DNA double-strand break repair equilibrium in tumour suppression and oncogenesis

Project Overview

DNA double-strand breaks (DSBs) are highly toxic and must usually be accurately repaired to counteract the threat of oncogenic mutations. However, some specialist tissues actually rely on mutagenic DSB repair as a means by which genetic material can be transferred between loci to create genetic diversity. To cope with this intrinsic discrepancy in desired DNA repair outcome between different tissues and cellular contexts, higher organisms have complex regulatory systems that maintain an appropriate equilibrium between competing DNA repair pathways and ensure DSBs are appropriately resolved. Failures in these systems are known to trigger and drive the evolution of both common hereditary cancer, and also spontaneously occurring tumours. Defective DSB repair also contributes to the pathologies of numerous monogenic syndromes such as Ataxia Telangiectasia, Nijmegen Breakage Syndrome, and Severe Combined Immunodeficiency (SCID), whose pathologies include developmental defects, infertility, immunodeficiency and cancer predisposition. 

Recent work from our laboratory has helped identify molecular defects that lead to imbalances in the usage of accurate and mutagenic DSB repair pathways, and shown these abnormalities link the DNA repair mechanisms responsible for creating genetic diversity in the adaptive immune system, to those that cause common human cancers. Specifically, a specialised branch of the non-homologous end joining (NHEJ) DSB repair pathway that is vital for mediating antibody gene rearrangements in lymphocytes, is additionally responsible for the genomic instability that triggers tumourigenesis in patients harbouring mutations in the BRCA breast and ovarian cancer tumour suppressor genes. Moreover, we have also shown that the repair activities of this branch of the NHEJ pathway can be harnessed in therapeutic treatment regimes to selectively kill cancer cells.

The aim of this project is to define the molecular mechanisms that regulate the choice between the accurate and mutagenic DNA repair pathways, and determine their contributions to adaptive immune system function, tumour suppression and oncogenesis. This will involve research to gain a mechanistic understanding of the 53BP1-dependent NHEJ pathway and its downstream protein components (see references below for examples of recent research from the laboratory in this area, including: Ghezraoui et al. Nature, 2018). Complementary experiments may aim to identify the precise molecular events in the 53BP1 pathway that are antagonised by the BRCA1-BARD1 complex to allow for accurate DSB repair by the homologous recombination pathway. This research will therefore help identify the molecular mechanisms that drive genomic instability and trigger tumourigenesis in BRCA1 mutation-associated homologous recombination-deficient cancers, and allow for the selective killing of BRCA1 mutant tumours using targeted therapeutics.

Funding: Research in the Chapman lab is supported by grants from Cancer Research UK, the Wellcome Trust, the Medical Research Council, and the European Commission via Horizon 2020.

Training Opportunities

The successful applicant will receive training in a wide range of modern molecular biology, biochemistry and cell biology techniques. Experimental approaches are likely to include protein interaction studies, mutational protein analyses, routine CRISPR-Cas9 cell-line engineering, and developing and analysing in vivo models to study the impact of DNA repair mechanisms and/or deficits in mammalian physiology and cancer. 

Housed at the WellcomCentre for Human Genetics, the candidate will profit from state-of-the-art core facilities that include high-throughput genomics (Next Generation and single-cell sequencing), bioinformatics, transgenics, conventional and super-resolution microscopy. The candidate will also benefit from the complementary work of other teams working in the institute, and interactions with the active genome stability community across the university.

It is expected that the applicant will also gain a broad range of other skills during the course of the project. This includes time and project management, supervision of junior staff members, use of scientific web resources, and scientific writing and reviewing. There will also be opportunities to travel to international conferences to present results obtained during the project.

Theme

Cancer Biology and Immunology & Infectious Disease

Admissions

Project reference number: 658

Funding and admissions information

Supervisors

Name Department Institution Country Email
Dr Ross Chapman Wellcome Trust Centre for Human Genetics Oxford University, Henry Wellcome Building of Genomic Medicine GBR ross.chapman@well.ox.ac.uk
Professor Richard J Cornall FMedSci FRCP Centre for Cellular and Molecular Physiology Oxford University, Henry Wellcome Building for Molecular Physiology GBR richard.cornall@ndm.ox.ac.uk

Ghezraoui H, Oliveira C, Becker JR, Bilham K, Moralli D, Anzilotti C, Fischer R, Deobagkar-Lele M, Sanchiz-Calvo M, Fueyo-Marcos E, Bonham S, Kessler BM, Rottenberg S, Cornall RJ, Green CM, Chapman JR. 2018. 53BP1 cooperation with the REV7-shieldin complex underpins DNA structure-specific NHEJ. Nature, 560 (7716), pp. 122-127. Read abstract | Read more

53BP1 governs a specialized, context-specific branch of the classical non-homologous end joining DNA double-strand break repair pathway. Mice lacking 53bp1 (also known as Trp53bp1) are immunodeficient owing to a complete loss of immunoglobulin class-switch recombination, and reduced fidelity of long-range V(D)J recombination. The 53BP1-dependent pathway is also responsible for pathological joining events at dysfunctional telomeres, and its unrestricted activity in Brca1-deficient cellular and tumour models causes genomic instability and oncogenesis. Cells that lack core non-homologous end joining proteins are profoundly radiosensitive, unlike 53BP1-deficient cells, which suggests that 53BP1 and its co-factors act on specific DNA substrates. Here we show that 53BP1 cooperates with its downstream effector protein REV7 to promote non-homologous end joining during class-switch recombination, but REV7 is not required for 53BP1-dependent V(D)J recombination. We identify shieldin-a four-subunit putative single-stranded DNA-binding complex comprising REV7, c20orf196 (SHLD1), FAM35A (SHLD2) and FLJ26957 (SHLD3)-as the factor that explains this specificity. Shieldin is essential for REV7-dependent DNA end-protection and non-homologous end joining during class-switch recombination, and supports toxic non-homologous end joining in Brca1-deficient cells, yet is dispensable for REV7-dependent interstrand cross-link repair. The 53BP1 pathway therefore comprises distinct double-strand break repair activities within chromatin and single-stranded DNA compartments, which explains both the immunological differences between 53bp1- and Rev7- deficient mice and the context specificity of the pathway. Hide abstract

Cuella-Martin R, Oliveira C, Lockstone HE, Snellenberg S, Grolmusova N, Chapman JR. 2016. 53BP1 Integrates DNA Repair and p53-Dependent Cell Fate Decisions via Distinct Mechanisms. Mol. Cell, 64 (1), pp. 51-64. Read abstract | Read more

The tumor suppressor protein 53BP1, a pivotal regulator of DNA double-strand break (DSB) repair, was first identified as a p53-interacting protein over two decades ago. However, its direct contributions to p53-dependent cellular activities remain undefined. Here, we reveal that 53BP1 stimulates genome-wide p53-dependent gene transactivation and repression events in response to ionizing radiation (IR) and synthetic p53 activation. 53BP1-dependent p53 modulation requires both auto-oligomerization and tandem-BRCT domain-mediated bivalent interactions with p53 and the ubiquitin-specific protease USP28. Loss of these activities results in inefficient p53-dependent cell-cycle checkpoint and exit responses. Furthermore, we demonstrate 53BP1-USP28 cooperation to be essential for normal p53-promoter element interactions and gene transactivation-associated events, yet dispensable for 53BP1-dependent DSB repair regulation. Collectively, our data provide a mechanistic explanation for 53BP1-p53 cooperation in controlling anti-tumorigenic cell-fate decisions and reveal these activities to be distinct and separable from 53BP1's regulation of DNA double-strand break repair pathway choice. Hide abstract

Barazas M, Annunziato S, Pettitt SJ, de Krijger I, Ghezraoui H, Roobol SJ, Lutz C, Frankum J, Song FF, Brough R, Evers B, Gogola E, Bhin J, van de Ven M, van Gent DC, Jacobs JJL, Chapman R, Lord CJ, Jonkers J, Rottenberg S. 2018. The CST Complex Mediates End Protection at Double-Strand Breaks and Promotes PARP Inhibitor Sensitivity in BRCA1-Deficient Cells. Cell Rep, 23 (7), pp. 2107-2118. Read abstract | Read more

Selective elimination of BRCA1-deficient cells by inhibitors of poly(ADP-ribose) polymerase (PARP) is a prime example of the concept of synthetic lethality in cancer therapy. This interaction is counteracted by the restoration of BRCA1-independent homologous recombination through loss of factors such as 53BP1, RIF1, and REV7/MAD2L2, which inhibit end resection of DNA double-strand breaks (DSBs). To identify additional factors involved in this process, we performed CRISPR/SpCas9-based loss-of-function screens and selected for factors that confer PARP inhibitor (PARPi) resistance in BRCA1-deficient cells. Loss of members of the CTC1-STN1-TEN1 (CST) complex were found to cause PARPi resistance in BRCA1-deficient cells in vitro and in vivo. We show that CTC1 depletion results in the restoration of end resection and that the CST complex may act downstream of 53BP1/RIF1. These data suggest that, in addition to its role in protecting telomeres, the CST complex also contributes to protecting DSBs from end resection. Hide abstract

Xu G, Chapman JR, Brandsma I, Yuan J, Mistrik M, Bouwman P, Bartkova J, Gogola E, Warmerdam D, Barazas M, Jaspers JE, Watanabe K, Pieterse M, Kersbergen A, Sol W, Celie PH, Schouten PC, van den Broek B, Salman A, Nieuwland M, de Rink I, de Ronde J, Jalink K, Boulton SJ, Chen J, van Gent DC, Bartek J, Jonkers J, Borst P, Rottenberg S. 2015. REV7 counteracts DNA double-strand break resection and affects PARP inhibition. Nature, 521 (7553), pp. 541-4. Read abstract | Read more

Error-free repair of DNA double-strand breaks (DSBs) is achieved by homologous recombination (HR), and BRCA1 is an important factor for this repair pathway. In the absence of BRCA1-mediated HR, the administration of PARP inhibitors induces synthetic lethality of tumour cells of patients with breast or ovarian cancers. Despite the benefit of this tailored therapy, drug resistance can occur by HR restoration. Genetic reversion of BRCA1-inactivating mutations can be the underlying mechanism of drug resistance, but this does not explain resistance in all cases. In particular, little is known about BRCA1-independent restoration of HR. Here we show that loss of REV7 (also known as MAD2L2) in mouse and human cell lines re-establishes CTIP-dependent end resection of DSBs in BRCA1-deficient cells, leading to HR restoration and PARP inhibitor resistance, which is reversed by ATM kinase inhibition. REV7 is recruited to DSBs in a manner dependent on the H2AX-MDC1-RNF8-RNF168-53BP1 chromatin pathway, and seems to block HR and promote end joining in addition to its regulatory role in DNA damage tolerance. Finally, we establish that REV7 blocks DSB resection to promote non-homologous end-joining during immunoglobulin class switch recombination. Our results reveal an unexpected crucial function of REV7 downstream of 53BP1 in coordinating pathological DSB repair pathway choices in BRCA1-deficient cells. Hide abstract

Chapman JR, Barral P, Vannier JB, Borel V, Steger M, Tomas-Loba A, Sartori AA, Adams IR, Batista FD, Boulton SJ. 2013. RIF1 is essential for 53BP1-dependent nonhomologous end joining and suppression of DNA double-strand break resection. Mol. Cell, 49 (5), pp. 858-71. Read abstract | Read more

The appropriate execution of DNA double-strand break (DSB) repair is critical for genome stability and tumor avoidance. 53BP1 and BRCA1 directly influence DSB repair pathway choice by regulating 5' end resection, but how this is achieved remains uncertain. Here we report that Rif1(-/-) mice are severely compromised for 53BP1-dependent class switch recombination (CSR) and fusion of dysfunctional telomeres. The inappropriate accumulation of RIF1 at DSBs in S phase is antagonized by BRCA1, and deletion of Rif1 suppresses toxic nonhomologous end joining (NHEJ) induced by PARP inhibition in Brca1-deficient cells. Mechanistically, RIF1 is recruited to DSBs via the N-terminal phospho-SQ/TQ domain of 53BP1, and DSBs generated by ionizing radiation or during CSR are hyperresected in the absence of RIF1. Thus, RIF1 and 53BP1 cooperate to block DSB resection to promote NHEJ in G1, which is antagonized by BRCA1 in S phase to ensure a switch of DSB repair mode to homologous recombination. Hide abstract

Chapman JR, Taylor MR, Boulton SJ. 2012. Playing the end game: DNA double-strand break repair pathway choice. Mol. Cell, 47 (4), pp. 497-510. Read abstract | Read more

DNA double-strand breaks (DSBs) are highly toxic lesions that can drive genetic instability. To preserve genome integrity, organisms have evolved several DSB repair mechanisms, of which nonhomologous end-joining (NHEJ) and homologous recombination (HR) represent the two most prominent. It has recently become apparent that multiple layers of regulation exist to ensure these repair pathways are accurate and restricted to the appropriate cellular contexts. Such regulation is crucial, as failure to properly execute DSB repair is known to accelerate tumorigenesis and is associated with several human genetic syndromes. Here, we review recent insights into the mechanisms that influence the choice between competing DSB repair pathways, how this is regulated during the cell cycle, and how imbalances in this equilibrium result in genome instability. Hide abstract

Chapman JR, Sossick AJ, Boulton SJ, Jackson SP. 2012. BRCA1-associated exclusion of 53BP1 from DNA damage sites underlies temporal control of DNA repair. J. Cell. Sci., 125 (Pt 15), pp. 3529-34. Read abstract | Read more

Following irradiation, numerous DNA-damage-responsive proteins rapidly redistribute into microscopically visible subnuclear aggregates, termed ionising-radiation-induced foci (IRIF). How the enrichment of proteins on damaged chromatin actually relates to DNA repair remains unclear. Here, we use super-resolution microscopy to examine the spatial distribution of BRCA1 and 53BP1 proteins within single IRIF at subdiffraction-limit resolution, yielding an unprecedented increase in detail that was not previously apparent by conventional microscopy. Consistent with a role for 53BP1 in promoting DNA double-strand break repair by non-homologous end joining, 53BP1 enrichment in IRIF is most prominent in the G0/G1 cell cycle phases, where it is enriched in dense globular structures. By contrast, as cells transition through S phase, the recruitment of BRCA1 into the core of IRIF is associated with an exclusion of 53BP1 to the focal periphery, leading to an overall reduction of 53BP1 occupancy at DNA damage sites. Our data suggest that the BRCA1-associated IRIF core corresponds to chromatin regions associated with repair by homologous recombination, and the enrichment of BRCA1 in IRIF represents a temporal switch in the DNA repair program. We propose that BRCA1 antagonises 53BP1-dependent DNA repair in S phase by inhibiting its interaction with chromatin proximal to damage sites. Furthermore, the genomic instability exhibited by BRCA1-deficient cells might result from a failure to efficiently exclude 53BP1 from such regions during S phase. Hide abstract

Lloyd J, Chapman JR, Clapperton JA, Haire LF, Hartsuiker E, Li J, Carr AM, Jackson SP, Smerdon SJ. 2009. A supramodular FHA/BRCT-repeat architecture mediates Nbs1 adaptor function in response to DNA damage. Cell, 139 (1), pp. 100-11. Read abstract | Read more

The Mre11/Rad50/Nbs1 protein complex plays central enzymatic and signaling roles in the DNA-damage response. Nuclease (Mre11) and scaffolding (Rad50) components of MRN have been extensively characterized, but the molecular basis of Nbs1 function has remained elusive. Here, we present a 2.3A crystal structure of the N-terminal region of fission yeast Nbs1, revealing an unusual but conserved architecture in which the FHA- and BRCT-repeat domains structurally coalesce. We demonstrate that diphosphorylated pSer-Asp-pThr-Asp motifs, recently identified as multicopy docking sites within Mdc1, are evolutionarily conserved Nbs1 binding targets. Furthermore, we show that similar phosphomotifs within Ctp1, the fission yeast ortholog of human CtIP, promote interactions with the Nbs1 FHA domain that are necessary for Ctp1-dependent resistance to DNA damage. Finally, we establish that human Nbs1 interactions with Mdc1 occur through both its FHA- and BRCT-repeat domains, suggesting how their structural and functional interdependence underpins Nbs1 adaptor functions in the DNA-damage response. Hide abstract

Kolas NK, Chapman JR, Nakada S, Ylanko J, Chahwan R, Sweeney FD, Panier S, Mendez M, Wildenhain J, Thomson TM, Pelletier L, Jackson SP, Durocher D. 2007. Orchestration of the DNA-damage response by the RNF8 ubiquitin ligase. Science, 318 (5856), pp. 1637-40. Read abstract | Read more

Cells respond to DNA double-strand breaks by recruiting factors such as the DNA-damage mediator protein MDC1, the p53-binding protein 1 (53BP1), and the breast cancer susceptibility protein BRCA1 to sites of damaged DNA. Here, we reveal that the ubiquitin ligase RNF8 mediates ubiquitin conjugation and 53BP1 and BRCA1 focal accumulation at sites of DNA lesions. Moreover, we establish that MDC1 recruits RNF8 through phosphodependent interactions between the RNF8 forkhead-associated domain and motifs in MDC1 that are phosphorylated by the DNA-damage activated protein kinase ataxia telangiectasia mutated (ATM). We also show that depletion of the E2 enzyme UBC13 impairs 53BP1 recruitment to sites of damage, which suggests that it cooperates with RNF8. Finally, we reveal that RNF8 promotes the G2/M DNA damage checkpoint and resistance to ionizing radiation. These results demonstrate how the DNA-damage response is orchestrated by ATM-dependent phosphorylation of MDC1 and RNF8-mediated ubiquitination. Hide abstract