Mesoscale and Nanoscale Technologies Integrated by Structures for DNA Repair Complexes (MANTIS-DRC)

PROJECT SUMMARY/ABSTRACT Cancer is linked to every human DNA repair (DR) pathway. Genomic instability, which results from DR defects, is a cancer hallmark. Due to cancer cell susceptibilities from oncogenic stress and frequent DR defects, DNA damaging approaches are widely used successful cancer therapies. Yet, cancers may escape these therapies. Furthermore, they can cause toxicities, aging, and secondary cancers making knowledge to combat therapeutic resistance and to design advanced therapies important. In fact, DNA damage effects depend upon poorly understood dynamic DR complexes that are also a target for precision oncology. This R35 renewal application for Mesoscale and Nanoscale Technologies Integrated by Structures for DNA Repair Complexes (MANTIS-DRC) will focus on structures, mechanisms, and cancer cell biology impacts from exemplary systems addressing three critical knowledge gaps: 1) RNA alkylation response impacts on cancer cells, 2) DDR adaptors and complexes determining repair pathway choice at replication forks and DNA double-strand breaks (DSBs), and 3) mitochondrial sensing and response to PARylation and resulting changes in NADH levels. We will harness AlphaFold structure predictions for experimental structures including functional dynamicity and combine them with data analyses from whole genome studies (WGS) to determine how cancer genomes respond to damage, develop genome instability, and elaborate synthetic lethality for inhibitors to DDR. Alkylation therapies are widely used, but their damage to RNA, which is both more exposed to this damage and is roughly 10-fold higher than DNA, has unknown cancer cell impacts. Knowledge of DR pathway choice at DSBs and stalled forks remains incomplete. Although energy production and mitochondrial complex 1 is a cancer drug target how mitochondria respond to DNA damage and parylation, which lowers NADH levels, is enigmatic. Based upon his current R35 progress, Prof. Tainer is poised to efficiently test and define mechanisms underlying the outcomes to RNA alkylation responses, repair at DSBs and replication forks, and the mitochondrial response to high NADH use in DDR. With R35 support, we developed time-resolved X-ray scattering and its integration with atomic detail for conformations and assemblies that help link structures to phenotypes and biological outcomes. To elucidate how dynamic multi-functional DDR complexes orchestrate cellular responses to RNA damage, DNA damage at replication forks and breaks, and NADH levels, we will map their dynamic conformations and kinetics with systematic analyses. Rather than correlating data sets, we will integrate quantitative measurements to collapse complex data into unifying insights and actionable knowledge. Leveraging cutting-edge clinical information at MD Anderson will enable testing the relevance and impact of MANTIS-DRC predictions on patient databases. Collective results will produce objective mechanistic measurements from molecules to cells to design dissection-of-function mutations and inhibitor tools and to predict DR outcomes and their links to innate immune responses for cancer biology and medicine.