Targeting BRCA1/2-deficient cells and tumours with G-quadruplex-binding compounds

Heterozygous BRCA1 and BRCA2 mutations increase the risk of breast and ovarian cancers. Genome profiling studies revealed that 30% of all ovarian tumours and 16% of all breast tumours carry either BRCA1 or BRCA2 gene inactivation, in the form of germline or somatic mutations or BRCA1 promoter methylation. At the molecular level, BRCA1 and BRCA2 proteins play essential roles in DNA replication and double-strand break repair by homologous recombination. Consequently, loss of BRCA1 or BRCA2 function triggers replication arrest and accumulation of unrepaired DNA lesions. The project proposed here aims to exploit the hypersensitivity of BRCA1- and BRCA2-deficient cancers to G-quadruplex (G4)-binding compounds, in particular pyridostatin (Zimmer et al., 2016), for the development of novel, specific therapies.

To elucidate the mechanism of action of pyridostatin, innovative END-seq technology (Canela et al., 2016) will be applied to determine the genome-wide location of DNA double-strand breaks induced by pyridostatin in BRCA2-deficient cells. We will focus on those mapping to actively transcribed genes. Transcriptional deregulation of G4-containing genes has been proposed to mediate pyridostatin toxicity (Rodriguez et al., 2012). We will thus determine the transcription profiles of BRCA2-proficient and -deficient cells treated with pyridostatin using RNA-seq. This will allow identification of genes or gene networks affected by pyridostatin. Integration of gene expression profiles with DNA breaks location determined by END-seq, will enable isolation and characterization of the gene subset whose transcriptional deregulation promotes BRCA2-deficient cell killing by pyridostatin. Alterations in expression of these genes upon pyridostatin treatment will be subsequently monitored in xenograft tumours established in nude mice.