# US 11,026,982 B2 · Method for reducing the likelihood of developing bladder or colorectal cancer in an individual human being

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- Number: US 11,026,982 B2
- Document ID: US11026982B2
- Status: Granted
- Kind: B2
- Application number: 17/027,953
- Filed: 2020-09-22
- Published: 2021-01-07
- Granted: 2021-06-08
- Earliest claimed: 2015-11-30
- Applicants: Joseph E. Kovarik
- Inventors: Joseph E. Kovarik
- Web page: https://patentgrep.com/patent/US11026982B2

## CPC

- A61K 35/74: Bacteria (therapeutic use of a bacterial protein A61K38/00)
- A61K 31/58: containing heterocyclic rings, e.g. danazol, stanozolol, pancuronium or digitogenin (digitoxin {A61K31/7048})
- A61K 31/715: Polysaccharides, i.e. having more than five saccharide radicals attached to each other by glycosidic linkages; Derivatives thereof, e.g. ethers, esters
- A61K 35/741: Probiotics (probiotic yeast, e.g. saccharomyces A61K36/06)
- A61K 38/1709: {from mammals}
- A61K 38/1758: {p53}
- A61K 38/465: {acting on ester bonds (3.1), e.g. lipases, ribonucleases}
- A61K 39/3955: {against proteinaceous materials, e.g. enzymes, hormones, lymphokines}
- A61P 31/04: Antibacterial agents
- A61P 35/00: Antineoplastic agents
- C07K 16/2818: {against CD28 or CD152}
- A61K 2035/11: {Medicinal preparations comprising living procariotic cells}
- A61K: PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES (devices or methods specially adapted for bringing pharmaceutical products into particular physical or administering forms A61J3/00; chemical aspects of, or use of materials for deodorisation of air, for disinfection or sterilisation, or for bandages, dressings, absorbent pads or surgical articles A61L; soap compositions C11D)
- A61P: SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- C07K: PEPTIDES (peptides in foodstuffs A23; obtaining protein compositions for foodstuffs, working-up proteins for foodstuffs A23J; preparations for medicinal purposes A61K; peptides containing beta-lactam rings C07D; cyclic dipeptides not having in their molecule any other peptide link than those which form their ring, e.g. piperazine-2,5-diones, C07D; ergot alkaloids of the cyclic peptide type C07D519/02; macromolecular compounds having statistically distributed amino acid units in their molecules, i.e. when the preparation does not provide for a specific; but for a random sequence of the amino acid units, homopolyamides and block copolyamides derived from amino acids C08G69/00; macromolecular products derived from proteins C08H1/00; preparation of glue or gelatine C09H; single cell proteins, enzymes C12N; genetic engineering processes for obtaining peptides C12N15/00; compositions for measuring or testing processes involving enzymes C12Q; investigation or analysis of biological material G01N33/00)

## Abstract

A method for treating an individual suffering from one of bladder cancer and colorectal cancer employs a CRISPR system to selectively kill or reduce the numbers of pathogenic bacteria within the individual and the individual is then administered an immune checkpoint inhibitor. In particular embodiments, the pathogenic bacteria is one of E. coli, Pseudomonas aeruginosa and Klebsiella bacteria, and the checkpoint inhibitor is selected from the group consisting of nivolumab, pembrolizumab, pidilizumab, AMP-224, AMP-514, STI-A1110, TSR-042, RG-7446, BMS-936559, MEDI-4736, MSB-0020718C, AUR-012 and STI-A1010. Further embodiments include enhancing the growth of a second bacteria in the individual, such bacteria including Akkermansia, Bacteroides, Bifidobacterium, Clostridium, Enterococcus, Fusobacterium, Lactobacillus, Propionibacterium, Ruminococcus, Veillonella, Prevotella, Escherichia and Streptococcus. Still other embodiments include increasing the levels of Roseburia and/or Faecalibacterium prausnitzii, in the individual's gut microbiome.

## Claims

### Claim 1

A method for treating an individual suffering from one of bladder cancer and colorectal cancer, comprising, using a clustered regularly interspaced short palindromic repeats (CRISPR) CRISPR associated protein (Cas) system or a CRISPR from Prevotella and Francisella 1 (Cpf1), selectively killing a pathogenic bacteria within the individual, said pathogenic bacteria selected from the group consisting of Escherichia coli, Pseudomonas aeruginosa and Klebsiella bacteria, and
administering to the individual an immune checkpoint inhibitor selected from the group consisting of nivolumab, pembrolizumab, pidilizumab, AMP-224, AMP-514, STI-A1110, TSR-042, RG-7446, BMS-936559, MEDI-4736, MSB-0020718C, AUR-012 and STI-A1010.

### Claim 2 (depends on 1)

The method of claim 1, further comprising enhancing the growth of a beneficial bacteria in the individual selected from the group consisting of Akkermansia, Bacteroides, Bifidobacterium, Clostridium, Enterococcus, Fusobacterium, Coprococcus, Lactobacillus, Propionibacterium, Ruminococcus, Veillonella, Prevotella, and Streptococcus bacteria.

### Claim 3 (depends on 1)

The method as set forth in claim 1, wherein a CRISPR-Cas or Cpf1 system is used to cut a gene expressed by the pathogenic bacteria.

### Claim 4

A method for treating an individual suffering from one of bladder cancer and colorectal cancer, comprising, using a clustered regularly interspaced short palindromic repeats (CRISPR) CRISPR associated protein (Cas) system or a CRISPR from Prevotella and Francisella 1 (Cpf1), selectively killing pathogenic bacteria within the individual, and administering to the individual an immune checkpoint inhibitor that specifically binds to an immune checkpoint protein selected from the group consisting of CTLA4, PD-1, PD-L1, PD-L2, A2AR, B7-H3, B7-H4, BTLA, KIR, LAG3, TIM-3 and VISTA.

### Claim 5 (depends on 4)

The method as set forth in claim 4, wherein the immune checkpoint inhibitor is selected from the group consisting of nivolumab, pembrolizumab, pidilizumab, AMP-224, AMP-514, STI-A1110, TSR-042, RG-7446, BMS-936559, MEDI-4736, MSB-0020718C, AUR-012 and STI-A1010.

### Claim 6 (depends on 4)

The method as set forth in claim 4, wherein a CRISPR-Cas or Cpf1 system is used to cut a gene expressed by the pathogenic bacteria.

### Claim 7 (depends on 4)

The method as set forth in claim 4, wherein the CRISPR-Cas or Cpf1 system is used to insert genes that have controllable elements such that the pathogenic bacteria cells are killed by triggering the expression of said inserted genes.

### Claim 8 (depends on 4)

The method as set forth in claim 4, wherein said pathogenic bacteria are selected from the group consisting of: Staphylococcus aureus; Pseudomonas aeruginosa; Klebsiella; Streptoccocus; Salmonella; Shigella; Mycobacterium tuberculosis; Enterococcus; E coli; Clostridium; Neisseria gonnorrhoea; Acinetobacter baumannii; and Campylobacter.

### Claim 9 (depends on 4)

The method as set forth in claim 4, wherein CRISPR-Cas or Cpf1 is used to facilitate RNA-guided site-specific DNA cleavage to kill the pathogenic bacteria.

### Claim 10 (depends on 4)

The method as set forth in claim 4, wherein using CRISPR-Cas systems, said pathogenic bacteria are killed while sparing other commensal bacteria.

### Claim 11 (depends on 4)

The method of claim 4, further comprising enhancing the growth of a beneficial bacteria in the individual selected from the group consisting of Akkermansia, Bacteroides, Bifidobacterium, Clostridium, Enterococcus, Fusobacterium, Lactobacillus, Propionibacterium, Ruminococcus, Veillonella, Prevotella, and Streptococcus bacteria.

### Claim 12

A method for treating an individual suffering from one of bladder cancer and colorectal cancer, comprising,
providing in the gut of an individual a population of beneficial bacteria selected from the group consisting of Lactobacillus species;
administering at least 6 grams per day of fiber to the individual to maintain a therapeutically effective amount of the beneficial bacteria in the gut of the individual human being;
increasing the levels of at least one of Faecalibacterium prausnitzii, Bifidobacterium, Lachnospira, Veillonella, Coprococcus, Akkermansia muciniphila and Rothia in the individual's gut microbiome,
administering to the individual an immune checkpoint inhibitor, and, using a clustered regularly interspaced short palindromic repeats (CRISPR) CRISPR associated protein (Cas) system or a CRISPR from Prevotella and Francisella 1(Cpf1) system, reducing the population of a second bacteria in the individual, said second bacteria selected from the group consisting of Staphylococcus aureus; Pseudomonas aeruginosa ; Klebsiella; Streptoccocus; Salmonella; Shigella; Mycobacterium tuberculosis; Enterococcus; Escherichia coli; Clostridium; Neisseria gonnorrhoea; Acinetobacter baumannii; and Campylobacter.

### Claim 13 (depends on 12)

The method as set forth in claim 12, wherein the immune checkpoint inhibitor is selected from the group consisting of nivolumab, pembrolizumab, pidilizumab, AMP-224, AMP-514, STI-A1110, TSR-042, RG-7446, BMS-936559, MEDI-4736, MSB-0020718C, AUR-012 and STI-A1010.

### Claim 14 (depends on 12)

The method as set forth in claim 12, wherein a CRISPR-Cas or Cpf1 system is used to cut a gene expressed by the second bacteria.

### Claim 15 (depends on 12)

The method as set forth in claim 12, wherein using CRISPR-Cas systems, said pathogenic second bacteria are killed while sparing other commensal bacteria.

### Claim 16 (depends on 1)

The method as set forth in claim 1, wherein the CRISPR Cas system comprises one of Cas3 or Cas9.

### Claim 17 (depends on 1)

The method as set forth in claim 1, wherein the CRISPR Cas system is delivered using a bacteriophage.

### Claim 18 (depends on 4)

The method as set forth in claim 4, wherein the CRISPR Cas system comprises Cas3.

### Claim 19 (depends on 12)

The method as set forth in claim 12, wherein the CRISPR Cas system comprises Cas3 and is delivered using a bacteriophage.