Resistance to therapy in BRCA2 mutant cells due to loss of the nucleosome remodeling factor CHD4

Abstract

Hereditary cancers derive from gene defects that often compromise DNA repair. Thus, BRCA-associated cancers are sensitive to DNA-damaging agents such as cisplatin. The efficacy of cisplatin is limited, however, by the development of resistance. One cisplatin resistance mechanism is restoration of homologous recombination (HR), which can result from BRCA reversion mutations. However, in BRCA2 mutant cancers, cisplatin resistance can occur independently of restored HR by a mechanism that remains unknown. Here we performed a genome-wide shRNA screen and found that loss of the nucleosome remodeling factor CHD4 confers cisplatin resistance. Restoration of cisplatin resistance is independent of HR but correlates with restored cell cycle progression, reduced chromosomal aberrations, and enhanced DNA damage tolerance. Suggesting clinical relevance, cisplatin-resistant clones lacking genetic reversion of BRCA2 show de novo loss of CHD4 expression in vitro. Moreover, BRCA2 mutant ovarian cancers with reduced CHD4 expression significantly correlate with shorter progression-free survival and shorter overall survival. Collectively, our findings indicate that CHD4 modulates therapeutic response in BRCA2 mutant cancer cells.

Restoration of Replication Fork Stability in BRCA1- and BRCA2-Deficient Cells by Inactivation of SNF2-Family Fork Remodelers

“…These findings are in agreement with previous observations that the chromosomal instability of BRCA1/2-deficient cells can be reduced by inhibiting the nuclease activity of MRE11 or by preventing the recruitment of MRE11 to stalled forks by PARP1, CHD4, MLL3/4 and PTIP (Ding et al, 2016; Guillemette et al, 2015; Ray Chaudhuri et al, 2016; Schlacher et al, 2011; Schlacher et al, 2012). Our observations that WT, but not fork remodeling-defective, SMARCAL1 and ZRANB3 proteins cause replication stress-induced DSBs in BRCA1-deficient cells (Figure 6C–D) indicate that the remodeling of stalled forks by SMARCAL1 and ZRANB3 causes genomic instability in BRCA1-deficient cells.…”

Multifaceted Impact of MicroRNA 493-5p on Genome-Stabilizing Pathways Induces Platinum and PARP Inhibitor Resistance in BRCA2-Mutated Carcinomas

“…CHD4 (Guillemette et al, 2015), MRE11 (Ding et al, 2016; Schlacher et al, 2011), and EXO1 (Lemaç on et al, 2017) are factors that contribute to destabilizing the replication fork in BRCA2 mutant cells and are recruited/stabilized at the fork by PTIP (Ray Chaudhuri et al, 2016). It is worth noting that silencing PTIP causes resistance to olaparib and cisplatin in Kuramochi and OVSAHO cells at a scale comparable to the impact of miR-493-5p (Figure S4C).…”

“…Beyond their role in DSB repair via HRR, BRCA1 and BRCA2 occupy an important role in limiting access of nucleases (such as MRE11 ) to single-strand DNA at stalled replication forks, thereby leading to replication fork protection. Recently, loss of PTIP , CHD4 , and EZH2 have been identified as a mechanism of resistance in BRCA2 -deficient cells (Ding et al, 2016; Guillemette et al, 2015; Ray Chaudhuri et al, 2016; Rondinelli et al, 2017). Specifically, deficiency in PTIP and CHD4 impedes recruitment of MRE11 , thereby protecting stalled replication forks from nucleolytic degradation in BRCA2 mutant cells.…”

“…Identifying the mechanism of platinum and PARPi resistance in BRCA2 -mutated carcinomas has been a challenge as HRR is not restored in cells expressing mutant BRCA2 . However, few recent studies have revealed that BRCA2 mutant carcinomas might still develop platinum and PARPi resistance without restoration of HRR proficiency via a complex mechanism where stalled DNA replication fork is protected from degradation by nucleases by downregulation of proteins such as PTIP , CHD4 , or EZH2 (Guillemette et al, 2015; Lai et al, 2017; Patch et al, 2015; Ray Chaudhuri et al, 2016; Rondinelli et al, 2017). Importantly, it is not clear how these factors would be downregulated in BRCA2 mutant cancers.…”

Homology-Directed Repair and the Role of BRCA1, BRCA2, and Related Proteins in Genome Integrity and Cancer

“…In this scenario, nascent strand degradation is prevented by precluding the recruitment of MRE11 nuclease to stalled replication forks, which can be achieved by ablation of PTIP, MLL3/4, CHD4, and even PARP1 itself (Ding et al 2016, Guillemette et al 2015, Ray Chaudhuri et al 2016). Interestingly, HDR activity is not restored in these cases, indicating in the cell types tested that fork protection alone is sufficient to confer chemoresistance.…”