Dr. John Paul Y.C. Shen
The University of Texas MD Anderson Cancer Center
Department of Gastrointestinal Medical Oncology
The Shen Lab is focused on better understanding the molecular aberrations (mutation, CNA, gene expression, epigenetic) that define colon cancer and applying this knowledge to develop new targeted therapies. Broadly two approaches are used:
(1) generating new data from wet lab experimentation, in particular functional genomic screens using CRISPR-Cas9 technology to perform single and double gene knockouts in cancer cells; and
(2) applying innovative systems and network biology analytical methods to existing data to derive new biological insights and hypothesis.
Hypotheses from either wet lab screens or computational analysis are tested in follow up assays to validate findings and to develop a better mechanistic understanding that is necessary to move forward into mouse experimentation and ultimately human clinical trials. Current projects in the lab include testing machine learning based predictions of drug sensitivity in PDX models, generation of new double knockout CRISPR libraries to identify new synthetic lethal interactions in colon cancer, and the analysis of MD Anderson’s MoClip database and ATTACC colon cancer clinical trial database to identify new biomarkers of drug sensitivity.
The potential for student led projects project is wide and includes both wet lab and computational projects (or a mix of both). Examples include developing and screening a new CRISPR knockout library, or identifying new synthetic lethal interactions from analysis of the MoClip database. The Shen lab is highly collaborative, and seeks to establish new connections; thus co-mentoring with another faculty member is a possibility.