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-11690880-B2
Application number	US-202218052379-A
Country	US
Kind code	B2
Filing date	Nov 3, 2022
Priority date	Apr 8, 2020
Publication date	Jul 4, 2023
Grant date	Jul 4, 2023

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 gene editing enzyme or system targeting a specific nucleotide sequence in a target bacteria,
wherein said gene editing enzyme or system 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 sequence, and
where 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 said genetic modification is a point mutation that results in a change of an amino acid in a mimic peptide, wherein said mimic peptide is a bacterial antigen that mimics a human protein.

10. The delivery vehicle of claim 1 , wherein the gene editing enzyme further comprises one or two uracil DNA glycosylase inhibitor domain(s) (UGI).

11. The delivery vehicle of claim 1 , wherein the gene editing enzyme further comprises Mu-GAM.

12. The delivery vehicle of claim 1 , wherein the gene editing enzyme is a dual base editor.

13. The delivery vehicle of claim 1 , wherein the gene editing enzyme further comprises a reverse transcriptase domain.

14. The delivery vehicle of claim 1 , wherein the gene editing enzyme further comprises an inhibitor of base repair.

15. The delivery vehicle of claim 1 , wherein the gene editing system is a retro based system.

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

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

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

19. 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
• Fernandez Rodriguez Jesus
• Brodel Andreas

Classifications

• A61K35/74 Primary

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

• 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