MRC DiMeN Doctoral Training Partnership: Regulation of transcription replication conflicts in cancer: mechanism and functional implications in acute myeloid leukemia

Description

This project focuses on the emerging field of transcription-replication conflicts (TRCs) in cancer.

In cancer cells, oncogenic transcription is essential for unrestricted cancer cell proliferation, yet it also causes genomic instability during DNA synthesis. Transcription interference with the replication fork induces replication stress, manifested as defective DNA synthesis, increased DNA damage and loss of important epigenetic information. Cancer cells have evolved mechanisms counteracting replication stress, allowing them to grow and develop resistance to treatments. Oncogenic transcription can cause TRCs by inducing R-loops. R-loops are RNA-DNA hybrid structures formed when newly synthesized RNA anneals to the template DNA, displacing complement DNA. When not resolved, R-loops can interfere with the replication fork causing replication stress and impeding cancer cell proliferation. Nevertheless, our understanding of how R-loops are counteracted in cancer is limited. This knowledge gap will be addressed in this project.

We demonstrated that the ATP-dependent chromatin remodelling INO80 complex promotes R-loop resolution, suppressing replication stress and maintaining proliferation and viability of cancer cells (Prendergast et al., Nature Communications 2020). This indicates that chromatin regulation plays an important, yet unclear role in protecting the genome from genotoxic R-loops.

Here, we will investigate the molecular mechanisms resolving R-loops to prevent transcription-replication conflicts and investigate their role and functional implications in a cancer of great unmet need, acute myeloid leukemia (AML).

AML is an aggressive blood and bone marrow cancer characterized by abnormal proliferation and differentiation of myeloid cells. Despite extensive research, poor understanding of AML pathology has impeded the development of effective treatments, resulting in dismal survival rates. Evidence suggests that R-loop resolution plays a critical role in AML, however the mechanisms remain poorly understood.

The goal of this project is to characterize novel regulatory pathways that counteract TRCs and maintain genome stability in AML. Using established AML cell lines and cancer cells from patients with AML, we will test the exciting hypothesis that R-loop resolution enables continuous oncogene-driven transcription to coordinate with replication, thereby preventing DNA damage and promoting AML growth.

Experimental Approach

This is a cross-cutting collaboration between a Chromatin (Dr Papamichos-Chronakis), an AML Biology (Prof David MacEwan), and a Computational Biology (Dr Aditi Kanhere) team. We will utilize lentiviral shRNA and CRISPR technologies to deplete factors and investigate their mechanisms. Employing a powerful combination of state-of-the-art and innovative genomics, transcriptomics and super-resolution microscopy technologies together with reporter-assays and advanced bioinformatics analysis in well-characterised AML cell lines and primary patient cells, this study will provide insight into the role and mechanism of resolution of transcription-replication conflicts in AML.

Novelty and Impact

Conflicts between transcription and replication have emerged as critical vulnerabilities in cancer cells. Understanding the mechanisms promoting TRC resolution and response to replication stress, a hallmark of cancer cells, will provide a deeper understanding of AML pathogenesis and cancer cell proliferation. Dissecting the molecular pathways for R-loop resolution and transcription-replication conflicts forms a rational, innovative and promising approach for identifying targets for new therapeutic intervention. Elucidating how AML cells counteract genotoxic conflicts between transcription and replication will pave the way for urgently-needed more effective treatments for the disease.

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, training opportunities or internships in science policy, science communication and beyond. Further information on the programme and how to apply can be found on our website:

https://www.dimen.org.uk/