Antonio Rios, a junior bioengineering major at Stanford University, characterized mutant TSC1 bladder cancer cell lines using differential gene expression analysis to better understand their pathogenicity.
Bladder cancer is the sixth most common cancer in the United States, with more than 74,000 new cases and 16,000 deaths every year. Inactivating mutations in the TSC1 gene have been shown to drive the formation of approximately 10-15% of bladder cancers. However, these TSC1-mutated bladder cancers have differing responses to clinical treatments. Growth mechanisms involved in bladder tumor formations require more analysis to determine which treatment options are more optimal.
The Broad has been one of the most inspiring environments I’ve been a part of, where the scientists have seemingly infinite amounts of scientific fortitude and resilience. Despite the program being virtual this due to the pandemic, I am confident in my decision to pursue biomedical research alongside my amazing BSRP cohort. I know the 14 of us will revolutionize science and conduct trailblazing research.
Using the Cancer Cell Line Encyclopedia (CCLE) dataset, we identified the differentially expressed (DE) genes between the TSC1-mutated RT-4 bladder cancer cell line and its TSC1- wildtype counterparts using DESeq2. Then, we used gene ontology analysis (GOseq) to investigate which biological processes the upregulated and downregulated DE genes are involved in. Both of these computational techniques will assist in the analysis of tumor growth mechanisms in TSC1-mutated bladder cancers.
The most significant biological processes the downregulated DE genes were a part of included extracellular organization, cell death, and cell motility. Conversely, the upregulated DE genes were implicated in metal ion transport, hypothalamus development, and limbic system development. These findings will help oncologists determine what biological processes are impacted in bladder cancer patients and assist in personalized treatment options. Further research should explore the pathogenesis of these biological processes.
Project: Identifying Differentially Expressed Genes Between a TSC1-mutated Bladder Cell Line and TSC1-wildtype Bladder Cancer Cell Lines
Mentor: Dr. Krinio Gianniakou, Kwiatkowski Lab