Selectively altering microbiota for immune modulation

• US 10,300,138 B2
• Filed: 07/05/2018
• Issued: 05/28/2019
• Est. Priority Date: 06/05/2016
• Status: Active Grant

• Current Assignee: Snipr Technologies Limited
• Original Assignee: Snipr Technologies Limited
• Inventors: Clube, Jasper
• Primary Examiner(s): Nickol, Gary B
• Assistant Examiner(s): Jackson-Tongue, Lakia J
• Application Number:
  US16/028,311
• Publication Number:
  US 20180303934A1
• Time in Patent Office: 327 Days
• CPC Class Codes: A61K 2039/505 comprising antibodies
• CPC Class Codes: A61K 31/7105 Natural ribonucleic acids, i.e. containing only riboses attached to adenine, guanine, cytosine or uracil and having 3'-5' phosphodiester links
• CPC Class Codes: A61K 35/15 Cells of the myeloid line, e.g. granulocytes, basophils, eosinophils, neutrophils, leucocytes, monocytes, macrophages or mast cells; Myeloid precursor cells; Antigen-presenting cells, e.g. dendritic cells presenting a specific antigen A61K39/00; therapeutic combinations of antibodies, or fragments thereof, and blood-derived cells A61K39/00
• CPC Class Codes: A61K 35/17 Lymphocytes; B-cells; T-cells; Natural killer cells; Interferon-activated or cytokine-activated lymphocytes when activated by a specific antigen A61K39/00
• CPC Class Codes: A61K 35/74 Bacteria therapeutic use of a bacterial protein A61K38/00
• CPC Class Codes: A61K 39/0011 Cancer antigens
• CPC Class Codes: A61K 39/3955 against proteinaceous materials, e.g. enzymes, hormones, lymphokines
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: A61P 37/00 Drugs for immunological or allergic disorders
• CPC Class Codes: C12N 2320/30 Special therapeutic applications
• CPC Class Codes: C12N 2320/50 Methods for regulating/modulating their activity

Abstract

The invention relates to methods of modulating immune cells in a patient by altering microbiota of the patient. The invention also relates to methods of modulating treatments or therapies in a subject organism by altering microbiota of the subject. The invention also relates to cell populations, systems, arrays, cells, RNA, kits and other means for effecting this. In an example, advantageously selective targeting of a particular species in a human gut microbiota using guided nucleic acid modification is carried out to effect the alteration.

Claims

1. A method for enhancing a therapy of a disease or condition in a human or animal patient, the method comprises selective killing or reducing growth of a target bacterial or archaeal sub-population of a microbiota using a guided nuclease, thereby increasing the relative proportion of a sub-population of gram negative bacteria in the microbiota, wherein the sub-population of gram negative bacteria comprise Akkermansia or Faecalibacterium, wherein the therapy comprises administration of an effective amount of an immune checkpoint inhibitor to the patient, and wherein the immune checkpoint inhibitor is a PD-1 (Programmed Cell Death Protein 1) inhibitor or a PD-L1 (Programmed Death-Ligand 1) inhibitor.

2. The method of claim 1, wherein the guided nuclease is a Cas, TALEN (Transcription Activator-like Effector Nuclease), meganuclease or zinc finger nuclease.

3. The method of claim 2, wherein the microbiota comprises a mixed population of human gut microbiota bacteria of different species, and wherein the selective killing comprises selectively killing cells of one or more of the different species and sparing cells of the other species.

4. The method of claim 1, wherein the sub-population of gram negative bacteria comprise Akkermansia.

5. The method of claim 1, wherein the immune checkpoint inhibitor is an antibody.

6. The method of claim 5, wherein the immune checkpoint inhibitor is nivolumab, pembrolizumab, pidilizumab, durvalumab, or atezolizumab.

7. The method of claim 1, wherein the microbiota is gut microbiota.

8. The method of claim 1, wherein the sub-population of gram negative bacteria comprise Akkermansia muciniphila.

9. The method of claim 1, wherein the disease is cancer.

10. The method of claim 9, wherein the cancer is melanoma, non-small-cell lung cancer (NSCLC), or renal cell carcinoma (RCC).

11. The method of claim 1, wherein the sub-population of gram negative bacteria comprise Faecalibacterium.

12. The method of claim 1, wherein the sub-population of gram negative bacteria comprise Faecalibacterium prausnitzii.

13. The method of claim 1, wherein the target sub-population comprises Bacteroidetes.

14. The method of claim 1, wherein the method comprises:

a. contacting the microbiota with an engineered nucleic acid sequence for producing a host modifying (HM) crRNA, and

b. producing the HM-crRNA in a host cell of the target sub-population, wherein the HM-crRNA is operable with a Cas nuclease in the host cell to form a HM-CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas system, and wherein the HM-crRNA comprises a sequence that is capable of hybridizing to a target sequence of the host cell to guide the Cas nuclease to the target sequence in the host cell, whereby the target sequence is modified by the HM-CRISPR/Cas system and the host cell is killed or growth of the target sub-population is reduced.

15. The method of claim 14, wherein the Cas nuclease is endogenous to the host cell.

16. The method of claim 14, wherein the Cas nuclease is a Type II Cas.

17. The method of claim 16, wherein the HM-CRISPR/Cas system comprises an endogenous tracrRNA of the host cell.

18. The method of claim 16, wherein the HM-CRISPR/Cas system comprises a tracrRNA, and wherein the tracrRNA is encoded by an engineered nucleic acid.

19. The method of claim 14, wherein the sub-population of gram negative bacteria comprise Akkermansia.

20. The method of claim 14, wherein the sub-population of gram negative bacteria comprise Faecalibacterium.