Decoding Cancer Variants of Unknown Significance for Helicase-Nuclease-RPA Complexes Orchestrating DNA Repair During Transcription and Replication.
AuthorsTsutakawa, Susan E
Tainer, John A
KAUST DepartmentBioscience Program
Biological and Environmental Science and Engineering (BESE) Division
KAUST Grant NumberOSR-2018-CRG7-3764
Permanent link to this recordhttp://hdl.handle.net/10754/675064
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AbstractAll tumors have DNA mutations, and a predictive understanding of those mutations could inform clinical treatments. However, 40% of the mutations are variants of unknown significance (VUS), with the challenge being to objectively predict whether a VUS is pathogenic and supports the tumor or whether it is benign. To objectively decode VUS, we mapped cancer sequence data and evolutionary trace (ET) scores onto crystallography and cryo-electron microscopy structures with variant impacts quantitated by evolutionary action (EA) measures. As tumors depend on helicases and nucleases to deal with transcription/replication stress, we targeted helicase-nuclease-RPA complexes: (1) XPB-XPD (within TFIIH), XPF-ERCC1, XPG, and RPA for transcription and nucleotide excision repair pathways and (2) BLM, EXO5, and RPA plus DNA2 for stalled replication fork restart. As validation, EA scoring predicts severe effects for most disease mutations, but disease mutants with low ET scores not only are likely destabilizing but also disrupt sophisticated allosteric mechanisms. For sites of disease mutations and VUS predicted to be severe, we found strong co-localization to ordered regions. Rare discrepancies highlighted the different survival requirements between disease and tumor mutations, as well as the value of examining proteins within complexes. In a genome-wide analysis of 33 cancer types, we found correlation between the number of mutations in each tumor and which pathways or functional processes in which the mutations occur, revealing different mutagenic routes to tumorigenesis. We also found upregulation of ancient genes including BLM, which supports a non-random and concerted cancer process: reversion to a unicellular, proliferation-uncontrolled, status by breaking multicellular constraints on cell division. Together, these genes and global analyses challenge the binary "driver" and "passenger" mutation paradigm, support a gradient impact as revealed by EA scoring from moderate to severe at a single gene level, and indicate reduced regulation as well as activity. The objective quantitative assessment of VUS scoring and gene overexpression in the context of functional interactions and pathways provides insights for biology, oncology, and precision medicine.
CitationTsutakawa, S. E., Bacolla, A., Katsonis, P., Bralić, A., Hamdan, S. M., Lichtarge, O., … Tsai, C.-L. (2021). Decoding Cancer Variants of Unknown Significance for Helicase–Nuclease–RPA Complexes Orchestrating DNA Repair During Transcription and Replication. Frontiers in Molecular Biosciences, 8. doi:10.3389/fmolb.2021.791792
SponsorsThis research was supported by National Institute of Health (NIH) grants (P01 CA092584, R35 CA220430, and P30 GM124169), a Robert A. Welch Chemistry Chair, Cancer Prevention and Research Institute of Texas (CPRIT) grant RP180813, and King Abdullah University of Science and Technology (KAUST) grant OSR-2018-CRG7-3764. This research used the Texas Advanced Computing Center, supported by National Science Foundation (NSF) grant ACI-1134872 and Bridges/Bridges2 Pittsburgh Supercomputing Center through the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation grants ACI-1445606 and ACI-1548562.
PublisherFrontiers Media SA
PubMed Central IDPMC8710748
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