WO2024254506A3 - Satseq : système modulaire pour coupler une mutagenèse à saturation, un codage par barres d'adn et un séquençage profond - Google Patents

Satseq : système modulaire pour coupler une mutagenèse à saturation, un codage par barres d'adn et un séquençage profond Download PDF

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Publication number
WO2024254506A3
WO2024254506A3 PCT/US2024/033082 US2024033082W WO2024254506A3 WO 2024254506 A3 WO2024254506 A3 WO 2024254506A3 US 2024033082 W US2024033082 W US 2024033082W WO 2024254506 A3 WO2024254506 A3 WO 2024254506A3
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Prior art keywords
satseq
saturation mutagenesis
deep sequencing
modular system
dna barcoding
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Ceased
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PCT/US2024/033082
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WO2024254506A2 (fr
Inventor
Ashley LAUGHNEY BAKHOUM
Matthew DEYELL
Samuel F. BAKHOUM
Jun Li
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Memorial Sloan Kettering Cancer Center Memorial Hospital For Cancer And Allied Diseases And Sloan Kettering Institute For Cancer Research
Cornell University
Original Assignee
Memorial Sloan Kettering Cancer Center Memorial Hospital For Cancer And Allied Diseases And Sloan Kettering Institute For Cancer Research
Cornell University
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Application filed by Memorial Sloan Kettering Cancer Center Memorial Hospital For Cancer And Allied Diseases And Sloan Kettering Institute For Cancer Research, Cornell University filed Critical Memorial Sloan Kettering Cancer Center Memorial Hospital For Cancer And Allied Diseases And Sloan Kettering Institute For Cancer Research
Priority to EP24739836.5A priority Critical patent/EP4724809A2/fr
Publication of WO2024254506A2 publication Critical patent/WO2024254506A2/fr
Publication of WO2024254506A3 publication Critical patent/WO2024254506A3/fr
Anticipated expiration legal-status Critical
Ceased legal-status Critical Current

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    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/5005—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells
    • G01N33/5008—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics
    • 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
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034—Isolating an individual clone by screening libraries
    • C12N15/1058—Directional evolution of libraries, e.g. evolution of libraries is achieved by mutagenesis and screening or selection of mixed population of organisms
    • 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
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/85—Vectors or expression systems specially adapted for eukaryotic hosts for animal cells
    • C12N15/86—Viral vectors
    • C—CHEMISTRY; METALLURGY
    • C40—COMBINATORIAL TECHNOLOGY
    • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B40/00—Libraries per se, e.g. arrays, mixtures
    • C40B40/04—Libraries containing only organic compounds
    • C40B40/06—Libraries containing nucleotides or polynucleotides, or derivatives thereof
    • C40B40/08—Libraries containing RNA or DNA which encodes proteins, e.g. gene libraries
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/5005—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells
    • G01N33/5008—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics
    • G01N33/502—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics for testing non-proliferative effects
    • G01N33/5023—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics for testing non-proliferative effects on expression patterns
    • 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
    • C12N2740/00—Reverse transcribing RNA viruses
    • C12N2740/00011—Details
    • C12N2740/10011—Retroviridae
    • C12N2740/16011—Human Immunodeficiency Virus, HIV
    • C12N2740/16041—Use of virus, viral particle or viral elements as a vector
    • C12N2740/16043—Use of virus, viral particle or viral elements as a vector viral genome or elements thereof as genetic vector
    • 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
    • C12N2830/00—Vector systems having a special element relevant for transcription
    • C12N2830/48—Vector systems having a special element relevant for transcription regulating transport or export of RNA, e.g. RRE, PRE, WPRE, CTE
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2563/00—Nucleic acid detection characterized by the use of physical, structural and functional properties
    • C12Q2563/179—Nucleic acid detection characterized by the use of physical, structural and functional properties the label being a nucleic acid
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2500/00—Screening for compounds of potential therapeutic value
    • G01N2500/04—Screening involving studying the effect of compounds C directly on molecule A (e.g. C are potential ligands for a receptor A, or potential substrates for an enzyme A)
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2500/00—Screening for compounds of potential therapeutic value
    • G01N2500/10—Screening for compounds of potential therapeutic value involving cells
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2500/00—Screening for compounds of potential therapeutic value
    • G01N2500/20—Screening for compounds of potential therapeutic value cell-free systems

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  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Chemical & Material Sciences (AREA)
  • Biomedical Technology (AREA)
  • Molecular Biology (AREA)
  • Genetics & Genomics (AREA)
  • Organic Chemistry (AREA)
  • Immunology (AREA)
  • Biotechnology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Health & Medical Sciences (AREA)
  • Biochemistry (AREA)
  • Zoology (AREA)
  • Hematology (AREA)
  • General Engineering & Computer Science (AREA)
  • Microbiology (AREA)
  • Wood Science & Technology (AREA)
  • Urology & Nephrology (AREA)
  • Physics & Mathematics (AREA)
  • Medicinal Chemistry (AREA)
  • Analytical Chemistry (AREA)
  • Tropical Medicine & Parasitology (AREA)
  • Pathology (AREA)
  • Plant Pathology (AREA)
  • General Physics & Mathematics (AREA)
  • Toxicology (AREA)
  • Food Science & Technology (AREA)
  • Biophysics (AREA)
  • Cell Biology (AREA)
  • Virology (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Ecology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • General Chemical & Material Sciences (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

La présente divulgation concerne une technologie SatSeq qui couple la mutagenèse à saturation, le codage par barres d'ADN et le séquençage profond. L'invention concerne des vecteurs, des systèmes et des procédés d'analyse de fonctions protéiques, de validation de cibles de médicament, d'identification d'effets de médicament sur cible, d'identification de médicaments qui se lient à des variants génétiquement pertinents, et/ou d'identification de modulateurs spécifiques de la voie d'un gène pléiotrope, par application de la technologie SatSeq.
PCT/US2024/033082 2023-06-08 2024-06-07 Satseq : système modulaire pour coupler une mutagenèse à saturation, un codage par barres d'adn et un séquençage profond Ceased WO2024254506A2 (fr)

Priority Applications (1)

Application Number Priority Date Filing Date Title
EP24739836.5A EP4724809A2 (fr) 2023-06-08 2024-06-07 Satseq : système modulaire pour coupler une mutagenèse à saturation, un codage par barres d'adn et un séquençage profond

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US202363471801P 2023-06-08 2023-06-08
US63/471,801 2023-06-08

Publications (2)

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WO2024254506A2 WO2024254506A2 (fr) 2024-12-12
WO2024254506A3 true WO2024254506A3 (fr) 2025-01-09

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PCT/US2024/033082 Ceased WO2024254506A2 (fr) 2023-06-08 2024-06-07 Satseq : système modulaire pour coupler une mutagenèse à saturation, un codage par barres d'adn et un séquençage profond

Country Status (2)

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EP (1) EP4724809A2 (fr)
WO (1) WO2024254506A2 (fr)

Family Cites Families (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US4861719A (en) 1986-04-25 1989-08-29 Fred Hutchinson Cancer Research Center DNA constructs for retrovirus packaging cell lines
US5278056A (en) 1988-02-05 1994-01-11 The Trustees Of Columbia University In The City Of New York Retroviral packaging cell lines and process of using same
US5670488A (en) 1992-12-03 1997-09-23 Genzyme Corporation Adenovirus vector for gene therapy
JP3866760B2 (ja) 1993-02-22 2007-01-10 ザ ロックフェラー ユニバーシティ 一過性トランスフェクションによる高力価のヘルパーフリーのレトロウイルスの生産
FR2712812B1 (fr) 1993-11-23 1996-02-09 Centre Nat Rech Scient Composition pour la production de produits thérapeutiques in vivo.
IL116816A (en) 1995-01-20 2003-05-29 Rhone Poulenc Rorer Sa Cell for the production of a defective recombinant adenovirus or an adeno-associated virus and the various uses thereof
US6013516A (en) 1995-10-06 2000-01-11 The Salk Institute For Biological Studies Vector and method of use for nucleic acid delivery to non-dividing cells

Non-Patent Citations (3)

* Cited by examiner, † Cited by third party
Title
AMOROSI CLARA J ET AL: "Massively parallel characterization of CYP2C9 variant enzyme activity and abundance", THE AMERICAN JOURNAL OF HUMAN GENETICS, AMERICAN SOCIETY OF HUMAN GENETICS , CHICAGO , IL, US, vol. 108, no. 9, 26 July 2021 (2021-07-26), pages 1735 - 1751, XP086761688, ISSN: 0002-9297, [retrieved on 20210726], DOI: 10.1016/J.AJHG.2021.07.001 *
MA LEYUAN ET AL: "CRISPR-Cas9-mediated saturated mutagenesis screen predicts clinical drug resistance with improved accuracy", PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES, vol. 114, no. 44, 16 October 2017 (2017-10-16), pages 11751 - 11756, XP055963805, ISSN: 0027-8424, DOI: 10.1073/pnas.1708268114 *
MARTON M J ET AL: "Drug target validation and identification of secondary drug target effects using DNA microarrays", NATURE MEDICINE, NATURE PUBLISHING GROUP US, NEW YORK, vol. 4, no. 11, 1 November 1998 (1998-11-01), pages 1293 - 1301, XP002168523, ISSN: 1078-8956, DOI: 10.1038/3282 *

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EP4724809A2 (fr) 2026-04-15
WO2024254506A2 (fr) 2024-12-12

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