Characterization of the functions and therapeutic potential of deubiquitinating enzymes in oncology

Abstract

DUBs are dysregulated in cancer and other diseases, but there is much that is unknown about the specific substrates and pathways that individual DUBs regulate and their clinical utility remains incompletely explored. In this work, I present characterization of the functions and therapeutic potential of DUBs in oncology through pharmacological and genetic studies coupled with analysis of publicly available datasets. First, I used phenotypic screens using early small molecule DUB inhibitors and target deconvolution to identify promising DUB targets in acute myeloid leukemia (AML) and breast cancer (chapter II). Specifically, I identify USP10 as the DUB responsible for stabilizing the oncoprotein, FMS-like receptor tyrosine kinase-3 (FLT3), in AML, and I identify USP7 as a DUB with selective proliferative effects based on subtype in breast cancer. Next, I used targeted studies with USP7 inhibitors to understand the functions of USP7 important for transcription and proliferation as well as characterize the polypharmacology of commonly used USP7 inhibitors. (chapter III). I conclude that p53 is central to the impact of USP7 on both proliferation and the transcriptome, but additional USP7 functions also impact proliferation to a lesser extent. Finally, I used parallel experimental and computational approaches with pharmacological and genetic tools coupled with multiple, publicly available omics datasets to systematically interrogate the function and therapeutic potential of each DUB (chapter IV), and these results comprise the majority of the work presented here. I use this multi-omics approach to identify candidate functions and interactors essential for proliferation for 35 DUBs and investigate the transcriptional impacts of DUB knock out and inhibition. Overall, in this thesis, I present novel insights into both well studied DUBs as well as understudied DUBs, identify promising therapeutic contexts for many individual DUBs, and create a resource of integrated omics datasets for further exploration of DUB function. For example, I determine that copy number loss of USPL1 is predictive of sensitivity to USPL1 loss and the role of USPL1 in the Little Elongation Complex is central to its impact on cancer cell proliferation and transcription.