Quantifying the impact of DNA repair dysregulation on intrinsic radiation sensitivity

Abstract

Variations in individual radiosensitivity are a key determinant of radiotherapy outcomes. However, treatments are not currently biologically optimised to consider the impact of individual genetics. Radiosensitivity models which effectively predict individual responses could be used to deliver more personalised treatments and improve patient outcomes. To develop robust radiosensitivity models, it is essential to understand in detail the impact of genetic alterations in DNA damage response pathways. DNA repair is a key component of the DNA damage response, and although the dysregulation of double strand break (DSB) repair pathways is known to impact radiosensitivity, the impact of single strand break (SSB) repair pathway disruption remains relatively underexplored. This work aimed to quantify the impact of SSB repair pathway dysregulation on intrinsic radiosensitivity, to determine if these pathways are important to consider for individual radiosensitivity model development. Cell line models deficient in each of the three SSB repair pathways, base excision repair (BER), nucleotide excision repair (NER) and mismatch repair (MMR), were generated using CRISPR-Cas9 gene editing to knock out key pathway genes in RPE-1 cells. The impact of gene loss on radiosensitivity was quantified through clonogenic survival analysis, and the mechanisms underpinning any observed sensitivities were explored by measuring the effects on cell cycle distribution and DNA damage (both DSB and non-DSB) following irradiation. The involvement of these pathways across different radiation qualities was quantified by measuring responses to X-rays, carbon ions, and alpha-particles. Finally, a targeted CRISPR radiosensitivity screen was performed to explore interactions between BER pathway genes and other DDR genes. Disruption of the BER and NER pathways resulted in small but statistically significant increases in X-ray radiosensitivity, which were linked to higher DSB yields due to delayed repair of non-DSB damages, as well as higher levels of unrepaired DSBs. As radiation quality increased, the loss of any SSB repair pathway resulted in a significant increase in radiosensitivity, which was associated with higher levels of persistent DSB damage. The CRISPR screen identified a small number of interactions between the BER genes PARP1 and XRCC1 and other DDR genes, highlighting pathway interactions which may be important to consider in future modelling. Overall, this work has demonstrated that the dysregulation of SSB repair pathways impacts cellular radiosensitivity. Although the observed effects were relatively small compared to DSB repair disruption, mutations in SSB repair pathways are common meaning the cumulative effect may be clinically relevant and important to consider for individual radiosensitivity models. Thesis embargoed until 31st December 2030