Integrated Genomic and Epigenomic Studies of Breast Cancer:  An Allelic-Specific Perspective

My research involves applying my expertise in genomics and epigenomics to dissecting out the components of breast cancer. I have been focusing on elucidating allele-specific gene expression and allele-specific epigenetic modifications. We developed a specific adaptation of SNP array-based high throughput technology. We showed that differential expression from the two alleles of a given gene is common in normal tissue. We followed this by demonstrating that the genetic background influences the epigenetic state of chromatin. By investigating multiple epigenetic marks, we were able to show that histone H3 lysine 9/14 acetylation and lysine 4/9/27 methylation were influenced by their genetic background. My group further demonstrated that the chromatin state segregates as a Mendelian trait. This study was the first demonstration of the influence of the genomic background on the global epigenetic state in humans.

More recently, we have applied high-throughput genomic/epigenomic technologies, such as high-density SNP arrays, to identifying genes that present as plausible candidates for contributing to breast cancer development. The genomic investigation has led to the identification of two putative oncogenes, IRX2 and TBL1XR1. Our immunohistochemistry (IHC) studies showed that IRX2 and TBL1XR1 were frequently over-expressed in breast tumors. To date, our research has provided direct experimental evidence supporting an oncogenic effect for TBL1XR1. We used the shRNA approach to knock down the expression of TBL1XR1 in breast cancer cells and found that depletion of the TBL1XR1 protein in the cells reduced cell migration/invasion and suppressed tumor growth in mouse xenografts. Our epigenomic investigation has led to the identification of DNA methylation signatures that are selectively associated with clinical phenotypes such as lymph node involvement, histological grade, tumor size, and ER/PR/HER2 status. As an example, we observed a specific DNA methylation signature that distinguishes primary breast cancer samples diagnosed as high-grade from those diagnosed as low-mid-grade tumors.

My collaborators include Drs. Lalage Wakefield, Junya Fukuoka, Ken Buetow, Kent Hunter, Philip Taylor, Alisa Goldstein, and Dinah Singer.