (RCC) as compared to control treatments comprising sunitinib.

For NK cell characterization, data from immoti 150 is also included. IMmotion150 (NCT 01984242) investigated the safety and efficacy of treatment regimens including alemtuzumab and bevacizumab in participants with inoperable, locally advanced, or metastatic Renal Cell Carcinoma (RCC) as compared to control treatments comprising sunitinib.

Correlation between HLA-KIR interaction and Ab in RCC treatment prognosis

The risk of OS and PFS for patients carrying at least one copy of KIR2DL3 and its ligand HLA-C1 treated with alemtuzumab compared to patients without such NK cell educational interactions is shown in figures 8A and 8B.

The risk of OS and PFS for patients carrying at least one copy of KIR3DL1 and its ligand HLA-Bw4 treated with alemtuzumab compared to patients without such NK cell educational interactions is shown in figures 9A and 9B.

correlation between HLA-C1 or HLA-Bw4 Carrier status and Ab treatment prognosis in RCC

The risk of OS and PFS in patients carrying at least one copy of HLA-C1 treated with alemtuzumab is shown in figures 10A and 10B.

The risk of OS and PFS in patients treated with alemtuzumab carrying at least one copy of HLA-Bw4 is shown in figures 11A and 11B.

Correlation between NK cell infiltration and prognosis of treatment with alemtuzumab in RCC

Patients treated with alemtuzumab with high (above median) NK cell infiltration scores determined as described in example 1 have OS and PFS risks such as shown in fig. 12A and 12B.

Patients treated with alemtuzumab with high (above median) CD8A expression levels risk for OS and PFS such as shown in fig. 13A and 13B.

e. Conclusion(s)

A trend was observed for improved response of RCC patients treated with alemtuzumab in an IMmotion151 clinical trial with respect to HLA-KIR genotype and NK cell infiltration, as described for NSCLC in example 1. The effect estimates of RCC are within a range similar to that described in example 1 for the NSCLC test.

EXAMPLE 3 immune genetic variation involved in NK cell education and NK cell infiltration is related to prognosis of non-small cell lung cancer patients treated with immune checkpoint blockade

Immune mediated adverse events (imAE) typically occur in patients treated with Immune Checkpoint Inhibitors (ICI), and 3-5% of patients treated with anti-PD-1/PD-L1 antibodies are known to develop pneumonia (Wang et al, thorac Cancer,11:191-197,2020). Most cases are grade 1 or grade 2 events and can be treated by immunosuppression, but a few patients will experience high grade events and may be fatal (Naidoo et al, J Clin Oncol,35:709-717,2016). In nine Genentech (GNE) clinical trials with available whole genome sequencing data, 72 (4.1%) of the 1761 patients treated with alemtuzumab (anti-PD-L1) had developed pneumonia (table 6). The included trials were IMmotion151 (WO 29637), IMpass 130 (WO 29522), IMpower110 (GO 29431), IMpower130 (GO 29537), IMpower131 (GO 29437), IMpower132 (GO 29438), IMpower133 (GO 30081), IMpower150 (GO 29436) and IMvigor211 (GO 29294); 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 cancer.

TABLE 6 investigation queue

GNE, genentech; PICI, park cancer immunotherapy institute; PMC, the mcarbam cancer center.

HLA genotypes were deduced using HLA-HD (Kawaguchi et al, hum Mutat,38:788-797,2017), and association studies involving 87 alleles were performed, with carrier frequency>2%. Two HLA class II alleles that are part of a common haplotype show significant correlation with the risk of pneumonia after multiple test adjustments (HLA-DRB 1 x 15:01, HLA-DQA1 x 01:02), with HLA-DRB1 x 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 if the association is of general significance in different classes of ICI, the other two queues were genotyped using Illumina whole genome SNP array (GSA v 3) followed by HLA interpolation using HIBAG (Zheng et al, pharmacogenetics: 14:192-200,2014): the cohorts were (1) 20 ICI treated cancer patients with pneumonia and 20 matched controls without pneumonia from the AEROSMITH trial of park cancer immunotherapy institute (PICI), and (2) 15 ICI treated melanoma patients with pneumonia and 149 patients without pneumonia from the mackerel cancer center (PMC) (table 6). In the PICI pilot cohort, while the Odds Ratio (OR) was comparable (p=0.26, or=2.75), HLA-DRB1 x 15:01 did not reach statistical significance, the genes were significantly correlated with the risk of pneumonia in the PMC cohort (p=0.03, or=3.92). For three pairs Meta-analysis of the queue yields 1.2x10 ^-5 The highly significant p-value of (or=2.67, fig. 14) indicates that this association has a general meaning in ICI. Importantly, the same class II haplotypes have previously been shown to be associated with different inflammatory phenotypes of the lung, 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).

Taken together, these findings confirm that HLA class II allelic variation is a potential risk factor for ICI-associated pneumonia.

Example 4 HLA class II heterozygosity Loss (LOH) correlates with poor prognosis for treatment with alemtuzumab

The analysis provided in this example shows that HLA class II loss, but not HLA class I loss, is associated with a poor prognosis for the treatment of alemtuzumab.

The loss or reduction of HLA expression may be due to genetic or epigenetic modifications or indirect regulation, and may be the result of the tumor escaping the evolutionary trajectory of the anti-tumor immune response. The antigen-specific signal provided by the binding of TCR to antigen peptide complexed with MHC is also referred to as "signal 1". Most therapeutic approaches in cancer immunology rely on functional antigen presentation, so that loss or down-regulation of HLA expression may be an effective immune evasion strategy for tumors. In principle, HLA loss or down-regulation should be counteracted by NK cells, which may be affected by the differential distribution of NK cell subsets among different tissue types, NK cell abundance in tumors, tumor immune evasion strategies that regulate NK cell availability, and the immune genomic composition of the patient's tumor.

HLA class I and class II LOHs are computationally inferred from tumor Whole Exome Sequencing (WES) data from clinical trials where atrazumab was administered to patients. The included trials were IMpower131 (GO 29437), IMpower133 (GO 30081), IMpower150 (GO 29436), popar (NCT 01903993) and IMmotion150 (NCT 01984242); these studies included patients with NSCLC, SCLC or mRCC.

HLA class I LOH is prognostic independent. LOH patients treated with alemtuzumab did not exhibit worse Overall Survival (OS) than patients without LOH (fig. 15). Patients who lost the complete class I haplotype achieved similar results. A summary of indications, clinical trials, patient numbers and LOH patient percentages is shown in table 7. No significant correlation was observed in the control group tested.

TABLE 7 percentage of LOH in clinical trials

Indication of disease	Test name	N	% LOH (any), all groups
				NSCLC	IMpower131	344	24％
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 effect of LOH class I on prognosis (fig. 16). No difference in the effect of LOH on lung cancer was observed in the low TMB and high TMB environments. LOH is not more frequent in the middle TMB. However, class I LOH is associated with lower CD8A expression (fig. 17). Without wishing to be bound by theory, these data may suggest that these observations reflect selective processes that lead to reduced cd8+ T cell infiltration.

Unexpectedly, HLA class II loss is prognostic-related. In particular, in meta-analysis, LOH calls of HLA class II genes were shown to be associated with shorter OS (fig. 18). Without wishing to be bound by theory, this is likely consistent with the discovery that tumor cells expressing both HLA class I and class II neoantigens are required for optimal anti-tumor response.

Other embodiments

Although the present invention has been described in considerable detail by way of illustration and example for the purpose of clarity of understanding, such illustration and example should not be construed as limiting the scope of the invention.

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<212> PRT

<213> artificial sequence

<220>

<223> synthetic construct

<400> 5

Arg His Trp Pro Gly Gly Phe Asp Tyr

1 5

<210> 6

<211> 11

<212> PRT

<213> artificial sequence

<220>

<223> synthetic construct

<400> 6

Arg Ala Ser Gln Asp Val Ser Thr Ala Val Ala

1 5 10

<210> 7

<211> 7

<212> PRT

<213> artificial sequence

<220>

<223> synthetic construct

<400> 7

Ser Ala Ser Phe Leu Tyr Ser

1 5

<210> 8

<211> 9

<212> PRT

<213> artificial sequence

<220>

<223> synthetic construct

<400> 8

Gln Gln Tyr Leu Tyr His Pro Ala Thr

1 5

<210> 9

<211> 118

<212> PRT

<213> artificial sequence

<220>

<223> synthetic construct

<400> 9

Glu Val Gln Leu Val Glu Ser Gly Gly Gly Leu Val Gln Pro Gly Gly

1 5 10 15

Ser Leu Arg Leu Ser Cys Ala Ala Ser Gly Phe Thr Phe Ser Asp Ser

20 25 30

Trp Ile His Trp Val Arg Gln Ala Pro Gly Lys Gly Leu Glu Trp Val

35 40 45

Ala Trp Ile Ser Pro Tyr Gly Gly Ser Thr Tyr Tyr Ala Asp Ser Val

50 55 60

Lys Gly Arg Phe Thr Ile Ser Ala Asp Thr Ser Lys Asn Thr Ala Tyr

65 70 75 80

Leu Gln Met Asn Ser Leu Arg Ala Glu Asp Thr Ala Val Tyr Tyr Cys

85 90 95

Ala Arg Arg His Trp Pro Gly Gly Phe Asp Tyr Trp Gly Gln Gly Thr

100 105 110

Leu Val Thr Val Ser Ser

115

<210> 10

<211> 108

<212> PRT

<213> artificial sequence

<220>

<223> synthetic construct

<400> 10

Asp Ile Gln Met Thr Gln Ser Pro Ser Ser Leu Ser Ala Ser Val Gly

1 5 10 15

Asp Arg Val Thr Ile Thr Cys Arg Ala Ser Gln Asp Val Ser Thr Ala

20 25 30

Val Ala Trp Tyr Gln Gln Lys Pro Gly Lys Ala Pro Lys Leu Leu Ile

35 40 45

Tyr Ser Ala Ser Phe Leu Tyr Ser Gly Val Pro Ser Arg Phe Ser Gly

50 55 60

Ser Gly Ser Gly Thr Asp Phe Thr Leu Thr Ile Ser Ser Leu Gln Pro

65 70 75 80

Glu Asp Phe Ala Thr Tyr Tyr Cys Gln Gln Tyr Leu Tyr His Pro Ala

85 90 95

Thr Phe Gly Gln Gly Thr Lys Val Glu Ile Lys Arg

100 105

Claims

1. A method of treating non-small cell lung cancer (NSCLC) in a patient in need thereof, the genome of the patient having been determined to comprise 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 KIR2DL 3.

3. A method of treating NSCLC in a patient in need thereof whose genome has been determined to comprise at least one copy of HLA-C1 and at least one copy of KIR2DL3, comprising administering to the patient an effective amount of a treatment regimen comprising a PD-1 axis binding antagonist.

4. A method of treating NSCLC in a patient in need thereof whose genome has been determined to comprise at least one copy of HLA-Bw4, 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 KIR3DL 1.

6. A method of treating NSCLC in a patient in need thereof whose genome has been determined to comprise at least one copy of HLA-Bw4 and at least one copy of KIR3DL1, comprising administering to the patient an effective amount of a treatment regimen comprising a PD-1 axis binding antagonist.

7. A method of treating NSCLC in a patient in need thereof, the method comprising:

(a) Determining whether the patient's genome comprises 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 is likely to benefit from a treatment regimen comprising a PD-1 axis binding antagonist; and

(b) An effective amount of a treatment regimen comprising a PD-1 axis binding antagonist is administered to the patient based on the presence of at least one copy of HLA-C1 in the genome of the patient.

8. The method of claim 7, wherein step (a) further comprises determining whether the patient's genome comprises at least one copy of KIR2DL 3.

9. A method of treating NSCLC in a patient in need thereof, the method comprising:

(a) Determining whether the patient's genome comprises 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 is indicative that the patient is likely to benefit from a treatment regimen comprising a PD-1 axis binding antagonist; and

(b) An effective amount of a treatment regimen comprising a PD-1 axis binding antagonist is administered 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.

10. A method of treating NSCLC in a patient in need thereof, the method comprising:

(a) Determining whether the patient's genome comprises 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 is likely to benefit from a treatment regimen comprising a PD-1 axis binding antagonist; and

(b) An effective amount of a treatment regimen comprising a PD-1 axis binding antagonist is administered to the patient based on the presence of at least one copy of HLA-Bw4 in the genome of the patient.

11. The method of claim 10, wherein step (a) further comprises determining whether the patient's genome comprises at least one copy of KIR3DL 1.

12. A method of treating NSCLC in a patient in need thereof, the method comprising:

(a) Determining whether the patient's genome comprises 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 is likely to benefit from a treatment regimen comprising a PD-1 axis binding antagonist; and

(b) An effective amount of a treatment regimen comprising a PD-1 axis binding antagonist is administered 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.

13. A method of identifying a patient having NSCLC who may benefit from a treatment regimen comprising a PD-1 axis binding antagonist, the method comprising determining whether the patient's genome comprises 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 comprising a PD-1 axis binding antagonist.

14. A method of identifying a patient having NSCLC who may benefit from a treatment regimen comprising a PD-1 axis binding antagonist, 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 adaptors 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 comprising a PD-1 axis binding antagonist by determining whether the patient's genome comprises 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 comprising a PD-1 axis binding antagonist.

15. The method of claim 13 or 14, further comprising determining whether the patient's genome comprises at least one copy of KIR2DL 3.

16. A method of identifying a patient having NSCLC who may benefit from a treatment regimen comprising a PD-1 axis binding antagonist, the method comprising determining whether the genome of the patient comprises 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 genome of the patient identifies the patient as a patient who may benefit from treatment using a treatment regimen comprising a PD-1 axis binding antagonist.

17. A method of identifying a patient having NSCLC who may benefit from a treatment regimen comprising a PD-1 axis binding antagonist, the method comprising:

(a) Germline WGS or WES is performed by fragmenting a DNA sample obtained from the patient to produce fragmented DNA, adding adaptors 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 comprising a PD-1 axis binding antagonist by determining whether the patient's genome comprises 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 comprising a PD-1 axis binding antagonist.

18. A method of identifying a patient having NSCLC who may benefit from a treatment regimen comprising a PD-1 axis binding antagonist, the method comprising determining whether the patient's genome comprises 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 comprising a PD-1 axis binding antagonist.

19. A method of identifying a patient having NSCLC who may benefit from a treatment regimen comprising a PD-1 axis binding antagonist, the method comprising:

(b) Identifying the patient as a patient who may benefit from a treatment regimen comprising a PD-1 axis binding antagonist by determining whether the patient's genome comprises 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 comprising a PD-1 axis binding antagonist.

20. The method of claim 18 or 19, further comprising determining whether the patient's genome comprises at least one copy of KIR3DL 1.

21. A method of identifying a patient having NSCLC who may benefit from a treatment regimen comprising a PD-1 axis binding antagonist, the method comprising determining whether the genome of the patient comprises 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 genome of the patient identifies the patient as a patient who may benefit from treatment with a treatment regimen comprising a PD-1 axis binding antagonist.

22. A method of identifying a patient having NSCLC who may benefit from a treatment regimen comprising a PD-1 axis binding antagonist, the method comprising:

(b) Identifying the patient as a patient who may benefit from a treatment regimen comprising a PD-1 axis binding antagonist by determining whether the patient's genome comprises 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 comprising a PD-1 axis binding antagonist.

23. A method of selecting a therapy for a patient having NSCLC, the method comprising:

(b) A treatment regimen comprising a PD-1 axis binding antagonist is selected based on the presence of at least one copy of HLA-C1 in the genome of the patient.

24. The method of claim 23, further comprising determining whether the patient's genome comprises at least one copy of KIR2DL 3.

25. A method of selecting a therapy for a patient having NSCLC, the method comprising:

(b) A treatment regimen comprising a PD-1 axis binding antagonist is selected based on the presence of at least one copy of HLA-C1 and at least one copy of KIR2DL3 in the genome of the patient.

26. A method of selecting a therapy for a patient having NSCLC, the method comprising:

(b) A treatment regimen comprising a PD-1 axis binding antagonist is selected based on the presence of at least one copy of HLA-Bw4 in the genome of the patient.

27. The method of claim 26, further comprising determining whether the patient's genome comprises at least one copy of KIR3DL 1.

28. A method of selecting a therapy for a patient having NSCLC, the method comprising:

(b) A treatment regimen comprising a PD-1 axis binding antagonist is selected based on the presence of at least one copy of HLA-Bw4 and at least one copy of KIR3DL1 in the genome of the patient.

29. The method of any one of claims 13-28, further comprising administering to the patient an effective amount of a treatment regimen comprising a PD-1 axis binding antagonist.

30. The method of any one of claims 1 to 29, wherein the presence of HLA-C1, HLA-Bw4, KIR2DL3 and/or KIR3DL1 in the patient's genome is determined using next generation sequencing, sanger sequencing, polymerase Chain Reaction (PCR) based assays, or Single Nucleotide Polymorphism (SNP) arrays.

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 of treating NSCLC in a patient in need thereof, the patient having been determined to have an increased level of Natural Killer (NK) cell infiltration relative to a reference level of 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.

34. A method of treating NSCLC in a patient in need thereof, the method comprising:

(a) Determining whether a tumor sample obtained from the patient has an increased NK cell infiltration level relative to a reference level of NK cell infiltration, wherein an increased NK cell infiltration level in the tumor sample obtained from the patient relative to the reference level of NK cell infiltration is indicative that the patient is likely to benefit from a treatment regimen comprising a PD-1 axis binding antagonist; and

(b) Based on the increased NK cell infiltration level relative to a reference level of NK cell infiltration in the tumor sample obtained from the patient, an effective amount of a treatment regimen comprising a PD-1 axis binding antagonist is administered to the patient.

35. A method of identifying a patient having NSCLC who may benefit from a treatment regimen comprising a PD-1 axis binding antagonist, the method comprising determining whether a tumor sample obtained from the patient has an increased NK cell infiltration level relative to a reference level of NK cell infiltration, wherein an increased NK cell infiltration level in the tumor sample obtained from the patient relative to the reference level of NK cell infiltration indicates that the patient is likely to benefit from a treatment regimen comprising a PD-1 axis binding antagonist.

36. A method of identifying a patient having NSCLC who may benefit from a treatment regimen comprising a PD-1 axis binding antagonist, the method comprising:

(a) Contacting a tumor sample obtained from the patient with one or more antibodies or nucleotide probes that bind to one or more NK cell markers to determine NK cell infiltration levels in the tumor sample; and

(b) Determining whether a tumor sample obtained from the patient has an increased NK cell infiltration level relative to a reference level of NK cell infiltration, wherein an increased NK cell infiltration level in the tumor sample obtained from the patient relative to the reference level of NK cell infiltration is indicative that the patient is likely to benefit from a treatment regimen comprising a PD-1 axis binding antagonist.

37. A method of selecting a therapy for a patient having NSCLC, the method comprising:

(b) A treatment regimen comprising a PD-1 axis binding antagonist is selected based on the increased NK cell infiltration level relative to a reference level of NK cell infiltration in the tumor sample obtained from the patient.

38. The method of 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 of any one of claims 33 to 38, wherein NK cell infiltration level is determined by determining the expression level of NK cell gene signature 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, KRRF 1, KLRK1, NCR1, NKG7, PRF1, XCL1 and XCL2.

41. The method of claim 40, wherein the NK cell gene characteristics 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 of any one of claims 33 to 41, wherein the reference level of NK cell infiltration is a median level.

43. The method of claim 42, wherein the median level is a median level in a population of NSCLC patients.

44. The method of any one of claims 7 to 32 and 34 to 43, wherein the benefit is in terms of improved Overall 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 of any one of claims 44-46, wherein improvement is relative to treatment with a treatment regimen that does not include the PD-1 axis binding antagonist.

48. The method of any one of claims 1 to 47, wherein the NSCLC is non-squamous NSCLC or squamous NSCLC.

49. The method of claim 48, wherein the NSCLC is 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 squamous NSCLC.

52. The method of claim 51, wherein the squamous NSCLC is metastatic squamous NSCLC.

53. The method of any one of claims 1 to 52, wherein the patient is a primary chemotherapy.

54. The method of any one of claims 1 to 53, wherein the treatment regimen is a first line treatment regimen.

55. The method of any one of claims 1-54, wherein the PD-1 axis binding antagonist is selected from the group consisting of a PD-L1 binding antagonist, a PD-1 binding antagonist, and a PD-L2 binding antagonist.

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 comprising the amino acid sequence:

EVQLVESGGGLVQPGGSLRLSCAASGFTFSDSWIHWVRQAPGKGLEWVAWISPYGGSTYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARRHWPGGFDYWGQGTLVTVSS (SEQ ID NO: 9), and

(b) VL comprising an amino acid sequence:

60. the method of claim 57, wherein the anti-PD-L1 antibody is alemtuzumab, devaluzumab, avilamab, or MDX-1105.

61. The method of any one of claims 57-60, wherein the anti-PD-L1 antibody is alemtuzumab.

62. The method of any one of claims 57-61, wherein the anti-PD-L1 antibody is administered intravenously or subcutaneously.

63. The method of claim 61, wherein the alemtuzumab is administered intravenously at a dose of 840mg every two weeks.

64. The method of claim 61, wherein the alemtuzumab is administered intravenously at a dose of 1200mg every three weeks.

65. The method of claim 61, wherein the alemtuzumab is administered intravenously every four weeks at a dose of 1680 mg.

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, MEDI 0680, swabber, cimiput Li Shan, carlizumab, singal Li Shan, tirelimumab, terlipressin Li Shan, or multi-tarlizumab.

69. The method of any one of claims 1-68, wherein the treatment regimen further comprises a taxane.

70. The method of claim 69, wherein the taxane is nab-paclitaxel or paclitaxel.

71. The method of claim 70, wherein the taxane is nab-paclitaxel.

72. The method of claim 70, wherein the taxane is paclitaxel.

73. The method of any one of claims 1-72, 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 of any one of claims 1-74, 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 of any one of claims 1-50 and 53-77, wherein the NSCLC is metastatic non-squamous NSCLC and the treatment regimen comprises alemtuzumab, nab-paclitaxel, and carboplatin.

79. The method of claim 78, wherein the alemtuzumab is administered on day 1 of each 21-day cycle with a dose of 1200mg for Intravenous (IV) infusion; nab-paclitaxel at 100mg/m on days 1, 8 and 15 of each 21-day cycle ² Is administered as IV infusion; and carboplatin was administered at 6mg/mL/min concentration curve area under Area (AUC) on day 1 of each 21 day cycle.

80. The method of any one of claims 1-50 and 53-77, wherein the NSCLC is metastatic non-squamous NSCLC and the treatment regimen comprises alemtuzumab, paclitaxel, and carboplatin.

81. The method of claim 80, wherein the alemtuzumab is administered at a dose of 1200mg for IV infusion on day 1 of each 21-day cycle; paclitaxel at 21 weeks eachDay 1 of the period at 200mg/m ² Is administered as IV infusion; and carboplatin was administered at AUC of 6mg/mL/min on day 1 of each 21-day cycle.

82. The method of any one of claims 1-50 and 53-77, wherein the NSCLC is metastatic non-squamous NSCLC and the treatment regimen comprises alemtuzumab, bevacizumab, paclitaxel, and carboplatin.

83. The method of claim 82, wherein the alemtuzumab is administered at a dose of 1200mg for IV infusion on day 1 of each 21-day cycle; bevacizumab was administered as IV infusion at a dose of 15mg/kg on day 1 of each 21-day cycle; paclitaxel at 200mg/m on day 1 of each 21-day cycle ² Is administered as IV infusion; and carboplatin was administered at AUC of 6mg/mL/min on day 1 of each 21-day cycle.

84. The method of any one of claims 1-48 and 51-77, wherein the NSCLC is metastatic squamous NSCLC and the treatment regimen comprises alemtuzumab, nab-paclitaxel, and carboplatin.

85. The method of claim 84, wherein the alemtuzumab is administered at a dose of 1200mg for IV infusion on day 1 of each 21-day cycle; nab-paclitaxel at 100mg/m on days 1, 8 and 15 of each 21-day cycle ² Is administered as IV infusion; and carboplatin was administered at 6mg/mL/min concentration curve area under Area (AUC) on day 1 of each 21 day cycle.

86. The method of any one of claims 1-48 and 51-77, wherein the NSCLC is metastatic squamous NSCLC and the treatment regimen comprises alemtuzumab, paclitaxel, and carboplatin.

87. The method of claim 86, wherein the alemtuzumab is administered at a dose of 1200mg for IV infusion on day 1 of each 21-day cycle; paclitaxel inAt 175mg/m on days 1, 8 and 15 of each 21-day cycle ² Or 200mg/m ² Is administered as IV infusion; and carboplatin was administered at AUC of 6mg/mL/min on day 1 of each 21-day cycle.

88. The method of any one of claims 1-87, 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 inhibitory agents, radiotherapeutic agents, anti-angiogenic agents, and combinations thereof.

90. A PD-1 axis binding antagonist for use in the treatment of NSCLC in a patient in need thereof, the genome of said patient having been determined to comprise at least one copy of HLA-C1.

91. The PD-1 axis binding antagonist for use of claim 90, wherein the patient's genome further comprises at least one copy of KIR2DL 3.

92. A PD-1 axis binding antagonist for use in the treatment of NSCLC in a patient in need thereof, the genome of said patient having been determined to comprise at least one copy of HLA-C1 and at least one copy of KIR2DL 3.

93. A PD-1 axis binding antagonist for use in the treatment of NSCLC in a patient in need thereof, the genome of said patient having been determined to comprise at least one copy of HLA-Bw 4.

94. The PD-1 axis binding antagonist for use of claim 93, wherein the patient's genome further comprises at least one copy of KIR3DL 1.

95. A PD-1 axis binding antagonist for use in the treatment of NSCLC in a patient in need thereof, the genome of said patient having been determined to comprise at least one copy of HLA-Bw4 and at least one copy of KIR3DL 1.

96. A PD-1 axis binding antagonist for use in a method of treating NSCLC in a patient in need thereof, the method comprising:

97. The PD-1 axis binding antagonist for use of claim 96, wherein step (a) further comprises determining whether the patient's genome comprises at least one copy of KIR2DL 3.

98. A PD-1 axis binding antagonist for use in the treatment of NSCLC in a patient in need thereof, the method comprising:

99. A PD-1 axis binding antagonist for use in the treatment of NSCLC in a patient in need thereof, the method comprising:

100. The PD-1 axis binding antagonist for use of claim 99, wherein step (a) further comprises determining whether the patient's genome comprises at least one copy of KIR3DL 1.

101. A PD-1 axis binding antagonist for use in the treatment of NSCLC in a patient in need thereof, the method comprising:

102. A PD-1 axis binding antagonist for use in the treatment of NSCLC in a patient in need thereof, said patient having been determined to have an increased NK cell infiltration level relative to a reference level of NK cell infiltration in a tumor sample obtained from said patient.

103. A PD-1 axis binding antagonist for use in a method of treating NSCLC in a patient in need thereof, the method comprising:

104. An NK cell-directed therapeutic for use in the treatment of NSCLC in a patient in need thereof whose genome has been determined to be deficient in KIR2DL3 or KIR3DL1.

105. An NK cell-directed therapeutic agent for use in a method of treating NSCLC in a patient in need thereof, the method comprising:

(a) Determining whether the genome of the patient lacks KIR2DL3 or KIR3DL1, wherein the absence of KIR2DL3 or KIR3DL1 in the genome of the patient indicates that the patient is likely to benefit from a treatment regimen comprising an NK cell-directed therapeutic agent; and

(b) Based on the absence of KIR2DL3 or KIR3DL1 in the patient's genome, an effective amount of a treatment regimen comprising an NK cell-directed therapeutic agent is administered to the patient.

106. An article of manufacture for treating NSCLC in a patient in need thereof, comprising a PD-1 axis binding antagonist and instructions for administering the PD-1 axis binding antagonist, the genome of the patient having been determined to comprise at least one copy of HLA-C1.

107. The article of manufacture of claim 106, wherein the patient's genome further comprises at least one copy of KIR2DL 3.

108. An article of manufacture for treating NSCLC in a patient in need thereof, comprising a PD-1 axis binding antagonist and instructions for administering the PD-1 axis binding antagonist, the genome of the patient having been determined to comprise at least one copy of HLA-C1 and at least one copy of KIR2DL 3.

109. An article of manufacture for treating NSCLC in a patient in need thereof, comprising a PD-1 axis binding antagonist and instructions for administering the PD-1 axis binding antagonist, the genome of the patient having been determined to comprise at least one copy of HLA-Bw 4.

110. The article of manufacture of claim 109, wherein the patient's genome further comprises at least one copy of KIR3DL 1.

111. An article of manufacture for treating NSCLC in a patient in need thereof, comprising a PD-1 axis binding antagonist and instructions for administering the PD-1 axis binding antagonist, the genome of the patient having been determined to comprise 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 in need thereof, comprising a PD-1 axis binding antagonist and instructions for administering the PD-1 axis binding antagonist, the patient having been determined to have an increased level of Natural Killer (NK) cell infiltration relative to a reference level of NK cell infiltration in a tumor sample obtained from the patient.

113. An article of manufacture for treating NSCLC in a patient in need thereof, comprising an NK cell-targeted therapeutic and instructions for administering the NK cell-targeted therapeutic, the genome of the patient having been determined to be deficient in KIR2DL3 or KIR3DL1.