Investigating roles of the SWI/SNF complex subunits in genome stability, chromatin organisation, innate immune signalling and replication stress

Abstract

The alterations of the SWI/SNF chromatin remodelling complex subunits happen in 30% of malignancies. The exact mechanisms by which SWI/SNF alterations contribute to tumourigenesis are still not entirely clear. Here, I investigated the contribution of key SWI/SNF complex subunits to genome stability, chromatin organisation, innate immune signalling, and replication stress. First, we found that PBRM1 is required for the p53-dependent maintenance of the G2/M checkpoint after ionising radiation (IR). When PBRM1 is deficient, p53-dependent upregulation of p21 is delayed, leading to defective repression of DREAM complex target genes, uncontrolled G2/M progression, and increased micronucleated cell formation. The ruptured micronuclei are sensed by the innate immune cGAS-STING pathway, inducing higher interferon responsive gene expression when PBRM1 is deficient after IR. Our findings reinforce the role of PBRM1 loss as a driver mutation in the development of clear cell renal cell carcinoma (ccRCC). Notably, ccRCC frequently loses PBRM1 but rarely loses p53, therefore it is possible to target this defect in ccRCC. First, we found that PBRM1 is required for the p53-dependent maintenance of the G2/M checkpoint. Second, we found that there is aberrant expression of genes involved in the (peri)centromere maintenance when PBRM1 is deficient. Preliminary FISH results showed greater centromere sizes with PBRM1 deficiency, suggesting a less compacted centromere organisation. Consistently, a subset of centromeric satellites is transcriptionally misregulated when PBRM1 is deficient. These RNA transcripts from repetitive elements are capable to activate dsRNA sensing innate immune pathway, and we found evidence of upregulated immune signalling gene sets when PBRM1 is deficient. Further work is required to determine whether this transcriptional misregulation directly impacts on immune signalling. Third, evidence suggests the ATPase subunit SMARCA4 is recruited to the collapsed replication forks and has roles during replication stress. We mapped the exact genomic locations of the DNA double strand breakends with or without replication stress in the isogenic parental and SMARCA4 KO cells. We have analysed the sequence composition, genomic locations and associated chromatin environment of the breakends under different contexts in order to provide additional insights into the contribution of the SWI/SNF complexes to replication stress responses.