Abstract LB-407: Global differential allele-specific expression (DASE) analysis in mammary epithelial transcriptome

Abstract

Abstract The significant mortality associated with breast cancer (BCa) suggests a clear need to improve current research strategies to identify new genes that predispose women to breast cancer. Differential allele-specific expression (DASE) has been shown to contribute to phenotypic variables in human and recently to the pathogenesis of cancer. We previously reported that nonsense-mediated mRNA decay (NMD) could lead to DASE of BRCA1/2 which is associated with elevated susceptibility to BCa. In addition to truncation mutations, multiple genetic and epigenetic factors, such as mutations in promoter regions, alteration in microRNA binding sites on 3′UTRs and changes in chromatin methylation status can contribute to DASE. Therefore, we hypothesize that DASE is a functional index for cis-acting variants and pathogenic mutations and global profiling of DASE in BCa precursor tissues can be used to identify novel causative alleles for BCa susceptibility. To test our hypothesis, we employed the Illumina® Omni1-Quad BeadChip in paired genomic DNA (gDNA) and double-stranded cDNA (ds-cDNA) samples prepared from of eight BCa patient-derived normal mammary epithelial lines (HMEC). We filtered original array data according to heterozygous genotype calls from 86,267 female transcriptome SNPs covered by the BeadChip and calculated DASE values using the Log ratio of cDNA allele intensity, which was normalized to the corresponding gDNA intensity to limit the potential technical variation cause by the design of oligo probes. We have developed two statistical methods, SNP- and gene-based approaches, which allowed us to identify 90 and 143 genes with a significant DASE>2 (P <= 0.01, FDR <= 0.05), respectively. Importantly, 60 candidate loci are identified by both approaches. Ingenuity Pathway Analysis of the 34 coding genes in top 60 candidates revealed two major interaction networks, which involves a variety of biological functions, including cell death and cell-to-cell signaling. One of the networks includes known cancer causative gene ZNF331 (DASE = 2.31, P = 0.0018, FDR = 0.040), USP6 (DASE = 4.80, P = 0.0013, FDR = 0.013) and breast cancer causative gene DMBT1 (DASE=2.03, P = 0.0017, FDR = 0.014). Sequencing of the 5′UTR of DMBT1 identified a genetic variant, rs2981745, which has been reported previously as a causative variant for breast cancer risk in DMBT1 locus. Further sequencing of 5′ RACE product of DMBT1 confirmed rs2981745 as the causal variant leading to DASE in DMBT1. This finding indicates that abnormalities in phenotypes of DASE reflect pathogenic genotypes. In summary, our study clearly demonstrated that global DASE profiling is a powerful new approach to identify BCa risk alleles. This work was kindly supported by the Susan G. Komen for the Cure (KG100274) and Eileen Stein Jacoby Fund. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr LB-407. doi:1538-7445.AM2012-LB-407