The aim or our research is to understand how genome stability is maintained in response to DNA double-strand breaks, and to exploit our findings to target cancer.
Exposure to ionizing radiation (IR) can cause chromosome breaks, in which both DNA strands are broken. In addition to causing cell death (the desired outcome during radiation therapy), such lesions can also cause chromosomal rearrangements and genome instability, a hallmark of cancer cells. We are focusing on the early events and chromatin modifications in DNA double-strand break (DSB) repair and misrepair. Further, we are exploiting our findings to develop novel targeted cancer therapies in the clinic.
A role for the chromatin mark H3K36me3 in DNA repair
DNA is tightly wrapped up around proteins called histones to form chromatin. We have studied a chromatin mark, (histone H3 lysine 36 trimethylation), which is frequently lost in some human cancers, including 60% of clear cell renal cell carcinomas (kidney cancers) and associated with poor prognosis. From our studies using the fission yeast Schizosaccharomyces pombe, we found a role for Set2, (the histone H3K36 methyltransferase) in facilitating DSB repair. We further defined a central role for H3 lysine 36 trimethylation (H3K36me3) in promoting homologous recombination (HR) repair of DSBs, and maintaining genome stability in human cells. We found that loss of SETD2, and subsequently other HR repair factors, including RPA, BRCA1 or BRCA2, led to significantly elevated levels of DSB misrepair through use of the microhomology-mediated end joining (MMEJ) pathway. Our findings have identified a more general role for HR repair factors in maintaining genome stability by both promoting error-free HR repair and by suppressing mutagenic MMEJ repair of DSBs.
Targeting histone H3K36me3-deficient cancers
We have exploited a powerful genetic approach (synthetic lethality) using yeast and human systems to identify drugs, which specifically kill histone H3K36me3-deficient cancers. From our initial observations in fission yeast, we identified a conserved synthetic lethal interaction between loss of SETD2 and WEE1 inactivation. Surprisingly, we found that cell death in this context arises through replicative catastrophe, resulting from critically low deoxyribonucleotide (dNTP) levels, leading to DNA damage and apoptosis. Mechanistic analysis indicated that H3K36me3 loss resulted in reduced expression of the ribonucleotide reductase subunit, RRM2, and to reduced dNTP supply. Further, WEE1 inhibition, using the potent WEE1 inhibitor AZD1775, led to degradation of RRM2, thus depleting dNTPs, and to elevated DNA replication origin firing, thereby increasing dNTP demand. Importantly, we found that treatment of H3K36me3-deficient cancer xenografts with AZD1775 caused cancer regression without signs of toxicity. Having developed a biomarker to detect H3K36me3 loss in patient samples, the use of the WEE1 inhibitor, AZD1775, has now been taken into clinical trials to target H3K36me3-deficient cancers.
Tim Humphrey is a senior group leader and a deputy director at the CRUK/MRC Oxford Institute for Radiation Oncology. Tim performed his doctoral studies at the University of Oxford and was an EMBO and HFSP post-doctoral research fellow at Harvard Medical School before returning to the UK to become a group leader at the MRC Genome Stability Unit, Oxfordshire. He was awarded tenure in 2003, and in 2008 he moved to the Gray Institute in Oxford and heads the Chromosome Integrity Group.
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, 2693-2705.
Bleuyard J-Y., Fournier M., Nakato R., Couturier A., Katou Y., Ralf C., Hester S., Dominguez D., Rhodes D., Humphrey T. C., Shirahige K., and Esashi F. (2017) MRG15-mediated tethering of PALB2 to unperturbed chromatin protects active genes from genotoxic stress. Proc. Natl. Acad. Sci. USA.114, 7671-7676
Ahrabi S., Sarkar S., Pfister S.X., Pirovano G., Higgins G.S., Porter A.C.G., Humphrey T.C. (2016) A role for human homologous recombination factors in suppressing microhomology-mediated end joining. Nucleic Acids Res. 44, 5743-5757.
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., Humphrey, T.C., (2015) Inhibiting WEE1 selectively kills histone H3K36me3-deficient cancers by dNTP starvation. Cancer Cell 28,557-568.
Gravells, P., Ahrabi, S., Vangala, RK, Tomita,K., Brash, JT, Brustle, L.A., Chung, C., Hong, J.M, Kaloudi, A., Humphrey, T.C., Porter A.C.W. (2015) Use of the HPRT gene to study nuclease-induced DNA double strand break repair. Hum. Mol. Genet. 24, 7079-7110.
K. Jha, D.K., Pfister, S.X., Humphrey, T.C., Strahl, B.D. (2014) SET-ting the stage for DNA repair, Nat Struct Mol Biol. 21, 655-7.
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, Humphrey,T.C.§ (2014) SETD2-Dependent Histone H3K36 Trimethylation Is Required for Homologous Recombination Repair and Genome Stability, Cell Reports 7, 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. Humphrey, T.C., (2014). A histone H3K36 chromatin switch coordinates DNA double-strand break repair pathway choice. Nature Communications (5):4091 10.1038/ncomms5091.