# US 7,410,758 B2 · Methods and compositions relating to HPV-associated pre-cancerous and cancerous growths, including CIN

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- Number: US 7,410,758 B2
- Document ID: US7410758B2
- Status: Granted
- Kind: B2
- Application number: 10/484,063
- Filed: 2002-07-19
- Published: 2005-03-03
- Granted: 2008-08-12
- Earliest claimed: 2001-07-20
- Assignees: Board of Regents, The University of Texas System
- Inventors: Jagannadha K. Sastry; Guillermo Tortolero-Luna; Michele Follen
- Web page: https://patentgrep.com/patent/US7410758B2

## CPC

- C07K 14/005: from viruses
- A61P 31/00: Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
- A61P 35/00: Antineoplastic agents
- G01N 33/505: {involving T-cells}
- G01N 33/56983: {Viruses}
- G01N 33/571: for venereal disease, e.g. syphilis, gonorrhoea {(herpes G01N33/56994; chlamydia G01N33/56927)}
- G01N 33/6863: {Cytokines, i.e. immune system proteins modifying a biological response such as cell growth proliferation or differentiation, e.g. TNF, CNF, GM-CSF, lymphotoxin, MIF or their receptors}
- A61K 2039/525: {Virus}
- C12N 2710/20022: New viral proteins or individual genes, new structural or functional aspects of known viral proteins or genes
- G01N 2333/025: Papovaviridae, e.g. papillomavirus, polyomavirus, SV40, BK virus, JC virus
- 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)
- A61P: SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- 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)
- 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)
- C12N: MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA (microbiological testing media C12Q1/00)

## Abstract

The present invention concerns the use of E6 and/or E7 peptides from human papilloma virus (HPV) to evaluate a cell-mediated response in a patient infected with HPV to determine the prognosis for that patient with respect to the development or recurrence of pre-cancerous or cancerous growths, including cervical intraepithelial neoplasia (CIN).

## Claims

### Claim 1

A method for determining the possibility of recurrence of a pre-cancerous or cancerous growth in a patient infected with human papilloma virus (HPV) or suspected of being infected with HPV, wherein the patient also has or had a pre-cancerous or cancerous growth on or around the cervix comprising determining whether the patient exhibits a cell-mediated response to at least one E6 or E7 peptide of HPV, wherein a cell-mediated response to such at least one peptide is indicative of a reduced risk of such a recurrence.

### Claim 2 (depends on 1)

The method of claim 1, wherein the sample is incubated with at least two E6 or at least two E7 peptides.

### Claim 3 (depends on 1)

The method of claim 1, wherein the sample is incubated with an E6 peptide of HPV.

### Claim 4 (depends on 3)

The method of claim 3, wherein the E6 peptide is K9L (SEQ ID NO:1), E10I (SEQ ID NO:2), C10R (SEQ ID NO:3), Q15L (SEQ ID NO:4), V10C (SEQ ID NO:5), P9L (SEQ ID NO:6), P10 I (SEQ ID NO:7), Q20P (SEQ ID NO:8), R16R (SEQ ID NO:9), or G10S (SEQ ID NO:10).

### Claim 5 (depends on 4)

The method of claim 4, wherein the E6 peptide is K9L (SEQ ID NO:l), E10I (SEQ ID NO:2), C10R (SEQ ID NO:3), Q15L (SEQ ID NO:4), V10C (SEQ ID NO:5), or a combination thereof.

### Claim 6 (depends on 1)

The method of claim 1, wherein the sample is incubated with an E7 peptide of HPV.

### Claim 7 (depends on 6)

The method of claim 6, wherein the E7 peptide is T10Q (SEQ ID NO:11), M9T (SEQ ID NO:12), D9L (SEQ ID NO:13), Q19D (SEQ ID NO:14), R9F (SEQ ID NO:15), R9V (SEQ ID NO:16), L9V (SEQ ID NO:17), G10C (SEQ ID NO:18), or D20C (SEQ ID NO:19).

### Claim 8 (depends on 7)

The method of claim 7, wherein the E7 peptide is Q19D (SEQ ID NO:19), R9F (SEQ ID NO:15), R9V (SEQ ID NO:16), L9V (SEQ ID NO:17), G10C (SEQ ID NO:18), or a combination thereof.

### Claim 9 (depends on 1)

The method of claim 1, wherein the sample is incubated with at least one E6 peptide and at least one E7 peptide.

### Claim 10 (depends on 1)

The method of claim 1, wherein the patient is known to be infected with HPV.

### Claim 11 (depends on 1)

The method of claim 1, further comprising determining whether the patient is infected with HPV.

### Claim 12 (depends on 1)

The method of claim 1, wherein the patient has or had a pre-cancerous growth.

### Claim 13 (depends on 12)

The method of claim 12, wherein the pre-cancerous growth is cervical intraepithelial neoplasia (CIN).

### Claim 14 (depends on 1)

The method of claim 1, wherein the patient no longer has the pre-cancerous or cancerous growth.

### Claim 15 (depends on 14)

The method of claim 14, wherein the patient no longer has a pre-cancerous growth.

### Claim 16 (depends on 15)

The method of claim 15, wherein the pre-cancerous growth is CIN.

### Claim 17 (depends on 1)

The method of claim 1, wherein the sample is blood.

### Claim 18 (depends on 1)

The method of claim 1, wherein the sample is obtained by a vaginal swab.

### Claim 19 (depends on 1)

The method of claim 1, wherein the sample comprises peripheral blood mononuclear cells.

### Claim 20 (depends on 1)

The method of claim 1, further comprising incubating the sample in media after obtaining the sample.

### Claim 21 (depends on 1)

The method of claim 1, wherein the assaying comprises contacting the sample with the peptide and measuring the sample for T-cell proliferation.

### Claim 22 (depends on 21)

The method of claim 21, wherein T-cell proliferation is assayed by measuring incorporation of tritiated thymidine.

### Claim 23 (depends on 22)

The method of claim 22, wherein the sample has an SI value of 2.0 or greater, indicating a cell-mediated immune response.

### Claim 24 (depends on 23)

The method of claim 23, wherein the sample has an SI value of 3.0 or greater, indicating a cell-mediated immune response.

### Claim 25 (depends on 1)

The method of claim 1, wherein the assaying comprises measuring an amount of a TH1 or TH2 cytokine.

### Claim 26 (depends on 25)

The method of claim 25, wherein the amount of a TH1 cytokine is measured.

### Claim 27 (depends on 26)

The method of claim 26, wherein the TH1 cytokine is IL-2, IFN-y, TNF-a, or TNF-p.

### Claim 28 (depends on 25)

The method of claim 25, wherein the amount of a TH2 cytokine is measured.

### Claim 29 (depends on 28)

The method of claim 28, wherein the TH2 cytokine is IL-4, IL-5, IL-10, or IL- 13.

### Claim 30 (depends on 25)

The method of claim 25, wherein the TH1 or TH2 cytokine is measured with an immunoassay.

### Claim 31 (depends on 30)

The method of claim 30, wherein the immunoassay is ELISA or a radioimmunoassay.

### Claim 32 (depends on 25)

The method of claim 25, wherein the TH1 or TH2 cytokine is measured by flow-cytometry.

### Claim 33 (depends on 1)

The method of claim 1, wherein the sample is assayed more than once.

### Claim 34 (depends on 33)

The method of claim 33, wherein the sample is assayed using different assays.

### Claim 35 (depends on 1)

The method of claim 1, wherein, further comprising obtaining a second sample from the patient and assaying the second sample for a cell-mediated immune response against at least one E6 or E7 peptide of HPV.

### Claim 36 (depends on 1)

The method of claim 1, wherein the sample is obtained from the patient at least one month after treatment for a pre-cancerous or cancerous growth.

### Claim 37 (depends on 1)

The method of claim 1, wherein the patient has undergone ablative treatment of a pre-cancerous or cancerous growth in the genitourinary tract.

### Claim 38 (depends on 1)

The method of claim 1, wherein determining whether the patient exhibits a cell-mediated response to at least one E6 or E7 peptide of HPV comprises:
a) incubating at least one E6 or E7 peptide of HPV with a sample from the patient; and
b) assaying the sample for a cell-mediated immune response against the peptide.

### Claim 39 (depends on 26)

The method of claim 26, wherein the TH1 cytokine is IL-12.

### Claim 40 (depends on 1)

The method of claim 1, wherein the patient has had a pre-cancerous or cancerous growth on or around the cervix, and, prior to the determining step, the growth has been successfully removed by ablation or surgery.