Modulation of microbiota function by gene therapy of the microbiome to prevent, treat or cure microbiome-associated diseases or disorders

Patent metadata

Field	Value
Publication number	US-11376286-B2
Application number	US-202117501110-A
Country	US
Kind code	B2
Filing date	Oct 14, 2021
Priority date	Apr 8, 2020
Publication date	Jul 5, 2022
Grant date	Jul 5, 2022

Abstract

The invention encompasses compositions, kits and methods for modifying bacteria, preferably naturally occurring bacteria, in situ. These can be used to treat, prevent or cure microbiome-associated diseases or disorders by modulating the molecules expressed and/or secreted by bacterial populations of the microbiome in a specific manner. The genomic modifications can modify the interactions between part or all of these populations and the host in a way that decreases their deleterious potential on host health. The compositions, kits and methods of the invention do not result in the direct death of these populations or a direct significant inhibition of their growth. The invention further includes methods for screening for genetic modifications in the bacteria, for determining the efficiency of vectors at inducing these genetic mutations, and for determining the effects of these mutations on bacterial growth.

First claim

We claim:

1. A delivery vehicle selected from a bacteriophage, bacterial virus particle, or packaged phagemid comprising a nucleic acid encoding a DNA base editor or a prime editor targeting a specific nucleotide sequence in a target bacteria,
wherein said DNA base editor or prime editor is designed to genetically modify a DNA sequence to generate at least one change in the targeted nucleotide sequence in the target bacteria without introducing a double strand break in the DNA sequence, and
wherein said genetic modification does not lead to the death of the target bacteria.

2. The delivery vehicle of claim 1 , wherein the target bacteria is a naturally occurring bacteria.

3. The delivery vehicle of claim 1 , wherein said bacteriophage, bacterial virus particle or packaged phagemid further comprises a conditional origin of replication which is inactive in the target bacteria.

4. The delivery vehicle of claim 1 , wherein said bacteriophage, bacterial virus particle or packaged phagemid is incapable of self-reproduction.

5. The delivery vehicle of claim 1 , wherein said genetic modification is a point mutation.

6. The delivery vehicle of claim 1 , wherein said genetic modification is a point mutation leading to gene disruption.

7. The delivery vehicle of claim 1 , wherein said targeted nucleotide sequence is a bacterial toxin gene.

8. The delivery vehicle of claim 1 , wherein the target bacteria is Bacteroides faecis or Bacteroides thetaiotaomicron and the targeted nucleotide sequence is the Bacteroides faecis or Bacteroides thetaiotaomicron beta-galactosidase gene.

9. The delivery vehicle of claim 1 , wherein the nucleic acid encodes the DNA base editor.

10. The delivery vehicle of claim 1 , wherein the nucleic acid encodes the prime editor.

11. The delivery vehicle of claim 1 , wherein the delivery vehicle comprises a nucleic acid sequence encoding a dCas9 (dead-Cas9).

12. The delivery vehicle of claim 1 , wherein the delivery vehicle comprises a nucleic acid sequence encoding an nCas9 (nickase Cas9).

13. The delivery vehicle of claim 11 , wherein the delivery vehicle comprises a nucleic acid sequence encoding a fusion protein of the dCas9 and a deaminase domain.

14. The delivery vehicle of claim 12 , wherein the delivery vehicle comprises a nucleic acid sequence encoding a fusion protein of the nCas9 and a deaminase domain.

15. The delivery vehicle of claim 1 , wherein said delivery vehicle is a bacteriophage.

16. The delivery vehicle of claim 1 , wherein said delivery vehicle is a bacterial virus particle.

17. The delivery vehicle of claim 1 , wherein said delivery vehicle is a packaged phagemid.

18. A pharmaceutical or veterinary composition comprising the delivery vehicle of claim 1 and a pharmaceutically acceptable vehicle.

Assignees

• Eligo Bioscience

Inventors

• Duportet Xavier
• Decrulle Antoine
• Gil-Cruz Cristina Del Carmen
• Pérez-Shibayama Christian Ivan
• Ludewig Burkhard
• Rodriguez Jesus Fernandez
• Brodel Andreas

Classifications

• C12N15/902

  using homologous recombination · CPC title

• C12N15/74

  Vectors or expression systems specially adapted for prokaryotic hosts other than E. coli, e.g. Lactobacillus, Micromonospora · CPC title

• C12N15/70 Primary

  Vectors or expression systems specially adapted for E. coli · CPC title

• C12N15/1079 Primary

  Screening libraries by altering the phenotype or phenotypic trait of the host (reporter assays C12N15/1086) · CPC title

• A61K35/74 Primary

  Bacteria (therapeutic use of a bacterial protein A61K38/00) · CPC title