Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0

DNA methylation profiling in the Carolina Breast Cancer Study


ABSTRACT: A microarray targeting promoters of cancer-related genes was used to evaluate DNA methylation at 935 CpG sites in 517 invasive breast tumors from the Carolina Breast Cancer Study (CBCS), a population-based study of invasive breast cancer. Concensus clustering using methylation (β) values for the 167 most variant CpG loci defined 4 clusters differing most distinctly in hormone receptor (HR) status, intrinsic subtype (luminal versus basal-like) and p53 mutation status. Supervised analyses for HR status, subtype, and p53 status identified differentially methylated CpG loci with considerable overlap (n=266). Concensus clustering also defined a hypermethylated luminal-enriched tumor cluster 3; gene ontology analysis of cluster 3 hypermethylated loci revealed enrichment for developmental genes, including homeobox domain genes (HOXB13, PAX6, IPF1, EYA4, DLK1, IHH, ISL1, TBX1, SOX1, SOX17). The hypermethylated luminal-enriched cluster 3 independently predicted poorer survival in multivariate Cox proportional hazard analysis, and this finding was confirmed in analysis of luminal A tumors. This study demonstrates epigenetic heterogeneity among breast tumors of a single intrinsic subtype, and shows that epigenetic patterns are strongly associated with HR status, subtype, and p53 mutation status. Among HR+ tumors, a gene signature characterized by hypermethylation of developmental genes may have prognostic value. Genes differentially methylated between clinically-important tumor subsets have roles in differentiation, development, and tumor growth and may be critical to inducing and maintaining tumor phenotypes and clinical outcomes. 517 breast tumors, 9 normal breast tissues

ORGANISM(S): Homo sapiens

SUBMITTER: Kathleen Dorsey 

PROVIDER: E-GEOD-51557 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

altmetric image

Publications

Body mass index is associated with gene methylation in estrogen receptor-positive breast tumors.

Hair Brionna Y BY   Troester Melissa A MA   Edmiston Sharon N SN   Parrish Eloise A EA   Robinson Whitney R WR   Wu Michael C MC   Olshan Andrew F AF   Swift-Scanlan Theresa T   Conway Kathleen K  

Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 20150112 3


<h4>Background</h4>Although obesity is associated with breast cancer incidence and prognosis, the underlying mechanisms are poorly understood. Identification of obesity-associated epigenetic changes in breast tissue may advance mechanistic understanding of breast cancer initiation and progression. The goal of this study, therefore, was to investigate associations between obesity and gene methylation in breast tumors.<h4>Methods</h4>Using the Illumina GoldenGate Cancer I Panel, we estimated the a  ...[more]

Similar Datasets

2015-04-07 | GSE51557 | GEO
2020-02-17 | GSE141338 | GEO
2007-02-20 | GSE3178 | GEO
2023-01-26 | GSE223700 | GEO
2014-06-30 | E-GEOD-52783 | biostudies-arrayexpress
2013-02-19 | E-GEOD-35629 | biostudies-arrayexpress
2008-06-12 | E-GEOD-3178 | biostudies-arrayexpress
2010-07-06 | E-GEOD-14457 | biostudies-arrayexpress
2011-08-14 | E-GEOD-27101 | biostudies-arrayexpress
2012-06-26 | E-GEOD-25307 | biostudies-arrayexpress