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Excessive transcription-replication conflicts are a vulnerability of BRCA1-mutant cancers

ABSTRACT: BRCA1 primarily functions to maintain genomic integrity; therefore, mutations in BRCA1 are associated with increased risk of developing breast (≥70%) and ovarian (≥40%) cancers. Additionally, tumors arising from BRCA1 mutations are typically high grade and recurrent in nature. Thus, there is an urgent need to identify novel optimal therapeutic options for the majority of these patients. Herein, we performed a targeted CRISPR-Cas9 dropout screen and identified Methylphosphate Capping Enzyme, MEPCE, as a potential synthetic lethal interactor of BRCA1. Mechanistically, depletion of MEPCE in a BRCA1-deficient setting results in increased RNA polymerase II redistribution, R-loop accumulation, as well as replication stress, concomitantly contributing to transcription-replication collision events. These factors compromise genomic integrity, thereby resulting in loss of viability of BRCA1-deficient tumor cells. We also identified RNA polymerase II-associated factor I, PAF1, as a synthetic lethal interactor of BRCA1. Similar to MEPCE depletion, loss of PAF1 in a BRCA1-deficient setting results in R-loop accumulation, transcription-replication conflicts, and cell death. Our study highlights the dependence of BRCA1-defective tumors on factors such as MEPCE and PAF1 that suppress transcription-replication conflicts through RNAPII pausing and release regulation to maintain genomic stability. This highlights the untapped potential of factors such as MEPCE as novel therapeutic targets for the treatment of cancers associated with BRCA1 mutations.

ORGANISM(S): Homo sapiens

PROVIDER: GSE173223 | GEO | 2023/04/25

REPOSITORIES: GEO

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The MYCN oncoprotein resolves conflicts of stalling RNA Polymerase with the replication fork [DP_EXOSC10_Screen]

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Project description:Heterozygous germline mutations in BRCA1 or BRCA2 predispose to breast, ovarian, as well as other cancers. The main physiological function of BRCA1 and BRCA2 is to facilitate DNA replication, by stabilising and re-starting stalled replication forks. Consequently, inactivation of either BRCA1 or BRCA2 genes leads to replication pathologies and accumulation of DNA double strand breaks. Similar to BRCA1/2 inactivation, oncogene overexpression interferes with replication and inflicts DNA damage. It remains unclear how the replication defects in the two settings differ from each other and what is their combined effect on cell viability. Here, we report that accumulation of β-catenin, an oncogene of the WNT signalling pathway, is synthetically lethal with BRCA1/2 inactivation. We identify two transcription-dependent mechanisms that mediate oncogene toxicity in the context of BRCA1/2 deficiency. Firstly, accumulation of -catenin activates E2F-dependent transcription, which accelerates G1/S transition, thus counteracting the delayed S-phase entry caused by BRCA1/2 abrogation. This, in turn, triggers illegitimate origin firing leading to fork collapse, DNA damage and deregulation of gene expression. Secondly, we find that β-catenin accumulation suppresses transcription of CDKN1A gene encoding p21, a modulator of fork progression. Decreased replication rates represent a hallmark of BRCA2 deficiency. Through p21 downregulation, β-catenin accelerates replication fork progression in BRCA2-deficient cells, thereby inflicting DNA damage and triggering cell death. Thus, our results demonstrate that oncogene-driven premature S-phase entry and increased replication rate are lethal in the context of BRCA1/2 abrogation, which explains the mutual exclusivity between oncogene activation and BRCA1/2 gene mutations in human tumours.

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