Cancer Genomics

Our lab uses the computational and experimental approaches to investigate new functional elements encoded in the human genome that function in human health and cancer. To gain fundamental insight into cancer development and maintenance, we decipher the cis-regulatory code that governs the transcriptional landscapes of malignancies.

The cancer transcriptome is generated by the spatiotemporal orchestration of cis-regulatory elements such as promoters and enhancers. In particular, enhancers are distal cis-regulatory DNA elements that are crucial for the establishment of cell type-specific function and identity.

To investigate the cis-regulatory code, we have developed a simple and robust technology, Native Elongating Transcript Cap Analysis of Gene Expression (NET-CAGE), to globally determine the 5’-ends of nascent RNAs, thereby sensitively detecting unstable transcripts including enhancer-derived RNAs. NET-CAGE enabled ultra-sensitive detection of a number of enhancers at single nucleotide resolution.

We are applying our original NET-CAGE technology to describe the active cis-regulatory landscape across hundreds of diverse tumors, discovering differentially regulated enhancers, genes, and long non-coding RNAs. Furthermore, using our unique atlas of active enhancer regions at single nucleotide resolution, we further aim to develop a series of original technologies to investigate connectivity and functionality of cis-regulatory elements at both population and single-cell levels. We believe in the importance of developing original technologies that can solve paradigms that cannot be otherwise solved.

Lastly, through integrated analysis of genomic and epigenomic data with clinical information, we explore molecular therapeutic targets and biomarkers.