MRC DiMeN Doctoral Training Partnership: Investigating the role of chromatin remodelling in resolution of oncogene-induced transcription-replication conflicts: Mechanism and Implications for Cancer Therapy

Cancer is a disease driven by uncontrollable cell proliferation. Activation of oncogenes induces abnormal gene expression, enabling cells to evade growth suppressors and escape cell cycle controls resulting in unlimited cell duplication and oncogenesis.

While oncogenic transcription is essential for cancer cell proliferation it is also conducive to genomic instability. Dysregulated transcription in cancers, induced by oncogenes and hormones, leads to the formation of extensive hybrids formed between newly synthesized RNA and template DNA, known as R-loops. R-loops play important roles in different biological pathways, however, unless resolved, they can be highly genotoxic. Persistent R-loops can trigger transcription-replication conflicts, leading to replication stress and DNA damage. Paradoxically, cancer cells proliferate under these inherently genotoxic conditions, strongly suggesting that resolving R-loops is critical for cancer progression. Nevertheless, the mechanisms counteracting transcription-replication conflicts in cancer remain largely unknown. This knowledge gap will be investigated in this project.

Eukaryotic chromosomal DNA is organized into the tightly compacted yet highly dynamic chromatin nucleoprotein structure. Chromatin remodelling factors shape the epigenetic landscape of the eukaryotic genome and control transcription and replication. Epigenetic regulation by chromatin plays an important role in oncogene-mediated gene expression and cancer cell proliferation. However, its role in cancer remains poorly understood. Our work has revealed a novel mechanism of R-loop resolution by chromatin remodelling essential for DNA replication and cancer cell proliferation (Prendergast et al., Nature Communications 2020).

Objectives

This project will test the exciting hypothesis that chromatin regulation of R-loops enables unremitting oncogene-driven transcription and coordinates it with replication. Our goal is to illuminate and characterize novel regulatory mechanisms of R-loops that suppress genomic instability and promote cancer cell proliferation. As resistance to radiation treatment is associated with increased replication stress, the potential synergy between inhibition of transcription-replication conflict resolution and radiotherapy will also be investigated. Specifically, using human cancer cells, this project will:

1.        Characterize how chromatin promotes R-loop resolution.

2.        Characterize the role of R-loop resolution in oncogenic transcription and coordination with DNA replication.

3.        Determine the functional role of chromatin-dependent R-loop-resolution in response to radiotherapy.

Impact and training

This cross-cutting project involves a powerful combination of genomics and single-cell imaging, together with advanced bioinformatics and molecular and cellular biology methods already established in our labs.  State-of-the art genome-wide and transcriptomics assays, cutting-edge super-resolution microscopy, unique radiotherapy resources (x-rays, plus proton beam therapy at the Clatterbridge Cancer Centre) and appropriate radiobiological assays will form an orthogonal approach that will allow us to dissect the mechanisms of R-loop resolution by chromatin and interrogate their biological relevance and impact to radioresistance.

The DTP student will benefit by the complementary and strong multidisciplinary expertise of Dr Papamichos-Chronakis in genome biology and chromatin (https://www.liverpool.ac.uk/systems-molecular-and-integrative-biology/staff/manolis-papamichos-chronakis/), Dr Parsons in radiobiology and cancer biology (https://www.liverpool.ac.uk/systems-molecular-and-integrative-biology/staff/jason-parsons/) and Dr Rico in epigenomics and big data analysis (https://www.ncl.ac.uk/medical-sciences/people/profile/danielrico.html).

This integrative approach will provide transformational insight into essential mechanisms for cell homeostasis, improve our understanding of how their dysregulation enables cancer cell proliferation, and help identify novel factors that can be targeted in cancer therapy.

Benefits of being in the DiMeN DTP:

This project is part of the Discovery Medicine North Doctoral Training Partnership (DiMeN DTP), a diverse community of PhD students across the North of England researching the major health problems facing the world today. Our partner institutions (Universities of Leeds, Liverpool, Newcastle, York and Sheffield) are internationally recognised as centres of research excellence and can offer you access to state-of the-art facilities to deliver high impact research.

We are very proud of our student-centred ethos and committed to supporting you throughout your PhD. As part of the DTP, we offer bespoke training in key skills sought after in early career researchers, as well as opportunities to broaden your career horizons in a range of non-academic sectors.

Being funded by the MRC means you can access additional funding for research placements, international training opportunities or internships in science policy, science communication and beyond. See how our current DiMeN students have benefited from this funding here: http://www.dimen.org.uk/overview/student-profiles/flexible-supplement-awards

Further information on the programme and how to apply can be found on our website:

http://www.dimen.org.uk/how-to-apply/application-overview