CBE Doctoral Dissertation Defense: “Bridging Transcription and Signaling to Study c-MYC Function and Regulation in Cancer Cells” (Reshma Kalyan Sundaram)

Abstract:

The transcription factor c-MYC (MYC) is a master regulator of gene expression and is frequently deregulated in human cancers. Despite the prevalent role of MYC in cancers, no MYC inhibitors are currently available for clinical use. In this work, we investigated the molecular mechanisms underlying MYC’s transcriptional function and deregulation using an integrated approach combining bioinformatics analyses and kinetic modeling. In studying MYC’s regulation of transcriptional function, we analyzed publicly available next-generation sequencing datasets (ChIP-seq and RNA-seq) in various cancer cell lines to characterize MYC’s DNA binding patterns and gene targets. We discovered that MYC indirectly binds the TRE sites specifically at enhancers over promoters. We also found that MYC co-occupied these TRE enhancer sites synergistically with the AP-1 family of TFs, and that MYC binding to these sites varied with MYC levels. Gene Ontology analysis revealed that MYC binding to TRE sites contributes to transcriptional rewiring of cells by modulating several cancer hallmarks like proliferation, apoptosis, and cell adhesion. We also investigated upstream regulatory mechanisms contributing to MYC deregulation. We built an Ordinary Differential Equation (ODE) based systems model incorporating extracellular growth and matrix signals (received by EGFR and integrins, respectively) and intracellular signaling pathways (MAPK, Rho/ROCK, and PI3K/Akt) that regulate MYC. The modeling results revealed that MYC regulation is primarily driven by EGFR in normal cells, whereas both EGFR and integrin signaling play a combined role in regulating MYC in cancerous conditions. Our findings highlight a novel role played by extracellular matrix (ECM) based microenvironmental cues in addition to the well-known growth signaling cues on MYC regulation. In summary, we identify an enhancer-specific mechanism through which MYC functions in concert with AP-1 to regulate gene expression, and demonstrate how extracellular cues, including ECM signaling, contribute to MYC regulation. These newly uncovered mechanisms provide deeper insights into MYC’s oncogenic functions, and suggest potential avenues for therapeutic targeting of MYC-driven cancers.