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WO2024197065A2 - Édition in vivo à base de nickase du gène lpa pour le traitement d'une maladie cardiovasculaire - Google Patents

Édition in vivo à base de nickase du gène lpa pour le traitement d'une maladie cardiovasculaire Download PDF

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Publication number
WO2024197065A2
WO2024197065A2 PCT/US2024/020769 US2024020769W WO2024197065A2 WO 2024197065 A2 WO2024197065 A2 WO 2024197065A2 US 2024020769 W US2024020769 W US 2024020769W WO 2024197065 A2 WO2024197065 A2 WO 2024197065A2
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Prior art keywords
sequence
spacer
nucleotides
guide
gene
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PCT/US2024/020769
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WO2024197065A3 (fr
Inventor
Peter Thomas HALLOCK
Liam Cornell
Sara Cristina De Almeida Pinto Garcia
Srinidhi Sridhar
Caroline REISS
Kui Wang
Christopher J. Cheng
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Verve Therapeutics, Inc.
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Publication of WO2024197065A2 publication Critical patent/WO2024197065A2/fr
Publication of WO2024197065A3 publication Critical patent/WO2024197065A3/fr

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/113—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
    • A61K31/7088—Compounds having three or more nucleosides or nucleotides
    • A61K31/7105—Natural ribonucleic acids, i.e. containing only riboses attached to adenine, guanine, cytosine or uracil and having 3'-5' phosphodiester links
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/10—Type of nucleic acid
    • C12N2310/20—Type of nucleic acid involving clustered regularly interspaced short palindromic repeats [CRISPRs]

Definitions

  • Lipoprotein(a) [Lp(a)] is a low-density lipoprotein (LDL) particle comprising apolipoprotein(a) [apo(a)] covalently linked to apolipoprotein B-100 (apoB-100), which is the primary protein component of LDL particles.
  • the apo(a) protein is encoded by the LPA gene, which is specifically expressed in hepatocytes in the liver of humans and certain non-human primates and secreted into the bloodstream where it is a constituent component of Lp(a).
  • LDL cholesterol (the quantified aggregate cholesterol content of LDL particles circulating in the bloodstream) is a well-established casual risk factor for atherosclerotic cardiovascular disease (ASCVD), which remains a leading cause of death worldwide notwithstanding the existence of approved chronic care drugs, including statins, ezetimibe, and proprotein convertase subtilisin/kexin type 9 (PCSK9) inhibitors.
  • ASCVD atherosclerotic cardiovascular disease
  • PCSK9 proprotein convertase subtilisin/kexin type 9
  • Lp(a) has been established to be a causal risk factor for calcific aortic valve disease, a distinct type of cardiovascular disease characterized by the stiffening or thickening of the aortic valves.
  • gRNA guide oligonucleotides
  • the disclosed gene editing technology is capable of in vitro and in vivo editing of the LPA gene, including specifically LPA genes found in human hepatocytes of the liver.
  • Various embodiments are disclosed that are directed to inactivating the LPA gene via the introduction of loss-of-function LPA variants that disrupt the production of apo(a) and/or Lp(a) protein thereby reducing the blood apo(a) and Lp(a) concentration to the substantial benefit of patients, such as those with existing cardiovascular disease or at risk of developing cardiovascular disease.
  • the gene editing and delivery systems, their respective components and elements, and the manufacture and/or use of those systems and components, described herein, alone and/or in any combination constitute individual aspects of the inventive subject matter disclosed herein.
  • compositions and methods disclosed herein to disrupt the production of apo(a) and/or Lp(a) protein and/or prevent and/or treat cardiovascular disease constitutes separate aspects of the inventive subject matter disclosed herein.
  • the location, nature and/or degree of the disruption of the LPA gene and/or commensurate disruption of the production of apo(a) and Lp(a) further constitute aspects of the inventive subject matter disclosed herein.
  • the invention provides pharmaceutical composition for in vivo editing of an LPA gene in a mammalian subject comprising an engineered, non-naturally occurring gene editing system and a delivery system.
  • the gene editing system includes one or more polynucleotides (e.g., mRNAs) encoding one or more CRISPR Cas nickases, a first guide oligonucleotide (e.g., gRNA), and a second guide oligonucleotide (e.g., gRNA).
  • the first guide oligonucleotide comprises a first spacer sequence and a first scaffold region.
  • the first spacer sequence is complementary to a first strand of the LPA gene at a first target sequence.
  • the first scaffold region serves as a binding scaffold for at least one of the one or more Cas nickases.
  • the second guide oligonucleotide comprises a second spacer sequence and a second scaffold region.
  • the second spacer sequence is complementary to a second strand of the LPA gene at a second target sequence.
  • the second scaffold region serves as a binding scaffold for at least one of the one or more Cas nickases.
  • the delivery system is engineered to deliver the one or more polynucleotides encoding one or more CRISPR Cas nickases, the first guide oligonucleotide, and/or the second guide oligonucleotide individually and/or collectively to the liver.
  • the first guide oligonucleotide and the at least one of the one or more Cas nickases are engineered to cause the at least one of the one or more Cas nickases to nick one of the first or second strands of the LPA gene at a first location of human chromosome 6 from position 160,664,275 to 160,531,482.
  • the second guide oligonucleotide and the at least one of the one or more Cas nickases are engineered to cause the at least one of the Cas nickases to nick the other of the first or second strands of the LPA gene at a second location of chromosome 6 from position 160,664,275 to 160,531,482.
  • expression of the edited LPA gene results in lowered production or lack of production of apo(a) protein in cells in which the LPA gene is edited. In some embodiments, expression of the edited LPA gene results in lowered production or lack of production of apo(a) protein in hepatocytes. In some embodiments, the hepatocytes are primary hepatocytes. [7] In some embodiments, expression of the edited LPA gene results in lowered amounts of LPA RNA, such as mRNA or pre-mRNA, in a cell in which the LPA gene is edited. Without intending to be bound by theory, it is believed that transcription of the edited LPA gene may, in some embodiments, result in nonsense-mediated decay of the LPA RNA.
  • expression of the edited LPA gene results in a lowering or a lack of production of apo(a) protein or the production of non-functional apo(a) protein, resulting in a reduced blood Lp(a) concentration.
  • the blood Lp(a) concentration is reduced to an extent to treat ASCVD and/or calcific aortic valve disease.
  • Lp(a) concentration in plasma is reduced.
  • blood concentration in serum is reduced.
  • Embodiments of the invention are directed to pharmaceutical compositions comprising one or more components (e.g., mRNA, gRNAs) of the LPA gene editing system, including pharmaceutical compositions thereof that allow for in vivo delivery.
  • the delivery system for the LPA gene editing system comprises lipid nanoparticles (LNPs) comprising: (a) one or more ionizable lipids, (b) cholesterol, (c) one or more PEG-lipids, (d) a phospholipid; and optionally including a targeting moiety, such as a GalNAc lipid.
  • LNPs lipid nanoparticles
  • the Cas nickase is a Cas9 nickase.
  • the Cas9 nickase when in operative interaction with the first or second guide oligonucleotide (e.g., gRNA), is engineered to nick the opposite strand of the LPA gene to which the operative guide is hybridized.
  • the Cas9 nickase when in operative interaction with the first or second guide oligonucleotide, is engineered to nick the same strand of the LPA gene to which the operative guide oligonucleotide (e.g., gRNA) is hybridized.
  • the Cas nickase comprises a Streptococcus pyogenes Cas9 nickase bearing a D10A mutation encoded within the polynucleotide (e.g., mRNA).
  • the first guide oligonucleotide e.g., gRNA
  • the second guide oligonucleotide has a second spacer sequence that is substantially identical to a second protospacer sequence adjacent to a second protospacer-adjacent motif (PAM) sequence on the other strand of the LPA gene
  • the Cas9 nickase bearing a D10A mutation in operation with the first and second guide oligonucleotides, makes two nicks on opposing strands (e.g., antisense and sense strands) of the LPA gene between the first and second protospacer- adjacent motifs (PAMs) in a “PAM-out” configuration (see, e.g., Figure 1A
  • the first guide oligonucleotide e.g., gRNA
  • the second guide oligonucleotide has a second spacer sequence that is substantially identical to a second protospacer sequence adjacent to a second protospacer-adjacent motif (PAM) sequence on the other strand of the LPA gene
  • the Cas9 nickase bearing a D10A mutation in operation with the first and second guide oligonucleotides, makes two nicks on opposing strands (e.g., antisense and sense strands) of the LPA gene outside the first and second protospacer- adjacent motifs (PAMs) in a “PAM-in” configuration (see, e.g., Figure 1C
  • the Cas nickase comprises Streptococcus pyogenes Cas9 nickase bearing a H840A mutation encoded within the polynucleotide (e.g., mRNA).
  • the first guide oligonucleotide e.g., gRNA
  • the second guide oligonucleotide has a second spacer sequence that is substantially identical to a second protospacer sequence adjacent to a second protospacer-adjacent motif (PAM) sequence on the other strand of the LPA gene
  • the Cas9 nickase bearing a H840A mutation in operation with the first and second guide oligonucleotides, makes two nicks on the first and second protospacer sequences on opposing strands (e.g., antisense and sense strands) of the LPA gene between the first and second protospacer-adjacent motifs (PAMs) in a “PAM-out”
  • the first guide oligonucleotide e.g., gRNA
  • the second guide oligonucleotide has a second spacer sequence that is substantially identical to a second protospacer sequence adjacent to a second protospacer-adjacent motif (PAM) sequence on the other strand of the LPA gene
  • the Cas9 nickase bearing a H840A mutation in operation with the first and second guide oligonucleotides, makes two nicks on the first and second protospacer sequences on opposing strands (e.g., sense and antisense strands) of the LPA gene outside the first and second protospacer-adjacent motifs (PAMs) in a “PAM-in”
  • the Cas9 nickase in operation with the first and second guide nucleotides nicks the DNA to generate nicks on opposing strands resulting in 5’ overhangs (e.g., as shown in Figures 1A and 1D).
  • the Cas9 nickase in operation with the first and second guide nucleotides nicks the DNA to generate nicks on opposing strands resulting in 3’ overhangs (e.g., as shown in Figures 1B and 1C).
  • the overhangs may have any length suitable to allow non-homologous end-joining. The length of the overhangs is defined by the distance between the nicks in DNA strands.
  • the length of the overhangs suitable to allow non-homologous end-joining may vary depending on a number of factors.
  • the overhangs have a length from 1 to 200 nucleotides, such as 10 to 150 nucleotides, 15 to 100 nucleotides, or 20 to 50 nucleotides.
  • the overhangs have a length of 10 nucleotides or greater, such as 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 nucleotides or greater.
  • the overhangs have a length of 200 nucleotides or less, such as 190, 180, 170, 160, 150, 140, 130, 120, 110, 100, 90, 80, 70, 60, or 50 nucleotides or less. In some embodiments, the overhangs have a length of 20 to 50 nucleotides, such as 23 to 45, 30 to 40, 31 to 40, 32 to 40, 33 to 40, 31 to 39, 32 to 39, 33 to 39, or 34 to 38 nucleotides. [18] In some embodiments, the sequences of the first and second scaffold regions of the first and second guide oligonucleotides are the same. In some embodiments, the sequences of the first and second scaffold regions are different.
  • the in vivo LPA gene editing system comprises one polynucleotide (e.g., mRNA) encoding one CRISPR Cas9 nickase.
  • the in vivo LPA gene editing system further comprises one or more polynucleotides (e.g., mRNA), each encoding a CRISPR Cas nickase.
  • the in vivo LPA gene editing system comprises a Cas nickase that is engineered to be directed to protospacer sequences within or in proximity to exon 20 of the LPA gene, which spans from chromosome 6, position 160,599,659, to chromosome 6, position 160,599,500, by the first and second guide oligonucleotides (e.g., gRNAs).
  • the gene editing system is configured to effect indel variants and/or non- synonymous variants in the LPA gene.
  • the in vivo LPA gene editing system comprises a Cas nickase that is engineered to be directed to protospacer sequences within or in proximity to exon 23 of the LPA gene, which spans from chromosome 6, position 160,591,101, to chromosome 6, position 160,590,944, by the first and second guide oligonucleotides (e.g., gRNAs).
  • the gene editing system is configured to effect indel variants and/or non- synonymous variants in the LPA gene.
  • the in vivo LPA gene editing system comprises a Cas nickase that is engineered to be directed to protospacer sequences within or in proximity to exon 25 of the LPA gene, which spans from chromosome 6, position 160,586,630, to chromosome 6, position 160,586,449, by the first and second guide oligonucleotides (e.g., gRNAs).
  • the gene editing system is configured to effect indel variants and/or non- synonymous variants in the LPA gene.
  • the in vivo LPA gene editing system comprises a Cas nickase that is engineered to be directed to protospacer sequences within or in proximity to exon 19 of the LPA gene, which spans from chromosome 6, position 160,601,098, to chromosome 6, position 160,600,917, by the first and second guide oligonucleotides (e.g., gRNAs).
  • the gene editing system is configured to effect indel variants and/or non- synonymous variants in the LPA gene.
  • the in vivo LPA gene editing system comprises a Cas nickase that is engineered to be directed to protospacer sequences within or in proximity to exon 31 of the LPA gene, which spans from chromosome 6, position 160,548,659, to chromosome 6, position 160,548,478, by the first and second guide oligonucleotides (e.g., gRNAs).
  • the gene editing system is configured to effect indel variants and/or non- synonymous variants in the LPA gene.
  • a plurality of different guide oligonucleotides e.g., gRNAs
  • the different guide oligonucleotides are delivered in vivo to the target human liver cells/tissues simultaneously and operate to effectuate the editing of the LPA gene of human liver cells.
  • the different guide oligonucleotides are delivered in vitro to the target human liver cells/tissues (e.g., HuH-7 cells) simultaneously and operate to effectuate the editing of the LPA gene of human liver cells.
  • one or more or all of the guide oligonucleotides are delivered to the target liver tissue and liver cells via lipid nanoparticles (LNPs), which may comprise an ionizable lipid, cholesterol, PEG-lipid, and a phospholipid and may also include a targeting moiety, such as a GalNAc lipid.
  • LNPs lipid nanoparticles
  • the phospholipid comprises distearoylphosphatidylcholine (DSPC).
  • DSPC distearoylphosphatidylcholine
  • the same or different LNPs may also serve to deliver mRNA encoding the gene editor, namely a Cas nickase (e.g., a Cas9 nickase).
  • the mRNA and/or guide oligonucleotides are selected from those specified herein.
  • the Cas nickase (gene editor) and guide oligonucleotides (e.g., gRNAs) may be selected from gene editing systems and configurations illustrated in Figures 1A-1D.
  • the in vivo gene editing system comprises mRNA that encodes a Cas nickase (gene editor) and comprises one or more guide oligonucleotides (e.g., gRNAs).
  • a first guide oligonucleotide may comprise a first spacer sequence and a first scaffold region.
  • a second guide oligonucleotide may comprise a second spacer sequence and a scaffold region that is different than or the same as the first scaffold region.
  • the first spacer sequence may correspond with a first protospacer sequence and be designed to be complementary or otherwise hybridize to the strand complementary to the first protospacer to facilitate a nick by the nickase (e.g., Cas nickase) on one or the other DNA strand.
  • the nickase e.g., Cas nickase
  • the second spacer sequence may correspond to a second protospacer sequence that is located on the opposite strand to the first protospacer sequence and is in operational proximity to the first protospacer sequence, wherein the second spacer sequence is complementary or otherwise designed to hybridize to the strand complementary to the second protospacer to facilitate a nick by the nickase on the strand that does not receive a nick via the action of the nickase in connection with the first guide oligonucleotide.
  • the present invention provides isolated oligonucleotides (e.g., gRNAs) or nucleic acids encoding the same.
  • the isolated oligonucleotides each comprise (i) a spacer sequence comprising about 15 to about 26 nucleotides, such as about 17 to about 23 nucleotides, that is identical to or substantially identical to a targeted protospacer sequence adjacent to a protospacer-adjacent motif (PAM) sequence within an LPA gene; and (ii) a scaffold region.
  • the isolated oligonucleotides serve as guide nucleic acids to direct the gene editor to effect the edit in the LPA gene.
  • the edit or edits are configured to modify the LPA gene to effect indel variants or non-synonymous variants.
  • the first protospacer is on the sense strand and the second protospacer is on the antisense strand of the LPA gene. In some embodiments, the first protospacer is on the antisense strand and the second protospacer is on the sense strand of the LPA gene.
  • the mRNA that encodes a Cas nickase comprises: (a) a 5’ untranslated region (UTR); (b) a 3’ UTR region; (c) a poly(A) tail proximate to the 3’ UTR as compared to the 5’ UTR, said poly(A) tail comprising a chain of 80-150 nucleotides that comprise adenine nucleotides; and (d) a gene editor coding region encoding an impaired CRISPR Cas endonuclease domain, said gene editor coding region extending between the 5’ UTR and the 3’ UTR.
  • the gene editor coding region also encodes a polymerase domain.
  • the mRNA has 90% or greater sequence identity to any of the mRNA sequences listed in Table 1.
  • the mRNA may have 91% or greater, 92% or greater, 93% or greater, 94% or greater, 95% or greater, 96% or greater, 97% or greater, 98% or greater, or 99% or greater sequence identity to any of the mRNA sequences listed in Table 1.
  • the Cas nickase is selected from: a Streptococcus pyogenes Cas9 variant, a Staphylococcus aureus Cas9 variant, or a Cas12a/Cpf1 variant.
  • the present disclosure describes a method of effecting a modification in an LPA gene to result in loss of function.
  • the method comprises delivering in vivo to a human liver cell, or administering to a mammalian subject, a pharmaceutical composition.
  • the pharmaceutical composition comprises a polynucleotide (e.g., mRNA) encoding the Cas nickase, the first and second guide oligonucleotides (e.g., gRNAs), and the delivery system.
  • the delivery system is engineered to deliver the polynucleotide encoding the Cas nickase, the first guide oligonucleotide, and/or the second guide oligonucleotide individually or collectively to the liver.
  • the delivery system comprises an LNP.
  • the method comprises delivering in vitro to a human liver cell (e.g., HuH-7 cell), or administering to a mammalian subject, a pharmaceutical composition.
  • the LNP is formulated with an mRNA: guide oligonucleotide (e.g., gRNA) weight ratio of 1:1 +/- 5%, 10%, 15%, 20%, 30%, 40%, 50% 60%, 70%, 80%, 90% or 100% of the mRNA or guide oligonucleotide or any therapeutically effective ratio.
  • a weight ratio of 1:1 +/- 100% includes weight ratios of 1:2 to 2:1.
  • a 1:1 weight ratio of mRNA: guide oligonucleotide refers to the cumulative weight ratios of all mRNAs and all guide oligonucleotides.
  • the weight ratio of the mRNA to the guide oligonucleotide will be the weight of the single mRNA relative to the combined weight of the two gRNAs in the formulation.
  • the LNP has an N/P ratio from about 4 to about 7, about 4, about 4.5, about 5, about 5.5, or about 6, about 6.5 or about 7 with each ratio +/- 5-20%.
  • the buffer solution containing the LNP has a pH of about 7.5 - 1.5 and comprises tris and/or sucrose.
  • the LNP has a mean diameter of about 70 nm +/- 20 nm, 70 nm +/- 10 nm, 70 nm +/- 5 nm; 60 nm +/- 20 nm, 60 nm +/- 10 nm, 60 nm +/- 5 nm; 50 nm +/- 20 nm, 50 nm +/- 10 nm, 50 nm +/- 5 nm; 45 nm +/- 20 nm, 45 nm +/- 10 nm, 45 nm +/- 5 nm.
  • the present disclosure describes a method for in vivo editing of an LPA gene in a mammalian subject in need thereof comprising administering to the subject a pharmaceutical composition.
  • the pharmaceutical composition comprises: (i) a polynucleotide (e.g., mRNA) encoding a CRISPR Cas nickase, (ii) a first guide oligonucleotide (e.g., gRNA) comprising a first spacer sequence and a scaffold region; and (iii) a second guide oligonucleotide (e.g., gRNA) comprising a second spacer sequence and a scaffold region, and (iv) a delivery system that is engineered to deliver the mRNA, the first gRNA, and/or the second gRNA individually and/or collectively to the liver, whereby in operation, the Cas nickase nicks each of the first and second strands of the LPA gene, in locations from chromosome
  • the mammalian subject is a human.
  • the subject has an elevated blood Lp(a) concentration.
  • the subject has an inversely associated apo(a) concentration.
  • the subject has cardiovascular disease associated with an elevated blood Lp(a) concentration.
  • the subject has cardiovascular disease associated with an inversely associated blood apo(a) concentration.
  • the in vivo editing of the LPA gene results in reduction of the blood Lp(a) concentration.
  • the in vivo editing of the LPA gene results in an inversely associated blood apo(a) concentration.
  • the invention provides a method for inactivating the LPA gene in vivo in a mammalian subject to treat and prevent cardiovascular disease comprising the step of: administering to the subject the pharmaceutical composition of the invention.
  • the invention provides a method for reducing blood Lp(a) concentration or inversely associated apo(a) concentration in a mammalian subject to treat and prevent cardiovascular disease comprising the step of: administering to the subject a pharmaceutical composition of the invention.
  • the invention provides a method for treating and/or preventing cardiovascular disease associated with the LPA gene in a mammalian subject comprising the step of: administering to the subject a pharmaceutical composition of the invention.
  • the invention provides a gene editing system for editing the LPA gene.
  • the gene editing system is produced by expressing in a cell one or more exogenous polynucleotides (e.g., mRNA) encoding one or more CRISPR Cas nickases and introducing first and second gRNAs into the cell.
  • the first guide oligonucleotide e.g., gRNA
  • the first guide oligonucleotide comprises (i) a first spacer sequence that is complementary to a first strand of the LPA gene at a first target sequence and (ii) a first scaffold region that serves as a binding scaffold for at least one of the one or more Cas nickases.
  • the second guide oligonucleotide (e.g., gRNA) comprises (i) a second spacer sequence that is complementary to a second strand of the LPA gene at a second target sequence and (ii) a second scaffold region that serves as a binding scaffold for at least one of the one or more Cas nickases.
  • the first gRNA and the at least one of the one or more Cas nickases are engineered to cause the at least one of the one or more Cas nickases to nick one of the first or second strands of the LPA gene at a first location of chromosome 6 from position 160,664,275 to 160,531,482.
  • the second gRNA and the at least one of the one or more Cas nickase are engineered to cause the at least one of the one or more Cas nickases to nick the other of the first or second strands of the LPA gene at a second location of chromosome 6 from position 160,664,275 to 160,531,482.
  • the invention provides a gene editing system comprising (i) a means for expressing one or more CRISPR Cas nickases in a cell; and (ii) a means for directing the one or more Cas nickases to first and second locations in the LPA gene and to cause the one or more Cas nickases to introduce a nick in a first strand of the LPA gene and to introduce a nick in a second strand of the LPA gene.
  • the invention provides a pharmaceutical composition for in vivo editing of an LPA gene, in a mammalian subject, comprising an engineered, non-naturally occurring gene editing system and a population of lipid nanoparticles that collectively encapsulate the gene editing system.
  • the gene editing system comprises (i) a nickase or one or more polynucleotides (mRNAs) encoding a nickase; (ii) a first guide oligonucleotide (gRNA) comprising a first spacer sequence that includes a region that is complementary to a first strand of the LPA gene at a first target sequence and a first scaffold region that serves as a binding scaffold for the nickase; and (ii) a second guide oligonucleotide (gRNA) comprising a second spacer sequence that includes a region that is complementary to a second strand of the LPA gene at a second target sequence and a second scaffold region that serves as a binding scaffold for the nickase.
  • mRNAs polynucleotides
  • the first and second strands are opposing strands.
  • the first spacer has a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% similar to or identical to, or is identical to the guide 1 protospacer listed in Table 2 or Table 5, and wherein the second spacer has a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% similar to or identical to, or is identical to the guide 2 protospacer listed in Table 2 or Table 5.
  • FIGS. 1A-1D are schematic drawings illustrating nickase-based editing systems and specifically dual nickase editing systems and configurations. Components of the gene editor and guide oligonucleotides (labeled as gRNAs) are identified and operationally described.
  • FIG. 1A illustrates one system and configuration that employs a nickase Cas9 protein with mutation of the RuvC domain, exemplified by Streptococcus pyogenes (S. pyogenes) Cas9 with a D10A mutation, with two guide oligonucleotides.
  • the first guide oligonucleotide has a spacer sequence that is identical to a first protospacer sequence on a bottom strand
  • the second guide oligonucleotide has a spacer sequence that is identical to a second protospacer sequence on a top strand, with the 5’ end of the first spacer sequence and the 5’ end of the second spacer sequence being proximate to one another as compared to the 3’ ends of the spacers.
  • the Cas9 nickase bearing a D10A mutation in operation with the first and second guide oligonucleotides, makes two nicks on respective target sequences on the top and bottom strands of the gene (e.g., LPA) between the first and second protospacer-adjacent motifs (PAMs) in a “PAM-out” configuration, in which the protospacer-adjacent motifs (PAMs) for the two protospacer sequences are separated by the length of the region spanned by the protospacer sequences. That is, the two PAMs are distal relative to one another and flank the two protospacer sequences in a “PAM-out” configuration.
  • LPA protospacer-adjacent motifs
  • Figure 1B illustrates one system and configuration that employs a nickase Cas9 protein with mutation of the HNH domain, exemplified by S. pyogenes Cas9 with an H840A mutation, with two guide oligonucleotides.
  • the first guide oligonucleotide has a spacer sequence that is identical to a first protospacer sequence on the bottom strand
  • the second guide oligonucleotide has a spacer sequence that is identical to a second protospacer sequence on the top strand, with the 5’ end of the first spacer sequence and the 5’ end of the second spacer sequence being proximate to one another as compared to the 3’ ends of the spacers.
  • the Cas9 nickase bearing a H840A mutation in operation with the first and second guide oligonucleotides, makes a first nicks on the first protospacer sequence and a second nick on the second protospacer sequences on the respective bottom and top strands of the gene (e.g., LPA) between the first and second protospacer-adjacent motifs (PAMs) in a “PAM-out” configuration.
  • the two PAMs depicted in Figure 1B are distal relative to one another and flank the two protospacer sequences in a “PAM-out” configuration.
  • Figure 1C illustrates one system and configuration that employs a nickase Cas9 protein with mutation of the RuvC domain, exemplified by S. pyogenes Cas9 with a D10A mutation, with two guide oligonucleotides.
  • the first guide oligonucleotide has a spacer sequence that is identical to a first protospacer sequence on the top strand
  • the second guide oligonucleotide has a spacer sequence that is identical to a second protospacer sequence on the bottom strand, with the 3’ end of the first spacer sequence and the 3’ end of the second spacer sequence being proximate to one another as compared to the 5’ ends of the spacers.
  • the Cas9 nickase bearing a D10A mutation in operation with the first and second guide oligonucleotides, makes two nicks on respective target bottom and top strands of the LPA gene outside the first and second protospacer-adjacent motifs (PAMs) in a “PAM-in” configuration, in which the PAMs for the two protospacer sequences are proximate relative to one another and are flanked by the protospacer sequences.
  • Figure 1D illustrates one system and configuration that employs a nickase Cas9 protein with mutation of the HNH domain, exemplified by S. pyogenes Cas9 with an H840A mutation, with two guide oligonucleotides.
  • the first guide oligonucleotide has a spacer sequence that is identical to a first protospacer sequence on the top strand
  • the second guide oligonucleotide has a spacer sequence that is identical to a second protospacer sequence on the bottom strand, with the 3’ end of the first spacer sequence and the 3’ end of the second spacer sequence being proximate to one another as compared to the 5’ ends of the spacers.
  • the Cas9 nickase bearing a H840A mutation in operation with the first and second guide oligonucleotides, makes a first nick on the first protospacer sequence and a second nick on the second protospacer sequence on respective top and bottom strands of the LPA gene outside the first and second protospacer-adjacent motifs (PAMs) in a “PAM-in” configuration, in which the PAMs for the two protospacer sequences are proximate relative to one another and are flanked by the protospacer sequences.
  • the arrows in the diagrams of Figs. 1A-1D indicate the location of the nicks.
  • D10A nickase is representative of nickases that nick the target strand
  • H840A nickase is representative of nickases that nick the non-target strand (e.g., the strand containing the protospacer).
  • other nickases may be used in connection with the nickase- based editing systems described herein.
  • Figure 2 is a plot of the percentages of LPA alleles edited in primary human hepatocytes (editing %, also referred to as editing efficiency) versus selected guide RNA pairs (first and second gRNAs) at relatively higher and lower doses, summarizing the LPA editing efficiencies in primary human hepatocytes using a gene editing system that comprises a Cas9 nickase with the specified pairs of first and second guide RNAs.
  • Specific guide RNA pairs are ranked by editing efficiency at the higher 2500 ng/ml total RNA dose. The lower total RNA dose is 312.5 ng/ml.
  • the Cas9 nickase is encoded within an mRNA (MS029) that was transfected into the primary human hepatocytes in a 1:1 total mRNA: total gRNA weight ratio.
  • Figure 3 shows dose response curves in human hepatocellular carcinoma immortalized cells (HuH-7) for five (5) pairs of first and second guide RNAs using a gene editing system that comprises a dual nickase Cas9 system as described in connection with Figure 2.
  • the Cas9 nickase is encoded within an mRNA (MS029) that was transfected into the HuH-7 cells in a 1:1 total mRNA: total gRNA weight ratio.
  • FIG. 4A is a schematic drawing illustrating the LPA genetic sequence to which spacers of guides GA1183, GA1184, GA1264, and GA1266 correspond. The corresponding amino acid sequence is provided below the genetic sequence and is numbered. Guide pairs (GA1183/GA1184, GA1264/GA1184, GA1266/GA1184) for dual nicking of the LPA gene are shown.
  • FIG. 4B is a plot illustrating editing efficiency (editing %) of primary human hepatocyte (PHH) cells incubated with LNPs (LNP 1, LNP 2, LNP 3 as described in the brief description of Figure 4A) in a dose responsive manner ranging from 0 to 40,000 ng/mL of total RNA (guides and mRNA).
  • FIG. 4B the gene editing system (guide pairs and mRNA encoding SpCas9-D10A nickase) resulted in an escalating response with increasing concentrations.
  • Figure 5 is a plot showing percent of apo(a) protein secreted from an HuH-7 reporter cell line exposed to varying concentrations of LNP ranging from 0 to 5000 ng/mL (total RNA).
  • the LNP corresponds to LNP 1 as described in the brief description of Figures 4A-B and includes the GA1183/GA1184 guide pair and mRNA encoding the SpCas9-D10A nickase (MS029).
  • the HuH-7 reporter cell line was generated by (i) infection with lentiviruses containing an expression cassette comprising an LPA open reading frame (ORF) followed by an internal ribosome entry site (IRES) and puromycin N-acetyltransferase (puro), driven by a cytomegalovirus (CMV) promoter, and (ii) selection with puromycin. As illustrated in Figure 5, the relative percent reduction in secreted apo(a) protein from the reporter cell line was reduced in a LNP dose-dependent manner.
  • ORF LPA open reading frame
  • IVS internal ribosome entry site
  • puro puromycin N-acetyltransferase
  • CMV cytomegalovirus
  • Figures 6A and 6B are graphs of LPA gene editing efficiency (indel %) in livers harvested from transgenic mice expressing the human LPA gene fourteen days after administration of a gene editing system (guide GA1296, guide GA1295, and MS029 mRNA).
  • the gene editing system was formulated into lipid nanoparticles (LNPs) and delivered to the transgenic mice via retro-orbital injection at various concentrations. Concentrations shown in Figures 6A and 6B correspond to mg total RNA (guide pair and mRNA) per kilogram (based on mouse weight).
  • gene editing efficiency increased in a dose- dependent manner with increasing dose of the gene editing system.
  • Figure 7 is a graph of percent change in plasma apo(a) protein level (measured as a percent change from baseline) in transgenic mice expressing the human LPA gene fourteen days after administration of a gene editing system (guide GA1296, guide GA1295, and MS029 mRNA).
  • the gene editing system was formulated into lipid nanoparticles (LNPs) and delivered to the transgenic mice via retro-orbital injection at various concentrations. Concentrations shown in Figure 7 correspond to mg total RNA (guide pair and mRNA) per kilogram (based on mouse weight). Plasma apo(a) concentrations were determined at baseline (–7 days) and 14 days following administration of the gene editing system.
  • Figure 8A is a graph of change in plasma apo(a) protein levels (measured as a percent change from baseline) in transgenic mice expressing the human LPA gene 7 and 14 days after administration of a gene editing system (guide GA1296, guide GA1295, and MS029 mRNA).
  • the gene editing system was formulated into lipid nanoparticles (LNPs) and delivered to the transgenic mice via retro-orbital injection at various concentrations. Concentrations shown in Figure 8A correspond to mg total RNA (guide pair and mRNA) per kilogram (based on mouse weight).
  • Plasma apo(a) concentrations were determined at baseline (–7 days) and 7 days and 14 days following administration of the gene editing system. As illustrated in Figure 8A, percent reduction in plasma apo(a) protein levels increased in a dose-dependent manner with increasing dose of the gene editing system.
  • Figure 8B is a graph of change in plasma apo(a) protein levels (measured as a percent change from baseline) in transgenic mice expressing the human LPA gene 14 days after administration of various gene editing systems (guide oligonucleotide pairs and MS029 mRNA). The gene editing system was formulated into lipid nanoparticles (LNPs) and delivered to the transgenic mice via retro-orbital injection at a 0.5 mg/kg dose.
  • LNPs lipid nanoparticles
  • FIG. 9 is a diagrammatic representation showing the locations at which the spacers of selected gRNAs described herein are complementary to the LPA gene and thereby are capable of hybridizing thereto. Due to the repetitive nature of some sequences of the LPA gene (e.g., the kringle type IV repeats), the spacers of some of the selected gRNAs are complementary to more than one location in the LPA gene.
  • compositions for LPA gene modification or editing and methods of using the same result in reduction of blood Lp(a) concentrations by inactivating the LPA gene.
  • editing of the LPA gene results in indel variants and non-synonymous variants in the LPA sequence.
  • Compositions and methods directed to editing the LPA gene using an editing system that can install the edit such as a Cas nickase (e.g., a Cas9 nicakse) and two guide oligonucleotides (e.g., gRNAs), are disclosed.
  • “about” can mean a range of up to 20%, up to 10%, up to 5%, or up to 1% of a given value.
  • the term can mean within an order of magnitude, within 5-fold, and more preferably within 2-fold, of a value.
  • the words “comprising” (and any form of comprising, such as “comprise” and “comprises”), “having” (and any form of having, such as “have” and “has”), “including” (and any form of including, such as “includes” and “include”) or “containing” (and any form of containing, such as “contains” and “contain”) are inclusive or open-ended and do not exclude additional, unrecited elements or method steps. It is contemplated that any embodiment discussed in this specification can be implemented with respect to any method or composition of the present disclosure, and vice versa. Furthermore, compositions of the present disclosure can be used to achieve methods of the present disclosure.
  • An article, composition, method, or the like that comprises one or more elements may consist of the one or more elements or may consist essentially of the one or more elements.
  • “consisting of” and any form of consisting of, such as “consists of” and “consist of”) means including and limited to.
  • an article, composition, method, or the like “consisting essentially of” (and any form of consisting essentially of, such as “consists essentially of” and “consist essentially of”) means the article, composition, method, or the like includes the specified enumerated elements; such as components, compounds, materials, steps, or the like, and may include additional elements that do not materially affect the basic and novel characteristics of the article, composition, method, or the like.
  • nucleic acid refers to a polymer containing at least two nucleotides (i.e., deoxyribonucleotides or ribonucleotides) in either single- or double-stranded form and includes DNA and RNA.
  • nucleotides contain a sugar deoxyribose (DNA) or ribose (RNA), a base, and a phosphate group. Nucleotides are linked together through the phosphate groups.
  • Bases include purines and pyrimidines, which further include natural compounds adenine (“A”), thymine (“T”), guanine (“G”), cytosine (“C”), uracil (“U”), inosine (“I”), and natural analogs, and synthetic derivatives of purines and pyrimidines, which include, but are not limited to, modifications which place new reactive groups such as, but not limited to, amines, alcohols, thiols, carboxylates, and alkylhalides.
  • A adenine
  • T thymine
  • G guanine
  • C cytosine
  • U uracil
  • I inosine
  • synthetic derivatives of purines and pyrimidines which include, but are not limited to, modifications which place new reactive groups such as, but not limited to, amines, alcohols, thiols, carboxylates, and alkylhalides.
  • Nucleic acids include nucleic acids containing known nucleotide analogs or modified backbone residues or linkages or modified sugar residues, or non-canonical/chemically-modified nucleobases and combinations thereof, which are synthetic, naturally occurring, and non-naturally occurring, and which have similar binding properties as the reference nucleic acid.
  • analogs and/or modified residues include, without limitation, phosphorothioates, phosphoramidates, methyl phosphonates, chiral- methyl phosphonates, 2'-O-methyl ribonucleotides, and peptide-nucleic acids (PNAs).
  • nucleic acid includes any oligonucleotide (e.g., gRNA) or polynucleotide (e.g., mRNA, genomic DNA), with fragments containing up to 150 nucleotides generally termed oligonucleotides, and longer fragments termed polynucleotides.
  • a deoxyribooligonucleotide consists of a 5-carbon sugar called deoxyribose joined covalently to phosphate at the 5' and 3' carbons of this sugar to form an alternating, unbranched polymer.
  • DNA may be in the form of, for example, antisense molecules, plasmid DNA, pre-condensed DNA, a PCR product, vectors, expression cassettes, chimeric sequences, chromosomal DNA, or derivatives and combinations of these groups.
  • a ribooligonucleotide consists of a similar repeating structure where the 5- carbon sugar is ribose. Accordingly, the terms “polynucleotide” and “oligonucleotide” can refer to a polymer or oligomer of nucleotide or nucleoside monomers consisting of naturally-occurring bases, sugars and intersugar (backbone) linkages.
  • polynucleotide and oligonucleotide can also include polymers or oligomers comprising non-naturally occurring monomers, or portions thereof, which function similarly. Such modified or substituted oligonucleotides are often preferred over native forms because of properties such as, for example, enhanced cellular uptake, reduced immunogenicity, and increased stability in the presence of nucleases. It should be understood that the terms “polynucleotide” and “oligonucleotide” can also include polymers or oligomers comprising both deoxy and ribonucleotide combinations or variants thereof in combination with backbone modifications, such as those described herein.
  • nucleic acid described herein may include one or more nucleotide variants, including nonstandard nucleotide(s), non–natural nucleotide(s), nucleotide analog(s), and/or modified nucleotides.
  • modified nucleotides include, but are not limited to diaminopurine, 5–fluorouracil, 5–bromouracil, 5–chlorouracil, 5–iodouracil, hypoxanthine, xantine, 4–acetylcytosine, 5–(carboxyhydroxylmethyl)uracil, 5–carboxymethylaminomethyl–2– thiouridine, 5–carboxymethylaminomethyluracil, dihydrouracil, beta–D–galactosylqueosine, inosine, N6–isopentenyladenine, 1–methylguanine, 1–methylinosine, 2,2–dimethylguanine, 2– methyladenine, 2–methylguanine, 3–methylcytosine, 5–methylcytosine, N6–adenine, 7– methylguanine, 5–methylaminomethyluracil, 5–methoxyaminomethyl–2–thiouracil, beta
  • nucleotides may include modifications in their phosphate moieties, including modifications to a triphosphate moiety.
  • modifications include phosphate chains of greater length (e.g., a phosphate chain having, 4, 5, 6, 7, 8, 9, 10 or more phosphate moieties) and modifications with thiol moieties (e.g., alpha–thiotriphosphate and beta–thiotriphosphates).
  • the nucleic acid described herein may be modified at the base moiety (e.g., at one or more atoms that typically are available to form a hydrogen bond with a complementary nucleotide and/or at one or more atoms that are not typically capable of forming a hydrogen bond with a complementary nucleotide), sugar moiety, or phosphate backbone.
  • Backbone modifications can include, but are not limited to, a phosphorothioate, a phosphorodithioate, a phosphoroselenoate, a phosphorodiselenoate, a phosphoroanilothioate, a phosphoraniladate, a phosphoramidate, and a phosphorodiamidate linkage.
  • a phosphorothioate linkage substitutes a sulfur atom for a non-bridging oxygen in the phosphate backbone and delay nuclease degradation of oligonucleotides.
  • a phosphorodiamidate linkage (N3’ ⁇ P5’) prevents nuclease recognition and degradation.
  • Backbone modifications can also include peptide bonds instead of phosphorous in the backbone structure (e.g., N-(2-aminoethyl)-glycine units linked by peptide bonds in a peptide nucleic acid) or linking groups including carbamate, amides, and linear and cyclic hydrocarbon groups. Oligonucleotides with modified backbones are reviewed in Micklefield, Curr. Med.
  • Nucleic acid molecules described herein may contain a sugar moiety that comprises ribose or deoxyribose, as present in naturally occurring nucleotides, or a modified sugar moiety or sugar analog.
  • Modified sugar moieties include, but are not limited to, 2’-O- methyl, 2’-O-methoxyethyl, 2’-O-aminoethyl, 2’-Fluoro, N3’ ⁇ P5’ phosphoramidate, 2’dimethylaminooxyethoxy, 2’ 2′dimethylaminoethoxyethoxy, 2′-guanidinidium, 2′-O- guanidinium ethyl, carbamate modified sugars, and bicyclic modified sugars.2’-O-methyl or 2’- O-methoxyethyl modifications may be included to promote the “A-form” or “RNA-like” conformation in oligonucleotides, increase binding affinity to RNA, and enhance nuclease resistance.
  • Modified sugar moieties can also include an extra bridge bond (e.g., a methylene bridge joining the 2’-O and 4’-C atoms of the ribose in a locked nucleic acid) or sugar analog such as a morpholine ring (e.g., as in a phosphorodiamidate morpholino).
  • an “isolated” or “purified” DNA molecule or RNA molecule is a DNA molecule or RNA molecule that exists apart from its native environment.
  • an isolated DNA molecule or RNA molecule may exist in a purified form or may exist in a non-native environment such as, for example, a transgenic host cell.
  • an “isolated” or “purified” nucleic acid molecule or biologically active portion thereof is substantially free of other cellular material, or culture medium when produced by recombinant techniques, or substantially free of chemical precursors or other chemicals when chemically synthesized.
  • an “isolated” nucleic acid is free of sequences that naturally flank the nucleic acid (i.e., sequences located at the 5’ and 3’ ends of the nucleic acid) in the genomic DNA of the organism from which the nucleic acid is derived.
  • polypeptide As used herein, the terms “protein,” “polypeptide,” and “peptide” are used interchangeably and refer to a polymer of amino acid residues linked via peptide bonds and which may be composed of two or more polypeptide chains.
  • the terms “polypeptide,” “protein,” and “peptide” refer to a polymer of at least two amino acid monomers joined together through amide bonds.
  • An amino acid may be the L–optical isomer or the D–optical isomer. More specifically, the terms “polypeptide,” “protein,” and “peptide” refer to a molecule composed of two or more amino acids in a specific order; for example, the order as determined by the base sequence of nucleotides in the gene or RNA coding for the protein.
  • Proteins are essential for the structure, function, and regulation of the body’s cells, tissues, and organs, and each protein has unique functions. Examples of proteins include hormones, enzymes, antibodies, and any fragments thereof.
  • a protein can be a portion of the protein, for example, a domain, a subdomain, or a motif of the protein.
  • a protein can be a variant (or mutant) of the protein, wherein one or more amino acid residues are inserted into, deleted from, and/or substituted into the naturally occurring (or at least a known) amino acid sequence of the protein.
  • a protein or a variant thereof can be naturally occurring or recombinant.
  • Methods for detection and/or measurement of polypeptides in biological material include, but are not limited to, Western blotting, flow cytometry, enzyme-linked immunosorbent assay (ELISA), radioimmunoassay (RIA), and various proteomics techniques, such as mass spectrometry.
  • An exemplary method to measure or detect a polypeptide is an immunoassay, such as an ELISA. This type of protein quantitation can be based on an antibody capable of capturing a specific antigen, and a second antibody capable of detecting the captured antigen.
  • the term “subject” or “patient” encompasses mammals.
  • mammals include, but are not limited to, any member of the mammalian class: humans, non-human primates such as chimpanzees, and other apes and monkey species; farm animals such as cattle, horses, sheep, goats, swine; domestic animals such as rabbits, dogs, and cats; laboratory animals including rodents, such as rats, mice, and guinea pigs; and the like.
  • a subject in need thereof refers to an individual who has a disease, a symptom of the disease, or a predisposition toward the disease, with the purpose to cure, heal, alleviate, relieve, alter, remedy, ameliorate, improve, or affect the disease, the symptom of the disease, or the predisposition toward the disease.
  • administering and its grammatical equivalents as used herein can refer to providing one or more drug substances (e.g., mRNA that encodes the editor proteins, guide oligonucleotides), drug products (e.g., LNPs that encapsulate the drug substances for delivery to the target cells/tissue), or pharmaceutical compositions thereof as described herein to a subject or a patient.
  • drug substances e.g., mRNA that encodes the editor proteins, guide oligonucleotides
  • drug products e.g., LNPs that encapsulate the drug substances for delivery to the target cells/tissue
  • pharmaceutical compositions thereof as described herein
  • administering can be performed by intravenous (i.v.) injection, subcutaneous (s.c.) injection, intradermal (i.d.) injection, intraperitoneal (i.p.) injection, intramuscular (i.m.) injection, intravascular injection, intracerebroventricular (i.c.v.) injection, intrathecal (i.t.) injection, infusion (inf.), oral routes (p.o.), topical (top.) administration, or rectal (p.r.) administration.
  • intravenous (i.v.) injection subcutaneous (s.c.) injection, intradermal (i.d.) injection, intraperitoneal (i.p.) injection, intramuscular (i.m.) injection, intravascular injection, intracerebroventricular (i.c.v.) injection, intrathecal (i.t.) injection, infusion (inf.), oral routes (p.o.), topical (top.) administration, or rectal (p.r.) administration.
  • i.v. subcutaneous
  • parenteral includes subcutaneous, intracutaneous, intravenous, intramuscular, intraarticular, intraarterial, intrasynovial, intrasternal, intracerebroventricular, intrathecal, intralesional, and intracranial injection or infusion techniques.
  • Parenteral administration can be, for example, by bolus injection or by gradual perfusion over time.
  • injectable depot routes of administration such as using 1-, 3-, or 6-month depot injectable or biodegradable materials and methods.
  • treat can include alleviating, abating, or ameliorating at least one symptom of a disease or a condition, preventing additional symptoms, inhibiting the disease or the condition, e.g., arresting the development of the disease or the condition, relieving the disease or the condition, causing regression of the disease or the condition, relieving a condition caused by the disease or the condition, or stopping the symptoms of the disease or the condition either prophylactically and/or therapeutically.
  • Treating may refer to administration of a composition comprising a nanoparticle, such as a lipid nanoparticle (LNP), to a subject before or after the onset, or suspected onset, of a disease or condition. “Treating” includes the concepts of “alleviating,” which refers to lessening the frequency of occurrence or recurrence, or the severity, of any symptoms or other ill effects related to a disease or condition and/or the side effects associated with the disease or condition.
  • a nanoparticle such as a lipid nanoparticle (LNP)
  • treating also encompasses the concept of “managing,” which refers to reducing the severity of a particular disease or disorder in a patient or delaying its recurrence, e.g., lengthening the period of remission in a patient who had suffered from the disease.
  • the term “treating” further encompasses the concept of “prevent,” “preventing,” and “prevention.” It is appreciated that, although not precluded, treating a disorder or condition does not require that the disorder, condition, or symptoms associated therewith be completely eliminated. [80]
  • the terms “prevent,” “preventing,” “prevention,” and the like refer to reducing the probability of developing a disease or condition in a subject, who does not have but is at risk of or susceptible to developing a disease or condition.
  • ameliorate can refer to decrease, suppress, attenuate, diminish, arrest, or stabilize the development or progression of a disease.
  • “delaying” the development of a disease means to defer, hinder, slow, retard, stabilize, and/or postpone progression of the disease. This delay can be of varying lengths of time, depending on the history of the disease and/or individuals being treated.
  • a method that “delays” or alleviates the development of a disease, or delays the onset of the disease is a method that reduces probability of developing one or more symptoms of the disease in a given time frame and/or reduces extent of the symptoms in a given time frame, when compared to not using the method.
  • “Development” or “progression” of a disease means initial manifestations and/or ensuing progression of the disease. Development of the disease can be detectable and assessed using standard clinical techniques as well known in the art. However, development also refers to progression that may be undetectable. For purpose of this disclosure, development or progression refers to the biological course of the symptoms. “Development” includes occurrence, recurrence, and onset. [84] As used herein “onset” or “occurrence” of a disease includes initial onset and/or recurrence.
  • therapeutic agent or “drug substance” can refer to any agent that, when administered to a subject, has a therapeutic, diagnostic, and/or prophylactic effect and/or elicits a desired biological and/or pharmacological effect.
  • Therapeutic agents can also be referred to as “actives” or “active agents.” Such agents include, but are not limited to, cytotoxins, radioactive ions, chemotherapeutic agents, small molecule drugs, proteins, and nucleic acids such as guide oligonucleotides and mRNA.
  • composition and its grammatical equivalents as used herein can refer to a mixture or solution comprising a therapeutically effective amount of an active pharmaceutical ingredient together with one or more pharmaceutically acceptable excipients, carriers, and/or a therapeutic agent to be administered to a subject, e.g., a human in need thereof.
  • pharmaceutically acceptable and its grammatical equivalents as used herein can refer to an attribute of a material which is useful in preparing a pharmaceutical composition that is generally safe, non-toxic, and neither biologically nor otherwise undesirable and is acceptable for veterinary as well as human pharmaceutical use.
  • “Pharmaceutically acceptable” can refer to a material, such as a carrier or diluent, that does not abrogate the biological activity or properties of the compound and is relatively nontoxic, i.e., the material may be administered to a subject without causing undesirable biological effects or interacting in a deleterious manner with any of the components of the pharmaceutical composition in which it is contained.
  • a “pharmaceutically acceptable excipient, carrier, or diluent” refers to an excipient, carrier, or diluent that can be administered to a subject, together with an agent, and which does not destroy the pharmacological activity thereof and is nontoxic when administered in doses sufficient to deliver a therapeutic amount of the agent.
  • a “pharmaceutically acceptable salt” may be an acid or base salt that is generally considered in the art to be suitable for use in contact with the tissues of human beings or animals without excessive toxicity, irritation, allergic response, or other problem or complication.
  • pharmaceutically acceptable salts include those listed by Remington's Pharmaceutical Sciences, 17th ed., Mack Publishing Company, Easton, PA, p.1418 (1985).
  • the term “therapeutically effective amount” means an amount of an agent to be delivered (e.g., nucleic acid, drug, payload, composition, therapeutic agent, diagnostic agent, prophylactic agent, etc.) that is sufficient, when administered to a subject suffering from or susceptible to an infection, disease, disorder, and/or condition, to treat, improve symptoms of, diagnose, prevent, and/or delay the onset of the infection, disease, disorder, and/or condition.
  • an agent to be delivered e.g., nucleic acid, drug, payload, composition, therapeutic agent, diagnostic agent, prophylactic agent, etc.
  • a range of 1 to 50 is understood to include any number, combination of numbers, or sub-range from the group consisting of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50, as well as all intervening decimal values between the aforementioned integers such as, for example, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, and 1.9.
  • sub-ranges “nested sub-ranges” that extend from either end point of the range are specifically contemplated.
  • a nested sub-range of an exemplary range of 1 to 50 may comprise 1 to 10, 1 to 20, 1 to 30, and 1 to 40 in one direction, or 50 to 40, 50 to 30, 50 to 20, and 50 to 10 in the other direction.
  • Numbers expressing quantities of components, molecular weights, and so forth used in the specification and claims are to be understood as being modified in all instances by the term "about.” Accordingly, unless otherwise indicated to the contrary, the numerical parameters set forth in the specification and claims are approximations that may vary depending upon the desired properties sought to be obtained by the present invention.
  • each numerical parameter should at least be construed in light of the number of reported significant digits and by applying ordinary rounding techniques.
  • a “spacer” sequence of a guide nucleic acid is considered to be “complementary” to a sequence of a target nucleic acid.
  • a sequence may be considered sufficiently “complementary” to a target sequence if it is capable of sufficiently hybridizing to the intended DNA strand so that it may be used to guide an editor protein to the target sequence to cause an intended edit.
  • a guide oligonucleotide is complementary if, for example, it is capable of sufficiently hybridizing to the intended DNA strand so that it operationally positions the editor in the desired location to facilitate the intended edit.
  • nucleic acid sequence that is “substantially identical” to another nucleic acid sequence is a nucleotide sequence that has 70% or more sequence identity to the other nucleic acid sequence.
  • a nucleic acid sequence that is “substantially identical” to another nucleic acid sequence has 75% or more, 80% or more, 85% or more, 90% or more, 91% or more, 92% or more, 93% or more, 94% or more, 95% or more, 96% or more, 97% or more, 98% or more, or 99% or more sequence identity to the other nucleic acid sequence.
  • sequence identity refers to the extent to which two optimally aligned nucleic acid sequences are invariant throughout a window of alignment of components, e.g., nucleotides. "Identity" can be readily calculated by known methods including, but not limited to, those described in: Computational Molecular Biology (Lesk, A. M., ed.) Oxford University Press, New York (1988); Biocomputing: Informatics and Genome Projects (Smith, D.
  • percent sequence identity refers to the percentage of identical nucleotides in a linear polynucleotide sequence of a reference (“query") nucleic acid (or its complementary strand) as compared to a test ("subject") nucleic acid (or its complementary strand) when the two sequences are optimally aligned. Percent sequence identity may be determined, when the compared sequences are aligned for maximum correspondence, as measured using a sequence comparison algorithm described below and as known in the art, or by visual inspection. [99] For sequence comparison, typically one sequence acts as a reference sequence to which test sequences are compared.
  • sequence comparison algorithm When using a sequence comparison algorithm, test and reference sequences are entered into a computer, subsequence coordinates are designated if necessary, and sequence algorithm program parameters are designated. The sequence comparison algorithm then calculates the percent sequence identity for the test sequence(s) relative to the reference sequence, based on the designated program parameters. Optimal alignment of sequences for aligning a comparison window are well known to those skilled in the art and may be conducted by tools such as the local homology algorithm of Smith and Waterman, the homology alignment algorithm of Needleman and Wunsch, the search for similarity method of Pearson and Lipman, and optionally by computerized implementations of these algorithms such as GAP, BESTFIT, FASTA, and TFASTA available as part of the GCG® Wisconsin Package® (Accelrys Inc., San Diego, CA).
  • Alignment of sequences may be analyzed using a Burrows-Wheeler transform such as BOWTIE open-source software available from https://github.com/BenLangmead/bowtie.
  • An "identity fraction" for aligned segments of a test sequence and a reference sequence is the number of identical components which are shared by the two aligned sequences divided by the total number of components in the reference sequence segment, i.e., the entire reference sequence or a smaller defined part of the reference sequence. Percent sequence identity is represented as the identity fraction multiplied by 100. [100] "Percent identity" may also be determined using BLASTX version 2.0 for translated nucleotide sequences and BLASTN version 2.0 for polynucleotide sequences.
  • HSPs high scoring sequence pairs
  • Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always > 0) and N (penalty score for mismatching residues; always ⁇ 0). Extension of the word hits in each direction are halted when the cumulative alignment score falls off by the quantity X from its maximum achieved value, the cumulative score goes to zero or below due to the accumulation of one or more negative-scoring residue alignments, or the end of either sequence is reached.
  • the BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment.
  • W word length
  • E expectation
  • N a comparison of both strands.
  • the BLAST algorithm also performs a statistical analysis of the similarity between two sequences (see, e.g., Karlin & Altschul, Proc. Natl. Acad. Sci. U. S. A.90: 5873-5787 (1993)).
  • One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance.
  • a test nucleic acid sequence is considered similar to a reference sequence if the smallest sum probability in a comparison of the test nucleotide sequence to the reference nucleotide sequence is less than about 0.1 to less than about 0.001.
  • Sequence “identity” refers to the amount of nucleotide or amino acid which match exactly between two different sequences. When comparing RNA and DNA sequences Uracil and Thymine bases are considered to be the same base. Gaps are not counted, and the measurement is typically in relation to the shorter of the two sequences.
  • sequence A AAGGCTT; B: AAGGC; and C: AAGGCAT
  • identity of sequence A compared to reference sequence B ((Identity(A,B)) is 100% (5 identical nucleotides / min(length(A),length(B)));
  • Identity of sequence B to reference sequence C is 100%; but identity of sequence A to reference sequence C is 85% ((6 identical nucleotides / 7).
  • Sequence “similarity” (or, e.g., “similar” sequences), as used herein, can be described as an optimal matching problem that finds the minimal number of edit operations (inserts, deletes, and substitutions) in order to transform a first sequence into an exact copy of a second sequence being aligned (edit distance). If the lengths of the first and second sequences are different, similarity is determined relative to the length of the shortest sequence. That is, sequence similarity is [1-(number of edit operations/length of the shortest sequence)].
  • sequence similarity for nucleotide sequences A: AAGGCTT; B: AAGGC; and C: AAGGCAT, similarity of sequence A and sequence B is 60%, similarity of sequence B and sequence C is 60%, and similarity of sequence A and sequence C is 86%.
  • comparisons of sequences may be determined including or excluding chemical modifications.
  • percent sequence identity is determined based on the sequences of nucleobases in the modified oligonucleotide, where modified nucleobases are considered equivalent to unmodified nucleobases from which the modified nucleobases are derived.
  • 2,4,-Dichlorotoluene, 2,4-Dibromotholuene, and 2,4-Diiodotolume are considered equivalent to Thymine for purposes of comparing sequence identity of a modified oligonucleotide to a reference unmodified oligonucleotide.
  • 4- methylbenzimidazole and 9-methylimidazo are considered equivalent to Adenine for purposes of comparing sequence identity of a modified oligonucleotide to a reference unmodified oligonucleotide.
  • the modified oligonucleotide comprises modifications to the linkage moiety (e.g., other than phosphate linker) and/or to the sugar (e.g., 2’ modified ribose or dideoxyribose)
  • the sequence of the nucleobases of the modified oligonucleotides is compared to the sequence of the nucleobases in the reference unmodified sequence to determine sequence identity. For example, for nucleotide sequences: A: mA*AGGCmT*mT; B: AAGGCTT; and C: AAGGCAT, identity of sequence A to reference sequence B is 100% (7 identical nucleotides / 7); identity of sequence A to reference sequence C is 85% (6 identical nucleotides / 7).
  • sequence similarity is determined based on the exact modifications of each nucleotide of the reference modified oligonucleotide (e.g., based on any modifications to the linker, the sugar moiety, and the nucleobase). Accordingly, an unmodified (or differently modified) nucleotide of an oligonucleotide is not considered identical to a corresponding modified oligonucleotide of a reference modified oligonucleotide.
  • a spacer sequence of a guide nucleic acid is considered to be “homologous” to a protospacer sequence of a target nucleic acid if a gene editor system comprising a guide oligonucleotide having the spacer sequence is capable of making a modification (e.g., nick) to the target nucleic acid (e.g., nick on sense strand or antisense strand of the target nucleic acid).
  • a spacer sequence that is homologous to a protospacer sequence may be identical or substantially identical to the protospacer sequence.
  • a first nucleotide sequence that is homologous to a second nucleotide sequence may hybridize to the complementary sequence of the second nucleotide sequence under stringent conditions or highly stringent conditions.
  • Stringent hybridization conditions and “stringent hybridization wash conditions” in the context of nucleic acid hybridization are sequence-dependent and are different under different environmental parameters. An extensive guide to the hybridization of nucleic acids is found in Tijssen, Laboratory Techniques in Biochemistry and Molecular Biology-Hybridization with Nucleic Acid Probes part I chapter 2 “Overview of principles of hybridization and the strategy of nucleic acid probe assays” Elsevier, New York (1993).
  • highly stringent hybridization and wash conditions are selected to be about 5°C lower than the thermal melting point Tm for the specific sequence at a defined ionic strength and pH.
  • the Tm is the temperature (under defined ionic strength and pH) at which 50% of the target sequence hybridizes to a perfectly matched probe.
  • Very stringent conditions are selected to be equal to the Tm for a particular probe.
  • An example of stringent hybridization conditions for hybridization of complementary nucleotide sequences which have more than 100 complementary residues on a filter in a Southern or Northern blot is 50% formamide with 1 mg of heparin at 42°C, with the hybridization being carried out overnight.
  • An example of highly stringent wash conditions is 0.15M NaCl at 72°C for about 15 minutes.
  • stringent wash conditions is a 0.2 ⁇ SSC wash at 65°C for 15 minutes (see, Sambrook and Russel, Molecular Cloning: A Laboratory Manual, 3 rd ed., Cold Spring Harbor Laboratory Press, 2001 for a description of SSC buffer). Often, a high stringency wash is preceded by a low stringency wash to remove background probe signal.
  • An example of a medium stringency wash for a duplex of, e.g., more than 100 nucleotides is 1 ⁇ SSC at 45°C for 15 minutes.
  • An example of a low stringency wash for a duplex of, e.g., more than 100 nucleotides is 4-6 ⁇ SSC at 40°C for 15 minutes.
  • stringent conditions typically involve salt concentrations of less than about 1.0 M Na ion, typically about 0.01 to 1.0 M Na ion concentration (or other salts) at pH 7.0 to 8.3, and a temperature typically at least about 30°C. Stringent conditions can also be achieved with the addition of destabilizing agents such as formamide.
  • effect or “effectuate” and their grammatical equivalents are used throughout this disclosure to refer to an action made that will induce creation of an intended result. The entire process by which the result is produced may not necessarily be performed by the system used to effect the edit. Cellular processing may, for example, play a role in completing the intended result.
  • a dual nickase in vivo editor system such as those illustrated in Figures 1A-1D that include a Cas9 nickase and two guide oligonucleotides may effect an edit in a gene without performing final processing steps that result in the edit being fully incorporated in both strands of the gene.
  • Cellular DNA repair enzymes may perform the final processing steps. While all the steps needed to complete the edit would not be performed by the dual nickase editor system, the system would still be said to have effected the edit.
  • activating the LPA gene and grammatical equivalents thereof refer to edits to the LPA gene by a gene editing system that result in decreased expression of apo(a), expression of a non-functional variant of apo(a), and/or expression of an apo(a) variant having reduced function relative to wild-type apo(a).
  • the edits to the LPA gene effected by the gene editing systems described herein may result in indel and/or non-synonymous variants.
  • the indel and/or non-synonymous variants of the LPA gene may result in production of pre-mRNA that is degraded via, for example, nonsense-mediated decay.
  • the indel and/or non-synonymous variants of the LPA gene may result in production of apo(a) variants having reduced function, and in some cases no function, relative to wild-type apo(a).
  • LPA gene is highly similar to the PLG (plasminogen) gene, from which it evolved in primates, and the protein products of the two genes have structural commonalities. They each have kringle type IV (KIV) and kringle type V (KV) domains and protease-like domains.
  • KIV kringle type IV
  • KV kringle type V
  • Apo(a) comprises 10 types of KIV domains (KIV 1 through KIV 10 ), with a variable number of repeat KIV2 domains ranging from 2 to more than 40, and single domains of the other 9 types, a single KV domain, and an inactive protease-like domain.
  • Blood Lp(a) concentrations are largely genetically determined and vary inversely with the number of KIV 2 repeats, as LPA alleles with fewer repeats result in smaller apo(a) isoforms that are more quickly produced and processed in hepatocytes. There is broad inter-individual variation in blood Lp(a) concentrations, with one in five individuals having elevated concentrations that signify substantially increased risk of cardiovascular disease.
  • Apolipoprotein(a) [apo(a)] is a defining component of Lp(a).
  • Apo(a) is understood to be primarily synthesized in the hepatocyte cells of the liver.
  • Apo(a) comprises single copies of the KIV1 domain and KIV3 through KIV10 domains, a variable number of repeat KIV2 domains ranging from 2 to more than 40, a single KV domain, and an inactive protease-like domain.
  • the wild-type apo(a) protein that is annotated in the reference human genome has six repeat KIV2 domains, is 2040 amino acids in length, and has the amino acid sequence below. It should be understood that the sequence below represents one of many isoforms of apo(a) present in the human population. [116] It should be understood that the foregoing sequence employs standard conventional nomenclature well known in the art with each letter denoting an amino acid.
  • a method includes identifying a subject having an elevated blood Lp(a) concentration and administering to the subject a composition comprising components capable of introducing indel or non-synonymous variants in the coding sequence of the LPA gene.
  • Administering the composition to the subject may comprise administering a therapeutically effective amount of the composition to the subject.
  • the effected edits of the LPA gene may result in reduced functionality of the apo(a) protein.
  • the effected edits of the LPA gene may result in a reduction of the blood Lp(a) concentration.
  • the compositions described herein that include a gene editing system include one or more guide nucleic acids designed to target one or more protospacer regions on the LPA gene. III. GENE EDITING/GENE MODIFICATION [124]
  • the term “gene editing” or “gene modification” and their grammatical equivalents as used herein refer to genetic engineering in which one or more nucleotides are modified, inserted, replaced, or removed from a genome. Gene editing can be performed using man-made non- naturally occurring gene editing systems that comprise one or more nucleases, which may be derived from naturally existing nucleases or artificially engineered.
  • Gene modification can include introducing a double-strand break, a nonsense variant, a frameshift variant, a splice site alteration, or an inversion in a polynucleotide sequence, e.g., a target polynucleotide sequence. Gene modification can also be accomplished using other editing systems, such as dual nickase editor systems such as those illustrated and described in Figures 1A-1D. [125] Any suitable gene editing system may be employed to effect the editing in the LPA gene.
  • the gene editing system may include a gene editor and a suitable guide nucleic acid for use with the gene editor.
  • a “gene editor system” that includes a nucleic acid capable of being translated, or transcribed and translated, into a gene editor protein or protein component of a gene editor is considered to be a gene editor system that includes a gene editor.
  • the nucleic acid may be, for example, a plasmid DNA or an mRNA.
  • the mRNA may be mature mRNA or pre-mRNA that may be processed, e.g., within a cell, to mature mRNA, which then may be translated, e.g., within a cell, to produce the gene editor.
  • a “gene editor system” that includes a nucleic acid capable of being transcribed to produce a gRNA is considered to be a gene editor system that comprises the gRNA.
  • the nucleic acid may be, for example, a plasmid DNA.
  • the gene editor is a Cas9 variant or related gene editor.
  • the gene editor is a nickase such as described in Figures 1A-1D.
  • A. Cas9 and related nucleic acid-directed editing proteins [126] A ribonucleoprotein complex from S. pyogenes capable of introducing double-strand breaks in double-stranded DNA was published by Jennifer Doudna’s group in 2012 (Jinek et al.
  • ribonucleoprotein is used to refer to a non-covalent assembly of RNA and protein.
  • Clustered regularly interspaced short palindromic repeats CRISPR
  • Cas CRISPR-associated protein
  • crRNA short sequences of RNA
  • tracrRNA trans-activating CRISPR RNA
  • gRNA guide RNA
  • the crRNA comprises a nucleotide sequence (known as a “spacer” or “spacer sequence”) that is complementary to the target strand of the DNA, whereas the tracrRNA serves as a binding scaffold for the Cas protein.
  • the Cas protein then may complex with the gRNA, and the ribonucleoprotein is targeted to a sequence substantially identical to the crRNA sequence.
  • the sequence that is substantially identical to the crRNA is known as the “protospacer” sequence, and it is directly adjacent to a “protospacer-adjacent motif” (PAM).
  • PAM is an “NGG” sequence, wherein N represents any standard nucleotide, and G represents guanine.
  • the Cas protein contains two nuclease domains capable of cutting the phosphate backbone of a nucleic acid, termed the HNH domain and the RuvC domain.
  • the HNH domain cuts the backbone of the strand complementary to the gRNA, referred to as the “target strand”, while the RuvC domain cuts the backbone of the opposite strand, also referred to as the “non- target strand” or “displaced strand” (i.e., the strand that contains the protospacer).
  • the gRNA-Cas complex binds a sequence of double-stranded DNA, each nuclease domain cuts the backbone of one strand of the DNA, causing a double-strand break (DSB).
  • the DSB may be repaired by the cell in several ways, including creation of an insertion or deletion (indel), homology-directed repair (HDR), microhomology-mediated end joining (MMEJ), or mismatch repair (MMR).
  • Indel insertion or deletion
  • HDR homology-directed repair
  • MMEJ microhomology-mediated end joining
  • MMR mismatch repair
  • Multiple Cas-based systems have been engineered to exploit each of these repair pathways.
  • Guide RNA design has been further characterized and engineered to improve editing efficiency and yield different editing results.
  • Other variants of Cas9 and Cas-type proteins have also been characterized.
  • each nuclease domains of the Cas9 may be mutated to impair the nuclease activity of the Cas9 protein to yield a “nickase” Cas9 protein (nCas9) that introduces a single-strand cut in a targeted DNA sequence, rather than a double-strand break.
  • “D10A” mutation of the RuvC domain results in a Cas9 protein that will cut only the strand complementary to the gRNA (i.e., the target strand).
  • Such nickases based on the “D10A” mutation of the RuvC domain of the Cas9 protein are used in base editing systems to nick the target strand, which is the strand opposite the strand that contains the protospacer.
  • “H840A” mutation of the HNH domain results in a Cas9 protein that will cut only the displaced strand (i.e., the strand that contains the protospacer sequence).
  • Such nickases based on the “H840A” mutation of the HNH domain of the Cas9 protein are used in template-based editing systems to nick the non-target strand or protospacer sequence. Mutations that impair both nuclease domains yield a catalytically dead Cas9 (also called “dCas9”), which is still capable of binding to a gRNA and targeting a region of a gene but does not inherently alter the target region.
  • dCas9 catalytically dead Cas9
  • Cas9 and Cas-type proteins include, but are not limited to, SpCas9 (e.g., dCas9 and nCas9), SaCas9 (e.g., SaCas9d, SaCas9d, SaKKH Cas9), NmeCas9, CasX, CasY, Cas12a/Cpf1, C2c1, C2c2, C2c3, and Argonaute.
  • a gene editor described herein may include a Cas9 or Cas-related domain or protein or suitable variants of the domain or protein.
  • a dual nickase gene editing system comprises one or more nickases, a first guide oligonucleotide, and a second guide oligonucleotide. At least one of the one or more nickases is configured to interact with the first guide oligonucleotide. In interaction with the first guide oligonucleotide, the nickase is engineered to nick one of a first or second strand of the LPA gene. At least one of the one or more nickases is configured to interact with the second guide oligonucleotide.
  • the nickase is engineered to nick the other of the first or second strands of the LPA gene.
  • the nickase(s) that interacts with the first and second guide oligonucleotides may be the same or different.
  • the resulting nicks on opposing strands in the LPA gene may activate a cellular DNA repair mechanism, which may result in an indel variant or non-synonymous variant in the LPA gene.
  • the dual nickase system may effect the indel variant or the non-synonymous variant.
  • Figures 1A-1D illustrate dual nickase editing systems that comprise a single nickase editor.
  • the nickase editor is a protein or protein complex capable of effecting indel variants or non-synonymous variants into a targeted DNA site using two guide nucleic acids.
  • the nickase editor may comprise a nickase Cas9.
  • a dual nickase editor system (the nickase protein and two guide nucleic acids) may be capable of locating a specific target in a gene or genome, nicking both strands at separate positions at a targeted DNA site.
  • the nickase protein may be catalytically inactivated or impaired such that it nicks or cuts at most one strand of a double-stranded nucleic acid target.
  • the “D10A” mutation of the RuvC domain of the Cas9 protein described above and the “H840A” mutation of the HNH domain of the Cas9 protein described above are examples of an impaired nuclease that is capable of being used in a dual nickase editor system.
  • Any suitable dual nickase editor system may be used to effect editing in the LPA gene of a cell or subject.
  • a cell or subject may be treated with an assembled lipid nanoparticle (LNP) encapsulating or otherwise comprising the nickase protein or a nucleic acid, such as an mRNA, encoding the nickase protein and two guide nucleic acids to effect the editing.
  • LNP lipid nanoparticle
  • the dual nickase editing process may occur as shown in Figure 1A or Figure 1C.
  • the targeted DNA site is engaged by the Cas9-D10A protein via the spacer region of the first guide nucleic acid, which is substantially identical to a protospacer sequence on one strand of the targeted DNA site.
  • the Cas9-D10A domain nicks the target strand of the first guide nucleic acid (i.e., the strand hybridized to the first spacer sequence).
  • the targeted DNA site is engaged by the Cas9-D10A protein via the spacer region of the second guide nucleic acid, which is substantially identical to a protospacer sequence on the other strand of the targeted DNA site.
  • the Cas9-D10A domain nicks the target strand of the second guide nucleic acid (i.e., the strand hybridized to the second spacer sequence).
  • the orientation of the protospacer sequences relative to each other dictates whether the two nick sites are some distance apart ( Figure 1A) or close together ( Figure 1C).
  • the two nicks on opposing DNA strands are subsequently repaired by the cell via non-homologous end-joining and may yield indel or non-synonymous variants.
  • the dual nickase editing process may occur as shown in Figure 1B or Figure 1D.
  • the targeted DNA site is engaged by the Cas9-H840A protein via the spacer region of the first guide nucleic acid, which is substantially identical to a protospacer sequence on one strand of the targeted DNA site.
  • the Cas9-H840A domain nicks the non-target strand of the first guide nucleic acid (i.e., the strand with the first protospacer sequence).
  • the targeted DNA site is engaged by the Cas9-H840A protein via the spacer region of the second guide nucleic acid, which is substantially identical to a protospacer sequence on the other strand of the targeted DNA site.
  • the Cas9-H840A domain nicks the non-target strand of the second guide nucleic acid (i.e., the strand with the second protospacer sequence).
  • the orientation of the protospacer sequences relative to each other dictates whether the two nick sites are close together ( Figure 1B) or some distance apart ( Figure 1D).
  • the two nicks on opposing DNA strands are subsequently repaired by the cell via non-homologous end-joining and may yield indel or non- synonymous variants.
  • the Cas9 nickase in operation with the first and second guide nucleotides nicks opposing strands of the DNA to generate 5’ overhangs (e.g., as shown in Figures 1A and 1D).
  • the Cas9 nickase in operation with the first and second guide nucleotides nicks opposing strands of the DNA to generate 3’ overhangs (e.g., as shown in Figures 1B and 1C).
  • the overhangs may have any length suitable to allow non-homologous end-joining.
  • the length of the overhangs suitable to allow non-homologous end-joining may vary based on, among other things, the composition of the overhangs.
  • the overhangs have a length from 1 to 200 nucleotides, such as 10 to 150 nucleotides, 15 to 100 nucleotides, or 20 to 50 nucleotides.
  • the overhangs have a length of 10 nucleotides or greater, such as 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 nucleotides or greater.
  • the overhangs have a length of 200 nucleotides or less, such as 190, 180, 170, 160, 150, 140, 130, 120, 110, 100, 90, 80, 70, 60, or 50 nucleotides or less. In some embodiments, the overhangs have a length of 20 to 50 nucleotides, such as 23 to 45, 30 to 40, 31 to 40, 32 to 40, 33 to 40, 31 to 39, 32 to 39, 33 to 39, or 34 to 38 nucleotides.
  • One implementation of a dual nickase editor system is the D10A mutation of the RuvC domain of the Streptococcus pyogenes Cas9 protein (SpCas9-D10A).
  • the protein and cDNA sequences of SpCas9-D10A are shown in Table 1. Also shown in Table 1 is a chemically modified mRNA sequence (MS029) that has been engineered to express SpCas9-D10A in cells, including with respect to editing in the LPA gene as is further described herein.
  • MS029 chemically modified mRNA sequence
  • One implementation of a dual nickase editor system is the H840A mutation of the RuvC domain of the Streptococcus pyogenes Cas9 protein (SpCas9-H840A).
  • the protein and cDNA sequences of SpCas9-H840A are shown in Table 1.
  • Table 1 Also shown in Table 1 is a chemically modified mRNA sequence that has been engineered to express SpCas9-H840A in cells, including with respect to editing in the LPA gene as is further described herein.
  • Table 1 Nickase SpCas9 protein, cDNA, and mRNA sequences Attorney Docket Number 0650.000010WO01
  • an mRNA encoding a nickase has a sequence of an mRNA listed in Table 1. In some embodiments, an mRNA encoding a nickase has a sequence that is at least about 90% identical, at least about 91% identical, at least about 92% identical, at least about 93% identical, at least about 94% identical, at least about 95% identical, at least about 96% identical, at least about 97% identical, at least about 98% identical, or at least about 99% identical to an mRNA sequence listed in Table 1. [139] In some embodiments, an mRNA encoding a nickase has a coding sequence of an mRNA listed in Table 1.
  • an mRNA encoding a nickase has a coding sequence that is at least about 90% identical, at least about 91% identical, at least about 92% identical, at least about 93% identical, at least about 94% identical, at least about 95% identical, at least about 96% identical, at least about 97% identical, at least about 98% identical, or at least about 99% identical to a coding sequence of an mRNA sequence listed in Table 1.
  • the coding sequence of an mRNA listed in Table 1 may be modified or optimized, the untranslated regions (UTRs), and/or the 5’ and 3’ ends (e.g., within three or within five nucleotides of the end) may be modified or optimized to enhance or alter stability and/or expression of the mRNA.
  • the mRNA may comprise one or more stabilizing motif, such as a 5’ and/or 3’ end stabilizing motif.
  • dual nickase editing systems are disclosed to effectuate editing in the LPA gene. IV.
  • a dual nickase editing system comprises more than one guide nucleic acid. In some embodiments, a dual nickase editing system comprises two guide nucleic acids.
  • a guide nucleic acid sequence directs a gene editor to a target genomic location. The guide nucleic acid may vary depending on the gene editor. The present disclosure refers to guide nucleic acids as guide nucleic acid sequences, guide RNAs, gRNAs and/or guide oligonucleotides. As described herein, guide RNAs may comprise an RNA sequence that may or may not be chemically modified.
  • Each guide nucleic acid may include a nucleotide sequence that is complementary to a targeted site in chromosomal DNA.
  • the portion of the guide nucleic acid that specifies the targeted site is referred to herein as the “spacer.” The spacer is typically located at the 5’ end of the guide nucleic acid.
  • each guide nucleic acid includes a spacer sequence that is identical to or substantially identical to a protospacer sequence of the LPA gene.
  • the gene editing system comprises two guide nucleic acids, each having different spacer sequences, wherein each spacer sequence is identical or substantially identical to a protospacer sequence specified in Table 2 or Table 5.
  • a guide oligonucleotide comprises a spacer comprising a sequence identical to or substantially identical to nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of a protospacer sequence specified in Table 2 or Table 5.
  • a guide oligonucleotide comprises a spacer comprising a sequence identical to or substantially identical to nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of a protospacer sequence specified in Table 2 or Table 5 with 0, 1, 2, 3, 4, or 5 mismatches.
  • a guide oligonucleotide comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, or at least about 95% identical to a protospacer sequence specified in Table 2 or Table 5. In some embodiments, a guide oligonucleotide comprises a spacer having a sequence that is identical to a protospacer sequence specified in Table 2 or Table 5.
  • a gene editing system described herein comprises a first guide oligonucleotide and a second guide oligonucleotide, where the first guide oligonucleotide comprises a spacer sequence identical to or substantially identical to a guide 1 protospacer sequence specified in Table 2 or Table 5, and the second guide oligonucleotide comprises a spacer sequence identical to or substantially identical to a corresponding (in the same row) guide 2 protospacer sequence specified in Table 2 or Table 5.
  • the first guide oligonucleotide comprises a spacer sequence identical to or substantially identical to nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of a guide 1 protospacer sequence specified in Table 2 or Table 5
  • the second guide oligonucleotide comprises a spacer sequence identical to or substantially identical to nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of a corresponding (in the same row) guide 2 protospacer sequence specified in Table 2 or Table 5.
  • the first guide oligonucleotide comprises a spacer sequence identical to or substantially identical to nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of a guide 1 protospacer sequence specified in Table 2 or Table 5 with 0, 1, 2, 3, 4, or 5 mismatches
  • the second guide oligonucleotide comprises a spacer sequence identical to or substantially identical to nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of a corresponding (in the same row) guide 2 protospacer sequence specified in Table 2 or Table 5 with 0, 1, 2, 3, 4, or 5 mismatches.
  • the first guide oligonucleotide comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, or at least about 95% identical to a guide 1 protospacer sequence specified in Table 2 or Table 5, and the second guide oligonucleotide comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, or at least about 95% identical to a corresponding (in the same row) guide 2 protospacer sequence specified in Table 2 or Table 5.
  • the first guide oligonucleotide comprises a spacer sequence identical to a guide 1 protospacer sequence specified in Table 2 or Table 5
  • the second guide oligonucleotide comprises a spacer sequence identical to a corresponding (in the same row) guide 2 protospacer sequence specified in Table 2 or Table 5.
  • Table 2 Examples of protospacers to which spacers of guide oligonucleotides may correspond
  • Each guide nucleic acid may include a portion that is recognized by and binds to the gene editor (e.g., the nickase).
  • the portion of the guide nucleic acid that recognizes and binds the gene editor may be referred to herein as the “scaffold” region.
  • the scaffold region may form one or more stem loop structures that are recognized by the gene editor.
  • a length of a loop and a stem can vary. In one or more embodiments, a loop can range from about 3 to about 10 nucleotides in length. In one or more embodiments, a stem can range from about 6 to about 20 nucleotides in length.
  • a stem can comprise one or more bulges of 1 to 10 nucleotides or about 10 nucleotides.
  • the overall length of a second region can range from about 16 to 60 nucleotides in length.
  • a loop can be about 4 nucleotides in length.
  • a stem can be about 12 nucleotides in length.
  • the scaffold region may include a region that does not form a stem loop structure. This portion lacking substantial secondary structure may have any suitable length, such as ranging from about 3 to about 100 nucleotides in length. The portion of the scaffold region lacking substantial secondary structure may be located at the 3’ end of the guide nucleic acid.
  • the scaffold region comprises a tracr sequence. In some embodiments, the scaffold region consists of, or consists essentially of, a tracr sequence.
  • the sequence of the scaffold region includes one of the following sequences: 5’- GUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAAC UUGAAAAAGUGGCACCGAGUCGGUGC -3’, or 5’- GUUUGAGAGCUAUGCUGGAAACAGCAUAGCAAGUUCAAAUAAGGCUAGUC CGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGC -3’.
  • the scaffold region may have a sequence that is at least 75%, at least 85%, at least 90%, or at least 95% identical to one of the sequences herein.
  • the appropriate scaffold region sequence and/or length may change depending on a number of factors, such as the editing protein used.
  • the scaffold region may include DNA and/or RNA nucleotides.
  • the scaffold region may be modified as described herein.
  • the sequence of the scaffold region comprises, consists essentially of, or consists of: 5’ - mGUUUUAGmAmGmCmUmAGmAmAmAmUmAmGmCmAmAGUUmAAmAAmUAmAm GmGmCmUmAGUmCmCGUUAmUmCAAmCmUmUGmAmAmAmAmAmGmUmGGmCm AmCmCmGmAmGmUmCmGmGmUmGmC 3’, where m of mN is 2′-O-methyl ribose.
  • a guide oligonucleotide may include an unstructured or a structured RNA motif, designed to be capable of preventing degradation of the nucleic acid.
  • the RNA motif may be located at the 3′ end of the nucleic acid.
  • the nucleic acid may include any suitable RNA motif, such as RNA motifs including the sequences listed below.
  • a guide oligonucleotide includes an RNA motif on the 5′ end of the nucleic acid.
  • the guide oligonucleotide includes an RNA motif on the 5′ end and the 3′ end.
  • a guide oligonucleotide may include an unstructured RNA motif that comprises, consists essentially of, or consists of the sequence 5′- UUU -3′.
  • the unstructured motif comprises modifications as follows: 5′-*mU*mU*mU -3′, where “mU*” indicates a phosphorothioated 2′-O-methyl uracil base, and “mU” indicates a 2′-O-methyl uracil base.
  • a guide oligonucleotide may include a tevopreQ1 motif.
  • a tevopreQ1 motif may be modified from a prequeosine1-1 riboswitch aptamer.
  • a guide oligonucleotide may include a tevopreQ1 motif that comprises, consists essentially of, or consists of the sequence 5′- CGCGGUUCUAUCUAGUUACGCGUUAAACCAACUAGAA -3′.
  • a guide oligonucleotide may include a mpknot motif.
  • a mpknot motif may be modified from a frameshifting pseudoknot from Moloney murine leukemia virus.
  • a guide oligonucleotide may include a mpknot motif that comprises, consists essentially of, or consists of the sequence 5′- GGGUCAGGAGCCCCCCCCCUGAACCCAGGAUAACCCUCAAAGUCGGGGGGCAACC C -3′.
  • a gRNA consists of, or consists essentially of, a sequence as follows: 5′- mN*mN*mN*NNNNNNNNNNNNNNNNNmGUUUUAGmAmGmCmUmAGmAmAmAmU mAmGmCmAmAGUUmAAmAAmUAmAmGmGmCmUmAGUmCmCGUUAmUmCAAmC mUmUGmAmAmAmAmAmGmUmGGmCmAmCmCmGmAmGmUmCmGmGmUmGmCmU *mU*mU*mU-3′, where N refers to any nucleotide, m of mN is 2′-O-methyl ribose, and * refers to a phosphorothioate linkage.
  • the first 20 nucleotides may correspond to a spacer sequence.
  • the spacer sequence may be identical to or substantially identical to a protospacer listed in Table 2 or Table 5.
  • a guide nucleic acid of a dual nickase editing system may have any suitable length. The length may depend on the CRISPR Cas component of the gene editor system and components used. For example, different Cas proteins from different bacterial species have varying optimal spacer sequence lengths.
  • the spacer sequence may comprise 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, or more than 50 nucleotides in length.
  • the spacer sequence comprises 15 to 24 nucleotides in length.
  • the spacer sequence comprises 18 to 24 nucleotides in length.
  • the spacer sequence comprises 19 to 21 nucleotides in length.
  • the spacer sequence comprises 20 nucleotides in length +/- 1 nucleotide, +/- 2 nucleotides, or +/- 3 nucleotides.
  • each guide nucleic acid includes a spacer sequence and otherwise conforms to a conventional 100-nucleotide Streptococcus pyogenes CRISPR gRNA sequence.
  • Each guide nucleic acid e.g., guide RNA
  • a guide nucleic acid includes DNA nucleotides. In one or more embodiments, a guide nucleic acid includes DNA and RNA. In one or more embodiments, a guide nucleic acid is an RNA, also referred to herein as a guide RNA or gRNA.
  • a guide nucleic acid is a modified nucleic acid.
  • a modified nucleic acid is a nucleic acid comprising at least one modified nucleobase, sugar, or backbone (e.g., linkage) moiety.
  • a guide nucleic acid may be synthesized.
  • the guide nucleic acid may comprise a spacer sequence configured to hybridize to the complementary sequence on a target strand under, for example, conditions within a cell.
  • the guide nucleic acid comprises a spacer sequence that is homologous to a protospacer sequence in an LPA gene.
  • the guide nucleic acid may comprise a spacer sequence that is identical to or substantially identical to a protospacer sequence.
  • the guide nucleic acid comprises a spacer having a sequence identical to or substantially identical to a protospacer set forth in Table 2 or Table 5.
  • the guide oligonucleotide may have a sequence set forth in Table 3 in which zero, one, or more than one nucleotide may be modified. Table 3. Example sequences of guide oligonucleotides
  • a guide oligonucleotide comprises one of more modified nucleotides.
  • the nucleotides may be modified in any suitable manner.
  • the nucleotide comprises a modified sugar moiety.
  • the sugar moiety may be modified in any suitable manner.
  • the modified sugar moieties comprise a 2’-O-methyl, 2’-O- methoxyethyl, 2’-O-aminoethyl, 2’-Fluoro, N3’ ⁇ P5’ phosphoramidate, 2’dimethylaminooxyethoxy, 2’ 2′dimethylaminoethoxyethoxy, 2′-guanidinidium, 2′-O- guanidinium ethyl, carbamate modified sugars, or bicyclic modified sugars.
  • the modified nucleotide comprises a 2’-O-methyl modification.
  • the nucleotide comprises a backbone modification.
  • the backbone modifications comprise a phosphorothioate, a phosphorodithioate, a phosphoroselenoate, a phosphorodiselenoate, a phosphoroanilothioate, a phosphoraniladate, a phosphoramidate, or a phosphorodiamidate linkage.
  • the backbone modification comprises a phosphorothioate linkage [165]
  • a spacer sequence of a guide oligonucleotide comprises from 1 to 20 modified nucleotides. In some embodiments, a spacer sequence comprises from 1 to 10 modified nucleotides.
  • a spacer sequence comprises from 1 to 5 modified nucleotides. In some embodiments, a spacer sequence comprises from 1 to 3 modified nucleotides. In some embodiments, one or more of the five 5′-most nucleotides of a spacer sequence are modified. In some embodiments, one or more of the five 5′-most nucleotides of a spacer sequence are modified to include a 2′-O-methyl group, a phosphorothioate linkage, or a combination thereof. In some embodiments, one or more of the three 5′-most nucleotides of a spacer sequence are modified.
  • one or more of the three 5′-most nucleotides of a spacer sequence are modified to include a 2′-O-methyl group, a phosphorothioate linkage, or a combination thereof. In some embodiments, the three 5′-most nucleotides of a spacer sequence are modified. In some embodiments, the three 5′-most nucleotides of a spacer sequence are modified to include a 2′-O-methyl group, a phosphorothioate linkage, or a combination thereof. In some embodiments, the three 5′-most nucleotides of a spacer sequence are modified to include a 2′-O-methyl group and a phosphorothioate linkage.
  • a scaffold sequence of a guide oligonucleotide comprises from 1 to 76 modified nucleotides, such as from 1 to 70 modified nucleotides, from 1 to 60 modified nucleotides, or from 1 to 55 modified nucleotides. In some embodiments, a scaffold sequence of a guide oligonucleotide comprises from 10 to 76 modified nucleotides, such as from 20 to 76 modified nucleotides, such as 30 to 76 modified nucleotides, 40 to 76 modified nucleotides, or 50 to 76 modified nucleotides.
  • a scaffold sequence of a guide oligonucleotide comprises from 20 to 70 modified nucleotides, such as from 30 to 65 modified nucleotides, from 40 to 60 modified nucleotides, or from 50 to 55 modified nucleotides. [167] In some embodiments, from 20% to 95% of the nucleotides of the scaffold sequence are modified. In some embodiments, from 30% to 90%, such as 40% to 85%, 45% to 80%, 50% to 75%, 60% to 75%, or 65% to 75% of the nucleotides of the scaffold sequence are modified. [168] In some embodiments, a modified scaffold nucleotide comprises a 2′ sugar modification.
  • a modified scaffold nucleotide comprises a 2′-O-methyl group.
  • from 20% to 95% of the nucleotides of the scaffold sequence comprise a 2′ sugar modification.
  • from 30% to 90%, such as 40% to 85%, 45% to 80%, 50% to 75%, 60% to 75%, or 65% to 75% of the nucleotides of the scaffold sequence comprise a 2′ sugar modification.
  • from 20% to 95% of the nucleotides of the scaffold sequence comprises a 2′-O-methyl group.
  • from 30% to 90%, such as 40% to 85%, 45% to 80%, 50% to 75%, 60% to 75%, or 65% to 75% of the nucleotides of the scaffold sequence comprise a 2′-O-methyl group.
  • Table 5 summarizes the percentages of LPA alleles edited in primary human hepatocytes (editing %, also referred to as editing efficiency) versus selected guide RNA pairs (first and second gRNAs) at relatively higher and lower doses, summarizing the LPA editing efficiencies in primary human hepatocytes using a gene editing system that comprises a Cas9 nickase with the specified pairs of first and second guide RNAs.
  • Table 6 shows the number of nucleotides between the nicks (the overhang length) for some of the gRNA pairs indicated in Table 5 and indicates the targeted exon. All nicking in Table 5 was in a PAM-out configuration. [171] In some embodiments, the location of the first nick and the location of the second nick are spaced apart from about 1 to 200 nucleotides, such as from 10 to 150 nucleotides, 15 to 100 nucleotides, or 20 to 50 nucleotides.
  • the distance between the first and second nicks is 10 nucleotides or greater, such as 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 nucleotides or greater.
  • the distance between nicks is 200 nucleotides or less, such as 190, 180, 170, 160, 150, 140, 130, 120, 110, 100, 90, 80, 70, 60, or 50 nucleotides or less.
  • the distance between nicks is from 20 to 50 nucleotides, such as 23 to 45, 30 to 40, 31 to 40, 32 to 40, 33 to 40, 31 to 39, 32 to 39, 33 to 39, or 34 to 38 nucleotides.
  • Table 4 provides the full gRNA sequences of the guides that were tested to produce the results presented in Table 5.
  • the tested guide oligonucleotides comprise RNA spacer sequences identical to the protospacer sequences shown in the table above, but with “U” substituted for “T”. Editing results are presented for those gRNA pairs that were evaluated by MessengerMax transfection. *Editing results for in vitro LNP delivery studies for guide pairs having spacer sequences corresponding to GA1264/GA1184 (GA1297/GA1296) and GA1266/GA1184 (GA1298/GA1296) are shown in Figure 4B and were similar to a guide pair having spacer sequences corresponding to GAI 183/GA1184 (GA1295/GA1296) - see, also, Table 4 and Table 7B.
  • the spacer for guide GA1265 overlaps with the spacers for GA1264 (and GA1297), GA1266 (and GA1298), and GAI 184 (and GA1295) (see Figure 4A for alignment of spacer/protospacer sequences of GA1297, GA1298, and GA1295) — the protospacer for GA1265 is between (and offset by one from) protospacer for GA1264 (and GA1297) and GA1266 (and GA1298).
  • a gene editing system described herein comprises a first guide oligonucleotide and a second guide oligonucleotide, where the first guide oligonucleotide comprises a spacer sequence identical to or substantially identical to a guide 1 protospacer sequence specified in Table 5, and the second guide oligonucleotide comprises a spacer sequence identical to or substantially identical to a corresponding (in the same row) guide 2 protospacer sequence specified in Table 5.
  • the first guide oligonucleotide comprises a spacer sequence identical to or substantially identical to a guide 1 protospacer sequence specified in Table 5
  • the second guide oligonucleotide comprises a spacer sequence identical to or substantially identical to a corresponding guide 2 protospacer sequence specified in Table 5, wherein the tested guide pair of Table 5 exhibited an editing of 20% or greater, of 30% or greater, of 40% or greater, of 50% or greater, of 60% or greater, of 70% or greater, of 80% or greater, of 85% or greater, or of 90% or greater at a concentration of 2500 ng/ml, or where the gRNA pair corresponds to GA1264/GA1184, GA1265/GA1184, or GA1266/GA1184.
  • the gene editing system comprises a first guide oligonucleotide and a second guide oligonucleotide, where the first guide oligonucleotide comprises a spacer sequence identical to or substantially identical to a guide 1 protospacer sequence specified in Table 5, and the second guide oligonucleotide comprises a spacer sequence identical to or substantially identical to a corresponding guide 2 protospacer sequence specified in Table 5 wherein the tested guide pair of Table 5 exhibited an editing of 50% or greater, of 60% or greater, of 70% or greater, of 80% or greater, of 85% or greater, or of 90% or greater at a concentration of 2500 ng/ml, or where the gRNA pair corresponds to GA1264/GA1184, GA1265/GA1184, or GA1266/GA1184.
  • the first guide oligonucleotide comprises a spacer sequence identical to or substantially identical to a guide 1 protospacer sequence specified in Table 5
  • the second guide oligonucleotide comprises a spacer sequence identical to or substantially identical to a corresponding guide 2 protospacer sequence specified in Table 5, wherein the tested guide pair exhibited an editing of 70% or greater, of 80% or greater, of 85% or greater, or of 90% or greater at a concentration of 2500 ng/ml, or where the guide pair corresponds to GA1264/GA1184, GA1265/GA1184, or GA1266/GA1184.
  • the first guide oligonucleotide comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’-CUGUCACCAGGCAUUGUGUC-3’; and the second guide oligonucleotide comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’-UGUCCUUGCAACUCUCACGG-3’.
  • an oligonucleotide comprising nucleotides 6 to 20 of 5’-CUGUCACCAGGCAUUGUGUC-3’ would comprise 5’- ACCAGGCAUUGUGUC-3’.
  • the first guide oligonucleotide comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’- CUGUCACCAGGCAUUGUGUC-3’
  • the second guide oligonucleotide comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’- UGUCCUUGCAACUCUCACGG-3’.
  • the first guide oligonucleotide comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- GUAGUAGCAGUCCUGUACCC-3’; and the second guide oligonucleotide comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- CAUUAUGGACAGAGUUACCG-3’.
  • the first guide oligonucleotide comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’- GUAGUAGCAGUCCUGUACCC-3’
  • the second guide oligonucleotide comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’- CAUUAUGGACAGAGUUACCG-3’.
  • the first guide oligonucleotide comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’-AGGACACUCGAUUCUGUCAC-3’; and the second guide oligonucleotide comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- CACAACUCCCACAGUGGCCC-3’.
  • the first guide oligonucleotide comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’- AGGACACUCGAUUCUGUCA-3’
  • the second guide oligonucleotide comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’- CACAACUCCCACAGUGGCCC-3’.
  • the first guide oligonucleotide comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’-CUGUCACUGGACAUUGUGUC-3’; and the second guide oligonucleotide comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’-AAGUGUCCUUGCGACGUCCA-3’.
  • the first guide oligonucleotide comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’- CUGUCACUGGACAUUGUGUC-3’
  • the second guide oligonucleotide comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’- AAGUGUCCUUGCGACGUCCA-3’.
  • the first guide oligonucleotide comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’-GGAGCAAAGCCCCACAGUCC-3’; and the second guide oligonucleotide comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’-GUUGGUGCUGAAAUUCAAAG-3’.
  • the first guide oligonucleotide comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’- GGAGCAAAGCCCCACAGUCC-3’
  • the second guide oligonucleotide comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’- GUUGGUGCUGAAAUUCAAAG-3’.
  • the first guide oligonucleotide comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’-GGAGCAAAGCCCCGGGGUCC-3’; and the second guide oligonucleotide comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’-GUUGGUGCUGAAAUUCAAAG-3’.
  • the first guide oligonucleotide comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’- GGAGCAAAGCCCCGGGGUCC-3’
  • the second guide oligonucleotide comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’- GUUGGUGCUGAAAUUCAAAG-3’.
  • the first guide oligonucleotide comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’-CUGGAACUGGGACCACCGU-3’; and the second guide oligonucleotide comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’-ACAGAGCUUCCUUCUGAAGA-3’.
  • the first guide oligonucleotide comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’- CUGGAACUGGGACCACCGU-3’
  • the second guide oligonucleotide comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’- ACAGAGCUUCCUUCUGAAGA-3’.
  • the first guide oligonucleotide comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’-AUGCCAGUGUGGUGUCAUAG-3’; and the second guide oligonucleotide comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’-ACCACAGAAUACUACCCAAA-3’.
  • the first guide oligonucleotide comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’- AUGCCAGUGUGGUGUCAUAG -3’
  • the second guide oligonucleotide comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’- ACCACAGAAUACUACCCAAA -3’.
  • the first guide oligonucleotide comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’-GGAGCCAGAAUAACAUUCGG-3’; and the second guide oligonucleotide comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’-CUAGAGGCUUUUUUUGAACA-3’.
  • the first guide oligonucleotide comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’- GGAGCCAGAAUAACAUUCGG -3’
  • the second guide oligonucleotide comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’- CUAGAGGCUUUUUUGAACA -3’.
  • the first guide oligonucleotide comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’-CAGAUGCUGAGAUUAGUCCU-3’; and the second guide oligonucleotide comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’-UGGAUUCCUGCAGUAGUUCC-3’.
  • the first guide oligonucleotide comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’- CAGAUGCUGAGAUUAGUCCU-3’
  • the second guide oligonucleotide comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’- UGGAUUCCUGCAGUAGUUCC-3’.
  • the first guide oligonucleotide comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’-UGACACCACAUUGGCAUCGG-3’; and the second guide oligonucleotide comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’-ACAUGUUCUUCCUGUGAUAG-3’.
  • the first guide oligonucleotide comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’- UGACACCACAUUGGCAUCGG-3’
  • the second guide oligonucleotide comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’- ACAUGUUCUUCCUGUGAUAG-3’.
  • the first guide oligonucleotide comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’-CAUAGAUGACCAAGAUUGAC-3’; and the second guide oligonucleotide comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’-UGAUACCACACUGGCAUCAG-3’.
  • the first guide oligonucleotide comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’- CAUAGAUGACCAAGAUUGAC-3’
  • the second guide oligonucleotide comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’- UGAUACCACACUGGCAUCAG-3’.
  • the first guide oligonucleotide comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’-CCAUCACUGGACAUUGCGUC-3’; and the second guide oligonucleotide comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’-AACUCUCCUCACAACUCCCA-3’.
  • the first guide oligonucleotide comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’- CCAUCACUGGACAUUGCGUC-3’
  • the second guide oligonucleotide comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’- AACUCUCCUCACAACUCCCA-3’.
  • the first guide oligonucleotide comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’-CUGCAUCUGAGCAUCGUGUC-3’; and the second guide oligonucleotide comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’-CGUCCCUCCGAAUGUUAUUC-3’.
  • the first guide oligonucleotide comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’- CUGCAUCUGAGCAUCGUGUC-3’
  • the second guide oligonucleotide comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’- CGUCCCUCCGAAUGUUAUUC-3’.
  • the first guide oligonucleotide comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’-AAACAGCCGUGGACGUCGCA-3’; and the second guide oligonucleotide comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’-UGAACAAGGUAAGAAGUCUC-3’.
  • the first guide oligonucleotide comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’- AAACAGCCGUGGACGUCGCA-3’
  • the second guide oligonucleotide comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’- UGAACAAGGUAAGAAGUCUC-3’.
  • the first guide oligonucleotide comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’-ACAGAGGCUCCUUCUGAACA-3’; and the second guide oligonucleotide comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’-GCUUGGAACCGGGGCCACUG-3’.
  • the first guide oligonucleotide comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’- ACAGAGGCUCCUUCUGAACA-3’
  • the second guide oligonucleotide comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’- GCUUGGAACCGGGGCCACUG-3’.
  • the first guide oligonucleotide comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’-AUGCCAGUGUGGUGUCAUAG-3’; and the second guide oligonucleotide comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’-ACAACAGAAUAUUAUCCAAA-3’.
  • the first guide oligonucleotide comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’- AUGCCAGUGUGGUGUCAUAG-3’
  • the second guide oligonucleotide comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’- ACAACAGAAUAUUAUCCAAA-3’.
  • the first guide oligonucleotide comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’-CUAUGACACCACAUUGGCAU-3’; and the second guide oligonucleotide comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’-ACAUGUUCUUCCUGUGAUAG-3’.
  • the first guide oligonucleotide comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’- CUAUGACACCACAUUGGCAU-3’
  • the second guide oligonucleotide comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’- ACAUGUUCUUCCUGUGAUAG-3’.
  • the first guide oligonucleotide comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’-AAUAACAUUCGGAGGGACGA-3’; and the second guide oligonucleotide comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’-UAUUCUGGCUCCAAGCCUAG-3’.
  • the first guide oligonucleotide comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’- AAUAACAUUCGGAGGGACGA-3’
  • the second guide oligonucleotide comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’- UAUUCUGGCUCCAAGCCUAG-3’.
  • the first guide oligonucleotide comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’-GUAGCAGUCCUGUACCCCGG-3’; and the second guide oligonucleotide comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’-CAUUAUGGACAGAGUUACCG-3’.
  • the first guide oligonucleotide comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’-GUAGCAGUCCUGUACCCCGG-3’
  • the second guide oligonucleotide comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’- CAUUAUGGACAGAGUUACCG -3’.
  • the first guide oligonucleotide comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’-AGUAGCAGUCCUGUACCCCG-3’; and the second guide oligonucleotide comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’-CAUUAUGGACAGAGUUACCG-3’.
  • the first guide oligonucleotide comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’-AGUAGCAGUCCUGUACCCCG-3’
  • the second guide oligonucleotide comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’- CAUUAUGGACAGAGUUACCG -3’.
  • the first guide oligonucleotide comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’-UAGUAGCAGUCCUGUACCCC-3’; and the second guide oligonucleotide comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’-CAUUAUGGACAGAGUUACCG-3’.
  • the first guide oligonucleotide comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’-UAGUAGCAGUCCUGUACCCC-3’
  • the second guide oligonucleotide comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’- CAUUAUGGACAGAGUUACCG -3’.
  • the first guide oligonucleotide comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’-UGGACCACAUGGCUUUGCUC-3’; and the second guide oligonucleotide comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’-ACGUACUCCACCACUGUCAC-3’.
  • the first guide oligonucleotide comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’-UGGACCACAUGGCUUUGCUC-3’
  • the second guide oligonucleotide comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’- ACGUACUCCACCACUGUCAC-3’.
  • Table 7A summarizes dose response curves in human hepatocellular carcinoma immortalized cells (HuH-7) for five (5) pairs of first and second guide RNAs using a gene editing system that comprises a dual nickase Cas9 system.
  • the Cas9 nickase is encoded within an mRNA (MS029) that was transfected into the HuH-7 cells in a 1:1 total mRNA: total gRNA weight ratio.
  • Table 7B summarizes dose response curves in HuH-7 cells tested in a separate experiment under similar conditions to those used to generate the results presented in Table 7A.
  • Table 7A Average editing % of selected pairs of guide RNA pairs at different doses Table 7B.
  • a guide oligonucleotide, or a portion(s) thereof is chemically modified.
  • Chemical modification of the guide oligonucleotide may provide improved stability when transfected into mammalian cells.
  • gRNAs can be chemically modified to comprise a combination of 2’-O-methylribosugar and phosphorothioate backbone modifications on at least one 5’ nucleotide and at least one 3’ nucleotide of each gRNA.
  • the three terminal 5’ nucleotides and three terminal 3’ nucleotides are chemically modified to comprise combinations of 2’-O-methylribosugar and phosphorothioate modifications.
  • the present disclosure also contemplates guide nucleic acids that comprise component portions (e.g., crRNA, tracrRNA or scaffold region that may comprise tracrRNA, and connector regions there between) of the guide nucleic acids specified above.
  • the guide oligonucleotides described herein can be synthesized chemically, enzymatically, or via a combination thereof.
  • the guide oligonucleotide can be synthesized using conventional phosphoramidite-based solid-phase synthesis methods.
  • a gRNA can be synthesized in vitro by operably linking DNA encoding the gRNA to a promoter control sequence that is recognized by, for example, a phage RNA polymerase.
  • suitable phage promoter sequences include, but are not limited to, T7, T3, SP6 promoter sequences, or variations thereof.
  • a guide oligonucleotide comprises two separate molecules (e.g., crRNA (which comprises the spacer) and tracrRNA or scaffold region, which may comprise tracrRNA).
  • One molecule guide oligonucleotide portion e.g., tracrRNA or scaffold region, which may comprise tracrRNA
  • the other molecule e.g., crRNA
  • Portions of the guide oligonucleotide can be ligated to one another via splint ligation or other suitable methods, thereby forming a larger unified guide oligonucleotide.
  • the guide oligonucleotide may include, in addition to RNA nucleotides, DNA nucleotides and/or nucleotide analogs.
  • a gRNA may comprise molecules other than RNA.
  • more than two guide nucleic acids may be used simultaneously to install edits at one or more target genomic locations.
  • a gene editing and delivery system as described herein may comprise a guide oligonucleotide having a spacer region engineered to bind to a target sequence on a strand of the human LPA gene opposing a protospacer within the LPA gene.
  • the gene editing system is configured such that the nickase in cooperation with a guide oligonucleotide nicks one strand of the LPA gene within, or in proximity to, the target sequence or the protospacer.
  • the gene editing system is engineered such that the nickase nicks within 5 nucleotides, within 4 nucleotides, within 3 nucleotides, within 2 nucleotides, within 1 nucleotide, or at the location between the 3’ end of the protospacer and the PAM or at a corresponding location in the target sequence. In embodiments, the gene editing system is engineered such that the gene editing system nicks within 2 or 3 nucleotides of the 3’ end of the protospacer or the corresponding location in the target sequence.
  • the gene editing system is engineered such that the gene editing system nicks (i) within the protospacer and within 2 or 3 nucleotides of the 3’ end of the protospacer or (ii) at the corresponding location in the target sequence.
  • the target sequence to which the spacer region of the guide oligonucleotide binds corresponds to (i.e., is complementary to) a protospacer sequence listed in Table 2 or Table 5.
  • the spacer sequence is identical to, or has at least about 75%, at least about 80%, at least about 85%, at least about 90%, or at least about 95% identity to, a protospacer listed in Table 2 or Table 5.
  • the guide oligonucleotide includes a spacer sequence that is identical or substantially identical to a protospacer listed in Table 2 or Table 5, or a 3′ portion thereof, with 0, 1, 2, 3, 4, or 5 mismatches.
  • the spacer region of the guide oligonucleotide comprises a sequence identical to the 15, 16, 17, 18, 19, or twenty 3’-most nucleotides of a protospacer listed in Table 2 or Table 5.
  • a spacer may comprise a sequence identical to the 15, 16, 17, 18, 19, or twenty 3’-most nucleotides of the protospacer in the first row and first column Table 2 (5’-GGAGCCAGAATAACATTCGG-3’), meaning that the spacer may comprise a sequence of 5’-GGAGCCAGAAUAACAUUCGG-3’, 5’-GAGCCAGAAUAACAUUCGG-3’, 5’-AGCCAGAAUAACAUUCGG-3’, 5’-GCCAGAAUAACAUUCGG-3, 5’- CCAGAAUAACAUUCGG-3’, or 5’-CAGAAUAACAUUCGG-3’.
  • the guide oligonucleotide comprises a spacer having a sequence identical to a protospacer listed in Table 2 or Table 5.
  • a gene editing and delivery system as described herein may comprise a first guide oligonucleotide and a second guide oligonucleotide.
  • the first guide oligonucleotide binds a first target sequence on a first strand of the human LPA gene
  • the second guide oligonucleotide binds a second target sequence on a second strand of the LPA gene.
  • the first target sequence opposes and is complementary to a first protospacer within the LPA gene.
  • the second target sequence opposes and is complementary to a second protospacer within the LPA gene.
  • the gene editing system is engineered such that one or more 97 nickases, in cooperation with the first guide oligonucleotide, nicks one strand of the LPA gene within, or in proximity to, the first target sequence or the first protospacer and, in cooperation with the second guide oligonucleotide, nicks the other strand of the LPA gene within, or in proximity to, the second target sequence or the second protospacer.
  • the gene editing system is engineered such that one or more nickases, in cooperation with the first guide oligonucleotide, nicks a strand of the LPA gene within 5 nucleotides, within 4 nucleotides, within 3 nucleotides, within 2 nucleotides, within 1 nucleotide, or at the location between the 3’ end of the first protospacer and the PAM or at a corresponding location in the first target sequence and, in cooperation with the second guide oligonucleotide, nicks the other strand of the LPA gene within 5 nucleotides, within 4 nucleotides, within 3 nucleotides, within 2 nucleotides, within 1 nucleotide, or at the location between the 3’ end of the second protospacer and the PAM or at a corresponding location in the second target sequence.
  • the gene editing system is engineered such that the gene editing system nicks a strand of the LPA gene within 2 or 3 nucleotides of the 3’ end of the first protospacer or the corresponding location in the first target sequence and nicks the other strand of the LPA gene within 2 or 3 nucleotides of the 3’ end of the second protospacer or the corresponding location in the second target sequence.
  • the gene editing system is engineered such that the gene editing system nicks a strand of the LPA gene (i) within the protospacer and within 2 or 3 nucleotides of the 3’ end of the first protospacer or (ii) at the corresponding location in the first target sequence and nicks the other strand of the LPA gene (i) within the second protospacer and within 2 or 3 nucleotides of the 3’ end of the second protospacer or (ii) at the corresponding location in the second target sequence.
  • the target sequence to which the spacer region of the first guide oligonucleotide binds corresponds to a guide 1 protospacer sequence listed in Table 2 or Table 5
  • the target sequence to which the spacer region of the second guide oligonucleotide binds corresponds to a guide 2 protospacer sequence listed in Table 2 or Table 5, where the guide 1 protospacer and the guide 2 protospacer are in the same row of Table 2 or Table 5.
  • the spacer sequence of the first guide oligonucleotide is identical to, or has at least about 75%, at least about 80%, at least about 85%, at least about 90%, or at least about 95% identity to, a guide 1 protospacer listed in Table 2 or Table 5, and the spacer sequence of the second guide oligonucleotide is identical to, or has at least about 75%, at least about 80%, at least about 85%, at least about 90%, or at least about 95% identity to, a guide 2 protospacer 98 listed in Table 2 or Table 5, where the guide 1 protospacer and the guide 2 protospacer are in the same row of Table 2 or Table 5.
  • the first guide oligonucleotide includes a spacer sequence that is identical or substantially identical to a guide 1 protospacer sequence listed in Table 2 or Table 5, or a 3′ portion thereof, with 0, 1, 2, 3, 4, or 5 mismatches
  • the second guide oligonucleotide includes a spacer sequence that is identical or substantially identical to a guide 2 protospacer sequence listed in Table 2 or Table 5, or a 3′ portion thereof, with 0, 1, 2, 3, 4, or 5 mismatches, where the guide 1 protospacer and the guide 2 protospacer are in the same row of Table 2 or Table 5.
  • the spacer region of the first guide oligonucleotide comprises a sequence identical to the 15, 16, 17, 18, 19, or twenty 3’-most nucleotides of a guide 1 protospacer listed in Table 2 or Table 5
  • the spacer region of the second guide oligonucleotide comprises a sequence identical to the 15, 16, 17, 18, 19, or twenty 3’-most nucleotides of a guide 2 protospacer listed in Table 2 or Table 5, where the guide 1 protospacer and the guide 2 protospacer are in the same row of Table 2 or Table 5.
  • the first guide oligonucleotide comprises a spacer having a sequence identical to a guide 1 protospacer listed in Table 2 or Table 5
  • the second guide oligonucleotide comprises a spacer having a sequence identical to a guide 2 protospacer listed in Table 2 or Table 5, where the guide 1 protospacer and the guide 2 protospacer are in the same row of Table 2 or Table 5.
  • V. GENE EDITOR SYSTEMS [207] The term “gene editor” is used throughout this disclosure to refer to a protein or protein complex that is capable of inserting, replacing, deleting, or nicking a DNA sequence in a genome in the presence of, or in operation with, a guide nucleic acid(s).
  • the guide nucleic acid(s) and the gene editor are collectively referred to herein as a “gene editor system” or “gene editing system.”
  • intracellular enzymes such as DNA repair enzymes, may facilitate or otherwise be required to finalize incorporation of the edit into the genome.
  • a gene editor that nicks a DNA strand may in operation interact with two different guide oligonucleotides to nick opposing strands of genomic DNA. The nicks on opposing strands may facilitate one or more DNA repair mechanisms to cause the edit (e.g., cause an indel variant or non-synonymous variant).
  • Gene editor systems are nucleotide-directed.
  • These systems generally include at least an editing protein and a guide nucleic acid.
  • the proteins and systems described above as Cas9, nucleotide-directed editing proteins, and nickases are encompassed by the term “gene editing system”.
  • the guide nucleic acids described above may also be a component of a “gene editing system”.
  • the editing proteins described herein are nickases, which in operation with a guide oligonucleotide nick a single strand of genomic DNA.
  • the nickase operates with a first guide oligonucleotide to nick one strand of the genomic DNA and operates with a second guide oligonucleotide to nick the other strand of the genomic DNA.
  • the first and second guide oligonucleotides comprise spacer sequences complementary to target sequences on opposing strands of the genomic DNA.
  • Such nickases are contrasted with nucleases (e.g., a Cas9 nuclease) that interact with a single guide RNA to catalyze double-strand cleavage of DNA.
  • the editing proteins described herein may include, but are not limited to, a Cas nickase such as a Streptococcus pyogenes Cas9 variant, a Staphylococcus aureus Cas9 variant, or a Cas12a/Cpf1 variant.
  • the editing protein may be provided as a recombinant protein.
  • the editing protein may alternately be transcribed and/or translated from a provided nucleotide such as mRNA or plasmid DNA.
  • the guide nucleic acid may include, but is not limited to, a spacer sequence and a scaffold region.
  • the guide nucleic acid components may be covalently attached to one another, may be assembled into a complex, or may be provided as individual strands.
  • the nucleotide components may alternately be transcribed from a provided nucleic acid, such as plasmid DNA.
  • the nucleotide components and the gene editor may be transcribed from a single nucleic acid, such as plasmid DNA or linear DNA. Protein components may then be translated from a transcript.
  • the nucleic acid encoding the gene editor is an mRNA.
  • the mRNA generates the gene editor upon translation in the targeted cell or subject after the administration.
  • the gene editor forms a ribonucleoprotein (RNP) complex in the targeted cell or subject.
  • RNP ribonucleoprotein
  • the editing of the present disclosure may comprise one or more additional features.
  • the gene editor may comprise cytoplasmic localization sequences, export sequences, such as nuclear export sequences, or other localization sequences, as well as sequence tags that are useful for solubilization, purification, or detection of the fusion proteins.
  • Suitable protein tags include, but are not limited to, biotin carboxylase carrier protein (BCCP) tags, myc-tags, calmodulin-tags, FLAG-tags, hemagglutinin (HA)-tags, polyhistidine tags, also referred to as histidine tags or His-tags, maltose binding protein (MBP)-tags, nus-tags, glutathione-S- transferase (GST)-tags, green fluorescent protein (GFP)-tags, thioredoxin-tags, S-tags, Softags (e.g. , Softag 1, Softag 3), strep-tags , biotin ligase tags, FlAsH tags, V5 tags, and SBP-tags.
  • BCCP biotin carboxylase carrier protein
  • MBP maltose binding protein
  • GST glutathione-S- transferase
  • GFP green fluorescent protein
  • Softags e.g. , Softag 1, Softag 3
  • the gene editor comprises one or more His tags.
  • the guide nucleic acids and compositions described herein may be administered to target cells or a subject in need thereof, in a therapeutically effective amount, to treat or prevent cardiovascular disease.
  • the subject has cardiovascular disease due at least in part to an elevated blood Lp(a) concentration, which may be directly correlated with apo(a) concentration or may be inversely correlated with size of the apo(a) protein.
  • the subject has atherosclerotic cardiovascular disease due at least in part to an elevated blood Lp(a) concentration, which may be directly correlated with apo(a) concentration or may be inversely correlated with the size of the apo(a) protein.
  • the subject has calcific aortic valve disease due at least in part to an elevated blood Lp(a) concentration, which may be directly correlated with apo(a) concentration or may be inversely correlated the size of the apo(a) protein.
  • the guide nucleic acids direct the gene editor to effect a modification in the LPA gene to reduce the blood Lp(a) concentration, which may be directly correlated with apo(a) concentration or may be inversely correlated with the size of the apo(a) protein in the subject.
  • the genetic alteration occurs in the cells of the liver (hepatocytes) in the subject.
  • the gene editor system includes an editing protein and guide nucleic acids, which may be introduced and/or expressed in a cell wherein target gene editing is desired, such as, for example, a liver cell (or hepatocyte), thereby allowing contact of the target gene with the guide nucleic acids, such as gRNAs, and the gene editor protein.
  • the binding of the editing protein to the target polynucleotide sequences in the target gene is directed by the guide nucleic acids, wherein the spacer sequence of each guide nucleic acid hybridizes with a complementary sequence in the target strand in the target gene.
  • the guide nucleic acids guide the editing protein to edit a polynucleotide sequence in the target gene.
  • the guide nucleic acids are co-introduced into a cell where editing is desired with the editing protein or with a nucleic acid encoding the editing protein.
  • the methods and compositions disclosed herein impair the function of the apo(a) protein encoded by the LPA gene to constitute Lp(a) particles. Impairment of function may be measured by the blood Lp(a) concentration in a subject to whom the method or composition disclosed herein has been administered. For example, the methods and compositions disclosed herein may reduce the blood Lp(a) concentration by at least 10-95 percent relative to a control.
  • the methods and compositions disclosed herein may reduce the blood Lp(a) concentration by at least 10 percent, at least 15 percent, at least 20 percent, at least 25 percent, at least 30 percent, at least 35 percent, at least 40 percent, at least 45 percent, at least 50 percent, at least 55 percent, at least 60 percent, at least 65 percent, at least 70 percent, at least 75 percent, at least 80 percent, at least 85 percent, at least 90 percent, or at least 95 percent relative to a control.
  • the method for treating or preventing cardiovascular disease in a subject in need thereof as described herein includes administering (i) guide nucleic acids and (ii) a nucleic acid encoding an editing protein to the subject.
  • the method for treating or preventing cardiovascular disease in a subject in need thereof as described herein includes administering a lipid nanoparticle (LNP) encapsulating or otherwise delivering a (i) guide nucleic acids or nucleic acids encoding the guide nucleic acids and/or (ii) an editing protein comprising a programmable DNA binding domain or a nucleic acid encoding the same, as such guide nucleic acids and editing proteins or nucleic acids encoding the same are described herein.
  • LNP lipid nanoparticle
  • the (i) guide nucleic acids or nucleic acids encoding the same and (ii) the editing protein comprising a programmable DNA binding domain or a nucleic acid encoding the same are enclosed in the same LNPs. In one or more aspects, they are enclosed in separate LNPs. VII. PHARMACEUTICAL COMPOSITIONS [220] In one or more aspects, provided herein is a pharmaceutical composition comprising the guide oligonucleotides or the gene editor system as provided herein and a pharmaceutically acceptable carrier or excipient.
  • a pharmaceutical composition for gene modification comprising guide nucleic acids, such as one or more gRNA, as described herein and an editing protein or a nucleic acid sequence encoding the editing protein and a pharmaceutically acceptable carrier.
  • Pharmaceutical compositions are formulated in a conventional manner using one or more pharmaceutically acceptable inactive ingredients that facilitate processing of the active compounds into preparations that can be used pharmaceutically. Suitable pharmaceutically acceptable additives are generally well known in the art. Proper formulation is dependent upon the route of administration chosen.
  • a pharmaceutical composition can comprise any suitable molar ratio of guide nucleic acids, such as gRNAs, as described herein or nucleic acid sequences encoding the guide RNAs to each other.
  • the weight ratio of one guide nucleic acid (or a nucleic acid sequence encoding the one guide RNA) to the other guide nucleic acid (or a nucleic acid sequence encoding the other guide RNA) is from 10:1 to 1:10, such as from 5:1 to 1:5, 3:1 to 1:3, or 2:1 to 1:2. In some embodiments, the weight ratio is 1:1 to 1:3. In some embodiments, the weight ratio is about 1:2. In some embodiments, the weight ratio is 1:1.5 to 1:2.5. Thus, for example, the weight ratio of one guide RNA to the other guide RNA may be 1:1 to 1:3 or 3:1.
  • a pharmaceutical composition can comprise any suitable molar ratio of guide nucleic acids, such as gRNAs, as described herein or nucleic acid sequences encoding the guide RNAs to the editing protein or a nucleic acid sequence encoding the editing protein.
  • the weight ratio of the guide nucleic acids (or nucleic acid sequences encoding the guide nucleic acids) to the editing protein (or nucleic acid encoding the editing protein) is from 10:1 to 1:10, such as from 5:1 to 1:5, 3:1 to 1:3, or 2:1 to 1:2.
  • the weight ratio is 1:1 to 1:3.
  • the weight ratio is about 1:2.
  • the ratio is 1:1.5 to 1:2.5.
  • a pharmaceutical composition can be a mixture of guide nucleic acids, such as gRNAs, as described herein or nucleic acid sequences encoding the guide RNAs and an editing protein or a nucleic acid sequence encoding the editing protein with one or more of other chemical components (i.e., pharmaceutically acceptable ingredients), such as carriers, excipients, binders, filling agents, suspending agents, flavoring agents, sweetening agents, disintegrating agents, dispersing agents, surfactants, lubricants, colorants, diluents, solubilizers, moistening agents, plasticizers, stabilizers, penetration enhancers, wetting agents, anti–foaming agents, antioxidants, preservatives, or one or more combination thereof.
  • other chemical components i.e., pharmaceutically acceptable ingredients
  • the pharmaceutical composition facilitates administration to an organism or a subject in need thereof.
  • the pharmaceutical compositions of the present disclosure can be administered to a subject using any suitable methods known in the art.
  • the pharmaceutical compositions described herein can be administered to the subject in a variety of ways, including parenterally, intravenously, intradermally, intramuscularly, colonically, rectally, or intraperitoneally.
  • the pharmaceutical compositions can be administered by intraperitoneal injection, intramuscular injection, subcutaneous injection, or intravenous injection of the subject.
  • the pharmaceutical compositions can be administered parenterally, intravenously, intramuscularly, or orally.
  • the pharmaceutical composition comprises a pharmaceutically acceptable solution comprising an LNP encapsulating one or more gRNAs and mRNAs encoding the editor protein(s) engineered to effect edits in the LPA gene, as described herein, that is administered intravenously to a subject in need thereof; the LNP may or may not include GalNAc (e.g., a GalNAc-lipid) as described herein.
  • a pharmaceutical composition for gene modification includes a further therapeutic agent. The additional therapeutic agent may modulate different aspects of the disease, disorder, or condition being treated and provide a greater overall benefit than administration of the therapeutic agent alone.
  • Therapeutic agents include, but are not limited to, a chemotherapeutic agent, a radiotherapeutic agent, a hormonal therapeutic agent, and/or an immunotherapeutic agent.
  • the therapeutic agent may be a radiotherapeutic agent.
  • the therapeutic agent may be a hormonal therapeutic agent.
  • the therapeutic agent may be an immunotherapeutic agent.
  • the therapeutic agent is a chemotherapeutic agent. Preparation and dosing schedules for additional therapeutic agents can be used according to manufacturers’ instructions or as determined empirically by a skilled practitioner. A.
  • compositions may be encapsulated in or comprise lipid nanoparticles (LNPs).
  • LNPs lipid nanoparticles
  • a “lipid nanoparticle (LNP) composition” or a “nanoparticle composition” is a composition comprising one or more described lipids.
  • LNP compositions or formulations, as contemplated herein, are typically sized on the order of micrometers or smaller and may include a lipid bilayer.
  • Nanoparticle compositions encompass lipid nanoparticles (LNPs), liposomes (e.g., lipid vesicles), and lipoplexes.
  • a nanoparticle composition or formulation as contemplated herein may be a liposome having a lipid bilayer with a diameter of 500 nm or less.
  • a LNP as described herein may have a mean diameter of from about 1 nm to about 2500 nm, from about 10 nm to about 1500 nm, from about 20 nm to about 1000 nm, from about 30 nm to about 150 nm, from about 40 nm to about 150 nm, from about 50 nm to about 150 nm, from about 60 nm to about 130 nm, from about 50 nm to 90 nm, from about 55 nm to 85 nm, from about 55 nm to 75 nm, from about 50 nm to about 80 nm, from about 60 nm to about 80 nm, from about 70 nm to about 110 nm, from about 70 nm to about 100 nm, from about 80 nm to about 100 nm, from about 90 n
  • the LNPs described herein can have a mean diameter of about 30 nm, 35 nm, 40 nm, 45 nm, 50 nm, 55 nm, 60 nm, 65 nm, 70 nm, 75 nm, 80 nm, 85 nm, 90 nm, 95 nm, 100 nm, 105 nm, 110 nm, 115 nm, 120 nm, 125 nm, 130 nm, 135 nm, 140 nm, 145 nm, 150 nm, or greater.
  • the mean diameter of the LNP is about 70 nm +/- 20 nm, 70 nm +/- 10 nm, 70 nm +/- 5 nm. In one embodiment the mean diameter of the LNP is about 60 nm +/- 20 nm, 60 nm +/- 10 nm, 60 nm +/- 5 nm. In one embodiment the mean diameter of the LNP is about 50 nm +/- 20 nm, 50 nm +/- 10 nm, 50 nm +/- 5 nm.
  • the LNPs described herein can be substantially non-toxic.
  • Lipid nanoparticles employ a non-viral drug delivery mechanism that is capable of passing through blood vessels and reaching hepatocytes (Am. J. Pathol.2010, 176,14–21).
  • Apolipoprotein E (apoE) proteins are capable of binding to the LNPs post PEG-lipid diffusion from the LNP surface with a near neutral charge in the bloodstream, and thereby function as an endogenous ligand against hepatocytes, which express the low-density lipoprotein receptor (LDLR) (Mol. Ther., 2010, 18, 1357–1364).
  • LDLR low-density lipoprotein receptor
  • Requirements for the efficient hepatic delivery of LNP include: 1) effective PEG-lipid shedding from the LNP surface in blood serum and 2) apoE binding to the LNP.
  • the endogenous apoE-mediated LDLR-dependent LNP delivery route is unavailable or a less effective path to achieve LNP-based hepatic gene delivery in patient populations that are LDLR deficient.
  • Efficient delivery to cells requires specific targeting and substantial protection from the extracellular environment, particularly serum proteins.
  • One method of achieving specific targeting is to conjugate a targeting moiety to an active agent or pharmaceutical effector such as a nucleic acid agent, thereby directing the active agent or pharmaceutical effector to particular cells or tissues depending on the specificity of the targeting moiety.
  • a targeting moiety can improve delivery is by receptor-mediated endocytotic activity.
  • This mechanism of uptake involves the movement of nucleic acid agent bound to membrane receptors into the interior of an area that is enveloped by the membrane via invagination of the membrane structure or by fusion of the delivery system with the cell membrane. This process is initiated via activation of a cell surface or membrane receptor following binding of a specific moiety, such as a ligand, to the receptor.
  • Receptor-mediated endocytotic systems include those that recognize sugars such as galactose, mannose, mannose-6-phosphate, peptides and proteins such as transferrin, asialoglycoprotein, vitamin B12, insulin, and epidermal growth factor (EGF).
  • Lipophilic moieties such as cholesterol or fatty acids, when attached to highly hydrophilic molecules such as nucleic acids can substantially enhance plasma protein binding and consequently circulation half-life. Lipophilic conjugates can also be used in combination with the targeting moieties in order to improve the intracellular trafficking of the targeted delivery approach.
  • the asialoglycoprotein receptor is a high-capacity receptor, which is abundant on hepatocytes. ASGPR shows a 50-fold higher affinity for N-Acetyl-D-Galactosamine (GalNAc) than D-Galactose. LNPs comprising receptor-targeting conjugates may be used to facilitate targeted delivery of the drug substances described herein.
  • the LNPs may include one or more receptor-targeting moiety on the surface or periphery of the particle at specified or engineered surface density ranging from relatively low to relatively high surface density.
  • the receptor-targeting conjugate may comprise a targeting moiety (such as a ligand), a linker, and a lipophilic moiety that is connected to the targeting moiety.
  • the receptor-targeting moiety (such as a ligand) targets a lectin receptor.
  • the lectin receptor is asialoglycoprotein receptor (ASGPR).
  • the receptor-targeting moiety is GalNAc or a derivative GalNAc that targets ASGPR.
  • the receptor-targeting conjugate comprises of one GalNAc moiety or derivative thereof. In another aspect, the receptor-targeting conjugate comprises two different GalNAc moieties or derivatives thereof. In another aspect, the receptor-targeting conjugate comprises three different GalNAc moieties or derivatives thereof. In another aspect, the receptor- targeting conjugate is lipophilic. In one or more embodiments, the receptor-targeting conjugate comprises one or more GalNAc moieties and one or more lipid moieties, i.e., GalNAc-Lipid. In one or more embodiments, the receptor-targeting conjugate is a GalNAc-Lipid.
  • LNP compositions comprising an amino lipid, a phospholipid, a PEG lipid, a cholesterol, or a derivative of a cholesterol, a payload, or any combination thereof and (ii) LNP compositions comprising an amino lipid, a phospholipid, a PEG-lipid, a cholesterol, a GalNAc-Lipid or a derivative thereof, a payload, or any combination thereof.
  • LNP compositions comprising an amino lipid, a phospholipid, a PEG-lipid, a cholesterol, a GalNAc-Lipid or a derivative thereof, a payload, or any combination thereof.
  • LNP compositions comprising the excipients amino lipid, phospholipid, PEG-Lipid, and cholesterol
  • a desired molar ratio of the four excipients is dissolved in a water-miscible organic solvent, e.g., ethanol.
  • the homogenous lipid solution is then rapidly in-line mixed with an aqueous buffer with acidic pH ranging from 4 to 6.5 containing nucleic acid payload to form the lipid nanoparticle (LNP) encapsulating the nucleic acid payload(s).
  • the LNPs thus formed undergo further downstream processing including concentration and buffer exchange to achieve the final LNP pharmaceutical composition with near neutral pH for administration into a cell line or animal disease model for evaluation, or to administer to human subjects.
  • the GalNAc-LNP pharmaceutical composition is mixed with the four lipid excipients in the water-miscible organic solvent prior to the preparation of the GalNAc-LNP.
  • the preparation of the GalNAc-LNP pharmaceutical composition then follow the same steps as described for the LNP pharmaceutical composition.
  • the mol% of the GalNAc-Lipid in the GalNAc-LNP preparation ranges from 0.001 to 2.0 of the total excipients.
  • the payload comprises guide nucleic acids, such as guide RNAs, targeting the LPA gene and an mRNA encoding a gene editor protein.
  • guide nucleic acids such as guide RNAs
  • the guide nucleic acid to mRNA weight ratio in the acidic aqueous buffer and in the final formulation is 6:1, 5:1, 4:1, 3:1, 2.5:1, 2:1, 1.5:1, 1:1, 1:1.5, 1:2, 1:2.5, 1:3, 1:5, or 1:6 by weight.
  • an LNP composition may be prepared as described in U.S.
  • the LNP composition comprises an amino lipid.
  • each asymmetric C-atom independently represents racemic, chirally pure R and/or chirally pure S isomer, or a combination thereof.
  • each of n, in, and q in Formula (I) is independently 0, 1, 2, or 3.
  • each of n, m, and q in Formula (I) is 1.
  • R 3 is - C0-C 10 alkylene-NR 7 R 8 , - C0-C 10 alkylene-heterocycloalkyl, or - C 0 -C 10 alkylene- heterocyclowyl, wherein the alkylene, heterocycloalkyl and heterocycloaryl is independently substituted or unsubstituted; each of R 4 is independently hydrogen or substituted or unsubstitutedC 1 -C 6 alkyl; R 5 is hydrogen or substituted or unsubstituted C 1 -C 6 alkyl; each of R 6 is independently substituted or unsubstituted C 3 -C 22 alkyl or substituted or unsubstituted C 3 -
  • each asymmetric C-atom independently represents racemic, chirally pure R and/or chirally pure S isomer, or a combination thereof.
  • R 1 and R 2 in Formula (I) and Formula (Ia) is independently C 3 -C 22 alkyl, C 3 -C 22 alkenyl, -C 2 -C 10 alkylene-L- R 6 , or , wherein each of the alkyl, alkylene, alkenyl, and cycloalkyl is independently substituted or unsubstituted.
  • R 1 and R 2 in Formula (I) and Formula (la) is independently C 10 -C20 alkyl, C 10 -C20 alkenyl. - C8-C7 alkylene-L- R 6 , or , wherein each of the alkyl, alkylene, alkenyl, and cycloalkyl is independently substituted or unsubstituted.
  • R 1 in Formula (I) and Formula (la) is [242]
  • each of R 6 in Formula (I) and Formula (Ia) is independently substituted or unsubstituted linear C 3 -C 22 alkyl or substituted or unsubstituted linear C 3 -C 22 alkenyl.
  • each of R 6 in Formula (I) and Formula (Ia) is independently substituted or unsubstituted C3-C20 alkyl or substituted or unsubstituted C3-C20 alkenyl. In one or more embodiments, each of R 6 in Formula (I) and Formula (Ia) is independently substituted or unsubstituted C 3 -C 10 alkyl or substituted or unsubstituted C 3 -C 10 alkenyl. In one or more embodiments, each of R 6 in Formula (I) and Formula (Ia) is independently substituted or unsubstituted C3-C 10 alkyl.
  • each of R 6 in Formula (I) and Formula (la) is independently substituted or unsubstituted linear C 3 -C 10 alkyl. In one or more embodiments, each of R 6 in Formula (I) and Formula (la) is independently substituted or unsubstituted n-pentyl, n-hexyl, n-heptyl, n-octyl, n-nonyl, n-decyl, n-undecyl, or n-dodecyl. In one or more embodiments, each of R 6 in Formula (I) and Formula (Ia) is independently substituted or unsubstituted n-octyl.
  • each of R 6 in Formula (I) and Formula (Ia) is n-octyl.
  • each of L in Formula (I) and Formula (Ia) is O.
  • each of L in Formula (I) and Formula (Ia) is -C 1 -C 3 alkylene-O-.
  • p in Formula (I) and Formula (Ia) is 1, 2, 3, 4, or 5.
  • p in Formula (I) and Formula (Ia) is 2. [245] In one or more embodiments, R 1 in Formula (I) and Formula (Ia) is
  • R 1 in Formula (I) and Formula (Ia) is R 2 .
  • each of R 4 in Formula (I) and Formula (Ia) is independently H or substituted or unsubstituted C 1 -C4 alkyl.
  • each of. R 4 in Formula (I) and Formula (Ia) is independently substituted or unsubstituted linear C 1 -C 4 alkyl.
  • each of R 4 in Formula (1) and Formula (la) is H.
  • R 2 in Formula (I) and Formula (Ia) is C3-C 22 alkyl, C3-C 22 alkenyl, - C 2 -C 10 alkylene-L- R 6 , or , wherein each of the alkyl, alkylene, alkenyl, and cycloalkyl is independently substituted or unsubstituted.
  • R 2 in Formula (I) and Formula (Ia) is substituted or unsubstituted C 7 -C 22 alkyl or substituted or unsubstituted C3-C 22 alkenyl.
  • R 2 in Formula (I) and Formula (la) is substituted or unsubstituted linear C7-C 22 alkyl or substituted or unsubstituted linear C 3 -C 22 alkenyl. In one or more embodiments, R 2 in Formula (I) and Formula (Ia) is substituted or unsubstituted C 10 -C20 alkyl or substituted or unsubstituted C 10 -C20 alkenyl. In one or more embodiments, R 2 in Formula (I) and Formula (Ia) is unsubstituted C 10 -C20 alkyl.
  • R 3 in Formula (I) and Formula (Ia) is -C0-C 10 alkylene- NR 7 R 8 or -C 0 -C 10 alkylene-heterocycloalkyl, wherein the alkylene and heterocycloalkyl is independently substituted or unsubstituted.
  • R 3 in Formula (I) and Formula (Ia) is -C0-C 10 alkylene-NR 7 R 8 .
  • R 3 in Formula (I) and Formula (Ia) is -C 1 -C 6 alkylene-NR 7 R 8 .
  • R 3 in Formula (I) and Formula (Ia) is - C 1 -C4 alkylene-NR 7 R 8 . In one or more embodiments, R 3 in Formula (I) and Formula (Ia) is -C 1 - alkylene-NR 7 R 8 . In one or more embodiments, R 3 in Formula (I) and Formula (Ia) is -C 2 -- alkylene-NR 7 R 8 . In one or more embodiments, R 3 in Formula (I) and Formula (Ia) is -C3- alkylene-NR 7 R 8 . In one or more embodiments, R 3 in Formula (I) and Formula (Ia) is -C4- alkylene- NR 7 R 8 .
  • R 3 in Formula (I) and Formula (Ia) is -C 5 - alkylene-NR 7 R 8 . In one or more embodiments, R 3 in Formula (I) and Formula (Ia) is - C 0 -C 10 alkylene-heterocycloalkyl. In one or more embodiments, R 3 in Formula (I) and Formula (Ia) is - C 1 -C 6 alkylene-heterocycloalkyl, wherein the heterocycloalkyl comprises 1 to 3 nitrogen and 0-2 oxygen. In one or more embodiments, R 3 in Formula (I) and Formula (la) is -C 1 -C 6 alkylene-heterocycloaryl.
  • each of R 7 and R 8 in Formula (I) and Formula (Ia) is independently hydrogen or substituted or unsubstituted C 1 -C 6 alkyl. In one or more embodiments, each of R 7 and R 8 is independently hydrogen or substituted or unsubstituted C 1 -C 3 alkyl. In one or more embodiments, each of R 7 and R 8 is independently substituted or unsubstituted C 1 -C3 alkyl. In one or more embodiments, each of R 7 and R 8 is independently - CH 3 , -CH 2 CH 3 , -CH 2 CH 2 CH 3 , or -CH(CH 3 ) 2 .
  • each of R and R 8 is CH 3 . In one or more embodiments, each of R 7 and R 8 is -CH 2 CH 3 . [255] In one or more embodiments, R 7 and R 8 in Formula (I) and Formula (Ia) taken together with the nitrogen to which they are attached form a substituted or unsubstituted C 2 -C6 heterocyclyl. In one or more embodiments, R 7 and R 8 taken together with the nitrogen to which they are attached form a substituted or unsubstituted C 2 -C 6 heterocycloalkyl.
  • R 7 and R 8 taken together with the nitrogen to which they are attached form a substituted or unsubstituted 3-7 membered heterocycloalkyl.
  • R 3 in Formula (I) and Formula (la) is [257] In one or more embodiments.
  • R 3 in Formula (I) and Formula (Ia) is [258] In one or more embodiments.
  • R 5 in Formula (I) and Formula (Ia) is hydrogen or substituted or unsubstituted C 1 -C3 alkyl.
  • R 5 in Formula (I) and Formula (Ia) is H, -CH 3 , - CH-)CH 3 , -CH2CH2CH3, or -CH(CH3)2.
  • R 5 in Formula (I) and Formula (Ia) is H. 2.
  • LNP Compositions Comprising Different Amino Lipids [268]
  • the LNP comprises a plurality of amino lipids having different formulas.
  • the LNP composition can comprise 2, 3, 4, 5, 6, 7, 8, 9, 10, or more amino lipids.
  • the LNP composition can comprise at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, or at least 20 amino lipids.
  • the LNP composition can comprise at most 2, at most 3, at most 4, at most 5, at most 6, at most 7, at most 8, at most 9, at most 10, at most 20, or at most 30 amino lipids.
  • the LNP composition comprises a first amino lipid.
  • the LNP composition comprises a first amino lipid and a second amino lipid.
  • the LNP composition comprises a first amino lipid, a second amino lipid, and a third amino lipid.
  • the LNP composition comprises a first amino lipid, a second amino lipid, a third amino lipid, and a fourth amino lipid.
  • the LNP composition does not comprise a fourth amino lipid. In one or more embodiments, the LNP composition does not comprise a third amino lipid. In one or more embodiments, a molar ratio of the first amino lipid to the second amino lipid is from about 0.1 to about 10. In one or more embodiments, a molar ratio of the first amino lipid to the second amino lipid is from about 0.20 to about 5. In one or more embodiments, a molar ratio of the first amino lipid to the second amino lipid is from about 0.25 to about 4. In one or more embodiments, a molar ratio of the first amino lipid to the second amino lipid is about 0.25, about 0.33, about 0.5, about 1, about 2, about 3, or about 4.
  • a molar ratio of the first amino lipid: the second amino lipid: the third amino lipid is about 4:1:1. In one or more embodiments, a molar ratio of the first amino lipid: the second amino lipid: the third amino lipid is about 1:1:1. In one or more embodiments, a molar ratio of the first amino lipid: the second amino lipid: the third amino lipid is about 2:1:1. In one or more embodiments, a molar ratio of the first amino lipid: the second amino lipid: the third amino lipid is about 2:2:1. In one or more embodiments, a molar ratio of the first amino lipid: the second amino lipid: the third amino lipid is about 3:2:1.
  • a molar ratio of the first amino lipid: the second amino lipid: the third amino lipid is about 3:1:1. In one or more embodiments, a molar ratio of the first amino lipid: the second amino lipid: the third amino lipid is about 5:1:1. In one or more embodiments, a molar ratio of the first amino lipid: the second amino lipid: the third amino lipid is about 3:3:1. In one or more embodiments, a molar ratio of the first amino lipid: the second amino lipid: the third amino lipid is about 4:4:1. 3. Additional Amino Lipid Embodiments [271] In one or more embodiments, the LNP composition comprises one or more amino lipids.
  • the one or more amino lipids comprise from about 40 mol% to about 65 mol% of the total lipid present in the particle. In one or more embodiments, the one or more amino lipids comprise about 40 mol%, about 41 mol%, about 42 mol%, about 43 mol%, about 44 mol%, about 45 mol%, about 46 mol%, about 47 mol%, about 48 mol%, about 49 mol%, about 50 mol%, about 51 mol%, about 52 mol%, about 53 mol%, about 54 mol%, about 55 mol%, about 56 mol%, about 57 mol%, about 58 mol%, about 59 mol%, about 60 mol%, about 61 mol%, about 62 mol%, about 63 mol%, about 64 mol%, or about 65 mol% of the total lipid present in the particle.
  • the first amino lipid comprises from about 1 mol% to about 99 mol% of the total amino lipids present in the particle. In one or more embodiments, the first amino lipid comprises from about 16.7 mol% to about 66.7 mol% of the total amino lipids present in the particle. In one or more embodiments, the first amino lipid comprises from about 20 mol% to about 60 mol% of the total amino lipids present in the particle. [272] In one or more embodiments, the amino lipid is an ionizable lipid. An ionizable lipid can comprise one or more ionizable nitrogen atoms. In one or more embodiments, at least one of the one or more ionizable nitrogen atoms is positively charged.
  • the amino lipid comprises a primary amine, a secondary amine, a tertiary amine, an imine, an amide, a guanidine moiety, a histidine residue, a lysine residue, an arginine residue, or any combination thereof.
  • the amino lipid comprises a primary amine, a secondary amine, a tertiary amine, a guanidine moiety, or any combination thereof. In one or more embodiments, the amino lipid comprises a tertiary amine. [273] In one or more embodiments, the amino lipid is a cationic lipid. In one or more embodiments, the amino lipid is an ionizable lipid. In one or more embodiments, the amino lipid comprises one or more nitrogen atoms. In one or more embodiments, the amino lipid comprises one or more ionizable nitrogen atoms.
  • Exemplary cationic and/or ionizable lipids include, but are not limited to, 3-(didodecylamino)- N1,N1,4-tri dodecyl-l-piperazineethan amine (KL10), N142- (didodecylamino)ethy1]-N1,N4,N4- tridodecyl-1,4-piperazinediethanamine (KL22), 14,25- ditridecy1-15,18,21 ,24-tetraaza-octatriacontane (KL25), 1,2-dilinoleyloxy-N,N- dimethylaminopropane (DLin-DMA), 2,2-dilinoley1-4- dimethylaminomethy1-[1,3]-dioxolane (DLin-K-DMA), heptatriaconta-6,9,28,31-tetraen-19-yl 4- (dimethylamino)butanoate
  • an amino lipid described herein can take the form of a salt, such as a pharmaceutically acceptable salt. All pharmaceutically acceptable salts of the amino lipid are encompassed by this disclosure. As used herein, the term "amino lipid” also includes its pharmaceutically acceptable salts, and its diastereomeric, enantiomeric, and epimeric forms. [275] In one or more embodiments, an amino lipid described herein possesses one or more stereocenters, and each stereocenter exists independently in either the R or S configuration. The lipids presented herein include all diastereomeric, enantiomeric, and epimeric forms as well as the appropriate mixtures thereof.
  • lipids provided herein include all cis, trans, syn, anti,
  • lipids described herein are prepared as their individual stereoisomers by reacting a racemic mixture of the compound with an optically active resolving agent to form a pair of diastereoisomeric compounds/salts, separating the diastereomers and recovering the optically pure enantiomers.
  • resolution of enantiomers is carried out using covalent diastereomeric derivatives of the compounds described herein.
  • diastereomers are separated by separation/resolution techniques based upon differences in solubility.
  • stereoisomers are obtained by stereoselective synthesis.
  • the lipids such as the amino lipids are substituted based on the structures disclosed herein. In one or more embodiments, the lipids such as the amino lipids are unsubstituted.
  • the lipids described herein are labeled isotopically (e.g., with a radioisotope) or by another other means, including, but not limited to, the use of chromophores or fluorescent moieties, bioluminescent labels, or chemiluminescent labels.
  • Lipids described herein include isotopically-labeled compounds, which are identical to those recited in the various formulae and structures presented herein, but for the fact that one or more atoms are replaced by an atom having an atomic mass or mass number different from the atomic mass or mass number usually found in nature.
  • isotopes examples include isotopes of hydrogen, carbon, nitrogen, oxygen, sulfur, fluorine, and chlorine, such as, for example, 2 H, 3 H, 13 C, 14 C, 15 N, 18 O, 17 O, 35 S, 18 F, and 36 Cl.
  • isotopically-labeled lipids described herein, for example those into which radioactive isotopes such as 3 H and 14 C are incorporated are useful in drug and/or substrate tissue distribution assays.
  • substitution with isotopes such as deuterium affords certain therapeutic advantages resulting from greater metabolic stability, such as, for example, increased in vivo half-life or reduced dosage requirements.
  • the asymmetric carbon atom of the amino lipid is present in enantiomerically enriched form. In certain embodiments, the asymmetric carbon atom of the amino lipid has at least 50% enantiomeric excess, at least 60% enantiomeric excess, at least 70% enantiomeric excess, at least 80% enantiomeric excess, at least 90% enantiomeric excess, at least 95% enantiomeric excess, or at least 99% enantiomeric excess in the (S)- or (R)-configuration. [279] In one or more embodiments, the disclosed amino lipids can be converted to N-oxides.
  • N-oxides are formed by a treatment with an oxidizing agent (e.g., 3- chloroperoxybenzoic acid and/or hydrogen peroxides).
  • an oxidizing agent e.g., 3- chloroperoxybenzoic acid and/or hydrogen peroxides.
  • the nitrogen in the compounds of the disclosure can be converted to N-hydroxy or N-alkoxy.
  • N-hydroxy compounds can be prepared by oxidation of the parent amine by an oxidizing agent such as ra- CPBA. All shown nitrogen-containing compounds are also considered.
  • N-hydroxy and N-alkoxy e.g., N-OR, wherein R is substituted or unsubstituted C 1 -C 6 alkyl, C 1 -C 6 alkenyl, C 1 -C 6 alkynyl, 3-14-membered carbocycle, or 3-14- membered heterocycle
  • the one or more amino lipids comprise from about 40 mol% to about 65 mol% of the total lipid present in the particle. 4.
  • PEG-Lipids [281]
  • the described LNP composition includes one or more PEG- lipids.
  • a “PEG lipid” or “PEG-lipid” refers to a lipid comprising a polyethylene glycol component.
  • suitable PEG-lipids also include, but are not limited to, PEG- modified phosphatidylethanolamines, PEG-modified phosphatidic acids, PEG-modified ceramides, PEG-modified dialkylamines, PEG-modified diacylglycerols, PEG-modified dialkylglycerols, and mixtures thereof.
  • the one or more PEG-lipids can comprise PEG-c-DOMG, PEG-DMG, PEG-DLPE, PEG-DMPE, PEG-DPPC, a PEG-DSPE lipid, or a combination thereof.
  • PEG-lipid comprises from about 0.1 mol% to about 10 mol% of the total lipid present in the particle. 5.
  • Phospholipid [283] In one or more embodiments, the described LNP composition includes one or more phospholipids. [284] In one or more embodiments, the phospholipid comprises from about 5 mol% to about 15 mol% of the total lipid present in the particle. 6.
  • the LNP composition includes a cholesterol or a derivative thereof. 7. GalNAc-Lipid [286] In one or more embodiments, the LNP composition includes a receptor targeting conjugate comprising a compound formula (V), Formula (V) wherein, a plurality of the A groups collectively comprise a receptor targeting moiety; each L 1 , L 2 , L 3 , L 4 , L 5 , L 6 , L 7 , L 8 , L 9 , L 10 and L 12 is independently substituted or unsubstituted C 1 -C 12 alkylene, substituted or unsubstituted C 1 -C 12 heteroalkylene, substituted or unsubstituted C 2 -C 12 alkenylene, substituted or unsubstituted C 2 -C 12 alkynylene, -(CH 2 CH 2 O) m -, -(OCH 2 CH 2 ) m -, -O-, -S-
  • each L 1 , L 4 , and L 7 is independently substituted or unsubstituted C 1 -C 12 alkylene. In one or more embodiments, each L 1 , L 4 , and L 7 is independently substituted or unsubstituted C 2 -C 6 alkylene. In one or more embodiments, each L 1 , L 4 , and L 7 is C 4 alkylene.
  • each L 3 , L 6 , and L 9 is independently substituted or unsubstituted C 1 -C 12 alkylene. In one or more embodiments, each L 3 is substituted or unsubstituted C 2 -C 6 alkylene. In one or more embodiments, L 3 is C 4 alkylene. In one or more embodiments, each L 6 and L 9 is independently substituted or unsubstituted C 2 -C 10 alkylene. In one or more embodiments, each L 6 and L 9 is independently substituted or unsubstituted C 2 -C 6 alkylene. In one or more embodiments, each L 6 and L 9 is C 3 alkylene. In one or more embodiments, A binds to a lectin.
  • the lectin is an asialoglycoprotein receptor (ASGPR).
  • A is N-acetylgalactosamine (GalNAc) or or a derivative thereof.
  • GalNAc N-acetylgalactosamine
  • Examples of such GalNAc lipids include the following: , wherein each of the p and q is independently an integer from 1 to 5, and n is an integer from 1 to 50; wherein n is an integer from 1 to 50; wherein each of the p and q is independently an integer from 1 to 5, and n is an integer from 1 to 50; ;
  • n is an integer from 1 to 50;
  • each of the p and q is independently an integer from 1 to 5, and n is an integer from 1 to 50; , wherein each of the p and q is independently an integer from 1 to 5, and n is an integer from 1 to 50; , wherein each of the p and q is independently an integer from 1 to 5, and n is an integer from 1 to 50; ; wherein each of the p and q is independently an integer from 1 to 5, and n is an integer from 33 to 39; , wherein n is an integer from 1-50; ; ; and .
  • the receptor targeting conjugate comprises from about 0.001 mol% to about 20 mol% of the total lipid content present in the nanoparticle composition.
  • Phosphate charge neutralizer [290]
  • the LNP described herein includes a phosphate charge neutralizer.
  • the phosphate charge neutralizer comprises arginine, asparagine, glutamine, lysine, histidine, cationic dendrimers, polyamines, or a combination thereof.
  • the phosphate charge neutralizer comprises one or more nitrogen atoms.
  • the phosphate charge neutralizer comprises a polyamine.
  • Suitable phosphate charge neutralizers to be used in LNP formulations include, but are not limited to, spermidine and 1,3-propanediamine.
  • Antioxidants [292]
  • the LNP described herein includes one or more antioxidants.
  • the one or more antioxidants function to reduce a degradation of the cationic lipids, the payload, or both.
  • the one or more antioxidants comprise a hydrophilic antioxidant.
  • the one or more antioxidants is a chelating agent such as ethylenediaminetetraacetic acid (EDTA) or citrate.
  • the one or more antioxidants comprise a lipophilic antioxidant.
  • the lipophilic antioxidant comprises a vitamin E isomer or a polyphenol.
  • the one or more antioxidants are present in the LNP composition at a concentration of at least 1 mM, at least 10 mM, at least 20 mM, at least 50 mM, or at least 100 mM.
  • the one or more antioxidants are present in the particle at a concentration of about 20 mM. 10.
  • the disclosed LNP compositions may comprise a helper lipid.
  • the disclosed LNP compositions comprise a neutral lipid.
  • the disclosed LNP compositions comprise a stealth lipid. In one or more embodiments, the disclosed LNP compositions comprise additional lipids. Neutral lipids can function to stabilize and improve processing of the LNPs.
  • Helper lipids can refer to lipids that enhance transfection (e.g., transfection of the nanoparticle (LNP) comprising the composition as provided herein, including the biologically active agent). The mechanism by which the helper lipid enhances transfection includes enhancing particle stability. In one or more embodiments, the helper lipid enhances membrane fusogenicity. Helper lipids can include steroids, sterols, and alkyl resorcinols.
  • Helper lipids suitable for use in the present disclosure can include, but are not limited to, cholesterol, 5- heptadecylresorcinol, and cholesterol hemisuccinate.
  • the helper lipid is cholesterol.
  • the helper lipid is cholesterol hemisuccinate.
  • Stealth lipids can refer to lipids that alter the length of time the nanoparticles can exist in vivo (e.g., in the blood). Stealth lipids can assist in the formulation process by, for example, reducing particle aggregation and controlling particle size. Stealth lipids used herein may modulate pharmacokinetic properties of the LNP.
  • Stealth lipids suitable for use in a lipid composition of the disclosure can include, but are not limited to, stealth lipids having a hydrophilic head group linked to a lipid moiety.
  • Stealth lipids suitable for use in a lipid composition of the present disclosure and information about the biochemistry of such lipids can be found in Romberg et al, Pharmaceutical Research, Vol.25, No.1, 2008, pg.55-71 and I- Toekstra et al, Biochimica et Biophysica Acta 1660 (2004) 41-52. Additional suitable PEG lipids are disclosed, e.g., in WO 2006/007712. [296] In one or more embodiments, the stealth lipid is a PEG-lipid.
  • the hydrophilic head group of stealth lipid comprises a polymer moiety selected from polymers based on PEG (sometimes referred to as poly(ethylene oxide)), poly(oxazoline), poly(vinyl alcohol), poly(glycerol), poly(N- vinylpyrrolidone), polyaminoacids, and poly N-(2- hydroxypropyl)methacrylamide].
  • PEG sometimes referred to as poly(ethylene oxide)
  • poly(oxazoline) poly(vinyl alcohol)
  • poly(glycerol) poly(N- vinylpyrrolidone)
  • polyaminoacids and poly N-(2- hydroxypropyl)methacrylamide.
  • Stealth lipids can comprise a lipid moiety.
  • the lipid moiety of the stealth lipid may be derived from diacylglycerol or diacylglycamide, including those comprising a dialkylglycerol or dialkylglycamide group having alkyl chain length independently comprising from about C4 to about C40 saturated or unsaturated carbon atoms, wherein the chain may comprise one or more functional groups such as, for example, an amide or ester.
  • the dialkylglycerol or dialkylglycamide group can further comprise one or more substituted alkyl groups.
  • helper lipids neutral lipids, stealth lipids, and/or other lipids are further described in W02017173054A1, W02019067999A1, US20180290965A1, US20180147298A1, US20160375134A1, US8236770, US8021686, US8236770B2, US7371404B2, US7780983B2, US7858117B2, US20180200186A1, US20070087045A1, W02018119514A1, and W02019067992A1, all of which are hereby incorporated by reference in their entirety.
  • LNP Formulations [298] Particular formulations of a nanoparticle composition comprising one or more described lipids are described herein.
  • the described nanoparticle compositions are capable of delivering a therapeutic agent such as an RNA to a particular cell, tissue, organ, or system or group thereof in a mammal's body.
  • Physiochemical properties of nanoparticle compositions may be altered in order to increase selectivity for particular bodily targets. For instance, particle sizes may be adjusted based on the fenestration sizes of different organs.
  • the therapeutic agent included in a nanoparticle composition may also be selected based on the desired delivery target or targets. For example, a therapeutic agent may be selected for a particular indication, condition, disease, or disorder and/or for delivery to a particular cell, tissue, organ, or system or group thereof (e.g., localized, or specific delivery).
  • a nanoparticle composition may include an mRNA encoding a polypeptide of interest capable of being translated within a cell to produce the polypeptide (e.g., gene editor) of interest.
  • a composition is capable of having specificity or affinity to a particular organ or cell type to facilitate drug substance delivery thereto, for example the liver or hepatocytes.
  • the amount of a therapeutic agent or drug substance (e.g., the mRNA that encodes for the gene editor and the guide nucleic acid, such as guide RNA) in an LNP composition may depend on the size, composition, desired target and/or application, or other properties of the nanoparticle composition.
  • the amount of an RNA in a nanoparticle composition may depend on the size, sequence, and other characteristics of the RNA.
  • the relative amounts of a therapeutic agent and other elements (e.g., lipids) in a nanoparticle composition may also vary.
  • the wt/wt ratio of the lipid component to a therapeutic agent in a nanoparticle composition may be from about 5:1 to about 60:1, such as about 5:1.6:1, 7:1, 8:1, 9:1, 10:1, 11:1, 12:1, 13:1, 14:1, 15:1, 16:1, 17:1, 18:1, 19:1, 20:1, 25:1, 30:1, 35:1, 40:1, 45:1, 50:1, and 60:1.
  • the wt/wt ratio of the lipid component to a therapeutic agent may be from about 10:1 to about 40:1. In certain embodiments, the wt/wt ratio is about 20:1.
  • the amount of a therapeutic agent in a nanoparticle composition can be measured using absorption spectroscopy (e.g., ultraviolet-visible spectroscopy).
  • an LNP formulation comprises one or more nucleic acids such as RNAs.
  • the one or more RNAs, lipids, and amounts thereof may be selected to provide a specific N/P ratio.
  • the N/P ratio can be selected from about 1 to about 30.
  • the N/P ratio can be selected from about 2 to about 12.
  • the N/P ratio is from about 0.1 to about 50. In one or more embodiments, the N/P ratio is from about 2 to about 8. In one or more embodiments, the N/P ratio is from about 2 to about 15, from about 2 to about 10, from about 2 to about 8, from about 2 to about 6, from about 3 to about 15, from about 3 to about 10, from about 3 to about 8, from about 3 to about 6, from about 4 to about 15, from about 4 to about 10, from about 4 to about 8, or from about 4 to about 6. In one or more embodiments, the N/P ratio is about 2, about 2.5, about 3, about 3.5, about 4, about 4.5, about 5, about 5.5, about 6, about 6.5, about 7, about 7.5, about 8, about 9, or about 10.
  • the N/P ratio is from about 4 to about 6. In one or more embodiments, the N/P ratio is about 4, about 4.5, about 5, about 5.5, or about 6. [302] As used herein, the “N/P ratio” is the molar ratio of ionizable (e.g., in the physiological pH range) nitrogen atoms in a lipid (or lipids) to phosphate groups in a nucleic acid molecular entity (or nucleic acid molecular entities), e.g., in a nanoparticle composition comprising a lipid component and an RNA.
  • ionizable e.g., in the physiological pH range
  • nitrogen atoms in a lipid or lipids
  • phosphate groups in a nucleic acid molecular entity or nucleic acid molecular entities
  • Ionizable nitrogen atoms can include, for example, nitrogen atoms that can be protonated at about pH 1, about pH 2, about pH 3, about pH 4, about pH 4.5, about pH 5, about pH 5.5, about pH 6, about pH 6.5, about pH 7, about pH 7.5, or about pH 8 or higher.
  • the physiological pH range can include, for example, the pH range of different cellular compartments (such as organs, tissues, and cells) and bodily fluids (such as blood, cerebrospinal fluid, gastric juice, milk, bile, saliva, tears, and urine).
  • the physiological pH range refers to the pH range of blood in a mammal, for example, from about 7.35 to about 7.45.
  • the N/P ratio can refer to a molar ratio of ionizable nitrogen atoms in the phosphate charge neutralizer to the phosphate groups in a nucleic acid.
  • ionizable nitrogen atoms refer to those nitrogen atoms that are ionizable within a pH range between 5 and 14.
  • the N/P ratio can refer to a molar ratio of ionizable nitrogen atoms in a lipid to the total negative charge in the payload.
  • the N/P ratio of an LNP composition can refer to a molar ratio of the total ionizable nitrogen atoms in the LNP composition to the total negative charge in the payload that is present in the composition.
  • the LNPs are formed with an average encapsulation efficiency ranging from about 50% to about 70%, from about 70% to about 90%, or from about 90% to about 100%. In one or more embodiments, the LNPs are formed with an average encapsulation efficiency ranging from about 75% to about 98%.
  • a lipid nanoparticle (LNP) comprising the composition as provided herein.
  • lipid nanoparticle (LNP) composition or a “nanoparticle composition” is a composition comprising one or more described lipids.
  • LNP compositions are typically sized on the order of micrometers or smaller and may include a lipid bilayer.
  • Nanoparticle compositions encompass lipid nanoparticles (LNPs), liposomes (e.g., lipid vesicles), and lipoplexes.
  • a LNP refers to any particle that has a diameter of less than 1000 nm, 500 nm, 250 nm, 200 nm, 150 nm, 100 nm, 75 nm, 50 nm, or 25 nm.
  • a nanoparticle may range in size from 1-1000 nm, 1-500 nm, 1-250 nm, 25-200 nm, 40-100 nm, 50-100 nm.50-90 nm, 50-80 nm, 50-70 nm, 55-95 nm, 55-80 nm, 55-75 nm, 60-100 nm, 60-90 nm, 60-80 nm, 60-70 nm, 25-100 nm, 25-80 nm, 40-80 nm, 45- 75 nm, 60-75nm, or 60-65 nm.
  • an LNP may be made from cationic, anionic, or neutral lipids.
  • an LNP may comprise neutral lipids, such as the fusogenic phospholipid 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE) or the membrane component cholesterol, as helper lipids to enhance transfection activity and nanoparticle stability.
  • DOPE fusogenic phospholipid 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
  • an LNP may comprise hydrophobic lipids, hydrophilic lipids, or both hydrophobic and hydrophilic lipids. Any lipid or combination of lipids that are known in the art can be used to produce an LNP.
  • lipids used to produce LNPs include, but are not limited to DOTMA (N[1-(2,3-dioleyloxy)propyl]-N,N,N- trimethylammonium chloride), DOSPA (N,N-dimethyl-N-([2-sperminecarboxamido]ethyl)-2,3- bis(dioleyloxy)-1-propaniminium pentahydrochloride), DOTAP (1,2-Dioleoyl-3- trimethylammonium propane), DMRIE (N-(2-hydroxyethyl)- N,N-dimethyl-2,3- bis(tetradecyloxy-1-propanaminiumbromide), DC-cholesterol (3 ⁇ -[N-(N',N'- dimethylaminoethane)-carbamoyl]cholesterol), DOTAP-cholesterol, GAP-DMORIE-DPyPE, and GL67A-DOPE-DMPE (1,2-Bis(di
  • cationic lipids include, but are not limited to, 98N12-5, C 1 2-200, DLin-K C 2 -DMA (KC2), DLin-MC3 -DMA (MC3), XTC, MD1, and 7C 1 .
  • neutral lipids include, but are not limited to, DPSC, DPPC (Dipalmitoylphosphatidylcholine), POPC (1-palmitoyl-2-oleoyl- sn-glycero-3-phosphocholine), DOPE, and SM (sphingomyelin).
  • PEG-modified lipids include, but are not limited to, PEG-DMG (Dimyristoyl glycerol), PEG-CerC 1 4, and PEG- CerC20.
  • the lipids may be combined in any number of molar ratios to produce an LNP.
  • the polynucleotide may be combined with lipid(s) in a wide range of molar ratios to produce an LNP.
  • substituted refers to the replacement of one or more hydrogen radicals in a given structure with the radical of a specified substituent including, but not limited to: halo, alkyl, alkenyl, alkynyl, aryl, heterocyclyl, thiol, alkylthio, oxo, thioxy, arylthio, alkylthioalkyl, arylthioallcyl, alkylsulfonyl, alkylsulfonylalkyl, arylsulfonylalkyl, alkoxy, aryloxy, aralkoxy, aminocarbonyl, alkylaminocarbonyl, aiylaminocarbonyl, alkoxycarbonyl, aryloxycarbonyl, haloalkyl, amino, trifluoromethyl, cyano, nitro, alkylamino, arylamino, alkylaminoal
  • substituent may be further substituted.
  • substituents include amino, alkylamino, and the like.
  • substituted means positional variables on the atoms of a core molecule that are substituted at a designated atom position, replacing one or more hydrogens on the designated atom, provided that the designated atom's normal valency is not exceeded, and that the substitution results in a stable compound. Combinations of substituents and/or variables are permissible only if such combinations result in stable compounds.
  • any carbon as well as heteroatom with valences that appear to be unsatisfied as described or shown herein is assumed to have a sufficient number of hydrogen atom(s) to satisfy the valences described or shown.
  • the point of attachment may be described, shown, or listed herein within a substituent group, wherein the structure may only show a single bond as the point of attachment to the core structure of Formula (I).
  • alkyl refers to a straight or branched hydrocarbon chain radical, having from one to twenty carbon atoms, and which is attached to the rest of the molecule by a single bond.
  • An alkyl comprising up to 10 carbon atoms is referred to as a C 1 -C 10 alkyl; likewise, for example, an alkyl comprising up to 6 carbon atoms is a C 1 -C 6 alkyl.
  • Alkyls (and other moieties defined herein) comprising other numbers of carbon atoms are represented similarly.
  • Alkyl groups include, but are not limited to, C 1 -C 10 alkyl, C 1 -C 9 alkyl, C 1 -C 8 alkyl.
  • C 1 -C 7 alkyl C 1 -C 6 alkyl, C 1 -C 5 alkyl, C 1 -C 4 alkyl, C 1 -C 3 alkyl, C 1 -C 2 alkyl, C 2 -C 8 alkyl, C 3 -C 8 alkyl and C 4 -C 8 alkyl.
  • alkyl groups include, but are not limited to, methyl, ethyl, n-propyl, 1- methylethyl (i-propyl), n-butyl, i-butyl, s-butyl, n- pentyl, 1,1-dimethylethyl (t-butyl), 3- methylhexyl, 2-methylhexyl, 1-ethyl-propyl, and the like.
  • the alkyl is methyl or ethyl.
  • the alkyl is -CH(CH3)2 or -C(CH3)3. Unless stated otherwise specifically in the specification, an alkyl group may be optionally substituted as described below.
  • Alkylene or “alkylene chain” refers to a straight or branched divalent hydrocarbon chain linking the rest of the molecule to a radical group.
  • the alkylene is -CI-12-, -CH2CH2-, or -CH2CH2CH2-.
  • the alkylene is -CH 2 -.
  • the alkylene is -CH 2 CH 2 -.
  • the alkylene is -CH 2 CH 2 CH 2 -.
  • alkenyl refers to a type of alkyl group in which at least one carbon-carbon double bond is present.
  • R is H or an alkyl.
  • an alkenyl is selected from ethenyl (i.e., vinyl), propenyl (i.e., allyl), butenyl, pentenyl, pentadienyl, and the like.
  • cycloalkyl refers to a monocyclic or polycyclic non-aromatic radical, wherein each of the atoms forming the ring (i.e., skeletal atoms) is a carbon atom.
  • cycloalkyls are saturated or partially unsaturated.
  • cycloalkyls are spirocyclic or bridged compounds.
  • cycloalkyls are fused with an aromatic ring (in which case the cycloalkyl is bonded through a non-aromatic ring carbon atom).
  • Cycloalkyl groups include groups having from 3 to 10 ring atoms.
  • Representative cycloalkyls include, but are not limited to, cycloalkyls having from three to ten carbon atoms, from three to eight carbon atoms, from three to six carbon atoms, or from three to five carbon atoms.
  • Monocyclic cycloalkyl radicals include, for example, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, and cyclooctyl.
  • the monocyclic cycloalkyl is cyclopropyl, cyclobutyl, cyclopentyl or cyclohexyl.
  • the monocyclic cycloalkyl is cyclopentenyl or cyclohexenyl.
  • the monocyclic cycloalkyl is cyclopenteny 1.
  • Polycyclic radicals include, for example, adamantyl, 1,2- dihydronaphthalenyl, 1,4-dihydronaphthalenyl, tetrainyl, decalinyl, 3,4-dihydronaphthalenyl-l(2H)-one, spiro[2.2]pentyl, norbomyl, and bicycle[1.1.1]pentyl.
  • a cycloalkyl group may be optionally substituted.
  • a cycloalkyl group can be monovalent or divalent (i.e., a cycloalkylene group).
  • heterocycle refers to heteroaromatic rings (also known as heteroaryls) and heterocycloalkyls (also known as heteroalicyclic groups) that includes at least one heteroatom selected from nitrogen, oxygen, and sulfur, wherein each heterocyclic group has from 3 to 12 atoms in its ring system, and with the proviso that any ring does not contain two adjacent O or S atoms.
  • heterocyclyl is a univalent group formed by removing a hydrogen atom from any ring atoms of a heterocyclic compound.
  • heterocycles are monocyclic, bicyclic, polycyclic, spirocyclic, or bridged compounds.
  • Non- aromatic heterocyclic groups include rings having 3 to 12 atoms in its ring system, and aromatic heterocyclic groups include rings having 5 to 12 atoms in its ring system.
  • the heterocyclic groups include benzofused ring systems. Examples of non- aromatic heterocyclic groups are pyrrolidinyl, tetrahydrofuranyl, dihydrofuranyl, tetrahydrothienyl, oxazolidinonyl, tetrahydropyranyl, dihydropyranyl, tetrahydrothiopyranyl, piperidinyl, morpholinyl.
  • thiomorpholinyl thioxanyl, piperazinyl, aziridinyl, azetidinyl, oxetanyl, thietanyl, homopiperidinyl, oxepanyl, thiepanyl, oxazepinyl, diazepinyl, thiazepinyl, 1,2,3,6-tetrahydropyridinyl, pyrrolin-2-yl, pyrrolin-3-yl, indolinyl, 2H-pyranyl, 4H-pyranyl, dioxanyl, 1,3-dioxolanyl, pyrazolinyl, dithianyl, dithiolanyl, dihydropyranyl, dihydrothienyl, dihydrofuranyl, pyrazolidinyl, imidazolinyl, imidazolidinyl, 3-azabicyclo[3.1.0]hexanyl, 3- azabicyclo
  • aromatic heterocyclic groups are pyridinyl, imidazolyl, pyrimidinyl, pyrazolyl, triazolyl, pyrazinyl, tetrazolyl, futyl, thienyl, isoxazolyl, thiazolyl, oxazolyl, isothiazolyl, pyrrolyl, quinolinyl, isoquinolinyl, indolyl, benzimidazolyl, benzofuranyl, cinnolinyl, indazolyl, indolizinyl, phthalazinyl, pyridazinyl, triazinyl, isoindolyl, pteridinyl, purinyl, oxadiazolyl, thiadiazolyl, furaz.anyl, benzofuraz.anyl, benzothiophenyl, benzothiazolyl, benzoxazolyl, quinazolinyl
  • a group derived from pyrrole includes both pyrrol-1-yl (N-attached) or pyrrol-3-yl (C-attached).
  • a group derived from imidazole includes imidazol-1-y1 or imidazol-3-yl (both N- attached) or imidazol-2-yl, imidazol-4-yl, or imidazol-5-yl (all C-attached).
  • the heterocyclic groups include benzo-fused ring systems.
  • at least one of the two rings of a bicyclic heterocycle is aromatic.
  • both rings of a bicyclic heterocycle are aromatic.
  • heterocycloalkyl refers to a cycloalkyl group that includes at least one heteroatom selected from nitrogen, oxygen, and sulfur.
  • the heterocycloalkyl radical may be a monocyclic, or bicyclic ring system, which may include fused (when fused with an aryl or a heterowyl ring, the heterocycloalkyl is bonded through a non-aromatic ring atom) or bridged ring systems.
  • the nitrogen, carbon, or sulfur atoms in the heterocyclyl radical may be optionally oxidized.
  • the nitrogen atom may be optionally quaternized.
  • the heterocycloalkyl radical is partially or fully saturated.
  • heterocycloalkyl radicals include, but are not limited to, dioxolanyl, thienyl[1,3]dithianyl, tetrahydroquinolyl, tetrahydroisoquinolyl, decahydroquinolyl, decahydroisoquinolyl, imidazolinyl, imidazolidinyl, isothiazolidinyl, isoxazolidinyl, morpholinyl, octahydroindolyl, octahydroisoindolyl, 2-oxopiperazinyl, 2-oxopiperidinyl, 2-oxopyrrolidinyl, oxazolidinyl, piperidinyl, piperazinyl, 4-piperidonyl, pyrrolidinyl, pyrazolidinyl, quinuclidinyl, thiazolidinyl, tetrahydrofuryl, trithianyl, t
  • heterocycloalkyl also includes all ring forms of carbohydrates, including but not limited to monosaccharides, disaccharides, and oligosaccharides. Unless otherwise noted, heterocycloalkyls have from 2 to 12 carbons in the ring. In one or more embodiments, heterocycloalkyls have from 2 to 10 carbons in the ring. In one or more embodiments, heterocycloalkyls have from 2 to 10 carbons in the ring and 1 or 2 N atoms. In one or more embodiments, heterocycloalkyls have from 2 to 10 carbons in the ring and 3 or 4 N atoms.
  • heterocycloalkyls have from 2 to 12 carbons, 0-2 N atoms, 0-2 O atoms, 0-2 P atoms, and 0-1 S atoms in the ring. In one or more embodiments, heterocycloalkyls have from 2 to 12 carbons, 1-3 N atoms, 0-1 O atoms, and 0-1 S atoms in the ring.
  • heterocycloalkyl refers to an aryl group that includes one or more ring heteroatoms selected from nitrogen, oxygen, and sulfur.
  • the heteroaryl is monocyclic or bicyclic.
  • monocyclic heteroaryls include pyridinyl, imidazolyl, pyrimidinyl, pyrazolyl, triazolyl, pyrazinyl, tetrazolyl, furyl, thienyl, isoxazolyl, thiazolyl, oxazolyl, isothiazolyl, pyrrolyl, pyridazinyl, triazinyl, oxadiazolyl, thiadiazolyl, furazanyl, indolizine, indole, benzofuran, benzothiophene, indazole, benzimidazole, purine, quinolizine, quinoline, isoquinoline, cinnoline, phthalazine, quinazoline, quinoxaline, 1,8-naphthyridine, and pteridine.
  • monocyclic heteroaryls include pyridinyl, imidazolyl, pyrimidinyl, pyrazolyl, triazolyl, pyrazinyl, tetrazolyl, furyl, thienyl, isoxazolyl, thiazolyl, oxazolyl, isothiazolyl, pyrrolyl, pyridazinyl, triazinyl, oxadiazolyl, thiadiazolyl, and furazanyl.
  • bicyclic heteroaryls include indolizine, indole, benzofuran, benzothiophene, indazole, benzimidazole, purine, quinolizine, quinoline, isoquinoline, cinnoline, phthalazine, quinazoline, quinoxaline, 1,8-naphthyridine, and pteridine.
  • heteroaryl is pyridinyl, pyrazinyl, pyrimidinyl, thiazolyl, thienyl, thiadiazolyl, or furyl.
  • a heteroaryl contains 0-6 N atoms in the ring.
  • a heteroaryl contains 1-4 N atoms in the ring. In one or more embodiments, a heteroaryl contains 4-6 N atoms in the ring. In one or more embodiments, a heteroaryl contains 0-4 N atoms, 0-1 O atoms, 0-1 P atoms, and 0-1 S atoms in the ring. In one or more embodiments, a heteroaryl contains 1-4 N atoms, 0-1 O atoms, and 0-1 S atoms in the ring. In one or more embodiments, heteroaryl is a C 1 -C9 heteroaryl. In one or more embodiments, monocyclic heteroaryl is a C 1 -C5 heteroaryl.
  • monocyclic heteroaryl is a 5- membered or 6- membered heteroaryl.
  • a bicyclic heteroaryl is a C 6 -C 9 heteroaryl.
  • a heteroaryl group is partially reduced to form a heterocycloalkyl group defined herein.
  • a heteroaryl group is fully reduced to form a heterocycloalkyl group defined herein.
  • amino lipids can contain at least one primary, secondary, or tertiary amine moiety that is protonatable (or ionizable) between pH range 4 and 14.
  • the amine moiety/moieties function as the hydrophilic headgroup of the amino lipids.
  • the nanoparticles can be termed as cationic lipid nanoparticles (cLNPs).
  • ionizable lipid nanoparticles ionizable lipid nanoparticles
  • the amino lipids that constitute cLNPs can be generally called cationic amino lipids (cLipids).
  • the amino lipids that constitute iLNPs can be called ionizable amino lipids (iLipids).
  • the amino lipid can be an iLipid or a cLipid at physiological pH.
  • LNP compositions or formulations are typically sized on the order of micrometers or smaller and may include a lipid bilayer.
  • Nanoparticle compositions encompass lipid nanoparticles (LNPs), liposomes, lipid vesicles, and lipoplexes.
  • a nanoparticle composition may be a liposome having a lipid bilayer with a diameter of 500 nm or less.
  • the LNPs described herein can have a mean diameter of from about 1 nm to about 2500 nm, from about 10 nm to about 1500 nm, from about 20 nm to about 1000 nm, from about 30 nm to about 150 nm, from about 40 nm to about 150 nm, from about 50 nm to about 150 nm, from about 60 nm to about 130 nm, from about 70 nm to about 110 nm, from about 70 nm to about 100 nm, from about 80 nm to about 100 nm, from about 90 nm to about 100 nm, from about 70 to about 90 nm, from about 80 nm to about 90 nm, or from about 70 nm to about 80 nm.
  • the LNPs described herein can have a mean diameter of about 30 nm, 35 nm, 40 nm, 45 nm, 50 nm, 55 nm, 60 nm, 65 nm, 70 nm, 75 nm, 80 nm, 85 nm, 90 nm, 95 nm, 100 nm, 105 nm, 110 nm, 115 nm, 120 nm, 125 nm, 130 nm, 135 nm, 140 nm, 145 nm, 150 nm, or greater.
  • the LNPs described herein can be substantially non-toxic.
  • a “phospholipid” can refer to a lipid that includes a phosphate moiety and one or more carbon chains, such as unsaturated fatty acid chains.
  • a phospholipid may include one or more multiple (e.g., double or triple) bonds.
  • a phospholipid may facilitate fusion to a membrane.
  • a cationic phospholipid may interact with one or more negatively charged phospholipids of a membrane (e.g., a cellular or intracellular membrane). Fusion of a phospholipid to a membrane may allow one or more elements of an LNP to pass through the membrane, i.e., delivery of the one or more elements to a cell. 12.
  • the LNPs described herein can be designed to deliver a payload, such as one or more therapeutic agent(s) or drug substances(s), to a target cell or organ of interest.
  • a LNP described herein encloses one or more components of a gene editor system as described herein.
  • a LNP may enclose one or more of a guide nucleic acid, such as a guide RNA, a nucleic acid encoding the guide nucleic acid, a vector encoding the guide nucleic acid, a gene editor fusion protein, a nucleic acid encoding the gene editor fusion protein, a programmable DNA binding domain, a nucleic acid encoding the programmable DNA binding domain, or all or any combination thereof.
  • the nucleic acid is a DNA.
  • the nucleic acid is an RNA, for example, an mRNA and/or a guide RNA.
  • the nucleic acid(s) is/are chemically modified.
  • the payload comprises one or more nucleic acid(s) (i.e., one or more nucleic acid molecular entities).
  • the nucleic acid is a single-stranded nucleic acid.
  • the single-stranded nucleic acid is a DNA.
  • the single-stranded nucleic acid is an RNA.
  • the nucleic acid is a double-stranded nucleic acid.
  • the double-stranded nucleic acid is a DNA.
  • the double-stranded nucleic acid is an RNA.
  • the double-stranded nucleic acid is a DNA-RNA hybrid.
  • the nucleic acid is a messenger RNA (mRNA), a microRNA, an asymmetrical interfering RNA (aiRNA), a small hairpin RNA (shRNA), an antisense oligonucleotide, or a Dicer-Substrate dsRNA.
  • mRNA messenger RNA
  • aiRNA asymmetrical interfering RNA
  • shRNA small hairpin RNA
  • antisense oligonucleotide or a Dicer-Substrate dsRNA.
  • the single- stranded nucleic acids form secondary structure, one or more stem-loops for example.
  • the single stranded nucleic acids contain one or more stem-loops and single-stranded regions within the molecule. 13.
  • Exemplary LNP Formulations [320] The following are example formulations of LPA LNPs.
  • the above LNPs may be formulated with an mRNA:gRNA weight ratio of 1:1 +/- 5%, 10%, 15%, 20%, 30%, 40%, 50% 60%, 70%, 80%, 90%, or 100% of the mRNA or gRNA or any therapeutically effective ratio.
  • an mRNA:gRNA weight ratio of 1:1 +/- 10% of gRNA would mean any mRNA:gRNA ratio between 1:0.9 to 1:1.1.
  • the N/P ratio of the LNP may be from about 4 to about 7, about 4, about 4.5, about 5, about 5.5, or about 6, about 6.5, or about 7, with each ratio +/- 5-20%.
  • the LNPs may be contained in a pharmaceutically acceptable solution that may, for example, comprise a buffer having a pH of about 7.5 +/- 1.5 and including tris and/or sucrose.
  • the gRNAs may comprise sequences substantially identical to those specified in Table 3.
  • one or more of the gRNA combinations set forth in Figure 2 may comprise the LNP payload.
  • the mean diameter of the LNPs may be about 70 nm +/- 20 nm, 70 nm +/- 10 nm, 70 nm +/- 5 nm; 60 nm +/- 20 nm, 60 nm +/- 10 nm, 60 nm +/- 5 nm; 50 nm +/- 20 nm, 50 nm +/- 10 nm, 50 nm +/- 5 nm; 45 nm +/- 20 nm, 45 nm +/- 10 nm, 45 nm +/- 5 nm.
  • kits including the compositions comprising guide nucleic acids, such as guide RNAs, as provided herein, the gene editor or gene editor system as provided herein, the compositions as provided herein, and/or the lipid nanoparticle formulations as provided herein for treating or preventing a condition.
  • kits and articles of manufacture for use with one or more methods described herein.
  • Such kits include a carrier, package, or container that is compartmentalized to receive one or more containers such as vials, tubes, and the like, each of the container(s) comprising one of the separate elements to be used in a method described herein.
  • Suitable containers include, for example, bottles, vials, syringes, and test tubes.
  • the containers are formed from a variety of materials such as glass or plastic.
  • the articles of manufacture provided herein contain packaging materials.
  • kits examples include, but are not limited to, blister packs, bottles, tubes, bags, containers, bottles, and any packaging material (including use and/or disposal instructions) suitable for a selected formulation and intended mode of administration and treatment.
  • the container(s) include a composition as described herein, and optionally in addition with therapeutic regimens or agents disclosed herein.
  • kits optionally include an identifying description or label or instructions relating to its use in the methods described herein.
  • a kit typically includes labels listing contents and/or instructions for use, and package inserts with instructions for use. A set of instructions will also typically be included.
  • a label is on or associated with the container.
  • a label is on a container when letters, numbers, or other characters forming the label are attached, molded, or etched into the container itself; a label is associated with a container when it is present within a receptacle or carrier that also holds the container, e.g., as a package insert.
  • a label is used to indicate that the contents are to be used for a specific therapeutic application. The label also indicates directions for use of the contents, such as in the methods described herein. IX.
  • DOSING [328] The skilled artisan will appreciate that certain factors may influence the dosage and frequency of administration required to effectively treat a subject, including but not limited to the severity of the disease or disorder, previous treatments, the general characteristics of the subject including health, sex, weight, and/or age of the subject, and other diseases present.
  • treatment of a subject with a therapeutically effective amount of the compositions can include a single treatment or, preferably, can include a series of treatments.
  • the effective dosage of the composition of the disclosure used for treatment may increase or decrease over the course of a particular treatment. Changes in dosage may result and become apparent from the results of diagnostic assays as described herein.
  • the therapeutically effective dosage will generally be dependent on the patient's status at the time of administration.
  • Frequency of administration may be determined and adjusted over the course of therapy, and is generally, but not necessarily, based on treatment and/or suppression and/or amelioration and/or delay of a disease.
  • sustained continuous release formulations of a polypeptide or a polynucleotide may be appropriate.
  • dosage is daily, every other day, every three days, every four days, every five days, or every six days.
  • dosing frequency is once every week, every 2 weeks, every 3 weeks, every 4 weeks, every 5 weeks, every 6 weeks, every 7 weeks, every 8 weeks, every 9 weeks, or every 10 weeks; or once every month, every 2 months, every 3 months, or longer.
  • the pharmaceutical composition comprising the gene editor system for effecting edits in the LPA gene, as described herein is dosed once to a subject in need with no need for additional dosing.
  • the pharmaceutical composition comprising the gene editor system for effecting edits in the LPA gene, as described herein is dosed twice with the second dose following sequentially after the first.
  • the pharmaceutical composition comprising the gene editor system for effecting edits in the LPA gene, as described herein, is dosed sequentially multiple times until a sufficient amount of therapeutically effective editing of the LPA gene, as described herein, is achieved, with the second dose following sequentially after the first.
  • the progress of this therapy is easily monitored by conventional techniques and assays and may be determined by monitoring blood Lp(a) concentrations, which may be directly correlated with apo(a) concentrations or may be inversely correlated the size of the apo(a) protein.
  • the subject may be dosed with LNPs that contain different gene editor system components (e.g., mRNA encoding the gene editor in one LNP and gRNAs in another, a mixture of mRNA and gRNAs in the same LNP, or different gRNAs in different LNPs with or without mRNA).
  • the dosing regimen can vary over time. In one or more embodiments, it is contemplated that for an adult subject of normal weight, doses ranging from about 0.01 to 1000 mg/kg may be administered. In one or more embodiments, the dose is between 1 to 200 mg/kg of subject body weight.
  • the dosing may be between 0.03 mg/kg to 3 mg/kg, 0.1 to 2 mg/kg, 0.5 to 1.5 mg/kg, or anywhere between any of the foregoing ranges.
  • the particular dosage regimen i.e., dose, timing, and repetition, will depend on the particular subject and that subject's medical history, as well as the properties of the polypeptide or the polynucleotide (such as the half-life of the polypeptide or the polynucleotide, and other considerations well known in the art).
  • compositions as described herein will depend on the specific agent (or compositions thereof) employed, the formulation and route of administration, the type and severity of the disease, whether the polypeptide or the polynucleotide is administered for preventive or therapeutic purposes, previous therapy, the subject's clinical history and response to the therapy, and the discretion of the attending physician. Typically, the clinician may administer a therapeutic agent until a dosage is reached that achieves the desired result.
  • Administration of one or more compositions can be continuous or intermittent, depending, for example, upon the recipient’s physiological condition, whether the purpose of the administration is therapeutic or preventative, and other factors known to skilled practitioners.
  • compositions may be essentially continuous over a preselected period of time or may be in a series of spaced doses, e.g., either before, during, or after developing a disease.
  • the methods and compositions of the disclosure described herein including embodiments thereof can be administered with one or more additional therapeutic regimens or agents or treatments, which can be co-administered to the mammal.
  • co-administering is meant administering one or more additional therapeutic regimens or agents or treatments and the composition of the disclosure sufficiently close in time to enhance the effect of one or more additional therapeutic agents, or vice versa.
  • composition of the disclosure described herein can be administered simultaneously with one or more additional therapeutic regimens or agents or treatments, at a different time, or on an entirely different therapeutic schedule (e.g., the first treatment can be daily, while the additional treatment is weekly).
  • the secondary therapeutic regimens or agents or treatments are administered simultaneously, prior to, or subsequent to the composition of the disclosure.
  • the means for editing the LPA gene, inactivating the LPA gene, or treating a disease include a gene editor system as described herein. In some embodiments, the means for editing the LPA gene, inactivating the LPA gene, or treating a disease include a delivery system comprising gene editor system as described herein. In some embodiments, the means for editing the LPA gene, inactivating the LPA gene, or treating a disease include a composition comprising gene editor system as described herein. In some embodiments, the means for editing the LPA gene, inactivating the LPA gene, or treating a disease include a pharmaceutical composition comprising gene editor system as described herein.
  • the means for editing the LPA gene, inactivating the LPA gene, or treating a disease include a lipid nanoparticle comprising gene editor system as described herein.
  • a delivery system, composition, or pharmaceutical composition may comprise the lipid nanoparticle.
  • Table 7A summarizes dose response curves in human hepatocellular carcinoma immortalized cells (HuH-7) for five (5) pairs of first and second guide RNAs using a gene editing system that comprises a dual nickase Cas9 system.
  • the sequences of the guide oligonucleotides are provided in Table 4.
  • the Cas9 nickase is encoded within an mRNA (MS029) that was transfected into the HuH-7 cells in a 1:1 total mRNA: total gRNA weight ratio.
  • Additional guide oligonucleotide pairs were tested with a similar experimental design. The results are presented in Table 7B (provided above in the Detailed Description).
  • RNA preparation From among the potential guide RNAs having spacer sequences corresponding to the protospacer sequences in Table 2, 58 guide RNAs identified in Table 5 (provided above in the Detailed Description) were manufactured and used for further cellular analysis. The spacer sequences of some of the gRNAs and the location of hybridization to the LPA gene for some of the guide oligonucleotides are shown in Figure 9.
  • Cell transfection For primary human hepatocytes: collagen-I coated 96-well plates were seeded with primary human hepatocytes (BioIVT, lot: OQA) at a density of 5 ⁇ 10 4 cells/well.
  • HuH-7 cells were plated into 100 ⁇ L of hepatocyte culture media and placed in an incubator for 4 hours, until they had attached and formed a monolayer.
  • HuH-7 cells 96-well plates were seeded with HuH-7 cells (Sekisui Xeno Tech) at a density of 2 ⁇ 10 4 cells/well. Cells were plated into 100 ⁇ L of DMEM + 10% FBS + 1% penicillin/streptomycin and placed in an incubator for 24 hours, until they had attached and formed a monolayer. Table 8.
  • transfection reactions were prepared by combining RNA for a total dose of 2500 ng/ml, as listed in Table 8, and then adding Lipofectamine MessengerMax diluted with OPTI-MEM and incubating for 15 minutes at room temperature.
  • transfection reagents were diluted 1:8, for a final dose of 312.5 ng/ml.
  • the hepatocyte culture medium was replaced with 90 ⁇ L of fresh hepatocyte culture medium, and 10 ⁇ L of each prepared transfection reaction was added to wells of cells in the 96- well plate for a total volume of 100 ⁇ L.
  • computational analysis was used to determine what fraction of the reads mapping to the specific targeted LPA genomic region contained the desired edits.
  • FIG. 1 shows edits for tested combinations of guide RNAs achieved with a higher dose (2500 ng/ml of RNA; closed circles) and a lower dose (312.5 ng/ml of RNA; open circles). More than half (31) of the tested guide pairs exceeded 50% editing at the higher (2500 ng/ml) dose; fifteen of the tested guide pairs exceeded 80% editing at the higher dose; and two of the tested guide pairs exceeded 90% editing at the higher dose. [349] Some selected guide pairs were further tested.
  • Figure 3 shows edits for tested combinations of guide RNAs achieved with a highest dose (10,000 ng/ml of RNA) and 1:2 dilutions of dose down to the lowest dose (78.125 ng/ml of RNA).
  • Guide 1:guide 2:mRNA weight ratios used were 1:1:2.
  • Each tested combination yielded some level of editing.
  • the highest level of editing observed with the highest RNA dose was 62% with guide pair GA1183/GA1184.
  • Each of the 5 guide pairs demonstrated good potency, which was titratable in relation to the dose used.
  • all guide RNAs introduced indel variants, and the edits were dose-dependent, validating the editing strategy.
  • the guide pairs tested in this example include GA1295/GA1296 (corresponding to LNP1); GA1297/GA1296 (corresponding to LNP2); and GA1298/GA1296 (corresponding to LNP3).
  • the sequences of the guide oligonucleotides are provided in Table 4.
  • LNPs comprising a guide pair GA1295/GA1296 (corresponding to LNP 1), GA1297/GA1296 (corresponding to LNP 2), or GA1298/GA1296 (corresponding to LNP 3) and comprising mRNA encoding SpCas9-D10A (MS029) were prepared with equal weights of each gRNA per guide pair and with a 1:1 weight ratio of total gRNA (guide 1 + guide 2) to mRNA.
  • each of the LNPs were an ionizable amino lipid (iLipid), a neutral helper lipid, a PEG-Lipid, and a sterol lipid, with optional inclusion of a ligand-targeting lipid, such as GalNAc.
  • iLipid ionizable amino lipid
  • PEG-Lipid a neutral helper lipid
  • sterol lipid a sterol lipid
  • a ligand-targeting lipid such as GalNAc.
  • Table 9 describes LNP formulations, excluding the drug substances (i.e., gRNA and mRNA).
  • the lipids in Table 9 may be substituted for other suitable lipids in the listed class.
  • the LNP comprises the amino lipid VL422 described in the International Published Patent Application WO 2022/060871 A1.
  • the amino lipid may be VL422 or a pharmaceutically acceptable salt or solvate thereof: .
  • the example mol% of lipids in Table 9 thus may be adjusted and that the mol% included in Table 9 are targeted excipient percentages of the LNP, which is intended to represent the aggregate mol% of all the LNPs formulated in a given batch and that specific LNPs within a batch may have varying mol%.
  • the mol% of one or more or all of the LNP components set forth in Table 9 may be adjusted, for example, by +/- 1 to 5%, +/- 5 to 10%, or +/- 10% to 20%. It is further contemplated herein that the mol% of one or more or all of the LNP components set forth in Table 9 with respect to a specific LNP, formulated in a given batch of LNPs formulated in accordance with desired target excipient percentages, may vary from the targeted mol%, for example, by +/- 1 to 5%, +/- 5 to 10%, +/-10 to 20%, or even greater than +/- 20%.
  • LNP components including non-lipid components
  • GalNAc ligand-targeting lipids such as those disclosed in International Published Patent Application WO 2021/178725 A1 may be added and the cholesterol mol% component reduced to account for the additional GalNAc conjugated lipid.
  • the mol% of cholesterol in the formulation would be reduced by 0.05%.
  • each of the p and q is independently an integer from 1 to 5, and n is an integer from 33 to 39; and .
  • the average LNP particle size may range from 40-90 nm, 50-80 nm, or 55-75 nm, +/- 15 nm.
  • PHA Primary human hepatocyte
  • EXAMPLE 4 Reduction in secreted LP(a) protein in HuH-7 cells by gene editing system
  • Lentiviruses containing an expression cassette comprising an LPA open reading frame (ORF) followed by an internal ribosome entry site (IRES) and puromycin N-acetyltransferase (puro), driven by a cytomegalovirus (CMV) promoter, were created.
  • HuH-7 cells were transfected with the lentiviruses and selected for integration of the expression cassette with puromycin.
  • LNPs LNP1 as described in Example 3 were administered to puromycin-resistant cells in which the expression cassette was integrated into the genome (the guide pair was GA1295/1296) at various concentrations ranging from 0 to 5,000 ng/ml (total RNA), and levels of apo(a) secreted from the cells were evaluated. Apo(a) protein concentration was assessed using a validated Lp(a) ELISA kit from Mercodia. [361] As shown in Figure 5, secreted apo(a) was reduced in a dose-dependent manner, illustrating that gene editing as described herein may be used to lower apo(a) levels.
  • EXAMPLE 5 Evaluation of off-target editing [362] Off-target analysis was performed and indicated a very favorable off-target profile (data not shown).
  • EXAMPLE 6 Gene editing in transgenic mice expressing human LPA gene [363] Transgenic mice expressing the human LPA gene (J:144538 Frazer KA, et al., The apolipoprotein(a) gene is regulated by sex hormones and acute-phase inducers in YAC transgenic mice. Nat Genet.1995 Apr;9(4):424-31) were obtained from The Jackson Laboratory.
  • mice two females and two males per group were split as follows: control vehicle (LNP), 0.05 mg/kg total dose RNA, 0.1 mg/kg total dose RNA, 0.5 mg/kg total dose RNA, 2 mg/kg total dose RNA, 4 mg/kg total dose RNA, and 10 mg/kg total dose RNA.
  • LNP control vehicle
  • the LNPs were prepared as described in Example 3 and included guide RNA pair GA1295/GA1296 and mRNA encoding SpCas9-D10A (MS029) in a ratio of 1:1:2 (or 1:1 based on total guide RNA to mRNA).
  • the sequences of the guide oligonucleotides are provided in Table 4.
  • LNP formulations were administered via retro-orbital injection.
  • Serum apo(a) protein concentrations were determined seven days prior to injecting the mice with LNPs, seven days following injection, and fourteen days following injection. Serum apo(a) protein concentrations were evaluated using a validated Lp(a) ELISA kit from Mercodia.
  • livers were harvested from the mice, and DNA extraction performed as described above in Example 2.
  • the average serum apo(a) protein concentration in female mice was about 50 ng/dL seven days prior to injection with the LNPs.
  • the average concentration in male mice was about 1.25 ng/dL seven days prior to injection with the LNPs.
  • the male apo(a) serum concentrations were about 40-fold less than the female serum concentrations.
  • the editing efficiency of the LPA gene occurred in a dose- dependent manner.
  • the EC50 was determined to be 0.18 mg/kg, and the EC90 was determined to be 0.67 mg/kg. Greater than 70% editing efficiency was achieved at the 2.0 mg/kg total RNA dose.
  • the experiment was repeated with slightly different doses and with LNPs having different average particle size (67 nm versus 77 nm for Figure 6A).
  • the results are presented in Figure 6B, which illustrates similar results to those illustrated in Figure 6A.
  • Plasma apo(a) concentrations were determined at baseline (–7 days) and 14 days following retro-orbital injection of the gene editing systems. The results are presented in Figure 8B. [373] The guide pair number shown in Figure 8B corresponds to the guide pairs listed in Table 10. The sequences of the gRNA are listed in Table 4. Table 10. Guide pair designators for guide pairs numbers shown in Figure 8B [374] Guide pair GA1303/GA1304 is interesting because the guide pair targets Exon 2 of the LPA gene and exhibits high editing efficiency. [375] The subject matter described herein and in the accompanying figures is done so with sufficient detail and clarity to permit the inclusion of claims, at any time, in means-plus- function format pursuant to 35 U.S.C. section 112, part (f).
  • the disclosure comprises specific embodiments and examples of base editing systems to effect a nucleobase alteration in a gene and methods of using same for treatment of disease including compositions that comprise such base editing systems, designs and modifications thereto; and specific examples and embodiments describing the synthesis, manufacture, use, and efficacy of the foregoing individually and in combination including as pharmaceutical compositions for treating disease and for in vivo and in vitro delivery of active agents to mammalian cells under described conditions.
  • any feature presented in one claim may be included in another claim; any feature presented in one claim may be removed from the claim to constitute a claim without that feature; and any feature presented in one claim may be combined with any feature in another claim, each of which is contemplated herein.
  • the following enumerated clauses are further illustrative examples of aspects and combination of aspects of the foregoing embodiments and examples: [380] Following is an example of enumerated clauses: 1.
  • a pharmaceutical composition for in vivo editing of an LPA gene, in a mammalian subject comprising: (i) an engineered, non-naturally occurring gene editing system, which comprises: (a) one or more polynucleotides (mRNAs) encoding one or more CRISPR Cas nickases; (b) a first guide oligonucleotide (gRNA) comprising a first spacer sequence that is complementary to a first strand of the LPA gene at a first target sequence and a first scaffold region that serves as a binding scaffold for at least one of the one or more Cas nickases; and (c) a second guide oligonucleotide (gRNA) comprising a second spacer sequence that is complementary to a second strand of the LPA gene at a second target sequence and a second scaffold region that serves as a binding scaffold for at least one of the one or more Cas nickases, and (ii) a delivery system that is engineered to deliver the one or more mRNA
  • the delivery system comprises lipid nanoparticles (LNPs), wherein the LNPs comprise: (a) one or more ionizable lipids, (b) cholesterol, (c) one or more PEG-lipids, (d) a phospholipid; and (e) optionally including a targeting moiety, such as a GalNAc lipid.
  • LNPs lipid nanoparticles
  • the LNPs comprise: (a) one or more ionizable lipids, (b) cholesterol, (c) one or more PEG-lipids, (d) a phospholipid; and (e) optionally including a targeting moiety, such as a GalNAc lipid.
  • first spacer sequence of the first guide oligonucleotide comprises about 15 to about 26 nucleotides and has a sequence that is identical to or substantially identical to a targeted first protospacer sequence adjacent to a protospacer-adjacent motif (PAM) sequence on the first strand of the LPA gene.
  • the gene editing system is engineered to edit the LPA gene to effect an indel or non-synonymous variant.
  • the first spacer sequence of the guide oligonucleotide has sequence that is identical to or substantially identical to a first protospace
  • first spacer sequence of the first guide oligonucleotide has a sequence that is identical to or substantially identical to a first protospacer sequence adjacent to a first protospacer- adjacent motif (PAM) sequence on the first strand of the LPA gene
  • second spacer sequence of the second guide oligonucleotide has a sequence that is identical to or substantially identical to a second protospacer sequence adjacent to a second protospacer-adjacent motif (PAM) sequence on the second strand of the LPA gene
  • the one or more Cas nickases in operation with the first and second guide oligonucleotides, is engineered to nick opposing strands of the LPA gene outside the first and second protospacer-adjacent motifs (PAMs) in a “PAM-in” configuration.
  • gRNAs guide oligonucleotides
  • gRNAs guide oligonucleotides
  • first guide oligonucleotide comprises a first spacer having a sequence identical to, or at least about 75%, at least about 80%, at least about 85%, at least about 90%, or at least about 95% identity to, a protospacer listed in Table 2 or Table 5; and the second guide oligonucleotide comprises a second spacer having a sequence identical to, or at least about 75%, at least about 80%, at least about 85%, at least about 90%, or at least about 95% identity to, a protospacer listed in Table 2 or Table 5, wherein the first spacer corresponds to a protospacer on one strand of the LPA gene and the second spacer corresponds to a protospacer on the other strand of the LPA gene.
  • first guide oligonucleotide comprises a first spacer having a sequence identical to, or at least about 75%, at least about 80%, at least about 85%, at least about 90%, or at least about 95% identity to, a guide 1 protospacer listed in Table 2 or Table 5; and the second guide oligonucleotide comprises a second spacer having a sequence identical to, or at least about 75%, at least about 80%, at least about 85%, at least about 90%, or at least about 95% identity to, a guide 2 protospacer listed in Table 2 or Table 5, wherein the guide 1 protospacer and the guide 2 protospacer are in a same row of Table 2 or Table 5. 22.
  • first guide oligonucleotide comprises a first spacer having a sequence identical or substantially identical to a guide 1 protospacer sequence listed in Table 2 or Table 5, or a 3′ portion thereof, with 0, 1, 2, 3, 4, or 5 mismatches
  • second guide oligonucleotide comprises a second spacer having a sequence identical or substantially identical to a guide 2 protospacer sequence listed in Table 2 or Table 5, or a 3′ portion thereof, with 0, 1, 2, 3, 4, or 5 mismatches, wherein the guide 1 protospacer and the guide 2 protospacer are in a same row of Table 2 or Table 5.
  • first guide oligonucleotide comprises a first spacer comprising a sequence identical to the 15, 16, 17, 18, 19, or twenty 3’-most nucleotides of a guide 1 protospacer sequence listed in Table 2 or Table 5; and the second guide oligonucleotide comprises a second spacer comprising a sequence identical to the 15, 16, 17, 18, 19, or twenty 3’-most nucleotides of a guide 2 protospacer sequence listed in Table 2 or Table 5, wherein the guide 1 protospacer and the guide 2 protospacer are in a same row of Table 2 or Table 5.
  • the first and second spacer sequences are identical to or substantially identical to protospacer sequences listed in Table 5 for which editing of 20% or greater was observed at 2500 ng/ml.
  • composition of any one of clauses 1 to 33 wherein at least one of the one or more polynucleotides is selected from any of the mRNA sequences listed in Table 1 or an mRNA having at least about 90% identity, at least about 91% identity, at least about 92% identity, at least about 93% identity, at least about 94% identity, at least about 95% identity, at least about 96% identity, at least about 97% identity, at least about 98% identity, or at least about 99% identity to any of the mRNA sequences listed in Table 1. 35.
  • composition of any one of clauses 1 to 35, wherein at least one of the one or more mRNAs that encodes the Cas nickase comprises: (a) a 5’ untranslated region (UTR); (b) a 3’ UTR region; (c) a poly(A) tail proximate to the 3’ UTR as compared to the 5’ UTR, said poly(A) tail comprising a chain of 80-150 nucleotides length that comprise adenine nucleotides; and (d) a gene editor coding region encoding an impaired CRISPR Cas9 endonuclease domain and a polymerase domain, said gene editor coding region extending between the 5’ UTR and the 3’ UTR. 37.
  • the scaffold region sequences of the first and second guide oligonucleotides are each independently selected from one of the following sequences or a sequence having at least about 75%, at least about 80%, at least about 85%, at least about 90%, or at least about 95% identity to one of the following sequences: 5’- GUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAAC UUGAAAAAGUGGCACCGAGUCGGUGC -3’, and 5’- GUUUGAGAGCUAUGCUGGAAACAGCAUAGCAAGUUCAAAUAAGGCUAGUC CGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGC -3’.
  • the LNP has a mean diameter of about 70 nm +/- 20 nm, 70 nm +/- 10 nm, 70 nm +/- 5 nm; 60 nm +/- 20 nm, 60 nm +/- 10 nm, 60 nm +/- 5 nm; 50 nm +/- 20 nm, 50 nm +/- 10 nm, 50 nm +/- 5 nm; 45 nm +/- 20 nm, 45 nm +/- 10 nm, 45 nm +/- 5 nm. 44.
  • composition according to any one of clauses 1 to 47, wherein the composition is engineered to generate nicks on the first strand and the second strand of the LPA gene, wherein the distance between the nicks is 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 nucleotides or greater. 49.
  • composition according to any one of clauses 1 to 48, wherein the composition is engineered to generate nicks on the first strand and the second strand of the LPA gene, wherein the distance between the nicks is between 20 and 50 nucleotides, such as between 23 and 45, between 30 and 40, between 31 and 40, between 32 and 40, between 33 and 40, between 31 and 39, between 32 and 39, between 33 and 39, or between 34 and 38 nucleotides. 50.
  • a method for in vivo editing of an LPA gene in a mammalian subject comprising: administering to the subject a pharmaceutical composition comprising: (i) one or more polynucleotides (mRNAs) encoding one or more CRISPR Cas nickases, (ii) a first guide oligonucleotide (gRNA) comprising a first spacer sequence and a scaffold region; and (iii) a second guide oligonucleotide (gRNA) comprising a second spacer sequence and a scaffold region, and (iv) a delivery system that is engineered to deliver the one or more mRNAs, the first gRNA, and/or the second gRNA individually or collectively to the liver, wherein the first gRNA and at least one of the one or more Cas nickases are engineered to cause the at least one of the one or more Cas nickases to nick one of the first or second strands of the LPA gene at a first location of chromos
  • LNPs lipid nanoparticles
  • the LNPS comprise: (a) one or more ionizable lipids, (b) cholesterol, (c) one or more PEG-lipids, (d) a phospholipid; and (e) optionally including a targeting moiety, such as a GalNAc lipid.
  • the mammalian subject is a human.
  • the first spacer sequence of the first guide oligonucleotide (gRNA) comprises about 15 to about 26 nucleotides and has a sequence that is identical to or substantially identical to a targeted first protospacer sequence adjacent to a protospacer-adjacent motif (PAM) sequence on the first strand of the LPA gene.
  • the one or more Cas nickase and the first and second gRNAs are engineered to effect an indel or non-synonymous variant.
  • first spacer sequence of the first guide oligonucleotide has a sequence that is identical to or substantially identical to a first protospacer sequence adjacent to a first protospacer-adjacent motif (PAM) sequence on the first strand of the LPA gene
  • second spacer sequence of the second guide oligonucleotide has a sequence that is identical to or substantially identical to a second protospacer sequence adjacent to a second protospacer-adjacent motif (PAM) sequence on the second strand of the LPA gene
  • the one or more Cas nickases in operation with the first and second guide oligonucleotides, nicks opposing strands of the LPA gene between the first and second protospacer-adjacent motifs (PAMs) in a “PAM-out” configuration.
  • the method for in vivo editing of an LPA gene according to any one of clauses 50 to 70, wherein at least one of the one or more polynucleotides comprises a coding sequence of any of the mRNA sequences listed in Table 1 or comprises a coding sequence having at least about 90% identity, at least about 91% identity, at least about 92% identity, at least about 93% identity, at least about 94% identity, at least about 95% identity, at least about 96% identity, at least about 97% identity, at least about 98% identity, or at least about 99% identity to any of the coding sequences of the SpCas9-D10A nickase mRNA sequences listed in Table 1. 72.
  • the method for in vivo editing of an LPA gene comprises: (a) a 5’ untranslated region (UTR); (b) a 3’ UTR region; (c) a poly(A) tail proximate to the 3’ UTR as compared to the 5’ UTR, said poly(A) tail comprising a chain of 80-150 nucleotides length that comprise adenine nucleotides; and (d) a gene editor coding region encoding an impaired CRISPR Cas endonuclease domain and a polymerase domain, said gene editor coding region extending between the 5’ UTR and the 3’ UTR.
  • scaffold region sequences of the first and second guide oligonucleotides are each independently selected from one of the following sequences or a sequence having at least about 75%, at least about 80%, at least about 85%, at least about 90%, or at least about 95% identity to one of the following sequences: 5’- GUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAAC UUGAAAAAGUGGCACCGAGUCGGUGC -3’, and 5’- GUUUGAGAGCUAUGCUGGAAACAGCAUAGCAAGUUCAAAUAAGGCUAGUC CGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGC -3’.
  • first guide oligonucleotide comprises a first spacer having a sequence identical to, or at least about 75%, at least about 80%, at least about 85%, at least about 90%, or at least about 95% identity to, a protospacer listed in Table 2 or Table 5; and the second guide oligonucleotide comprises a second spacer having a sequence identical to, or at least about 75%, at least about 80%, at least about 85%, at least about 90%, or at least about 95% identity to, a protospacer listed in Table 2 or Table 5, wherein the first spacer corresponds to a protospacer on one strand of the LPA gene and the second spacer corresponds to a protospacer on the other strand of the LPA gene.
  • the first guide oligonucleotide comprises a first spacer having a sequence identical to, or at least about 75%, at least about 80%, at least about 85%, at least about 90%, or at least about 95% identity to, a guide 1 protospacer listed in Table 2 or Table 5; and the second guide oligonucleotide comprises a second spacer having a sequence identical to, or at least about 75%, at least about 80%, at least about 85%, at least about 90%, or at least about 95% identity to, a guide 2 protospacer listed in Table 2 or Table 5, wherein the guide 1 protospacer and the guide 2 protospacer are in a same row of Table 2 or Table 5.
  • first guide oligonucleotide comprises a first spacer having a sequence identical or substantially identical to a guide 1 protospacer sequence listed in Table 2 or Table 5, or a 3′ portion thereof, with 0, 1, 2, 3, 4, or 5 mismatches
  • second guide oligonucleotide comprises a second spacer having a sequence identical or substantially identical to a guide 2 protospacer sequence listed in Table 2 or Table 5, or a 3′ portion thereof, with 0, 1, 2, 3, 4, or 5 mismatches, wherein the guide 1 protospacer and the guide 2 protospacer are in a same row of Table 2 or Table 5.
  • first guide oligonucleotide comprises a first spacer comprising a sequence identical to the 15, 16, 17, 18, 19, or twenty 3’-most nucleotides of a guide 1 protospacer sequence listed in Table 2 or Table 5; and the second guide oligonucleotide comprises a second spacer comprising a sequence identical to the 15, 16, 17, 18, 19, or twenty 3’-most nucleotides of a guide 2 protospacer sequence listed in Table 2 or Table 5, wherein the guide 1 protospacer and the guide 2 protospacer are in a same row of Table 2 or Table 5.
  • the first guide oligonucleotide comprises a first spacer sequence identical to or substantially identical to a guide 1 protospacer listed in Table 5; and the second guide oligonucleotide comprises a second spacer sequence identical to or substantially identical to a corresponding (in a same row) guide 2 protospacer listed in Table 5.
  • the first and second spacer sequences are identical to or substantially identical to protospacer sequences listed in Table 5 for which editing of 20% or greater was observed at 2500 ng/ml. 80.
  • the method for in vivo editing of an LPA gene according to clause 89 wherein the LNP has an N/P ratio from about 4 to about 7, about 4, about 4.5, about 5, about 5.5, or about 6, about 6.5, or about 7, with each ratio +/- 5-20%.
  • the buffer solution containing the LNP has a pH of about 7.5 +/- 1.5 and comprises tris and/or sucrose.
  • the method for in vivo editing of an LPA gene according to any one of clauses 89 to 91, wherein the LNP has a mean diameter of about 70 nm +/- 20 nm, 70 nm +/- 10 nm, 70 nm +/- 5 nm; 60 nm +/- 20 nm, 60 nm +/- 10 nm, 60 nm +/- 5 nm; 50 nm +/- 20 nm, 50 nm +/- 10 nm, 50 nm +/- 5 nm; 45 nm +/- 20 nm, 45 nm +/- 10 nm, 45 nm +/- 5 nm. 93.
  • a method for inactivating the LPA gene in vivo in a mammalian subject to treat and prevent cardiovascular disease comprising the step of: administering to the subject a pharmaceutical composition of any one of clauses 1 to 49.
  • a method for reducing blood Lp(a) concentration in a mammalian subject to treat and prevent cardiovascular disease comprising the step of: administering to the subject a pharmaceutical composition of any one of clauses 1 to 49.
  • a method for treating and/or preventing cardiovascular disease associated with the LPA gene in a mammalian subject comprising the step of: administering to the subject a pharmaceutical composition of any one of clauses 1 to 49. 96.
  • a gene editing system for editing the LPA gene produced by expressing in a cell one or more exogenous polynucleotides (mRNA) encoding one or more CRISPR Cas nickases and introducing first and second gRNAs into the cell, wherein the first guide oligonucleotide (gRNA) comprises (i) a first spacer sequence that is complementary to a first strand of the LPA gene at a first target sequence and (ii) a first scaffold region that serves as a binding scaffold for at least one of the one or more Cas nickases, wherein the second guide oligonucleotide (gRNA) comprises (i) a second spacer sequence that is complementary to a second strand of the LPA gene at a second target sequence and (ii) a second scaffold region that serves as a binding scaffold for at least one of the one or more Cas nickases, wherein the first gRNA and the at least one of the one or more Cas nickases are engineered to cause the at
  • a method comprising: formulating a delivery system comprising one or more exogenous polynucleotides (mRNA) encoding one or more CRISPR Cas nickases, a first guide oligonucleotide (gRNA), and a second guide oligonucleotide (gRNA), wherein the first guide oligonucleotide (gRNA) comprises (i) a first spacer sequence that is complementary to a first strand of the LPA gene at a first target sequence and (ii) a first scaffold region that serves as a binding scaffold for at least one of the one or more Cas nickases, wherein the second guide oligonucleotide (gRNA) comprises (i) a second spacer sequence that is complementary to a second strand of the LPA gene at a second target sequence and (ii) a second scaffold region that serves as a binding scaffold for at least one of the one or more Cas nickases, wherein the first gRNA and the at least one of
  • a gene editing system comprising: a means for expressing one or more CRISPR Cas nickases in a cell; and a means for directing the one or more Cas nickases to first and second locations in the LPA gene and to cause the one or more Cas nickases to introduce a nick in a first strand of the LPA gene and to introduce a nick in a second strand of the LPA gene.
  • a pharmaceutical composition comprising the gene editing system of clause 100 and a delivery system.
  • composition of clause 102 wherein the delivery system comprises means for delivering to the cell the means for expressing one or more CRISPR Cas nickases and the means for directing the one or more Cas nickases to first and second locations in the LPA gene. 104.
  • a gene editing system comprising: wherein the first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a first spacer having a sequence identical to, or at least about 75%, at least about 80%, at least about 85%, at least about 90%, or at least about 95% identity to, a protospacer listed in Table 2 or Table 5; and the second guide oligonucleotide comprises a second scaffold region that serves as a binding scaffold for the nickase and comprises a second spacer having a sequence identical to, or at least about 75%, at least about 80%, at least about 85%, at least about 90%, or at least about 95% identity to, a protospacer listed in Table 2 or Table 5, wherein the first spacer corresponds to a protospacer on one strand of the LPA gene and the second spacer corresponds to a protospacer on the other strand of the LPA gene.
  • a gene editing system comprising: a first guide oligonucleotide comprising a first scaffold region that serves as a binding scaffold for a nickase and comprising a first spacer having a sequence identical to, or at least about 75%, at least about 80%, at least about 85%, at least about 90%, or at least about 95% identity to, a guide 1 protospacer listed in Table 2 or Table 5; and a second guide oligonucleotide comprising a second scaffold region that serves as a binding scaffold for the nickase and comprising a second spacer having a sequence identical to, or at least about 75%, at least about 80%, at least about 85%, at least about 90%, or at least about 95% identity to, a guide 2 protospacer listed in Table 2 or Table 5, wherein the guide 1 protospacer and the guide 2 protospacer are in a same row of Table 2 or Table 5.
  • a gene editing system comprising: a first guide oligonucleotide comprising a first scaffold region that serves as a binding scaffold for a nickase and comprising a first spacer having a sequence identical or substantially identical to a guide 1 protospacer sequence listed in Table 2 or Table 5, or a 3′ portion thereof, with 0, 1, 2, 3, 4, or 5 mismatches; and a second guide oligonucleotide comprising a second scaffold region that serves as a binding scaffold for the nickase and comprising a second spacer having a sequence identical or substantially identical to a guide 2 protospacer sequence listed in Table 2 or Table 5, or a 3′ portion thereof, with 0, 1, 2, 3, 4, or 5 mismatches, wherein the guide 1 protospacer and the guide 2 protospacer are in a same row of Table 2 or Table 5.
  • a gene editing system comprising: a first guide oligonucleotide comprising a first scaffold region that serves as a binding scaffold for a nickase and comprising a first spacer comprising a sequence identical to the 15, 16, 17, 18, 19, or twenty 3’-most nucleotides of a guide 1 protospacer sequence listed in Table 2 or Table 5; and a second guide oligonucleotide comprising a second spacer comprising a second scaffold region that serves as a binding scaffold for the nickase and comprising a sequence identical to the 15, 16, 17, 18, 19, or twenty 3’-most nucleotides of a guide 2 protospacer sequence listed in Table 2 or Table 5, wherein the guide 1 protospacer and the guide 2 protospacer are in a same row of Table 2 or Table 5.
  • a gene editing system comprising: a first guide oligonucleotide having a first scaffold region that serves as a binding scaffold for a nickase and comprising a first spacer sequence identical to or substantially identical to a guide 1 protospacer listed in Table 5; and a second guide oligonucleotide having a second scaffold region that serves as a binding scaffold for the nickase and comprising a second spacer sequence identical to or substantially identical to a corresponding (in a same row) guide 2 protospacer listed in Table 5.
  • the gene editing system of clause 108 wherein the first and second spacer sequences are identical to or substantially identical to protospacer sequences listed in Table 5 for which editing of 20% or greater was observed at 2500 ng/ml. 110.
  • 111. The gene editing system of clause 108, wherein the first and second spacer sequences are identical to or substantially identical to protospacer sequences listed in Table 5 for which editing of 40% or greater was observed at 2500 ng/ml. 112.
  • the gene editing system of clause 108 wherein the first and second spacer sequences are identical to or substantially identical to protospacer sequences listed in Table 5 for which editing of 50% or greater was observed at 2500 ng/ml. 113.
  • the gene editing system of clause 108, wherein the first and second spacer sequences are identical to or substantially identical to protospacer sequences listed in Table 5 for which editing of 70% or greater was observed at 2500 ng/ml. 115.
  • a gene editing system comprising: a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- CUGUCACCAGGCAUUGUGUC-3’; and a second guide oligonucleotide comprises a second scaffold region that serves as a binding scaffold for the nickase and comprises a spacer sequence comprising 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- UGUCCUUGCAACUCUCACGG-3’.
  • a gene editing system comprising: a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’-CUGUCACCAGGCAUUGUGUC-3’; and a second guide oligonucleotide comprises a second scaffold region that serves as a binding scaffold for the nickase and comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’- UGUCCUUGCAACUCUCACGG-3’.
  • a gene editing system comprising: a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- GUAGUAGCAGUCCUGUACCC-3’; and a second guide oligonucleotide comprises a second scaffold region that serves as a binding scaffold for the nickase and comprises a spacer sequence comprising 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- CAUUAUGGACAGAGUUACCG-3’.
  • a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- CAUUA
  • a gene editing system comprising: a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’-GUAGUAGCAGUCCUGUACCC-3’, and a second guide oligonucleotide comprises a second scaffold region that serves as a binding scaffold for the nickase and comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’-CAUUAUGGACAGAGUUACCG-3’.
  • a gene editing system comprising: a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- AGGACACUCGAUUCUGUCAC-3’; and a second guide oligonucleotide comprises a second scaffold region that serves as a binding scaffold for the nickase and comprises a spacer sequence comprising 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- CACAACUCCCACAGUGGCCC-3’.
  • a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- AGGACACUCG
  • a gene editing system comprising: a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’-AGGACACUCGAUUCUGUCA-3’, and a second guide oligonucleotide comprises a second scaffold region that serves as a binding scaffold for the nickase and comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’-CACAACUCCCACAGUGGCCC-3’.
  • a gene editing system comprising: a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- CUGUCACUGGACAUUGUGUC-3’; and a second guide oligonucleotide comprises a second scaffold region that serves as a binding scaffold for the nickase and comprises a spacer sequence comprising 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- AAGUGUCCUUGCGACGUCCA-3’.
  • a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- AAGUG
  • a gene editing system comprising: a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’-CUGUCACUGGACAUUGUGUC-3’, and a second guide oligonucleotide comprises a second scaffold region that serves as a binding scaffold for the nickase and comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’-AAGUGUCCUUGCGACGUCCA-3’.
  • a gene editing system comprising: a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- GGAGCAAAGCCCCACAGUCC-3’; and a second guide oligonucleotide comprises a second scaffold region that serves as a binding scaffold for the nickase and comprises a spacer sequence comprising 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- GUUGGUGCUGAAAUUCAAAG-3’.
  • a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- GUUGGU
  • a gene editing system comprising: a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’-GGAGCAAAGCCCCACAGUCC-3’, and a second guide oligonucleotide comprises a second scaffold region that serves as a binding scaffold for the nickase and comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’-GUUGGUGCUGAAAUUCAAAG-3’.
  • a gene editing system comprising: a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- GGAGCAAAGCCCCGGGGUCC-3’; and a second guide oligonucleotide comprises a second scaffold region that serves as a binding scaffold for the nickase and comprises a spacer sequence comprising 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- GUUGGUGCUGAAAUUCAAAG-3’.
  • a gene editing system comprising: a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’-GGAGCAAAGCCCCGGGGUCC-3’, and a second guide oligonucleotide comprises a second scaffold region that serves as a binding scaffold for the nickase and comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’-GUUGGUGCUGAAAUUCAAAG-3’.
  • a gene editing system comprising: a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- CUGGAACUGGGACCACCGU-3’; and a second guide oligonucleotide comprises a second scaffold region that serves as a binding scaffold for the nickase and comprises a spacer sequence comprising 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- ACAGAGCUUCCUUCUGAAGA-3’.
  • a gene editing system comprising: a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’-CUGGAACUGGGACCACCGU-3’, and a second guide oligonucleotide comprises a second scaffold region that serves as a binding scaffold for the nickase and comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’-ACAGAGCUUCCUUCUGAAGA-3’.
  • a gene editing system comprising: a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- AUGCCAGUGUGGUGUCAUAG-3’; and a second guide oligonucleotide comprises a second scaffold region that serves as a binding scaffold for the nickase and comprises a spacer sequence comprising 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- ACCACAGAAUACUACCCAAA-3’.
  • a gene editing system comprising: a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’-AUGCCAGUGUGGUGUCAUAG -3’, and a second guide oligonucleotide comprises a second scaffold region that serves as a binding scaffold for the nickase and comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’-ACCACAGAAUACUACCCAAA -3’.
  • a gene editing system comprising: a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- GGAGCCAGAAUAACAUUCGG-3’; and a second guide oligonucleotide comprises a second scaffold region that serves as a binding scaffold for the nickase and comprises a spacer sequence comprising 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- CUAGAGGCUUUUUUGAACA-3’. 135.
  • a gene editing system comprising: a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’-GGAGCCAGAAUAACAUUCGG -3’, and a second guide oligonucleotide comprises a second scaffold region that serves as a binding scaffold for the nickase and comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’-CUAGAGGCUUUUUUGAACA -3’.
  • a gene editing system comprising: a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- CAGAUGCUGAGAUUAGUCCU-3’; and a second guide oligonucleotide comprises a second scaffold region that serves as a binding scaffold for the nickase and comprises a spacer sequence comprising 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- UGGAUUCCUGCAGUAGUUCC-3’.
  • a gene editing system comprising: a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’-CAGAUGCUGAGAUUAGUCCU-3’, and a second guide oligonucleotide comprises a second scaffold region that serves as a binding scaffold for the nickase and comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’-UGGAUUCCUGCAGUAGUUCC-3’.
  • a gene editing system comprising: a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- UGACACCACAUUGGCAUCGG-3’; and a second guide oligonucleotide comprises a second scaffold region that serves as a binding scaffold for the nickase and comprises a spacer sequence comprising 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- ACAUGUUCUUCCUGUGAUAG-3’.
  • a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- ACAUGU
  • a gene editing system comprising: a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’-UGACACCACAUUGGCAUCGG-3’, and a second guide oligonucleotide comprises a second scaffold region that serves as a binding scaffold for the nickase and comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’-ACAUGUUCUUCCUGUGAUAG-3’.
  • a gene editing system comprising: a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- CAUAGAUGACCAAGAUUGAC-3’; and a second guide oligonucleotide comprises a second scaffold region that serves as a binding scaffold for the nickase and comprises a spacer sequence comprising 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- UGAUACCACACUGGCAUCAG-3’.
  • a gene editing system comprising: a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’-CAUAGAUGACCAAGAUUGAC-3’, and a second guide oligonucleotide comprises a second scaffold region that serves as a binding scaffold for the nickase and comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’-UGAUACCACACUGGCAUCAG-3’.
  • a gene editing system comprising: a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- CCAUCACUGGACAUUGCGUC-3’; and a second guide oligonucleotide comprises a second scaffold region that serves as a binding scaffold for the nickase and comprises a spacer sequence comprising 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- AACUCUCCUCACAACUCCCA-3’.
  • a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- AACU
  • a gene editing system comprising: a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’-CCAUCACUGGACAUUGCGUC-3’, and a second guide oligonucleotide comprises a second scaffold region that serves as a binding scaffold for the nickase and comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’-AACUCUCCUCACAACUCCCA-3’.
  • a gene editing system comprising: a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- CUGCAUCUGAGCAUCGUGUC-3’; and a second guide oligonucleotide comprises a second scaffold region that serves as a binding scaffold for the nickase and comprises a spacer sequence comprising 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- CGUCCCUCCGAAUGUUAUUC-3’.
  • a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- CGUCC
  • a gene editing system comprising: a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’-CUGCAUCUGAGCAUCGUGUC-3’, and a second guide oligonucleotide comprises a second scaffold region that serves as a binding scaffold for the nickase and comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’-CGUCCCUCCGAAUGUUAUUC-3’.
  • a gene editing system comprising: a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- AAACAGCCGUGGACGUCGCA-3’; and a second guide oligonucleotide comprises a second scaffold region that serves as a binding scaffold for the nickase and comprises a spacer sequence comprising 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- UGAACAAGGUAAGAAGUCUC-3’. 147.
  • a gene editing system comprising: a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’-AAACAGCCGUGGACGUCGCA-3’, and a second guide oligonucleotide comprises a second scaffold region that serves as a binding scaffold for the nickase and comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’-UGAACAAGGUAAGAAGUCUC-3’.
  • a gene editing system comprising: a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- ACAGAGGCUCCUUCUGAACA-3’; and a second guide oligonucleotide comprises a second scaffold region that serves as a binding scaffold for the nickase and comprises a spacer sequence comprising 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- GCUUGGAACCGGGGCCACUG-3’. 149.
  • a gene editing system comprising: a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’-ACAGAGGCUCCUUCUGAACA-3’, and a second guide oligonucleotide comprises a second scaffold region that serves as a binding scaffold for the nickase and comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’-GCUUGGAACCGGGGCCACUG-3’.
  • a gene editing system comprising: a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- AUGCCAGUGUGGUGUCAUAG-3’; and a second guide oligonucleotide comprises a second scaffold region that serves as a binding scaffold for the nickase and comprises a spacer sequence comprising 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- ACAACAGAAUAUUAUCCAAA-3’.
  • a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- ACAACAGA
  • a gene editing system comprising: a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’-AUGCCAGUGUGGUGUCAUAG-3’, and a second guide oligonucleotide comprises a second scaffold region that serves as a binding scaffold for the nickase and comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’-ACAACAGAAUAUUAUCCAAA-3’.
  • a gene editing system comprising: a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- CUAUGACACCACAUUGGCAU-3’; and a second guide oligonucleotide comprises a second scaffold region that serves as a binding scaffold for the nickase and comprises a spacer sequence comprising 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- ACAUGUUCUUCCUGUGAUAG-3’.
  • a gene editing system comprising: a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’-CUAUGACACCACAUUGGCAU-3’, and a second guide oligonucleotide comprises a second scaffold region that serves as a binding scaffold for the nickase and comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’-ACAUGUUCUUCCUGUGAUAG-3’.
  • a gene editing system comprising: a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- AAUAACAUUCGGAGGGACGA-3’; and a second guide oligonucleotide comprises a second scaffold region that serves as a binding scaffold for the nickase and comprises a spacer sequence comprising 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- UAUUCUGGCUCCAAGCCUAG-3’.
  • a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- UAUUC
  • a gene editing system comprising: a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’-AAUAACAUUCGGAGGGACGA-3’, and a second guide oligonucleotide comprises a second scaffold region that serves as a binding scaffold for the nickase and comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’-UAUUCUGGCUCCAAGCCUAG-3’.
  • a gene editing system comprising: a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- GUAGCAGUCCUGUACCCCGG-3’; and a second guide oligonucleotide comprises a second scaffold region that serves as a binding scaffold for the nickase and comprises a spacer sequence comprising 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- CAUUAUGGACAGAGUUACCG-3’.
  • a gene editing system comprising: a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’-GUAGCAGUCCUGUACCCCGG-3’, and a second guide oligonucleotide comprises a second scaffold region that serves as a binding scaffold for the nickase and comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’-CAUUAUGGACAGAGUUACCG-3’.
  • a gene editing system comprising: a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- AGUAGCAGUCCUGUACCCCG-3’; and a second guide oligonucleotide comprises a second scaffold region that serves as a binding scaffold for the nickase and comprises a spacer sequence comprising 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- CAUUAUGGACAGAGUUACCG-3’.
  • a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- AGUAGCAG
  • a gene editing system comprising: a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’-AGUAGCAGUCCUGUACCCCG-3’, and a second guide oligonucleotide comprises a second scaffold region that serves as a binding scaffold for the nickase and comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’-CAUUAUGGACAGAGUUACCG-3’.
  • a gene editing system comprising: a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- UAGUAGCAGUCCUGUACCCC-3’; and a second guide oligonucleotide comprises a second scaffold region that serves as a binding scaffold for the nickase and comprises a spacer sequence comprising 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- CAUUAUGGACAGAGUUACCG-3’.
  • a gene editing system comprising: a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’-UAGUAGCAGUCCUGUACCCC-3’, and a second guide oligonucleotide comprises a second scaffold region that serves as a binding scaffold for the nickase and comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’-CAUUAUGGACAGAGUUACCG-3’.
  • a gene editing system comprising: a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer sequence comprising nucleotides 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- UGGACCACAUGGCUUUGCUC-3’; and a second guide oligonucleotide comprises a second scaffold region that serves as a binding scaffold for the nickase and comprises a spacer sequence comprising 6 to 20, 5 to 20, 4 to 20, 3 to 20, 2 to 20, or 1 to 20 of the following sequence 5’- ACGUACUCCACCACUGUCAC-3’. 163.
  • a gene editing system comprising: a first guide oligonucleotide comprises a first scaffold region that serves as a binding scaffold for a nickase and comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’-UGGACCACAUGGCUUUGCUC-3’, and a second guide oligonucleotide comprises a second scaffold region that serves as a binding scaffold for the nickase and comprises a spacer having a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’-ACGUACUCCACCACUGUCAC-3’.
  • a gene editing system comprising the one or more nucleic acids of clause 164.
  • 166 The gene editing system of any one of clauses 104 to 163 or 165, further comprising a gene editor or a nucleic acid encoding the gene editor.
  • 167 The gene editing system of clause 166, wherein the gene editor comprises a Cas nickase or a nucleic acid encoding the Cas nickase. 168.
  • a gene editing system for editing the LPA gene comprising: a Cas nickase or a nucleic acid encoding the Cas nickase; a first guide oligonucleotide comprising (i) a first spacer sequence that is complementary to a first strand of the LPA gene at a first target sequence and (ii) a first scaffold region that serves as a binding scaffold for the Cas nickase; a second guide oligonucleotide comprising (i) a second spacer sequence that is complementary to a second strand of the LPA gene at a second target sequence and (ii) a second scaffold region that serves as a binding scaffold for the Cas nickase, wherein the first guide oligonucleotide and the Cas nickase are engineered to cause the Cas nickase to nick one of the first or second strands of the LPA gene at a first location, wherein the second guide oligonucleotide and the
  • the backbone modification comprises a phosphorothioate, a phosphorodithioate, a phosphoroselenoate, a phosphorodiselenoate, a phosphoroanilothioate, a phosphoraniladate, a phosphoramidate, or a phosphorodiamidate linkage. 176.
  • the gene editing system, pharmaceutical composition, or method of 182 wherein one or more of the five 5′-most nucleotides of the first and/ or second spacer sequence are modified to include a 2′-O-methyl group, a phosphorothioate linkage, or a combination thereof.
  • the gene editing system, pharmaceutical composition, or method of 184 wherein one or more of the three 5′-most nucleotides of the first and/ or second spacer sequence are modified to include a 2′-O-methyl group, a phosphorothioate linkage, or a combination thereof.
  • the scaffold sequence of the first and/or second guide oligonucleotide comprises from 30 to 65 modified nucleotides.
  • the gene editing system, pharmaceutical composition, or method of any one of clauses 170 to 187 wherein from 45% to 80% of the nucleotides of the scaffold sequence of the first and/or second guide oligonucleotide are modified.
  • 195. The gene editing system, pharmaceutical composition, or method of any one of clauses 170 to 187, wherein from 65% to 75% of the nucleotides of the scaffold sequence of the first and/or second guide oligonucleotide are modified.
  • the gene editing system, pharmaceutical composition, or method of any clause 196 wherein from 60% to 75% of the nucleotides of the scaffold sequence of the first and/or second guide oligonucleotide comprises a 2′ sugar modification.
  • 200 The gene editing system, pharmaceutical composition, or method of any clause 196, wherein from 65% to 75% of the nucleotides of the scaffold sequence of the first and/or second guide oligonucleotide comprises a 2′ sugar modification.
  • 201. The gene editing system, pharmaceutical composition, or method of any one of clauses 170 to 196, wherein the scaffold sequence of the first and/or second guide oligonucleotide comprises a nucleotide having a 2′-O-methyl group.
  • the gene editing system, pharmaceutical composition, or method of clause 201 wherein from 30% to 90% of the nucleotides of the scaffold sequence of the first and/or second guide oligonucleotide comprises a 2′-O-methyl group.
  • the gene editing system, pharmaceutical composition, or method of clause 201 wherein from 45% to 80% of the nucleotides of the scaffold sequence of the first and/or second guide oligonucleotide comprises a 2′-O-methyl group.
  • the gene editing system, pharmaceutical composition, or method of clause 201 wherein from 60% to 75% of the nucleotides of the scaffold sequence of the first and/or second guide oligonucleotide comprises a 2′-O-methyl group.
  • nucleic acid encoding the Cas9-H840A nickase is an mRNA comprising the sequence of SpCas9-H840A in Table 1 or an mRNA having at least about 90% identity, at least about 91% identity, at least about 92% identity, at least about 93% identity, at least about 94% identity, at least about 95% identity, at least about 96% identity, at least about 97% identity, at least about 98% identity, or at least about 99% identity to the mRNA sequence of SpCas9-H840A listed in Table 1. 208.
  • nucleic acid encoding the Cas9-D10A nickase is an mRNA comprising the sequence of SpCas9-D10A in Table 1 or an mRNA having at least about 90% identity, at least about 91% identity, at least about 92% identity, at least about 93% identity, at least about 94% identity, at least about 95% identity, at least about 96% identity, at least about 97% identity, at least about 98% identity, or at least about 99% identity to the mRNA sequence of SpCas9-D10A listed in Table 1.
  • the gene editor comprises the nucleic acid encoding the Cas9-D10A nickase
  • nucleic acid encoding the Cas9-D10A nickase is an mRNA comprising the sequence of SpCas9-D10A in Table 1 or an mRNA having at least about 90% identity, at least about 91% identity, at least about 92% identity, at least about 93% identity, at least about 94% identity, at least about 95% identity
  • first guide oligonucleotide and/or the second guide oligonucleotide comprise a scaffold, wherein the scaffold comprises the following nucleotide sequence: 5’- GUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAAC UUGAAAAAGUGGCACCGAGUCGGUGC -3’. 211.
  • the scaffold comprises one or more of the modified nucleotides in the following nucleotide sequence: 5’ - mGUUUUAGmAmGmCmUmAGmAmAmAmUmAmGmCmAmAGUUmAAmAAmU AmAmGmGmCmUmAGUmCmCGUUAmUmCAAmCmUmUGmAmAmAmAmAmG mUmGGmCmAmCmCmGmAmGmUmCmGmGmUmGmGmUmGmC 3’, where m of mN is 2′-O- methyl ribose. 212.
  • RNA motif comprises, consists essentially of, or consists of 5′- UUU -3′.
  • RNA motif comprises, consists essentially of, or consists of 5′- mU*mU*mU*mU -3′, where “mU*” indicates a phosphorothioated 2′-O-methyl uracil base, and “mU” indicates a 2′-O-methyl uracil base. 1A.
  • a pharmaceutical composition for in vivo editing of an LPA gene, in a mammalian subject comprising: (i) an engineered, non-naturally occurring gene editing system, which comprises: (a) one or more polynucleotides (mRNAs) encoding one or more nickases; (b) a first guide oligonucleotide (gRNA) comprising a first spacer sequence that is complementary to a first strand of the LPA gene at a first target sequence and a first scaffold region that serves as a binding scaffold for at least one of the one or more nickases; and (c) a second guide oligonucleotide (gRNA) comprising a second spacer sequence that is complementary to a second strand of the LPA gene at a second target sequence and a second scaffold region that serves as a binding scaffold for at least one of the one or more nickases, and (ii) a delivery system that is engineered to deliver the one or more mRNAs, the first gRNA, and
  • the pharmaceutical composition of clause 1A wherein the first spacer has a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’-CUGUCACCAGGCAUUGUGUC-3’, and the second spacer has a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’- UGUCCUUGCAACUCUCACGG-3’, wherein the first spacer has a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’-GUAGUAGCAGUCCUGUACCC-3’, and the second spacer has a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’- CAUUAUGGACAGAGUU
  • composition of clause 8A wherein at least one of the one or more polynucleotides (mRNAs) encoding the one or more Cas nickases encodes a Streptococcus pyogenes Cas9 nickase bearing a H840A mutation.
  • mRNAs polynucleotides
  • 10A The pharmaceutical composition of any one of clauses 1A to 7A, wherein at least one of the one or more Cas nickases, when in operative interaction with the first or second guide oligonucleotide (gRNA), is engineered to nick the same strand of the LPA gene to which the operative guide is hybridized.
  • gRNA guide oligonucleotide
  • composition of clause 10A wherein at least one of the one or more polynucleotides (mRNAs) encoding the one or more Cas nickases encodes a Streptococcus pyogenes Cas9 nickase bearing a D10A mutation. 12A.
  • mRNAs polynucleotides
  • composition of any one of clauses 1A to 11A, wherein at least one of the one or more polynucleotides (mRNAs) comprises: (a) a 5’ untranslated region (UTR); (b) a 3’ UTR region; (c) a poly(A) tail proximate to the 3’ UTR as compared to the 5’ UTR, said poly(A) tail comprising a chain of 80-150 nucleotides length that comprise adenine nucleotides; and (d) a gene editor coding region encoding an impaired CRISPR Cas9 endonuclease domain and a polymerase domain, said gene editor coding region extending between the 5’ UTR and the 3’ UTR. 13A.
  • composition of any one of clauses 1A to 7A wherein at least one of the one or more polynucleotides is selected from any of the mRNA sequences listed in Table 1 or an mRNA having at least about 90% identity, at least about 91% identity, at least about 92% identity, at least about 93% identity, at least about 94% identity, at least about 95% identity, at least about 96% identity, at least about 97% identity, at least about 98% identity, or at least about 99% identity to any of the mRNA sequences listed in Table 1. 14A.
  • composition of any one of clauses 1A to 7A wherein at least one of the one or more polynucleotides comprises a coding sequence of any of the mRNA sequences listed in Table 1 or comprises a coding sequence having at least about 90% identity, at least about 91% identity, at least about 92% identity, at least about 93% identity, at least about 94% identity, at least about 95% identity, at least about 96% identity, at least about 97% identity, at least about 98% identity, or at least about 99% identity to any of the coding sequences of the SpCas9-D10A nickase mRNA sequences listed in Table 1. 15A.
  • the delivery system comprises lipid nanoparticles (LNPs), wherein the LNPs comprise: (a) one or more ionizable lipids, (b) cholesterol, (c) one or more PEG-lipids, (d) a phospholipid; and (e) optionally including a targeting moiety, such as a GalNAc lipid.
  • LNPs lipid nanoparticles
  • the LNPs comprise: (a) one or more ionizable lipids, (b) cholesterol, (c) one or more PEG-lipids, (d) a phospholipid; and (e) optionally including a targeting moiety, such as a GalNAc lipid.
  • the pharmaceutical composition of clause 15A wherein the LNPs are formulated to comprise: (a) 40 to 60 molar percent of the one or more ionizable lipids, 28 to 48 molar percent of the cholesterol, 5 to 13 molar percent of the phospholipid, and 2 to 5 molar percent of the PEG-lipid, (b) 50 +/- 10% molar percent of the one or more ionizable lipids, 38 +/- 10% molar percent of the cholesterol, 9 +/- 10% molar percent of the phospholipid, and 3 +/- 10% molar percent of the PEG-lipid, (c) 40 to 60 molar percent of the one or more ionizable lipids, 27.95 to 47.95 molar percent of the cholesterol, 5 to 13 molar percent of the phospholipid, 2 to 5 molar percent of the PEG-lipid, and 0.02 to 0.09 molar percent of the GalNAc-lipid; or (d) 50 +/- 10% molar percent of the one or
  • RNA motif comprises, consists essentially of, or consists of 5′-*mU*mU*mU -3′, where “mU*” indicates a phosphorothioated 2′-O-methyl uracil base, and “mU” indicates a 2′-O-methyl uracil base.
  • 24A The pharmaceutical composition according to any one of clauses 1A to 23A, wherein administration of the composition to hepatocytes results in 40% or greater editing efficiency.
  • 25A The pharmaceutical composition according to clause 24A, wherein the hepatocytes are primary hepatocytes.
  • 26A The pharmaceutical composition according to clause 24A or 25A, wherein the hepatocytes are human hepatocytes.
  • a method for inactivating the LPA gene in vivo in a mammalian subject to treat and prevent cardiovascular disease comprising the step of: administering to the subject a pharmaceutical composition of any one of clauses 1A to 26A.
  • a method for reducing blood Lp(a) concentration in a mammalian subject to treat and prevent cardiovascular disease comprising the step of: administering to the subject a pharmaceutical composition of any one of clauses 1A to 26A.
  • 29A A method for treating and/or preventing cardiovascular disease associated with the LPA gene in a mammalian subject comprising the step of: administering to the subject a pharmaceutical composition of any one of clauses 1A to 26A. 30A.
  • a method for in vivo editing of an LPA gene in a mammalian subject comprising: administering to the subject a pharmaceutical composition comprising: (i) one or more polynucleotides (mRNAs) encoding one or more CRISPR Cas nickases, (v) a first guide oligonucleotide (gRNA) comprising a first spacer sequence and a scaffold region; and (vi) a second guide oligonucleotide (gRNA) comprising a second spacer sequence and a scaffold region, and (vii) a delivery system that is engineered to deliver the one or more mRNAs, the first gRNA, and/or the second gRNA individually or collectively to the liver, wherein the first gRNA and at least one of the one or more Cas nickases are engineered to cause the at least one of the one or more Cas nickases to nick one of the first or second strands of the LPA gene at a first location of chromosome 6 from position
  • a gene editing system for editing the LPA gene produced by expressing in a cell one or more exogenous polynucleotides (mRNA) encoding one or more CRISPR Cas nickases and introducing first and second gRNAs into the cell, wherein the first guide oligonucleotide (gRNA) comprises (i) a first spacer sequence that is complementary to a first strand of the LPA gene at a first target sequence and (ii) a first scaffold region that serves as a binding scaffold for at least one of the one or more Cas nickases, wherein the second guide oligonucleotide (gRNA) comprises (i) a second spacer sequence that is complementary to a second strand of the LPA gene at a second target sequence and (ii) a second scaffold region that serves as a binding scaffold for at least one of the one or more Cas nickases, wherein the first gRNA and the at least one of the one or more Cas nickases are engineered to cause
  • a gene editing system comprising: a means for expressing one or more CRISPR Cas nickases in a cell; and a means for directing the one or more Cas nickases to first and second locations in the LPA gene and to cause the one or more Cas nickases to introduce a nick in a first strand of the LPA gene and to introduce a nick in a second strand of the LPA gene.
  • 33A A pharmaceutical composition comprising the gene editing system of clause 32A and a delivery system. 34A.
  • composition of clause 33A wherein the delivery system comprises means for delivering to the cell the means for expressing one or more CRISPR Cas nickases and the means for directing the one or more Cas nickases to first and second locations in the LPA gene. 35A.
  • a gene editing system for editing the LPA gene comprising: a Cas nickase or a nucleic acid encoding the Cas nickase; a first guide oligonucleotide comprising (i) a first spacer sequence that is complementary to a first strand of the LPA gene at a first target sequence and (ii) a first scaffold region that serves as a binding scaffold for the Cas nickase; a second guide oligonucleotide comprising (i) a second spacer sequence that is complementary to a second strand of the LPA gene at a second target sequence and (ii) a second scaffold region that serves as a binding scaffold for the Cas nickase, wherein the first guide oligonucleotide and the Cas nickase are engineered to cause the Cas nickase to nick one of the first or second strands of the LPA gene at a first location, wherein the second guide oligonucleotide and the
  • a pharmaceutical composition for in vivo editing of an LPA gene, in a mammalian subject comprising: (i) an engineered, non-naturally occurring gene editing system, which comprises: (a) one or more polynucleotides (mRNAs) encoding a nickase; (b) a first guide oligonucleotide (gRNA) comprising a first spacer sequence that includes a region that is complementary to a first strand of the LPA gene at a first target sequence and a first scaffold region that serves as a binding scaffold for the nickase; and (c) a second guide oligonucleotide (gRNA) comprising a second spacer sequence that includes a region that is complementary to a second strand of the LPA gene at a second target sequence and a second scaffold region that serves as a binding
  • mRNAs polynucleotides
  • gRNA first guide oligonucleotide
  • gRNA second guide oligonucleot
  • the pharmaceutical composition of clause 1B wherein the first spacer has a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’-CUGUCACCAGGCAUUGUGUC-3’, and the second spacer has a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’- UGUCCUUGCAACUCUCACGG-3’, wherein the first spacer has a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’-GUAGUAGCAGUCCUGUACCC-3’, and the second spacer has a sequence that is at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95% identical to, or is identical to 5’- CAUUAUGGACAGAGUU
  • composition of any one of clauses 1B to 14B, wherein at least one of the one or more polynucleotides (mRNAs) comprises: (a) a 5’ untranslated region (UTR); (b) a 3’ UTR region; (c) a poly(A) tail proximate to the 3’ UTR as compared to the 5’ UTR, said poly(A) tail comprising a chain of 80-150 nucleotides length that comprise adenine nucleotides; and (d) a gene editor coding region encoding an impaired CRISPR Cas9 endonuclease domain and a polymerase domain, said gene editor coding region extending between the 5’ UTR and the 3’ UTR. 16B.
  • composition of any one of clauses 1B to 15B wherein at least one of the one or more polynucleotides is selected from any of the mRNA sequences listed in Table 1 or an mRNA having at least about 90% identity, at least about 91% identity, at least about 92% identity, at least about 93% identity, at least about 94% identity, at least about 95% identity, at least about 96% identity, at least about 97% identity, at least about 98% identity, or at least about 99% identity to any of the mRNA sequences listed in Table 1. 17B.
  • the LNPs comprise: (a) one or more ionizable lipids, (b) cholesterol, (c) one or more PEG-lipids, (d) a phospholipid; and (e) optionally including a targeting moiety, such as a GalNAc lipid. 19B.
  • any one or clauses 1B to 23B, wherein the scaffold comprises the following sequence or a sequence having at least about 75%, at least about 80%, at least about 85%, at least about 90%, or at least about 95% identity to following sequence: 5’ - mGUUUUAGmAmGmCmUmAGmAmAmAmUmAmGmCmAmAGUUmAAmAAmU AmAmGmGmCmUmAGUmCmCGUUAmUmCAAmCmUmUGmAmAmAmAmAmG mUmGGmCmAmCmCmGmAmGmUmCmGmGmUmGmGmUmGmC 3’, where m of mN is 2′-O- methyl ribose.
  • RNA motif comprises, consists essentially of, or consists of 5′- *mU*mU*mU -3′, where “mU*” indicates a phosphorothioated 2′-O-methyl uracil base, and “mU” indicates a 2′-O-methyl uracil base.
  • a method for inactivating the LPA gene in vivo in a mammalian subject to treat and prevent cardiovascular disease comprising the step of: administering to the subject a pharmaceutical composition of any one of clauses 1B to 34B.
  • 36B. A method for reducing blood Lp(a) concentration in a mammalian subject to treat and prevent cardiovascular disease comprising the step of: administering to the subject a pharmaceutical composition of any one of clauses 1B to 34B. 37B.
  • a method for treating and/or preventing cardiovascular disease associated with the LPA gene in a mammalian subject comprising the step of: administering to the subject a pharmaceutical composition of any one of clauses 1B to 34B. 38B.
  • a method for in vivo editing of an LPA gene in a mammalian subject comprising the step of: administering to the subject a pharmaceutical composition of any one of clauses 1B to 34B. 39B.
  • a method for in vivo editing of an LPA gene in a mammalian subject comprising: administering to the subject a pharmaceutical composition comprising: (i) one or more polynucleotides (mRNAs) encoding one or more CRISPR Cas nickases, (ii) a first guide oligonucleotide (gRNA) comprising a first spacer sequence and a scaffold region; and (iii) a second guide oligonucleotide (gRNA) comprising a second spacer sequence and a scaffold region, and (iv) a delivery system that is engineered to deliver the one or more mRNAs, the first gRNA, and/or the second gRNA individually or collectively to the liver, wherein the first gRNA and at least one of the one or more Cas nickases are engineered to cause the at least one of the one or more Cas nickases to nick one of the first or second strands of the LPA gene at a first location of chromos
  • a gene editing system for editing the LPA gene produced by expressing in a cell one or more exogenous polynucleotides (mRNA) encoding one or more CRISPR Cas nickases and introducing first and second gRNAs into the cell, wherein the first guide oligonucleotide (gRNA) comprises (i) a first spacer sequence that is complementary to a first strand of the LPA gene at a first target sequence and (ii) a first scaffold region that serves as a binding scaffold for at least one of the one or more Cas nickases, wherein the second guide oligonucleotide (gRNA) comprises (i) a second spacer sequence that is complementary to a second strand of the LPA gene at a second target sequence and (ii) a second scaffold region that serves as a binding scaffold for at least one of the one or more Cas nickases, wherein the first gRNA and the at least one of the one or more Cas nickases are engineered to cause
  • a gene editing system comprising: a means for expressing one or more CRISPR Cas nickases in a cell; and a means for directing the one or more Cas nickases to first and second locations in the LPA gene and to cause the one or more Cas nickases to introduce a nick in a first strand of the LPA gene and to introduce a nick in a second strand of the LPA gene.
  • a pharmaceutical composition comprising the gene editing system of clause 41B and a delivery system. 43B.
  • composition of clause 42B wherein the delivery system comprises means for delivering to the cell the means for expressing one or more CRISPR Cas nickases and the means for directing the one or more Cas nickases to first and second locations in the LPA gene. 44B.
  • a gene editing system for editing the LPA gene comprising: a Cas nickase or a nucleic acid encoding the Cas nickase; a first guide oligonucleotide comprising (i) a first spacer sequence that is complementary to a first strand of the LPA gene at a first target sequence and (ii) a first scaffold region that serves as a binding scaffold for the Cas nickase; a second guide oligonucleotide comprising (i) a second spacer sequence that is complementary to a second strand of the LPA gene at a second target sequence and (ii) a second scaffold region that serves as a binding scaffold for the Cas nickase, wherein the first guide oligonucleotide and the Cas nickase are engineered to cause the Cas nickase to nick one of the first or second strands of the LPA gene at a first location, wherein the second guide oligonucleotide and the

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Abstract

Sont prévus des systèmes et des compositions d'édition de gènes destinés à effectuer des éditions in vivo dans le gène LPA. Est divulgué un système de traitement ou de prévention d'une maladie cardiovasculaire par l'interruption de la production d'apo(a) par édition de gènes et la réduction de la concentration de lipoprotéine de sang(a) [Lp(a)]. Sont divulgués des systèmes d'édition de gènes à base de nickase conçus pour effectuer l'installation d'insertions et/ou de délétions (variants d'indel) et/ou de variants non synonymes dans la séquence de codage de LPA. Les systèmes d'édition de gènes à base de nickase comprennent généralement un ou plusieurs ARNm qui codent une ou plusieurs nickases et une pluralité d'oligonucléotides guides (p.ex., des ARNg) et peuvent être administrés in vivo à un sujet mammifère en ayant besoin par l'intermédiaire d'un système d'administration approprié, tel que des nanoparticules lipidiques (LNP) (avec ou sans fractions de ciblage de GalNAc) par voie intraveineuse, ou autrement, administrés à un sujet en tant qu'agent thérapeutique potentiellement unique. Sont également divulguées la fabrication, l'utilisation et la formulation des systèmes et des compositions d'édition de gènes.
PCT/US2024/020769 2023-03-20 2024-03-20 Édition in vivo à base de nickase du gène lpa pour le traitement d'une maladie cardiovasculaire WO2024197065A2 (fr)

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