[129] Distinct ER Negative Breast Cancer Subtype-Specific Methylation Profiles

Dhananjay A Chitale, George W Divine, Kang Mei Chen, Maria J Worsham. Henry Ford Hospital, Detroit, MI

Background: Currently available markers routinely used in clinical practice are of limited value to patients with estrogen receptor-negative (ER-) breast cancer (basal-like and HER2neu {HER2} positive {HER+}), an aggressive subtype. Our aim was to identify differentially methylated genes informative of the biology of ER- breast cancer (BC) to aid in a refined classification of ER- subtypes of basal-like and HER2+.
Design: Whole-genome methylation array analysis was carried out using the Illumina Infinium HumanMethylation27 Bead- Chip on a 22 fresh frozen DNA samples: 14 primary BC: 5 ER+, 4 triple negative (TNBC), 5 ER-HER2+, and 8 matched normal, to quantify the proportion of methylated cytosines (5mC) to total cytosines at 27,578 different CpG dinucleotides. Data were analyzed by GenomeStudio software (Illumina). Locus methylation was calculated as a β-value (low to high ranging from 0 to 1). With 8 sets of paired tumor/normal tissue, GEE was performed to account for the correlation among such pairs which permitted the 6 unpaired tumor samples to be included in the same analysis. To identify methylated genes associated with ER- subtypes (TNBC and ER-HER2+) and distinct from ER+, a 3-tiered approach to call out genes in which methylation changed dramatically between ER+ and ER- subtypes was used. Tier 1: computed adjusted FDR values for all CpGs/ (or their averages for each gene) to be 0.05 or lower. Tier 2: the CpGs/genes to include genes with a 2-fold change (ratio >= 2.0 or ratio <= 0.5). Tier 3: CpGs/genes to include genes with an absolute difference between the mean β of =>0.2.
Results: When compared to normal, 2454 were differentially methylated genes (DMG) in BC at Tier 1, 342 at Tier 2 (238 hyper & 104 hypomethylated), and 77 genes at Tier 3 (75 hyper & 2 hypomethylated). For ER+ vs TNBC, of the 187 DMG at Tier 2 (172 hypermethylated, 15 hypomethylated), Tier 3 restriction included 91 such genes, 87 hyper- and 4 hypomethylated. For ER+ vs ER-HER+, of 101 significantly DMG (70 hyper-, 31 hypomethylated) at Tier 2, Tier 3 restriction held on to 52 such differentially methylated genes (48 hyper-, 4 hypomethylated). For TNBC vs HER2+, there were no DMG at Tiers 2 and 3. However, at Tier 1, only 2 FDR adjusted genes were noted: HAL (hypermethylated) and HGDF (hypomethylated).
Conclusions: ER+ BC are typified by many genes that are hypermethylated relative to normal tissue or to the TNBC and HER2+subtypes. The study shows feasibility of distinguishing ER- subtypes of basal-like and HER2+ breast cancers, and this suggests the potential to predict outcome based on CpG DNA methylation.
Category: Breast

Tuesday, March 5, 2013 9:30 AM

Poster Session III # 10, Tuesday Morning

 

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