Chromosome Integrity
RESEARCH SUMMARY
The aim of the Chromosome Integrity Group is to understand how genome stability is maintained in response to DNA double-strand breaks (DSBs), which can arise through normal DNA metabolism or through exposure to DNA damaging agents such as ionizing radiation, and to exploit our findings to target cancer. DSBs are usually repaired by either the non-homologous end joining (C-NHEJ), or homologous recombination (HR) repair pathways. However, cancer cells frequently exhibit large scale chromosomal rearrangements and instability, which is thought to provide a selective growth advantage over normal cells. Therefore, understanding how genome stability is maintained in response to DSBs is of both biological and clinical importance.
Using the fission yeast Schizosaccharomyces pombe and mammalian cells we have identified a number of conserved factors and pathways which contribute to DSB repair and genome stability. Moreover, we are exploring the underlying mechanisms by which DSB misrepair can drive genome instability. To facilitate our studies in fission yeast, we have developed a DNA double-strand break assay, in which a site-specific DSB can be introduced within a non-essential minichromosome, thereby facilitating the quantification and analysis of chromosome loss or rearrangements. This assay has been useful for the identification and characterization of novel determinants of radiation sensitivity, leading to new roles for DSB repair factors, checkpoint proteins, proteins involved in ubiquitylation, and RNA processing factors. It has also provided insights into how failure to repair a DSB can lead to chromosomal rearrangements, including de novo telomere addition at the break-site, to isochromosome formation, and recently, widespread chromosomal instability across the resultant population
IMPACT
We are interested in exploring how the DNA damage response can be exploited to target particular cancers. We have previously established roles for SETD2-dependent histone H3 lysine 36 trimethylation (H3K36me3) in both DSB repair and in response to DNA replication stress, and find H3K36me3 is frequently lost or depleted in particular cancer types, including metastatic kidney cancers. We have exploited a synthetic lethal interaction between loss of Set2 and Wee1, which is evolutionarily conserved between fission yeast and humans, to selectively kill H3K36me3-deficient human cancers, using the WEE1 inhibitor, Adavosertib (AZD1775) through targeting DNA replication stress. These findings have entered clinical trials to target SETD2-deficient cancers. Moreover, through a collaboration with our clinical colleagues, Adavosertib was included in the MRC FOCUS4 clinical trial where it was found to significantly extend progression free survival in both TP53 and RAS mutant metastatic colorectal cancers. We are currently exploring further ways in which the DNA damage response can be exploited to target particular cancers.
ALUMNI & NEXT DESTINATIONS
- Junetha Syed Jabarulla (2021) post-doc/lab manager - Chief Scientist, Oxford Cancer Analytics
- Fiona Okonjo (2018-2021) Post-doc - Nanosyrinx Biotech.
- Sophia Toumazou (2018-2021) DPhil student (co-supervised) - Jan Boots, consultant.
- Linda van Bijsterveldt (2017-2021) DPhil student - Post-doc, Jason Chin & Julian Sale, MRC LMB
- Samuel Durley (2017-2020) Post-doc - Ordinand-Ripon College Cuddesdon
- Sofia Tundo (2017) Erasmus student- PhD student, Roche, University of Basel, Switzerland
- Kirsten Lopez (2015-2019) DPhil student - Post-doc ICR, Sutton
- Lee Armfield (2015-2019) DPhil student - Associate with Deallus consultancy
- Sophia Pfister (2012-2015) DPhil student, Post-doc - Alan Ashworth, UCSF
- Sara Ahrabi (2013-2017) DPhil student - Post doc, Marc Mansour, UCL
- Elizabeth Blaikley (2010-2014) DPhil Student - Scientist, CRUK Manchester Institute
- Chen-Chun Pai (2009-2021) Post-doc - Scientist, IBME University of Oxford
- Torben Kasparek (2009-2013) DPhil Student - Norvartis Pharmaceuticals, Switzerland
- Rachel Deegan (2008-2012) DPhil student - Patent attorney
- Jennifer Moss (2007-2011) DPhil student - Teacher training
- Lydia Hulme (2009-2013) Post-doc - Post-doc, Ji-Long Liu lab, University of Oxford
- Dr Andrew Savory (2006-2009) Post-doc - Teacher, Winchester College
- Helen Tinline-Purvis (2005-2009) DPhil student - Post-doc, NHS, Bristol
- Jason Cullen (2004-2007) DPhil student - Post-doc, Brisbane University, Australia
- Boon-Yu Wee (2003-2006) DPhil student - Post-doc, Singapore
- Vinoj George (2001-2005) DPhil student - Post-doc, University Southampton
- Dr Wendy (Bridge) Cox (2005-2007) Post - doc position- Lonza
- Joanne Evans (2000-2004) DPhil student - Medicine, London
- Sharon Hussey (2000-2004) DPhil student - Post-doc, Mike Resnick Lab, NIH, USA
- Dr Anoushka Davé (2004-2008) Post-doc - Post-doc, A. Bianchi, GDSC, Sussex
- John Prudden (1998-2002) DPhil student - Post-doc, M. Boddy, Scripps, USA
- Isabelle Dunand-Sauthier (1997-2001) DPhil student - Post-doc, Stuart Clarkson, Geneva
- Dr Matloob Qureshi (1997-1998) Post-doc - Bioinformatics, EMBL
- Carol Walker (1997-2020) Lab Manager - retired.
GROUP INFORMATION
Sovan Sarkar - Post-doctoral Researcher
Swati Pendharkar - Post-doctoral Researcher
Asmita Sharda - Post-doctoral Researcher
Kanggeon Kim - Post-doctoral Researcher
Hira Javaid - DPhil student
Majd Abdulghani - DPhil student
Paul Guy - DPhil student
SELECTED PUBLICATIONS
- Sharda, A. & Humphrey, T.C. (2022) The role of histone H3K36me3 writers, readers and erasers in maintaining genome stability, DNA Repair, 119, 103407
- Seligmann, J.F., Fisher, D.J., Brown, L.C., Adams, R.A., Graham, J., Quirke, P., Richman, S.D., Butler, R., Domingo, E., Blake, A., Yates.E, Braun M., Collinson F., Jones R., Brown E., de Winton E., Humphrey, T.C., Kaplan,R., Wilson, R., Seymour, M. and Maughan, T.S., on behalf of the FOCUS4 Trial Investigators. (2021) Inhibition of WEE1 Is Effective in TP53- and RAS-Mutant Metastatic Colorectal Cancer: A Randomized Trial (FOCUS4-C) Comparing Adavosertib (AZD1775) With Active Monitoring, Journal of Clinical Oncology, 39, pp. 3705-3715.
- Dave, A., Pai, C.C., Durley, S.C., Hulme, L., Sarkar, S., Wee, B.Y., Prudden, J., Tinline-Purvis, H., Cullen, J.K., Walker, C., Watson, A., Carr, A.M., Murray, J.M., Humphrey, T.C. (2020) Homologous recombination repair intermediates promote efficient de novo telomere addition at DNA double-strand breaks, Nucleic Acids Research 48, pp. 1271-1284.
- Pai, C.C., Hsu, K.F., Durley, S.C., Keszthelyi, A., Kearsey, S.E., Rallis, C., Folkes, L.K., Deegan, R., Wilkins, S.E., Pfister, S.X., De Leόn N, Schofield CJ, Bähler J, Carr AM, Humphrey T.C. (2019) An essential role for dNTP homeostasis following CDK-induced replication stress, Journal of Cell Science, 132.
- Pai, C.C., Kishkevich, A., Deegan R.S., Keszthelyi A., Folkes, L., Kearsey, S.E., De León, N., Soriano I., de Bruin, R.A.M., Carr, A.M. and Humphrey, T.C. (2017) Set2 methyltransferase facilitates DNA replication and promotes genotoxic stress responses through MBF-dependent transcription. Cell Reports, 20, pp. 2693-2705.
- Pfister, S.X., Markkanen, E., Jiang,Y., Sarkar,S., Woodcock, M., Orlando, G., Mavrommati, I., Pai, C-C., Zalmas,L-P., Drobnitzky, N., Dianov, GL., Verrill, C., Macaulay, V.M., Ying, S., La Thangue, N.B., D’Angiolella, V., Ryan, A. and Humphrey, T.C. (2015) Inhibiting WEE1 selectively kills histone H3K36me3-deficient cancers by dNTP starvation, Cancer Cell, 28,pp. 557-568.
- Pfister,S.X., Ahrabi,S., Zalmas,PL., Sarkar,S., Aymard,F., Bachrati,C.Z., Helleday,T., Legube,G., LaThangue, N.B., Porter, A.C.G and Humphrey, T.C. (2014) SETD2-Dependent Histone H3K36 Trimethylation Is Required for Homologous Recombination Repair and Genome Stability, Cell Reports, 7, pp. 2006-2018.
- Pai, C-C., Deegan, R.S., Gal, C., Subramanian, L., Sarkar,S., Blaikley, E.J., Walker, C., Hulme, L., Bernhard, E., Codlin, S., Bähler, J., Allshire, R., Whitehall, S. and Humphrey, T.C. (2014) A histone H3K36 chromatin switch coordinates DNA double-strand break repair pathway choice, Nature Communications, 5, 4091.
- Blaikley, E.J., Tinline-Purvis, H., Kasparek, T.R., Marguerat, S., Sarkar,S. Hulme, L. Hussey, S., Wee, B-Y., Deegan, R.S., Walker, C.A., Pai, C-C., Bähler, J., Nakagawa, T. and Humphrey, T.C. (2014) The DNA damage checkpoint pathway promotes extensive resection and nucleotide synthesis to facilitate homologous recombination repair and genome stability in fission yeast, Nucleic Acids Research, 42, pp. 5644-5656.
- Moss, J., Tinline-Purvis, H., Walker, C., Folkes L., Stratford, M., Hayles, J., Hoe, K., Kim, D., Park, H., Kearsey, S., Fleck, O., Holmberg, C., Nielsen, O. and Humphrey, T.C. (2010) Break-induced ATR and Ddb1-Cul4(Cdt)(2) ubiquitin ligase-dependent nucleotide synthesis promotes homologous recombination repair in fission yeast, Genes & Development, 24, pp. 2705-2716.