WO2017112859A1 - Engineered meganucleases with recognition sequences found in the human beta-2 microglobulin gene - Google Patents

Engineered meganucleases with recognition sequences found in the human beta-2 microglobulin gene Download PDF

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Publication number
WO2017112859A1
WO2017112859A1 PCT/US2016/068289 US2016068289W WO2017112859A1 WO 2017112859 A1 WO2017112859 A1 WO 2017112859A1 US 2016068289 W US2016068289 W US 2016068289W WO 2017112859 A1 WO2017112859 A1 WO 2017112859A1
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seq
meganuclease
cell
sequence
nos
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English (en)
French (fr)
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Victor Bartsevich
Christina PHAM
Aaron Martin
Derek Jantz
James Jefferson Smith
Michael G. Nicholson
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Precision Biosciences Inc
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Precision Biosciences Inc
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Priority to CA3009637A priority Critical patent/CA3009637A1/en
Priority to JP2018533097A priority patent/JP6846429B2/ja
Priority to AU2016379393A priority patent/AU2016379393B2/en
Priority to US16/065,756 priority patent/US20190017075A1/en
Priority to EP21193857.6A priority patent/EP3988655A3/en
Priority to EP16825979.4A priority patent/EP3394253B1/en
Application filed by Precision Biosciences Inc filed Critical Precision Biosciences Inc
Priority to ES16825979T priority patent/ES2901000T3/es
Publication of WO2017112859A1 publication Critical patent/WO2017112859A1/en
Anticipated expiration legal-status Critical
Priority to US17/074,135 priority patent/US20210032664A1/en
Priority to AU2023202035A priority patent/AU2023202035A1/en
Priority to US18/491,484 priority patent/US20240052373A1/en
Ceased legal-status Critical Current

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    • 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
    • C12N15/87—Introduction of foreign genetic material using processes not otherwise provided for, e.g. co-transformation
    • C12N15/90—Stable introduction of foreign DNA into chromosome
    • C12N15/902—Stable introduction of foreign DNA into chromosome using homologous recombination
    • C12N15/907—Stable introduction of foreign DNA into chromosome using homologous recombination in mammalian cells
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K40/00—Cellular immunotherapy
    • A61K40/10—Cellular immunotherapy characterised by the cell type used
    • A61K40/11—T-cells, e.g. tumour infiltrating lymphocytes [TIL] or regulatory T [Treg] cells; Lymphokine-activated killer [LAK] cells
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K40/00—Cellular immunotherapy
    • A61K40/30—Cellular immunotherapy characterised by the recombinant expression of specific molecules in the cells of the immune system
    • A61K40/31—Chimeric antigen receptors [CAR]
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K40/00—Cellular immunotherapy
    • A61K40/40—Cellular immunotherapy characterised by antigens that are targeted or presented by cells of the immune system
    • A61K40/41—Vertebrate antigens
    • A61K40/42—Cancer antigens
    • A61K40/4202—Receptors, cell surface antigens or cell surface determinants
    • A61K40/421—Immunoglobulin superfamily
    • A61K40/4211—CD19 or B4
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K47/00—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
    • A61K47/50—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates
    • A61K47/69—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the conjugate being characterised by physical or galenical forms, e.g. emulsion, particle, inclusion complex, stent or kit
    • A61K47/6901—Conjugates being cells, cell fragments, viruses, ghosts, red blood cells or viral vectors
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P37/00—Drugs for immunological or allergic disorders
    • A61P37/02—Immunomodulators
    • A61P37/04—Immunostimulants
    • 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
    • C12N15/52—Genes encoding for enzymes or proenzymes
    • 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
    • C12N15/62—DNA sequences coding for fusion proteins
    • 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
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/14—Hydrolases (3)
    • C12N9/16—Hydrolases (3) acting on ester bonds (3.1)
    • C12N9/22—Ribonucleases [RNase]; Deoxyribonucleases [DNase]
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
    • C07K14/70503—Immunoglobulin superfamily
    • C07K14/7051—T-cell receptor (TcR)-CD3 complex
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/01—Fusion polypeptide containing a localisation/targetting motif
    • C07K2319/03—Fusion polypeptide containing a localisation/targetting motif containing a transmembrane segment

Definitions

  • the recombinant meganuclease comprises the amino acid sequence of any one of SEQ ID NOs: 101-113.
  • the nucleic acid encoding the sequence of interest is introduced into the eukaryotic cell using a single-stranded DNA template.
  • the eukaryotic cell is a human T cell, or a cell derived therefrom.
  • the eukaryotic cell has been genetically- modified to exhibit reduced cell-surface expression of an endogenous T cell receptor when compared to a control cell.
  • the nucleic acid comprising the exogenous sequence of interest is introduced into the eukaryotic cell by a viral vector.
  • the nucleic acid sequence encoding the endonuclease and the nucleic acid sequence encoding the sequence of interest are introduced into the eukaryotic cell by the same viral vector or, alternatively, by separate viral vectors.
  • the viral vector is a retroviral vector, a lentiviral vector, an adenoviral vector, or an AAV vector.
  • the viral vector is a recombinant AAV vector.
  • the non-human eukaryotic cell is selected from the group consisting of a gamete, a zygote, a blastocyst cell, an embryonic stem cell, and a protoplast cell.
  • the present disclosure provides a genetically-modified eukaryotic cell described herein for use as a medicament.
  • the present disclosure further provides the use of a genetically-modified eukaryotic cell described herein in the manufacture of a medicament for treating a disease in a subject in need thereof.
  • the medicament is useful in the treatment of cancer.
  • the medicament is useful in the treatment of cancer using immunotherapy.
  • the present disclosure provides a pharmaceutical composition
  • a pharmaceutical composition comprising a genetically-modified eukaryotic cell, or a population of genetically-modified eukaryotic cells, described herein and a pharmaceutically acceptable carrier.
  • the genetically-modified eukaryotic cells are genetically-modified T cells, or cells derived therefrom.
  • the genetically-modified T cells express a chimeric antigen receptor and exhibit reduced cell surface expression of beta-2
  • SEQ ID NO:6 sets forth the nucleic acid sequence of the B2M 7-8 recognition sequence (sense).
  • SEQ ID NO: 11 sets forth the amino acid sequence of the LAGLIDADG motif.
  • SEQ ID NO:24 sets forth the amino acid sequence of the B2M 13-14x.93 EEY66 meganuclease.
  • SEQ ID NO:32 sets forth the amino acid sequence of the B2M 13-14x.14 meganuclease.
  • SEQ ID NO:37 sets forth the amino acid sequence of the B2M 13-14x.96 meganuclease.
  • SEQ ID NO:40 sets forth the amino acid sequence of the B2M 13-14x.105 meganuclease.
  • SEQ ID NO:45 sets forth the amino acid sequence of the B2M 13-14x.146 meganuclease.
  • SEQ ID NO:49 sets forth the amino acid sequence of the B2M 13-14x.182 meganuclease.
  • SEQ ID NO:61 sets forth the amino acid sequence of the B2M 13-14x.285 meganuclease.
  • SEQ ID NO:69 sets forth the amino acid sequence of the B2M 13-14x.338 meganuclease.
  • SEQ ID NO:75 sets forth the amino acid sequence of the B2M 13-14x.371 meganuclease.
  • SEQ ID NO:76 sets forth the amino acid sequence of the B2M 13-14x.372 meganuclease.
  • SEQ ID NO:77 sets forth the amino acid sequence of the B2M 13-14x.375 meganuclease.
  • SEQ ID NO: 119 sets forth the amino acid sequence of the B2M 7-8x.2 meganuclease.
  • SEQ ID NO: 133 sets forth the B2M13 half-site binding subunit of the B2M 13- 14x.287 meganuclease.
  • SEQ ID NO: 156 sets forth the B2M13 half-site binding subunit of the B2M 13- 14x.85 meganuclease.
  • SEQ ID NO: 169 sets forth the B2M13 half-site binding subunit of the B2M 13- 14x. l82 meganuclease.
  • SEQ ID NO: 197 sets forth the B2M13 half-site binding subunit of the B2M 13- 14x.375 meganuclease.
  • SEQ ID NO:208 sets forth the B2M13 half-site binding subunit of the B2M 13- 14x.464 meganuclease.
  • SEQ ID NO:218 sets forth the B2M13 half-site binding subunit of the B2M 13- 14x.82 meganuclease.
  • SEQ ID NO:223 sets forth the B2M14 half-site binding subunit of the B2M 13- 14x.377 meganuclease.
  • SEQ ID NO:254 sets forth the B2M14 half-site binding subunit of the B2M 13- 14x. l46 meganuclease.
  • SEQ ID NO:271 sets forth the B2M14 half-site binding subunit of the B2M 13- 14x.286 meganuclease.
  • SEQ ID NO: 309 sets forth the B2M14 half-site binding subunit of the B2M 13- 14x.32 meganuclease.
  • SEQ ID NO:324 sets forth the B2M6 half-site binding subunit of the B2M 5-6x.5 meganuclease.
  • SEQ ID NO:343 sets forth the B2M7 half-site binding subunit of the B2M 7-8x.6 meganuclease.
  • SEQ ID NO: 365 sets forth the nucleic acid sequence of a E2A element.
  • SEQ ID NO 368 sets forth the nucleic acid sequence of a TRC-T2A-B2M bicistronic mRNA.
  • SEQ ID NO :370 sets forth the nucleic acid sequence of a TRC-E2A-B2M bicistronic mRNA.
  • SEQ ID NO: 375 sets forth the nucleic acid sequence of a B2M-E2A-TRC bicistronic mRNA.
  • the term "corresponding to” is used to indicate that a specified modification in the first protein is a substitution of the same amino acid residue as in the modification in the second protein, and that the amino acid position of the modification in the first proteins corresponds to or aligns with the amino acid position of the modification in the second protein when the two proteins are subjected to standard sequence alignments ⁇ e.g., using the BLASTp program).
  • residues X and Y correspond to each other in a sequence alignment, and despite the fact that X and Y are different numbers.
  • nuclease proteins can be delivered into cells to cleave genomic DNA, which allows for homologous recombination or non-homologous end-joining at the cleavage site with a sequence of interest, by a variety of different mechanisms known in the art.
  • engineered nuclease proteins are combined with amphiphilic molecules that self-assemble into micelles (Tong et al. (2007) J Gene Med. 9(11): 956-66).
  • Polymeric micelles may include a micellar shell formed with a hydrophilic polymer (e.g., polyethyleneglycol) that can prevent aggregation, mask charge interactions, and reduce nonspecific interactions outside of the cell.
  • a hydrophilic polymer e.g., polyethyleneglycol
  • cancers of B-cell origin include, without limitation, B-lineage acute lymphoblastic leukemia, B-cell chronic lymphocytic leukemia, and B-cell non-Hodgkin's lymphoma.
  • endonuclease gene expression to be regulated in a spatio-temporal manner by selecting when and to which tissues the small-molecule inducer is delivered.
  • the requirement to include the inducer in the viral genome which has significantly limited carrying capacity, creates a drawback to this approach.
  • variants of a particular polynucleotide of the embodiments will have at least about 40%, about 45%, about 50%, about 55%, about 60%, about 65%, about 70%, about 75%, about 80%, about 85%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99% or more sequence identity to that particular polynucleotide as determined by sequence alignment programs and parameters described elsewhere herein.
  • B2M 13-14 meganucleases Recombinant meganucleases (SEQ ID NOs: 12-100), collectively referred to herein as "B2M 13-14 meganucleases,” were engineered to recognize and cleave the B2M 13-14 recognition sequence (SEQ ID NO:2), which is present in the human beta-2 microglobulin gene (SEQ ID NO: l).
  • Each B2M 13-14 recombinant meganuclease comprises an N-terminal nuclease-localization signal derived from SV40, a first meganuclease subunit, a linker sequence, and a second meganuclease subunit.
  • a first subunit in each B2M 13-14 meganuclease binds to the B2M13 recognition half-site of SEQ ID NO:2, while a second subunit binds to the
  • meganuclease binds to the B2M5 recognition half-site of SEQ ID NO:4, while a second subunit binds to the B2M6 recognition half-site (see Fig. 1).
  • B2M 13- 14x.479 mRNAs were enriched for B2M-negative cells with a biotinylated antibody against B2M and an anti-biotin magnetic separation kit (Stem Cell Technologies).
  • B2M-negative and control B2M-positive cells were labeled with 2 ⁇ CellTrace Violet (Life Technologies) in accord with manufacturer's instructions.
  • donor human T cells were obtained and stimulated with ImmunoCult (Stem Cell Technologies) for 3 days prior to electroporation.
  • 3 ⁇ g/lxl0 6 cells were then electroporated with the bicistronic B2M-IRES-TRC mRNA described above using the Amaxa 4D-Nucleofector (Lonza) according to the manufacturer's instructions.
  • Cells were immediately transduced with a recombinant AAV vector encoding an anti-CD 19 CAR flanked by homology arms to the TRC 1-2 recognition site locus.
  • As controls cells were electroporated with ⁇ g of TRCl-2x87EE RNA prior to AAV transduction.
  • B2M-IRES-TRC and TRC l-2x.87 EE electroporated cells were mock transduced.

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PCT/US2016/068289 2015-12-23 2016-12-22 Engineered meganucleases with recognition sequences found in the human beta-2 microglobulin gene Ceased WO2017112859A1 (en)

Priority Applications (10)

Application Number Priority Date Filing Date Title
ES16825979T ES2901000T3 (es) 2015-12-23 2016-12-22 Meganucleasas de ingeniería con secuencias de reconocimiento encontradas en el gen de la microglobulina beta-2 humana
JP2018533097A JP6846429B2 (ja) 2015-12-23 2016-12-22 ヒトβ−２ミクログロブリン遺伝子に見られる認識配列を有する操作されたメガヌクレアーゼ
AU2016379393A AU2016379393B2 (en) 2015-12-23 2016-12-22 Engineered meganucleases with recognition sequences found in the human beta-2 microglobulin gene
US16/065,756 US20190017075A1 (en) 2015-12-23 2016-12-22 Engineered meganucleases with recognition sequences found in the human beta-2 microglobulin gene
EP21193857.6A EP3988655A3 (en) 2015-12-23 2016-12-22 Engineered meganucleases with recognition sequences found in the human beta-2 microglobulin gene
CA3009637A CA3009637A1 (en) 2015-12-23 2016-12-22 Engineered meganucleases with recognition sequences found in the human beta-2 microglobulin gene
EP16825979.4A EP3394253B1 (en) 2015-12-23 2016-12-22 Engineered meganucleases with recognition sequences found in the human beta-2 microglobulin gene
US17/074,135 US20210032664A1 (en) 2015-12-23 2020-10-19 Engineered meganucleases with recognition sequences found in the human beta-2 microglobulin gene
AU2023202035A AU2023202035A1 (en) 2015-12-23 2023-04-03 Engineered meganucleases with recognition sequences found in the human beta-2 microglobulin gene
US18/491,484 US20240052373A1 (en) 2015-12-23 2023-10-20 Engineered meganucleases with recognition sequences found in the human beta-2 microglobulin gene

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US201562387318P 2015-12-23 2015-12-23
US62/387,318 2015-12-23
US201662416513P 2016-11-02 2016-11-02
US62/416,513 2016-11-02

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US17/074,135 Continuation US20210032664A1 (en) 2015-12-23 2020-10-19 Engineered meganucleases with recognition sequences found in the human beta-2 microglobulin gene

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WO2018208837A1 (en) * 2017-05-08 2018-11-15 Precision Biosciences, Inc. Nucleic acid molecules encoding an engineered antigen receptor and an inhibitory nucleic acid molecule and methods of use thereof
JP2018536390A (ja) * 2015-10-05 2018-12-13 プレシジョン バイオサイエンシズ，インク． ヒトｔ細胞受容体アルファ定常領域遺伝子中に見出される認識配列に対して操作されたメガヌクレアーゼ
WO2019097083A1 (en) * 2017-11-20 2019-05-23 Tessa Therapeutics Pte. Ltd. Modified k562 cell
WO2019200122A1 (en) * 2018-04-12 2019-10-17 Precision Biosciences, Inc. Optimized engineered nucleases having specificity for the human t cell receptor alpha constant region gene
WO2020146807A1 (en) * 2019-01-10 2020-07-16 Precision Biosciences, Inc. Genetically-modified cells comprising a modified transferrin gene
US10729725B2 (en) 2017-05-12 2020-08-04 Crispr Therapeutics Ag Materials and methods for engineering cells and uses thereof in immuno-oncology
WO2020206248A1 (en) 2019-04-03 2020-10-08 Precision Biosciences, Inc. Genetically-modified immune cells comprising a microrna-adapted shrna (shrnamir)
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WO2020227534A1 (en) 2019-05-07 2020-11-12 Precision Biosciences, Inc. Optimization of engineered meganucleases for recognition sequences
JP2021506243A (ja) * 2017-12-13 2021-02-22 ヤンセン バイオテツク，インコーポレーテツド Ｔ細胞受容体及びβ２ミクログロブリン発現を排除するように遺伝子改変された不死化ＣＡＲ−Ｔ細胞
US11053484B2 (en) 2017-06-30 2021-07-06 Precision Biosciences, Inc. Genetically-modified T cells comprising a modified intron in the T cell receptor alpha gene
US11166985B2 (en) 2017-05-12 2021-11-09 Crispr Therapeutics Ag Materials and methods for engineering cells and uses thereof in immuno-oncology
WO2021231259A1 (en) 2020-05-11 2021-11-18 Precision Biosciences, Inc. Self-limiting viral vectors encoding nucleases
US11254912B2 (en) 2018-05-11 2022-02-22 Crispr Therapeutics Ag Methods and compositions for treating cancer
WO2022040582A1 (en) * 2020-08-21 2022-02-24 Precision Biosciences, Inc. Engineered meganucleases having specificity for a recognition sequence in the transthyretin gene
US11268065B2 (en) 2015-10-05 2022-03-08 Precision Biosciences, Inc. Genetically-modified cells comprising a modified human T cell receptor alpha constant region gene
US11389481B2 (en) 2019-04-30 2022-07-19 Crispr Therapeutics Ag Allogeneic cell therapy of B cell malignancies using genetically engineered T cells targeting CD19
WO2023070002A3 (en) * 2021-10-19 2023-07-06 Precision Biosciences, Inc. Gene editing methods for treating alpha-1 antitrypsin (aat) deficiency
WO2024236547A1 (en) 2023-05-18 2024-11-21 Inceptor Bio, Llc Modified phagocytic cells expressing chimeric antigen receptors comprising a herpes virus entry mediator (hvem) co-stimulatory domain and uses thereof
WO2025046513A1 (en) 2023-08-29 2025-03-06 Inceptor Bio, Llc Methods of manufacturing myeloid-derived cells from hematopoietic stem cells and compositions and uses thereof

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WO2017112859A1 (en) * 2015-12-23 2017-06-29 Precision Biosciences, Inc. Engineered meganucleases with recognition sequences found in the human beta-2 microglobulin gene
BR112019007450A2 (pt) 2016-10-14 2020-07-07 Precision Biosciences, Inc. meganucleases modificadas específicas para sequências de reconhecimento no genoma do vírus da hepatite b
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