Targeting DNA repair to overcome cancer therapy resistance

THE PROJECT
DNA cross-linking drugs and radiotherapy (RT) are used to treat a range of tumours including many hard-to-treat cancers (e.g. pancreas, oesophageal, lung) for which survival rates remain low. DNA repair pathways counteract the cancer-killing effects of crosslinking drugs and RT, by removing the toxic DNA damage they produce. Consequently, resistance to these therapies remains a major problem, often limiting their effective use.

The XPF-ERCC1 nuclease is critical to a number of DNA repair pathways including DNA crosslink and double-strand break repair. Therefore, inhibition of XPF-ERCC1 will effectively stall the repair of the DNA damage induced by crosslinking drugs and RT, making it attractive drug target. In our previous studies we have explored how the activity of XPF-ERCC1 is controlled by accessory proteins such as replication protein A (RPA) and SLX4. SLX4 is known to act as a ‘scaffold’ protein recruiting XPF-ERCC1 to the sites of damage, and both RPA and SLX4 have dramatic effects on the activity of XPF-ERCC1. In this studentship, we would like to identify the molecular mechanism of the regulation of XPF-ERCC1 activity by RPA and SLX4. We will solve the structure of human XPF-ERCC1 in complex with SLX4 and RPA bound to the DNA substrates modelling damaged replication forks. We will use a number of complementary approaches to achieve this including cryo-electron microscopy, X-ray crystallography and SAXS. This detailed analysis of the structure of XPF-ERCC1 bound to its key regulatory partners will reveal structural elements that are essential for DNA substrate recognition and will identify the key residues mediating the interaction between XPF-ERCC1 and accessory proteins. Armed with this information we will use cell-based approaches to confirm the importance of interactions and repair complex architecture identified in vivo. The structural information will also be used to guide the design of small molecule inhibitors that can be used in combination with chemotherapeutic agents and radiation with the aim of increasing the potency of existing anti-cancer treatments.

THE TRAINING
Training in protein purification and analysis, structural biology (X-ray crystallography and cryo-Electron Microscopy), biochemistry, cell biology, genome editing and developing cellular models of cancer treatment.

PUBLICATIONS
Abdullah UB, McGouran JF, Brolih S, Ptchelkine D, El-Sagheer AH, Brown T, and McHugh PJ. RPA activates the XPF-ERCC1 endonuclease to initiate processing of DNA interstrand crosslinks. EMBO J, 2017, 14;36(14):2047-2060.

Wang AT, Sengerová B, Cattell E, Inagawa T, Hartley JM, Kiakos K, Burgess-Brown N, Enzlin JH, Schofield CJ, Gileadi O, Hartley JA, McHugh PJ. Human SNM1A and XPF-ERCC1 collaborate to initiate DNA interstrand cross-link repair. Genes and Development 2011; 25 (17):1859-70.

De Silva IU, McHugh PJ, Clingen PH, Hartley JA. Defining the roles of nucleotide excision repair and recombination in the repair of DNA interstrand cross-links in mammalian cells. Mol Cell Biol. 2000; 20(21): 7980-90