Insights into MYC biology through investigation of synthetic lethal interactions with MYC deregulation

MYC (or c-myc) is a bona fide "cancer driver" oncogene that is deregulated in up to 70% of human tumors. In addition to its well-characterized role as a transcription factor that can directly promote tumorigenic growth and proliferation, MYC has transcription-independent functions in vital cellular processes including DNA replication and protein synthesis, contributing to its complex biology. MYC expression, activity, and stability are highly regulated through multiple mechanisms. MYC deregulation triggers genome instability and oncogene-induced DNA replication stress, which are thought to be critical in promoting cancer via mechanisms that are still unclear. Because regulated MYC activity is essential for normal cell viability and MYC is a difficult protein to target pharmacologically, targeting genes or pathways that are essential to survive MYC deregulation offer an attractive alternative as a means to combat tumor cells with MYC deregulation. To this end, we conducted a genome-wide synthetic lethal shRNA screen in MCF10A breast epithelial cells stably expressing an inducible MYCER transgene. We identified and validated FBXW7 as a high-confidence synthetic lethal (MYC-SL) candidate gene. FBXW7 is a component of an E3 ubiquitin ligase complex that degrades MYC. FBXW7 knockdown in MCF10A cells selectively induced cell death in MYC-deregulated cells compared to control. As expected, cellular MYC levels are stabilized when FBXW7 expression is attenuated. Notably, stabilization of MYC is more pronounced compared to other FBXW7 targets. FBXW7 knockdown with MYC deregulation results in cell cycle defects, as well as CDC45 accumulation on chromatin, suggesting DNA replication stress. Intriguingly, FBXW7 and MYC expression correlate most strongly in the luminal A-subtype of breast cancer associated with low to normal MYC expression. Together, our results suggest that knockdown of FBXW7 increases cellular MYC levels and promotes cell death possibly through accumulation of MYC-dependent genomic stress, and that FBXW7 inhibition may be selectively synthetic lethal with breast cancers that retain MYC-dependence. We also identified UVSSA and ERCC8, two genes involved in transcription-coupled repair (TCR), as MYC-SL candidates from our genome-wide screen. TCR is a DNA damage repair pathway associated with active RNA polymerase II-transcription complexes. We show that both UVSSA and ERCC8 knockdown confer increased lethality selectively in MYC-deregulated cells. This MYC-SL interaction is not exacerbated by exogenous UV irradiation, suggesting that TCR may be required for survival upon MYC deregulation independently of its role in UV damage repair. UVSSA knockdown with MYC deregulation results in cell cycle defects and CHK2 activation, suggesting genomic stress. Intriguingly, we observe that lethality associated with UVSSA down-regulation in cells expressing MYCER is alleviated by inhibiting transcription. This suggests that transcription-dependent aberrant genomic structures generated during MYC deregulation may require TCR for maintaining survival. Taken together, our results suggest that increased levels of transcription-dependent genomic stress may accumulate with MYC deregulation, and that TCR may have functions outside of repairing UV-induced damage in resolving these lesions or structures