Molecular characterisation of hypoxia-induced R-loops
About the research:
Most solid tumours include cells which experience insufficient oxygen (hypoxia). Tumour hypoxia plays critical roles in tumourigenesis and therapy response. Studies in multiple tumour types have shown that hypoxic tumours are more aggressive, harder to treat and negatively impact patient prognosis. Therefore, there is an urgent need to understand the biological response to hypoxia and use this knowledge to develop novel therapeutic approaches. We have demonstrated that at the levels of hypoxia most associated with therapy resistance, the DNA damage response is also initiated and is characterised by replication stress and an abundance of single stranded DNA. Further work has shown that this single stranded DNA occurs at both stalled replication forks as well as R-loops. R-loops are formed during transcription when DNA hybridises with RNA to leave a single stranded DNA loop. Our hypothesis is that these regions of single stranded DNA offer a unique vulnerability which could be exploited to target hypoxic cancer cells. The accumulation of R-loops, in hypoxia was somewhat surprising as transcription rates are extremely low in these conditions. Moreover, we found that an RNA/DNA helicase with key roles in R-loop resolution, senataxin, was induced in hypoxia through a unique mechanism. To build on these studies we plan to ask a series of simple but informative questions including using sequencing based techniques to determine where in the genome R-loops occur in hypoxic conditions. Knowing where the R-loops accumulate in hypoxia will provide insight into how they form and could also identify potential therapeutic targets, for example molecules which if inhibited lead to DNA breaks in the single stranded DNA. Our goal is to increase DNA damage in hypoxic cancer cells as this should lead to increased sensitivity to both radio and immunotherapy.
Training in the Hammond lab ensures a cross-disciplinary and collaborative research experience. We have strong collaborations with chemists, bioinformaticians, imaging scientists and mathematicians which deliver publications and joint funding. We regularly reach out to local experts who can assist us with specific techniques, and this has included students visiting these labs to receive training and/or carry out specific experiments. Students usually attend at least one national and one international conference during their DPhil and present at local meetings. Lab meetings are held weekly and include work in progress sessions, journal club and presentations from individuals. In addition, Prof Hammond meets with her students 1-to-1 at least once every two weeks. Students will receive training in cell and molecular biology including tissue culture, western blotting, gene expression studies (qPCR/RNA-seq), confocal microscopy and assays critical to pre-clinical studies.
Replication catastrophe induced by cyclic hypoxia leads to increased APOBEC3B activity. Bader SB, Ma TS, Simpson CJ, Liang J, Maezono SEB, Olcina MM, Buffa FM, Hammond EM. Nucleic Acids Res. 2021 Jul 21;49(13):7492-7506.
Hypoxia-induced SETX links replication stress with the unfolded protein response. Ramachandran S, Ma TS, Griffin J, Ng N, Foskolou IP, Hwang MS, Victori P, Cheng WC, Buffa FM, Leszczynska KB, El-Khamisy SF, Gromak N, Hammond EM. Nat Commun. 2021 Jun 17;12(1):3686.
Links between the unfolded protein response and the DNA damage response in hypoxia: a systematic review. Bolland H, Ma TS, Ramlee S, Ramadan K, Hammond EM. Biochem Soc Trans. 2021 Jun 30;49(3):1251-1263.