Genome-wide methylation analysis and use to identify genes specific to breast cancer hormone receptor status and risk of recurrence

Patent metadata

Field	Value
Publication number	US-10316361-B2
Application number	US-201214232981-A
Country	US
Kind code	B2
Filing date	Jul 16, 2012
Priority date	Jul 15, 2011
Publication date	Jun 11, 2019
Grant date	Jun 11, 2019

Abstract

To better understand the biology of hormone receptor-positive and negative breast cancer and to identify methylated gene markers of disease progression, a genome-wide methylation array analysis was performed on 103 primary invasive breast cancers and 21 normal breast samples using the Illumina Infinium HumanMethylation27 array that queried 27,578 CpG loci. Forty CpG loci showed differential methylation specific to either ER-positive or ER-negative tumors. Each of the 40 ER-subtype-specific loci was validated in silico using an independent, publicly available methylome dataset from The Cancer Genome Atlas (TCGA). In addition, 100 methylated CpG loci were identified that were significantly associated with disease progression. Arrays containing the ER-subtype-specific loci and their use in methods of diagnosis and treatment of breast cancer are provided.

First claim

The invention claimed is:

1. A method for treatment of a subject having breast cancer, the method comprising the steps of:
(a) extracting DNA from a biological sample comprising DNA from breast cancer tissue from the subject;
(b) performing bisulfite modification to the DNA in (a);
(c) contacting the DNA from (b) with a platform comprising an array of oligonucleotide probes for identifying specific methylated target DNA gene loci in a sample, comprising two oligonucleotide probes that each selectively bind the specific methylated loci in the target DNA genes ADAMTSL1 at locus cg00116234 and ARFGAP3 at locus cg00079563 wherein the probes are immobilized on the platform; or,
(d) contacting the DNA from (b) with a platform comprising an array of oligonucleotide probes for identifying specific methylated target DNA gene loci in a sample, comprising two oligonucleotide probes that each selectively bind the specific methylated loci in the target DNA genes ADHFE1 at locus cg08090772 and PDXK at locus cg23178308;
(e) providing a non-neoplastic control breast tissue sample; and performing steps (b)-(d) on the control breast tissue sample;
(f) comparing the methylation of the two target DNA gene loci in the suspect sample from the subject to the methylation of the two target DNA gene loci in the control breast tissue sample;
(g) detecting that the level of methylation of the target DNA gene loci from (c) is greater than the level of methylation of the target DNA gene loci from (e), identifying said human subject as having ER+ breast cancer, and
(h) administering to the subject treatment comprising surgery, radiation, and chemotherapeutic treatment with adjuvant endocrine therapy or continuing said treatment; or
(i) detecting that the level of methylation of the target DNA gene loci from (d) is greater than the level of methylation of the target DNA gene loci from (e), identifying said human subject as having ER− breast cancer, and
(j) administering to the subject treatment comprising surgery and radiation.

2. The method of claim 1 , wherein the methylation level of the target DNA gene loci is measured using a BeadChip.

3. The method of claim 1 , wherein at step c) the platform further comprises an additional oligonucleotide probe that selectively binds the specific methylated locus in the target DNA gene ACADL at locus cg09068528; or wherein at step d) the platform further comprises additional oligonucleotide probes that selectively bind the specific methylated loci in the target DNA gene DAB2IP at loci cg27650175, cg14063008, cg07981910, and cg05684891.

4. The method of claim 1 , wherein at step c) the platform further comprises an additional oligonucleotide probe that selectively binds the specific methylated locus in the target DNA gene B3GAT1 at locus cg07845566; or wherein at step d) the platform further comprises additional oligonucleotide probes that selectively bind the specific methylated locus in the target DNA gene DYNLRB2 at locus cg00720137.

5. The method of claim 1 , wherein at step c) the platform further comprises an additional oligonucleotide probe that selectively binds the specific methylated locus in the target DNA gene CDCA7 at locus cg08690031; or wherein at step d) the platform further comprises additional oligonucleotide probes that selectively bind the specific methylated locus in the target DNA gene HSD17B4 at locus cg14874121.

6. The method of claim 1 , wherein at step c) the platform further comprises an additional oligonucleotide probe that selectively binds the specific methylated locus in the target DNA gene ETS1 at locus cg14998713; or wherein at step d) the platform further comprises additional oligonucleotide probes that selectively bind the specific methylated locus in the target DNA gene HSD17B8 at locus cg07433344.

7. The method of claim 1 , wherein at step c) the platform further comprises an additional oligonucleotide probe that selectively binds the specific methylated locus in the target DNA gene EVI1 at locus cg14228238; or wherein at step d) the platform further comprises additional oligonucleotide probes that selectively bind the specific methylated locus in the target DNA gene IRF7 at locus cg16541031.

8. The method of claim 1 , wherein at step c) the platform further comprises an additional oligonucleotide probe that selectively binds the specific methylated locus in the target DNA gene FAM78A at locus cg12998491; or wherein at step d) the platform further comprises additional oligonucleotide probes that selectively bind the specific methylated locus in the target DNA gene PER1 at locus cg01980637.

9. The method of claim 1 , wherein at step c) the platform further comprises an additional oligonucleotide probe that selectively binds the specific methylated locus in the target DNA gene FAM89A at locus cg00679738; or wherein at step d) the platform further comprises additional oligonucleotide probes that selectively bind the specific methylated locus in the target DNA gene PISD at locus cg01980637.

10. The method of claim 1 , wherein at step c) the platform further comprises an additional oligonucleotide probe that selectively binds the specific methylated locus in the target DNA gene FLJ31951 at locus cg01657408; or wherein at step d) the platform further comprises additional oligonucleotide probes that selectively bind the specific methylated locus in the target DNA gene WNK4 at locus cg08108311.

Assignees

• Sukumar Saraswati V
• Umbricht Christopher Benedict
• Wolff Antonio C
• Fackler Mary Jo Steele
• Zhang Zhe
• Cope Leslie M
• Visvanathan Kala
• Huang Peng
• Univ Johns Hopkins

Inventors

• Sukumar Saraswati V
• Umbricht Christopher Benedict
• Wolff Antonio C
• Fackler Mary Jo Steele
• Zhang Zhe
• Cope Leslie M
• Visvanathan Kala
• Huang Peng

Classifications

• C12Q2600/112

  Disease subtyping, staging or classification · CPC title

• C12Q2600/118

  Prognosis of disease development · CPC title

• C12Q1/6874 Primary

  involving nucleic acid arrays, e.g. sequencing by hybridisation · CPC title

• C12Q2600/154

  Methylation markers · CPC title

• C12Q1/6886 Primary

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