EP3973052A1 - Phage et particules de transduction - Google Patents

Phage et particules de transduction

Info

Publication number
EP3973052A1
EP3973052A1 EP20727987.8A EP20727987A EP3973052A1 EP 3973052 A1 EP3973052 A1 EP 3973052A1 EP 20727987 A EP20727987 A EP 20727987A EP 3973052 A1 EP3973052 A1 EP 3973052A1
Authority
EP
European Patent Office
Prior art keywords
phage
dna
cell
composition
target
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Withdrawn
Application number
EP20727987.8A
Other languages
German (de)
English (en)
Inventor
Jakob KRAUSE HAABER
Szabolcs SEMSEY
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.)
SNIPR Biome ApS
Original Assignee
SNIPR Biome ApS
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by SNIPR Biome ApS filed Critical SNIPR Biome ApS
Publication of EP3973052A1 publication Critical patent/EP3973052A1/fr
Withdrawn legal-status Critical Current

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Classifications

    • 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
    • C12N7/00—Viruses; Bacteriophages; Compositions thereof; Preparation or purification thereof
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K35/00—Medicinal preparations containing materials or reaction products thereof with undetermined constitution
    • A61K35/66—Microorganisms or materials therefrom
    • A61K35/76—Viruses; Subviral particles; Bacteriophages
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K48/00—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy
    • A61K48/0008—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy characterised by an aspect of the 'non-active' part of the composition delivered, e.g. wherein such 'non-active' part is not delivered simultaneously with the 'active' part of the composition
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K48/00—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy
    • A61K48/005—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy characterised by an aspect of the 'active' part of the composition delivered, i.e. the nucleic acid delivered
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P1/00—Drugs for disorders of the alimentary tract or the digestive system
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P11/00—Drugs for disorders of the respiratory system
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P15/00—Drugs for genital or sexual disorders; Contraceptives
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/04—Antibacterial agents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P7/00—Drugs for disorders of the blood or the extracellular fluid
    • 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
    • C12N15/70—Vectors or expression systems specially adapted for E. coli
    • 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]
    • 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
    • C12N2795/00—Bacteriophages
    • C12N2795/00011—Details
    • C12N2795/10011—Details dsDNA Bacteriophages
    • C12N2795/10111—Myoviridae
    • C12N2795/10121—Viruses as such, e.g. new isolates, mutants or their genomic sequences
    • 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
    • C12N2795/00—Bacteriophages
    • C12N2795/00011—Details
    • C12N2795/10011—Details dsDNA Bacteriophages
    • C12N2795/10111—Myoviridae
    • C12N2795/10122—New viral proteins or individual genes, new structural or functional aspects of known viral proteins or genes
    • 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
    • C12N2795/00—Bacteriophages
    • C12N2795/00011—Details
    • C12N2795/10011—Details dsDNA Bacteriophages
    • C12N2795/10111—Myoviridae
    • C12N2795/10141—Use of virus, viral particle or viral elements as a 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
    • C12N2795/00—Bacteriophages
    • C12N2795/00011—Details
    • C12N2795/10011—Details dsDNA Bacteriophages
    • C12N2795/10111—Myoviridae
    • C12N2795/10141—Use of virus, viral particle or viral elements as a vector
    • C12N2795/10142—Use of virus, viral particle or viral elements as a vector virus or viral particle as vehicle, e.g. encapsulating small organic molecule

Definitions

  • the second DNA is devoid of a nucleotide sequence (eg, a packaging signal) required for packaging the second DNA into phage particles;
  • a nucleotide sequence eg, a packaging signal
  • a composition comprising a population of first phage, wherein the first phage require helper phage according to the First Configuration for replication; and wherein less than [20%] of total phage comprised by the composition are such helper phage.
  • step (c) Wherein the host bacterial cell comprises helper phage or wherein helper phage are introduced into the bacterial cell simultaneously or sequentially with step (b);
  • a non-self replicative transduction particle comprising said MGE or vector of the invention.
  • a phage packaging sequence (optionally pac, cos or a homologue thereof);
  • a method of making a plurality of transduction particles comprising culturing a plurality of host cells according to the invention, optionally inducing a lytic cycle of the helper phage, and incubating the cells under conditions wherein transducing particles comprising packaged copies of the plasmid are created, and optionally separating the particles from the cells to obtain a plurality of transduction particles.
  • An embodiment provides a bacterial cell comprising the first and second DNAs.
  • the cell is devoid of a functional CRISPR/Cas system before transfer therein of a first DNA, eg, a first DNA comprising a component of a CRISPR/Cas system that is toxic to the target bacterium.
  • An embodiment provides an antibacterial composition comprising a plurality of cells, wherein each cell is optionally according to this paragraph, for administration to a human or animal subject for medical use.
  • a method of treating an infection of target bacteria in a human or animal subject comprising exposing the bacteria to a population of phage particles obtainable by the production method, wherein the phage infect and kill the target bacteria.
  • 0.00000001% of total phage particles comprised by the composition are particles of such helper phage.
  • the horizontal transfer can be transfer of a plasmid (such as a conjugative plasmid) to the target bacteria or first phage infection of the target bacteria, wherein the first phage have been prior packaged in the carrier.
  • a carrier is useful too for oral administration or other routes where the carrier can provide protection for the phage, helper or composition from the acid stomach or other harsh environments in the subject.
  • the carrier can be formulated into a beverage, for example, a probiotic drink, eg, an adapted Yakult (trademark), Actimel (trademark), Kevita (trademark),
  • the component(s) comprise (i) a DNA sequence encoding a guide RNA (eg, a single guide RNA) or comprising a CRISPR array for producing guide RNA, wherein the guide RNA is capable of targeting the genome of target bacteria; (ii) a Cas (eg, Cas9, Cas3, Cpfl, CasX or CasY) nuclease-encoding DNA sequence; and/or (iii) a DNA sequence encoding one or more components of Cascade (eg, CasA).
  • a guide RNA eg, a single guide RNA
  • a CRISPR array for producing guide RNA
  • the guide RNA is capable of targeting the genome of target bacteria
  • a Cas eg, Cas9, Cas3, Cpfl, CasX or CasY
  • a DNA sequence encoding one or more components of Cascade eg, CasA
  • the system is devoid of a helper phage production factor (F1PF) that is required for forming helper phage particles that package the first DNA, or is devoid of an expressible nucleotide sequence that encodes a functional F1PF; or the system comprises a nucleotide sequence that comprises or encodes a functional F1PF, the system further comprising means for targeted inactivation in the host cell of the HPF sequence to eliminate or minimise production of helper phage comprising the first DNA;
  • F1PF helper phage production factor
  • the kit, DNA(s), first phage, helper phage or composition is comprised by a personal hygiene composition (eg, shampoo, soap or deodorant) or cosmetic formulation.
  • the kit, DNA(s), first phage, helper phage or composition is comprised by a detergent formulation.
  • the kit, DNA(s), first phage, helper phage or composition is comprised by a cleaning formulation, eg, for cleaning a medical or industrial device or apparatatus.
  • the kit, DNA(s), first phage, helper phage or composition is comprised by foodstuff, foodstuff ingredient or foodstuff processing agent.
  • target cells and targeting of antibiotic resistance in such cells using the present invention are as follows
  • the target bacteria are Pseudomonas aeuroginosa cells, eg, resistant to an antibiotic selected from cephalosporins (eg, ceftazidime), carbapenems (eg, imipenem or
  • the target bacteria are Shigella cells, eg, resistant to an antibiotic selected from ciprofloxacin and azithromycin.
  • the target bacteria are mycobacterium tuberculosis cells, eg, resistant to an antibiotic selected from Resistance to isoniazid (INH), rifampicin (RMP), fluoroquinolone, amikacin, kanamycin and capreomycin and azithromycin.
  • composition of Clause 53, 54 or 55, wherein the Cas is a Cas3, Cas9, Casl3, CasX, CasY or Cpfl.
  • composition of any one of Clauses 1 to 58, wherein the first species or strain is a gram negative species or strain.
  • target cells are sensitised to an antibiotic, whereby the antibiotic is toxic to the cells.
  • a bacterial host cell comprising a first phage and a MGE, vector or particle as recited in any one of Clauses 1 to 66, wherein the agent is not toxic to the host cell, but the agent is toxic to second cells of a species or strain that is different from the species or strain of the host cell, wherein the MGE is mobilizable in transduction particles producible by the host cell that are capable of transferring the MGE or a copy thereof into a said second cell, whereby the second cell is exposed to the antibacterial agent.
  • a bacterial host cell comprising the genome of a helper phage that is incapable of self replication, optionally wherein the genome is present as a prophage, and a plasmid according to any one of Clauses 95 to 98, wherein the helper phage is operable to package copies of the plasmid in transduction particles, wherein the particles are capable of infecting bacterial target cells to which the antibacterial agent is toxic.
  • the target bacteria are comprised by an environment as follows.
  • the environment is a microbiome of a human, eg, the oral cavity microbiome or gut microbiome or the bloodstream.
  • the environment is not an environment in or on a human.
  • the environment is not an environment in or on a non-human animal.
  • the environment is an air environment.
  • the environment is an agricultural environment.
  • the environment is an oil or petroleum recovery environment, eg, an oil or petroleum field or well.
  • the environment is an environment in or on a foodstuff or beverage for human or non-human animal consumption.
  • the packaging signal, NPF and/or HPF consists or comprises SEQ ID NO: 2 or a nucleotide sequence that is at least 70, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98 or 99% identical thereto.
  • arthritis osteoarthritis, rheumatoid arthritis (RA), psoriatic arthritis
  • the second DNA is devoid of a nucleotide sequence required for packaging the second DNA into phage particles;
  • kits of Paragraph 6 wherein the phage particle of (i) is capable of infecting a target bacterium, the phage comprising a nucleotide sequence of interest (NSI) that is capable of expressing a protein or RNA in the target bacterium, wherein the presence in the target bacterium of the NSI- encoded protein or RNA mediates target cell killing, or downregulation of target cell growth or propagation.
  • NBI nucleotide sequence of interest
  • the NSI encodes a Cas9, and a tracrRNA and a CRISPR array for producing guide RNA.
  • composition of Paragraph 33 wherein the antibacterial means comprises a nucleic acid encoding a guided nuclease, such as a Cas nuclease, TALEN, zinc finger nuclease or meganuclease
  • a guided nuclease such as a Cas nuclease, TALEN, zinc finger nuclease or meganuclease
  • the second DNA is required for packaging first DNA to produce particles, wherein the DNAs are operable in the cell for producing transduction particles comprising phage structural proteins that package copies of the first DNA.

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  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Genetics & Genomics (AREA)
  • Organic Chemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Health & Medical Sciences (AREA)
  • Medicinal Chemistry (AREA)
  • Veterinary Medicine (AREA)
  • Public Health (AREA)
  • Animal Behavior & Ethology (AREA)
  • Wood Science & Technology (AREA)
  • Zoology (AREA)
  • Pharmacology & Pharmacy (AREA)
  • Biotechnology (AREA)
  • Biomedical Technology (AREA)
  • General Engineering & Computer Science (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Nuclear Medicine, Radiotherapy & Molecular Imaging (AREA)
  • Microbiology (AREA)
  • General Chemical & Material Sciences (AREA)
  • Molecular Biology (AREA)
  • Biochemistry (AREA)
  • Epidemiology (AREA)
  • Virology (AREA)
  • Plant Pathology (AREA)
  • Biophysics (AREA)
  • Immunology (AREA)
  • Physics & Mathematics (AREA)
  • Communicable Diseases (AREA)
  • Endocrinology (AREA)
  • Reproductive Health (AREA)
  • Pulmonology (AREA)
  • Diabetes (AREA)
  • Hematology (AREA)
  • Oncology (AREA)
  • Mycology (AREA)
  • Micro-Organisms Or Cultivation Processes Thereof (AREA)
  • Medicines Containing Material From Animals Or Micro-Organisms (AREA)

Abstract

La présente invention concerne une production de phage et de particules de transduction utilisant des ADN (par exemple, des plasmides et un phage auxiliaire, des éléments génétiques mobiles (MGE) ou des plasmides ayant des gènes de phage auxiliaire chromosomiquement intégrés), ainsi qu'un phage, un phage auxiliaire, des kits, des compositions et des procédés impliquant ces derniers. Les particules sont particulièrement utiles pour administrer des charges toxiques dans des bactéries cibles en vue d'une action antibactérienne. Des modes de réalisation de l'invention permettent la production de compositions très pures de telles particules pour une utilisation sur le plan médical ou environnemental et pour le confinement des particules, qui peuvent être utiles pour contenir l'action antibactérienne.
EP20727987.8A 2019-05-22 2020-05-21 Phage et particules de transduction Withdrawn EP3973052A1 (fr)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
GBGB1907242.0A GB201907242D0 (en) 2019-05-22 2019-05-22 Dna methods etc ii
PCT/EP2020/064225 WO2020234428A1 (fr) 2019-05-22 2020-05-21 Phage et particules de transduction

Publications (1)

Publication Number Publication Date
EP3973052A1 true EP3973052A1 (fr) 2022-03-30

Family

ID=67385351

Family Applications (1)

Application Number Title Priority Date Filing Date
EP20727987.8A Withdrawn EP3973052A1 (fr) 2019-05-22 2020-05-21 Phage et particules de transduction

Country Status (8)

Country Link
EP (1) EP3973052A1 (fr)
JP (1) JP2022542742A (fr)
CN (1) CN114144517A (fr)
AU (1) AU2020278898A1 (fr)
CA (1) CA3137804A1 (fr)
GB (1) GB201907242D0 (fr)
SG (1) SG11202111779PA (fr)
WO (1) WO2020234428A1 (fr)

Families Citing this family (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN112391357A (zh) * 2019-08-14 2021-02-23 宁波大学 温和气单胞菌高效裂解性噬菌体vB_AsoP-yong及其应用
CN115418324B (zh) * 2020-07-15 2023-09-01 北京工商大学 北工商梅泽氏菌新菌种及其应用
CN113046328B (zh) * 2021-04-13 2023-07-25 吉林大学 一株化脓隐秘杆菌噬菌体及其医用用途
WO2023056413A1 (fr) * 2021-09-30 2023-04-06 Board Of Regents, The University Of Texas System Vecteurs modifiés et organismes les contenant pour la conversion d'isoflavones dans l'intestin
CN114934059B (zh) * 2022-03-04 2023-02-21 深圳先进技术研究院 高通量简化噬菌体基因组骨架的方法

Family Cites Families (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CA2541941C (fr) * 2003-10-06 2015-05-26 Gangagen, Inc. Compositions anti-bacteriennes a base de bacteriophages et leur utilisation
US10351452B2 (en) * 2014-01-29 2019-07-16 Synphagen Llc Compositions for in vivo expression of therapeutic sequences in the microbiome
AU2015228372B2 (en) 2014-03-12 2018-05-31 Yeda Research And Development Co. Ltd Reducing systemic regulatory T cell levels or activity for treatment of disease and injury of the CNS
WO2017009399A1 (fr) * 2015-07-13 2017-01-19 Institut Pasteur Amélioration des agents antimicrobiens spécifiques à une séquence par le blocage de la réparation de l'adn

Also Published As

Publication number Publication date
GB201907242D0 (en) 2019-07-03
CA3137804A1 (fr) 2020-11-26
JP2022542742A (ja) 2022-10-07
WO2020234428A1 (fr) 2020-11-26
CN114144517A (zh) 2022-03-04
SG11202111779PA (en) 2021-12-30
AU2020278898A1 (en) 2021-12-16

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