Abstract B40: Methylation signatures specific to triple negative breast cancer subtypes

Abstract

Abstract Objective: We identify methylation signatures specific to triple negative breast cancer (TNBC) subtypes using publicly available data, and examine their association with expression. Materials and Methods: DNA methylation, RNAseq expression and clinical data from breast invasive carcinoma patients were obtained from The Cancer Genome Atlas (TCGA) Data portal. The classification of each patient sample as TNBC was defined according to a combination of FISH and/or IHC results for ER, PR and HER2 negativity. Each TNBC specimen was classified into one of the following molecular subtypes by applying the gene expression-based model of Lehman (2011): basal-like 1 (BL1), basal-like 2 (BL2), immunomodulatory (IM), mesenchymal (MES), mesenchymal stem-like (MSL), luminal androgen receptor (LAR), and unstable (UNS). Among the 116 identified TNBC specimens, 61 had level-three data available on both methylation and RNAseq expression. For methylation, beta values were extracted based on Illumina's Infinium Human DNA Methylation 450K platform; for expression, RNAseqV2 Expectation/Maximization normalized counts (RSEM: Li and Dewey, 2011) were extracted on 20,531 genes and a logarithmic transformation applied. Data were filtered to identify methylation changes specific to each TNBC subtype based on a novel, generalized statistic (Switchenko and Kowalski, 2013) and tested for median difference between subtypes using p < 0.10 to define significance. Results: Among the 61 TNBC samples, the following molecular subtypes were represented: BL1 (n=6), BL2 (n=6), IM (n=12), LAR (n=5), MES (n=15), MSL (n=4), and UNS (n=13). A number of genes were determined to be hypermethylated with corresponding decreased expression by RNAseq in several subtypes. Methylated genes specific to the LAR TNBC subtype included IGF1R (61% LAR vs. 2% other) and N4BP2L1 (44% LAR vs. 3% other). Methylated genes in the MES subtype included ACSL5 (80% vs. 50%), RHOH (82% vs. 6%) and OAS2 (26% vs. 7%), and specific to the BL2 subtype were EN1 (35% vs. 8%) and TRAFIP3 (60% vs. 35%). Two hypomethylated genes, PIK3CD and CD69, associated with respective subtypes, MSL and IM, showed corresponding increased expression levels. Conclusion: Our results provide further insight into the molecular heterogeneity surrounding TNBC patients by examining methylation changes specific to molecular subtypes, which may be further examined for their effect on clinical outcome. Citation Format: Jeanne Kowalski, Jeffery M. Switchenko, Bhakti Dwivedi, Dana Nickleach, Carlos S. Moreno. Methylation signatures specific to triple negative breast cancer subtypes. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Jun 19-22, 2013; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2013;73(13 Suppl):Abstract nr B40.