Interrogating DNA replication stress and DNA damage responses via phenotypic and functional CRISPR/Cas9 screens

DNA double-strand breaks are believed to be one of the most cytotoxic DNA lesions, posing a constant threat for genome integrity and cell survival. Consequently, various DNA repair processes and pathways have evolved to deal with different DNA lesions and ensure genome stability. The tumour suppressor ATM is one of the apical kinases in the DNA damage response (DDR), occupying a key position in the DNA damage response network to regulate signalling responses and repair processes upon DNA damage. Disruption of the ATM gene sensitises cells to DNA damage-inducing chemotherapeutics. To identify genetic suppressors of this hypersensitivity, we performed a genome-wide CRISPR/Cas9 screen in ATM-deficient cells treated with the topoisomerase I poison topotecan. This dissertation describes two distinct resistance mechanisms in Atm-/- cells towards TOP1 inhibitors, resulting from the inactivation of the non-homologous end-joining (NHEJ) machinery or alternatively the absence of the BRCA1-A complex. Accordingly, I establish that the catalytic activity of DNA ligase 4 (LIG4) is crucial for topotecan toxicity in Atm-/- cells and mutating the catalytic site of Lig4 reinstates cellular survival of ATM-deficient cells in the presence of topotecan. In contrast, the absence of the BRCA1-A complex increases DNA end-resection kinetics, a pivotal initial step during homologous recombination-mediated repair of DNA double strand breaks. Moreover, I show that the accurate repair of topotecan-induced DNA damage occurs via homologous recombination, and in this context ATM prevents toxic end- joining of broken replication forks. Inactivation of NHEJ or increased end-resection in the absence of BRCA1-A supresses toxic end-joining, thus enabling cellular survival in the presence of topotecan. Additionally I describe that the end-resection defect of BRCA1- deficient cells can be counteracted by the inactivation of genes encoding the SHIELDIN complex, which causes resistance of BRCA1-mutant cells to PARP inhibitors. Lastly, I conceptualised and performed functional genome-wide CRISPR/Cas9 screens, utilising the chromatinisation of RPA as a read-out for DNA repair processes, to identify novel factors involved in the DNA damage response. Based on these screens, I provide evidence for the deubiquitinating enzyme USP37 regulating RPA loading and DNA repair during DNA replication.

Name dc:type.qualificationname

Doctor of Philosophy (PhD)

Level dc:type.qualificationlevel

Doctoral

Grantor dc:publisher.institution

University of Cambridge

Year dc:date.issued

2021

Author dc:creator

• Pilger, Domenic

Advisor dc:contributor.advisor

• Jackson, Stephen

• DNA repair

Licence

• https://apollo8-f-pro.lib.cam.ac.uk/bitstreams/6a92ed83-98fb-404e-bc6b-36bf78bb0ea1/download
• http://purl.org/NET/rdflicense/allrightsreserved

Language dc:language

eng

Author Identifier

0000-0001-7339-0685
0000-0001-9317-7937

OAI identifier oai:identifier

oai:www.repository.cam.ac.uk:1810/335063