# US 10,501,741 B2 · Methods and compositions for inhibiting growth and epithelial to mesenchymal transition (EMT) in cancer cells

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- Number: US 10,501,741 B2
- Document ID: US10501741B2
- Status: Granted
- Kind: B2
- Application number: 15/321,561
- Filed: 2015-06-25
- Published: 2017-07-27
- Granted: 2019-12-10
- Earliest claimed: 2014-06-25
- Assignees: Cold Spring Harbor Laboratory; Rutgers, The State University of New Jersey
- Applicants: Cold Spring Harbor Laboratory; Rutgers, The State University of New Jersey
- Inventors: Raffaella Sordella; Serif Senturk; Luca Cartegni; Zhan Yao
- Web page: https://patentgrep.com/patent/US10501741B2

## CPC

- C12N 15/1137: {against enzymes (viral enzymes C12N15/1131; receptors C12N15/1138)}
- A61K 31/198: Alpha-amino acids, e.g. alanine or edetic acid [EDTA] (betaine A61K31/205; proline A61K31/401; tryptophan A61K31/405; histidine A61K31/4172; peptides not degraded to individual amino acids A61K38/00)
- A61K 31/445: Non condensed piperidines, e.g. piperocaine
- A61K 31/713: Double-stranded nucleic acids or oligonucleotides
- A61K 38/13: Cyclosporins
- A61K 45/06: Mixtures of active ingredients without chemical characterisation, e.g. antiphlogistics and cardiaca
- A61P 35/00: Antineoplastic agents
- C12Y 502/01008: Peptidylprolyl isomerase (5.2.1.8), i.e. cyclophilin
- G01N 33/575: for cancer
- G01N 33/57557: {of other specific parts of the body, e.g. brain}
- G01N 33/57595: {involving intracellular compounds}
- C12N 2310/11: Antisense
- C12N 2310/14: interfering nucleic acids [NA]
- C12N 2310/20: involving clustered regularly interspaced short palindromic repeats [CRISPR]
- C12N 2320/30: Special therapeutic applications
- C12N 2320/31: Combination therapy
- G01N 2333/4748: p53
- G01N 2800/52: Predicting or monitoring the response to treatment, e.g. for selection of therapy based on assay results in personalised medicine; Prognosis
- C12N: MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA (microbiological testing media C12Q1/00)
- 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
- C12Y: ENZYMES
- G01N: INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES (measuring or testing apparatus or processes other than immunoassay, involving enzymes or microorganisms C12M, C12Q)

## Abstract

Provided herein are methods and compositions for inhibiting epithelial to mesenchymal transition of a cell.

## Claims

### Claim 1

A method of inhibiting cancer cells, comprising:
(a) determining whether cancer cells express p53Ψ, wherein the cancer cells are in a population of cells; and
(b) if the cancer cells in (a) express p53Ψ, administering a cyclophilin D (CypD) inhibitor in an effective amount that results in inhibition of p53Ψ protein activity.

### Claim 2 (depends on 1)

The method of claim 1, wherein the population of cells is in an individual.

### Claim 3 (depends on 1)

The method of claim 1, wherein the cancer cells are in a mammal.

### Claim 4 (depends on 3)

The method of claim 3, wherein the mammal is a human.

### Claim 5 (depends on 1)

The method of claim 1, wherein the CypD inhibitor is a pharmacologic inhibitor, a RNA interference (RNAi) molecule, an antisense oligonucleotide (ASO) or a CRISPR/Cas9 system that mediates gene editing.

### Claim 6 (depends on 5)

The method of claim 5, wherein the pharmacologic inhibitor is cyclosporine.

### Claim 7 (depends on 1)

The method of claim 1, further comprising administering a ROS inhibitor.

### Claim 8 (depends on 7)

The method of claim 7, wherein the ROS inhibitor is a ROS scavenger or an inhibitor that reduces production of ROS and activity of one or more ROS-mediated signaling component required for p53Ψ activity.

### Claim 9 (depends on 8)

The method of claim 8, wherein the ROS scavenger is N-acetyl cysteine or Tempol.

### Claim 10 (depends on 1)

The method of claim 1, further comprising evaluating one or more characteristics of the cancer cells prior to, during, or after administering the inhibitor, wherein the one or more characteristics of the cancer cells is selected from: morphology, invasive ability, motility, and expression of a cell biomarker.

### Claim 11 (depends on 10)

The method of claim 10, wherein increased expression of at least one cell biomarker selected from E-cadherin, CD24, CD104, MUC-1, MUC-4, MUC16, A33, CD143, CD166, PD-L1, B7-H2, B7-H3, Nectin-1, Nectin-2, Nectin-3, Nectin-4, cytokeratin, ZO-1, Laminin-1, Entactin, collagen, and miR200 family microRNAs indicates that a cell is epithelial cell-like.

### Claim 12 (depends on 10)

The method of claim 10, wherein decreased expression of a cell biomarker selected from CD44, CD45, N-cadherin, Vimentin, Zeb1, Twist, Slug, or Fibronectin indicates that a cell is epithelial cell-like.

### Claim 13 (depends on 1)

The method of claim 1, wherein the cancer cells in (a), also express one or more cell biomarkers of the mesenchymal state.

### Claim 14

A method of inhibiting growth of cancer cells in an individual, comprising:
(a) assessing cells in a population of cells obtained from an individual for expression of p53Ψ;
(b) identifying the cells from (a) that express p53Ψ; and
(c) if the cells assessed in (a) express p53Ψ, administering to the individual from whom the population of cells was obtained, a cyclophilin D (CypD) inhibitor in an effective amount that inhibits growth of cancer cells in the individual.

### Claim 15 (depends on 14)

The method of claim 14, further comprising (d) assessing the cells in a population of cells for expression of the one or more cell markers of the mesenchymal state, expression of one or more markers of the epithelial state, or both expression of the one or more cell markers of the mesenchymal state and expression of one or more markers of the epithelial state, wherein if there is a decrease in expression of the one or more markers of the mesenchymal state, an increase in expression of one or more markers of the epithelial state, or both a decrease in expression of the one or more cell markers of the mesenchymal state and an increase in expression of one or more markers of the epithelial state, cancer cell growth is inhibited.

### Claim 16 (depends on 15)

The method of claim 15, wherein markers of epithelial cell state and markers of mesenchymal cell state are selected from E-cadherin, CD24, CD104, CD44, CD45, N-cadherin, MUC-1, MUC-4, MUC16, A33, CD143, CD166, PD-L1, B7-H2, B7-H3, Nectin-1, Nectin-2, Nectin-3, Nectin-4, Vimentin, Zeb1, Twist, Slug, Fibronectin, cytokeratin, ZO-1, Laminin-1, Entactin, collagen, and a miR200 family microRNA.

### Claim 17 (depends on 14)

The method of claim 14, wherein the CypD inhibitor is a pharmacologic inhibitor, a RNA interference (RNAi) molecule, an antisense oligonucleotide (ASO) or a CRISPR/Cas9 system that mediates gene editing.

### Claim 18 (depends on 17)

The method of claim 17, wherein the pharmacologic inhibitor is cyclosporine.

### Claim 19 (depends on 14)

The method of claim 14, wherein increased expression of at least one of E-cadherin, CD24, CD104, MUC-1, MUC-4, MUC16, A33, CD143, CD166, PD-L1, B7-H2, B7-H3, Nectin-1, Nectin-2, Nectin-3, Nectin-4, cytokeratin, ZO-1, Laminin-1, Entactin, collagen, and miR200 family microRNAs indicates that a cell is epithelial cell-like.

### Claim 20 (depends on 14)

The method of claim 14, wherein decreased expression of CD44, CD45, N-cadherin, Vimentin, Zeb1, Twist, Slug, or Fibronectin indicates that a cell is epithelial cell-like.

### Claim 21 (depends on 14)

The method of claim 14, wherein the cells assessed in (a) that express p53Ψ also express one or more cell markers of the mesenchymal state.

### Claim 22

A method of treating an individual who has cancer cells that express p53Ψ, comprising administering to the individual in need thereof a CypD inhibitor in an effective amount that results in inhibition of p53Ψ.

### Claim 23

A method of identifying an individual suffering from cancer as a candidate for treatment with a CypD inhibitor, comprising
(a) determining whether cancer cells from the individual are CD44+ and CD24−;
(b) determining whether the cancer cells from the individual express p53Ψ;
(c) identifying the individual as a candidate for treatment if the cancer cells in (a) and (b) are CD44+ and CD24− and express p53Ψ; and
(d) administering to the individual who has been identified as a candidate for treatment, a CypD inhibitor in an effective amount that results in inhibition of p534Ψ activity.

### Claim 24 (depends on 23)

The method of claim 23, further comprising administration of a reactive oxygen species (ROS) inhibitor, wherein administration of the ROS inhibitor results in inhibition of signaling mediated by ROS required for the manifestation of p53Ψ mediated phenotypes.

### Claim 25 (depends on 24)

The method of claim 24, further comprising administering an inhibitor of p53Ψ in an effective amount by route that results in entry of a sufficient amount of the p53Ψ inhibitor into the cell and inhibition of p53Ψ.