Open Collections

Fournier, Louis-Alexandre

University of British Columbia

Mutations in ARID1A, the DNA-binding subunit of the BAF chromatin remodeling complex, occur in about 7% of all cancers. Loss of ARID1A in cancer results in the dysregulation of epigenetic and transcriptional programs, and disturbs normal genome integrity maintenance resulting in genome instability. Genome instability, which consists of a higher frequency of mutation rates, is a hallmark feature of cancer that contributes to initiation and progression of the disease. The accumulation of RNA:DNA hybrid structures in the genome, called R-loops, has become increasingly appreciated as a form of stress that contributes to genome instability. R-loops regulate a variety of processes within the cell, including mitochondrial DNA replication, splicing and gene expression. To provide a better understanding of the breadth of factors that regulate R-loop in human cells, I used machine learning and CRISPR screening approaches to identify R-loop binding and modulating proteins (RLBPs) in human cells. This analysis identified features unique to RLBPs, produced a comprehensive functional network of R-loop associated factors, and identified novel RLBPs in FXR1, LIG1 and ARID1A. Validation work revealed that ARID1A prevents R-loop mediated DNA replication stress via the regulation of TOP2A localization. To gain insight on new therapeutic avenues against ARID1A-deficient cancers, I conducted genome-wide dropout CRISPR screens to identify synthetic lethal partners of ARID1A. I focused on the validation of one of the hits, KEAP1, and confirmed that ARID1A- deficient cells are sensitive to inhibition of KEAP1. I found that inhibition of KEAP1 in ARID1A-KO cells results in an exacerbation of genome instability phenotypes. While the mechanism remains unclear, my data suggests that NRF2-independent functions of KEAP1 are likely responsible for the synthetic lethality between ARID1A and KEAP1. Overall, my results highlight the diversity of proteins that regulate R-loop homeostasis in human cells and uncover a previously unrecognized role for ARID1A in R-loop mitigation and the maintenance of genome integrity. I also document for the first time that cells lacking ARID1A are sensitive to KEAP1 inhibition, resulting in a new body of knowledge on the consequences of ARID1A deficiency and informing on a potentially novel approach for the treatment of such tumours.

Text

2023-12-18

Attribution-NonCommercial-NoDerivatives 4.0 International

http://hdl.handle.net/2429/86964

Interdisciplinary Oncology

University of British Columbia

UBCV

http://creativecommons.org/licenses/by-nc-nd/4.0/