Recent genome-wide association studies (GWAS) have identified multiple common inherited genetic susceptibility factors that may play a role in a variety of human diseases and outcomes. The primary goal of my research is to identify the functional links between these genetic associations and molecular phenotypes.
Some single nucleotide polymorphisms (SNPs) can affect coding sequence, and lead to disease-causing changes in proteins. However, the majority of the associated markers point to non-coding regions of the genome. We use a wide range of methods to identify molecular interactions within the genome, including DNA sequencing and genotyping, RNA sequencing, protein expression studies, DNA-protein interaction analysis, cell culture, and epigenetic studies.
Functional Studies of Genetic Variants Identified through GWAS
The first wave of genome-wide association studies has yielded several candidate areas of interest within the genome. My laboratory is conducting follow-up studies on findings from several GWAS including breast, prostate, and bladder cancers, as well as outcomes of HCV infection. This work involves additional genetic and functional studies to further understand the mechanisms underlying cancer risk.
My laboratory has analyzed the chromosome 1p11.2 region that includes the breast cancer-associated SNP rs11249433 (Thomas et al., Nature Genetics 2009). Through our studies on mRNA expression, we found that the rs11249433 genotype is associated with expression of the NOTCH2 gene, and that this association is stronger in estrogen receptor (ER) positive tumors compared with ER negative tumors (Fu et al., Molecular Cancer 2010).
My laboratory is also performing genetic and functional analysis of associations within the JAZF1 gene and prostate cancer risk (Thomas et al., Nature Genetics 2008). My lab has re-sequenced the region around a prostate cancer-associated SNP, identified all genetic variants in high linkage disequilibrium, and performed further genotyping and association studies. Through a grant from the Center of Excellence in Integrative Cancer Biology and Genomics (CEICBG, in collaboration with Drs. Natasha Caplen and Stefan Ambs, CCR/NCI), we are combining studies of mRNA expression, siRNA, and pathways analysis to better understand the function of JAZF1.
Efforts are underway to follow-up on several novel candidate regions identified by bladder cancer GWAS (Rothman et al., Nature Genetics 2010). These regions include the UGT1A region, PSCA, and CCNE1 genes. My laboratory is using the combined approaches of sequencing, imputation, genotyping, mRNA and protein expression studies to identify relevant functional mechanisms associated with genetic variants within these regions.
Molecular Genetics of HCV Infection
Persistent infection with hepatitis C virus (HCV) is a primary etiological factor for the development of chronic liver disease, including cirrhosis of the liver and cancer. A recent study identified occludin (OCLN), an integral tight junction protein, as one of the key factors for HCV entry into cells (Ploss et al., Nature 2009). Through further investigation of the OCLN gene in human liver samples, we found that splicing diversity of the OCLN gene may be associated with permissiveness or resistance to HCV infection (Kohaar et al., JVI 2010). Additional work will identify genetic variants within OCLN that may contribute to susceptibility to HCV infection.
The current therapy for chronic HCV infection includes treatment with ribovirin. Recent GWAS have identified an association between several SNPs from the IL28B region and patient response to this treatment and natural clearance of HCV infection. We continue to explore the molecular mechanisms of this association in collaboration with Drs. Thomas O’Brien (DCEG), Barbara Rehermann (NIDDK) and Raymond Donnelly (FDA).