QMAT-seq: a novel CRISPR/Cas9 based assay for studying DNA-repair-associated mutations

Mutations are a root cause of cancer. In skin and lung cancers, they often result from exposure to environmental mutagens such as cigarette smoke or UV light. However, in other cancers, their causes remain unexplained. Restoration of DNA repair in mice with BRCA1 deficiency prevents tumour formation revealing that defective DNA repair contributes to cancer. The alternative non-homologous-end-joining (A-EJ) pathway has recently been discovered and has been shown to promote genome instability and therapy resistance in BRCA1-deficient cancers but only few components of the A-EJ pathway are known. In addition the causes of their activation remain elusive. Inhibition of A-EJ could be an effective therapy for cancers associated with DNA repair deficiency.

In pump-priming experiments that will establish proof of concept, I will develop a novel quantitative laboratory assay for A-EJ employing CRISPR/Cas9 genome editing, high-throughput sequencing and a machine learning algorithm. My long-term goal is to elucidate A-EJ regulation, to identify new members of the A-EJ pathway and to define its mutational footprints that will serve as a biomarker of DNA repair deficiency.

The outcomes of this seed funding will enable me to study A-EJ in cancer and its potential in cancer stratification and personalised therapy.