Shen Laboratory

Epigenomic Analysis in Human Disease

The Shen Laboratory focuses on the epigenome and its interaction with the genome in various diseases, with a specific emphasis on female cancers and cross-cancer comparisons. The Shen team uses bioinformatics as a tool to understand the etiology, cell of origin, and epigenetic mechanisms of various diseases and to devise better approaches for cancer prevention, detection, therapy, and monitoring. Team members have extensive experience with genome-scale DNA methylation profiles in primary human samples and have made major contributions to epigenetic analysis within The Cancer Genome Atlas (TCGA).

DNA methylation is ideally suited to deconstruct heterogeneity among cell types within a tissue sample. In cancer research, this approach can be used for both cancer cell clonal evolution studies or for quantifying normal cell infiltration and stromal composition. The latter can provide insights into the tumor microenvironment. For non-cancer studies, this method is a useful tool to accurately estimate different cell populations and provide insights into lineage structures and population shifts in disease. The Shen lab also is interested in translational applications of epigenomic technology. To this end, the lab translates markers that emerge from bioinformatics analysis into clinical assay development, marker panel assembly, and optimization, with the ultimate goal of clinical testing and validation.