Grading, staging, and prognosing cancer using osteopontin-c

Patent metadata

Field	Value
Publication number	US-2018119232-A1
Application number	US-201715840611-A
Country	US
Kind code	A1
Filing date	Dec 13, 2017
Priority date	Oct 16, 2007
Publication date	May 3, 2018
Grant date	—

Abstract

The present disclosure provides methods and kits that can be used to determine the grade or stage of a breast or other cancer, such as a ductal carcinoma in situ (DCIS). By determining the grade, stage, or aggressiveness of a cancer, appropriate therapeutic regiments can be selected and administered to the patient with the cancer. The method includes detecting osteopontin-c (OPN-c), wherein the presence of high amounts of OPN-c in the cancer sample indicates that the subject has a more aggressive form of cancer (e.g., grade 3).

First claim

We claim:

1 . A method of treating a patient having a triple negative breast cancer tumor, the method comprising:
(I) grading the triple negative breast cancer tumor by:
(1) obtaining a sample of the triple negative breast cancer tumor;
(2) detecting an expression level of an OPN-c mRNA in the sample; and
(3) quantifying the expression level of the OPN-c mRNA detected in the sample in (I)(2); and
(4) grading the tumor on the basis of OPN-c mRNA expression level; and
(II) treating the patient with:
(1) an aggressive therapeutic protocol when the triple negative breast cancer tumor has a grade of 2 or 3 on the basis of OPN-C mRNA expression level, wherein the aggressive therapeutic protocol comprises mastectomy or lumpectomy combined with radiotherapy and/or chemotherapy; and
(2) a less aggressive therapeutic protocol when the triple negative breast cancer tumor has a grade of 1 on the basis of OPN-C mRNA expression level, wherein the less aggressive therapeutic protocol consists of lumpectomy.

2 . The method of claim 1 , wherein the triple negative breast cancer is ductal carcinoma in situ (DCIS).

3 . The method of claim 1 , wherein the triple negative breast cancer tumor has no detectable level of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2).

4 . The method of claim 1 , wherein the OPN-c mRNA is detected by a method comprising a procedure selected from the group consisting of Northern blotting and a PCR-based assay.

5 . The method of claim 4 , wherein the PCR-based assay is real time RT-PCR.

6 . The method of claim 1 , wherein the OPN-c mRNA is detected by a method comprising contacting the sample with a nucleic acid probe that hybridizes to an OPN-c mRNA OR OPN-c cDNA.

7 . The method of claim 6 , wherein the nucleic acid probe is capable of hybridizing to the OPN-c nucleic acid when hybridization is performed at 42° C. in a hybridization solution containing 25 mM KPO 4 (pH 7.4), 5×SSC, 5× Denhart's solution, 50 μg/mL denatured, sonicated salmon sperm DNA, 50% formamide, 10% Dextran sulfate, and from 1 ng/mL to 15 ng/mL probe, with washes performed at 65° C. with a wash solution containing 0.2×SSC and 0.1% sodium dodecyl sulfate.

8 . The method of claim 1 , wherein the tumor grade is obtained by comparing the expression level of the OPN-c mRNA to a reference value, wherein the reference value of a grade 3 cancer is higher than a reference value of a grade 2 cancer, and wherein the reference value of a grade 2 cancer is higher than a reference value of a grade 1 cancer.

9 . The method of claim 1 , wherein the expression level of OPN-c is normalized against the expression level of a housekeeping gene.

10 . A method for treating a breast cancer patient, the method comprising:
(I) assessing the breast cancer patient by:
(1) obtaining a breast cancer tumor sample from the patient; and
(2) detecting an expression level of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) in the tumor sample, and
(3) determining whether the expression level of ER, PR, and HER2 is indicative of triple negative breast cancer;
(II) grading the tumor sample when triple negative breast cancer is indicated in (I)(2) by:
(1) detecting an expression level of an OPN-c mRNA in the sample; and
(2) quantifying the expression level of the OPN-c mRNA detected in the sample in (II)(1); and
(3) grading the tumor on the basis of OPN-c mRNA expression level; and
(III) treating the patient with:
(1) an aggressive therapeutic protocol when the triple negative breast cancer tumor has a grade of 2 or 3 on the basis of OPN-c mRNA expression level, wherein the aggressive therapeutic protocol comprises mastectomy or lumpectomy combined with radiotherapy and/or chemotherapy; and
(2) a less aggressive therapeutic protocol when the triple negative breast cancer tumor has a grade of 1 on the basis of OPN-c mRNA expression level, wherein the less aggressive therapeutic protocol consists of lumpectomy.

11 . The method of claim 10 , wherein the triple negative breast cancer is ductal carcinoma in situ (DCIS).

12 . The method of claim 10 , wherein the triple negative breast cancer tumor has no detectable level of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2).

13 . The method of claim 10 , wherein the OPN-c mRNA is detected by a method comprising a procedure selected from the group consisting of Northern blotting, Southern blotting, PCR, and DNA arrays.

14 . The method of claim 10 , wherein the OPN-c mRNA is detected by a method comprising real time RT-PCR.

15 . The method of claim 10 , wherein the OPN-c mRNA is detected by a method comprising contacting the sample with a nucleic acid probe that hybridizes to an OPN-c mRNA OR OPN-c cDNA.

16 . The method of claim 15 , wherein the nucleic acid probe is capable of hybridizing to the OPN-c nucleic acid when hybridization is performed at 42° C. in a hybridization solution containing 25 mM KPO4 (pH 7.4), 5×SSC, 5× Denhart's solution, 50 μg/mL denatured, sonicated salmon sperm DNA, 50% formamide, 10% Dextran sulfate, and from 1 ng/mL to 15 ng/mL probe, with washes performed at 65° C. with a wash solution containing 0.2×SSC and 0.1% sodium dodecyl sulfate.

17 . The method of claim 10 , wherein the tumor grade is obtained by comparing the expression level of the OPN-c mRNA to a reference value, wherein the reference value of a grade 3 cancer is higher than a reference value of a grade 2 cancer, and wherein the reference value of a grade 2 cancer is higher than a reference value of a grade 1 cancer.

18 . The method of claim 10 , wherein the expression level of OPN-c mRNA is normalized against the expression level of a housekeeping gene.

19 . A kit, comprising:
(a) a nucleic acid probe or primer that specifically hybridizes to a estrogen receptor (ER) nucleic acid molecule; a nucleic acid probe or primer that specifically hybridizes to a progesterone receptor (PR) nucleic acid molecule; a nucleic acid probe or primer that specifically hybridizes to a HER2 nucleic acid molecule; and a nucleic acid probe or primer that specifically hybridizes to a OPN-c nucleic acid molecule; and/or (b) an antibody that specifically binds estrogen receptor (ER); an antibody that specifically binds progesterone receptor (PR); an antibody that specifically binds HER2; and an antibody that specifically binds OPN-c.

20 . The kit of claim 19 , further comprising one or more control samples with known amounts of ER, PR, HER2 and OPN-c.

21 . The kit of claim 19 , further comprising a nucleic acid probe or primer that specifically hybridizes to a housekeeping gene or a message of a housekeeping gene; and/or an antibody that specifically binds to a protein expressed by a housekeeping gene.

22 . A method selected from the group consisting of:
(a) a method of grading cancer in a subject, comprising: determining the expression level of osteopontin-c (OPN-c) in a cancer sample, wherein the presence of greater OPN-c levels indicates that the subject has a higher grade of cancer and the presence of lower OPN-c levels indicates that the subject has a lower grade of cancer., and (b) a method of staging cancer in a subject, comprising: determining the expression level of osteopontin-c (OPN-c) in a cancer sample, wherein the presence of greater OPN-c levels indicates that the subject has a higher s

Assignees

• Ventana Med Syst Inc
• Univ Cincinnati

Inventors

• Mirza Mana
• Shaughnessy Elizabeth
• Hurley John K
• Vanpatten Kristie A
• Pestano Gary
• Weber Georg F

Classifications

• C12Q2600/106

  Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism · CPC title

• A61K47/6855

  the tumour determinant being from breast cancer cell · CPC title

• C12Q1/6886 Primary

  for cancer (immunoassay for cancer G01N33/575) · CPC title

• C12Q2600/158

  Expression markers · CPC title

• C12Q2600/112

  Disease subtyping, staging or classification · CPC title