As we start 2023, I’ve been thinking about some of the highlights of the last year. We started 2022 in lockdown (again) due to the emergence of the omicron variant, but the first highlight of the year was the return to on-site working, in late January. I’m pleased to say that we continued to work on-site for the rest of the year.

Through the year we have had a lot of success with grant funding, which has enabled a number of new researchers to join the group, including Chay and Marian, who are researching early detection of pre-cancerous disease, and Samson and Sidi, who are studying the evolution of prostate cancer.

We are also pleased to have hosted several visiting scientists from around the globe. I would like to give a specific mention to Nadiah Zamri, who visited us for over a year until May 2023 and has now returned to her home in Malaysia.

Throughout 2022, the lab have published papers on a variety of topics, ranging from the identification of novel bacteria in the urine of prostate cancer patients to the discovery of mutational signatures, and from the transmission of cancer between twins in utero to the effect of APOBEC enzymes on genomic instability. Perhaps my favourite paper of the year reported the discovery of molecular subtypes of prostate cancer with high prevalence amongst Black men in South Africa. The prevalence of prostate cancer is twice as high in Black men as White men and this paper is a step towards explaining why.

I was honoured to receive a Making a Difference award from the University of Manchester in May, recognising my group’s research in South Africa, as well as our studies of breast cancer in Nigeria and of oesophageal cancer in Kenya.

Two PhD students submitted their thesis in October. Haoqi had a successful viva in December, and Noora has her viva coming up in the New Year. In October, a number of new PhD students joined the group: Laura, whose primary affiliation is to the Wedge group, and Diego and Lucy, who are primarily supervised by Prof Rob Bristow.

In 2023, I look forward to Natalia submitting her PhD thesis, the development of new projects focused on multiomic analysis of cancer and to finally publishing our work in the 100,000 genomes project.

A full breakdown of the infographic

Publications

• Cooke, D.P., Wedge, D.C. and Lunter, G., 2022. Benchmarking small-variant genotyping in polyploids. Genome research, 32(2), pp.403-408.
• Katz-Summercorn, A.C., Jammula, S., Frangou, A., Peneva, I., O’Donovan, M., Tripathi, M., Malhotra, S., di Pietro, M., Abbas, S., Devonshire, G. and Januszewicz, W., 2022. Multi-omic cross-sectional cohort study of pre-malignant Barrett’s esophagus reveals early structural variation and retrotransposon activity. Nature communications, 13(1), pp.1-17.
• Hurst, R., Meader, E., Gihawi, A., Rallapalli, G., Clark, J., Kay, G.L., Webb, M., Manley, K., Curley, H., Walker, H. and Kumar, R., 2022. Microbiomes of urine and the prostate are linked to human prostate cancer risk groups. European Urology Oncology.
• Palles, C., West, H.D., Chew, E., Galavotti, S., Flensburg, C., Grolleman, J.E., Jansen, E.A., Curley, H., Chegwidden, L., Arbe-Barnes, E.H. and Lander, N., 2022. Germline MBD4 deficiency causes a multi-tumor predisposition syndrome. The American Journal of Human Genetics, 109(5), pp.953-960.
• Sousos, N., Ní Leathlobhair, M., Simoglou Karali, C., Louka, E., Bienz, N., Royston, D., Clark, S.A., Hamblin, A., Howard, K., Mathews, V. and George, B., 2022. In utero origin of myelofibrosis presenting in adult monozygotic twins. Nature Medicine, pp.1-5.
• Burns, D., Anokian, E., Saunders, E.J., Bristow, R.G., Fraser, M., Reimand, J., Schlomm, T., Sauter, G., Brors, B., Korbel, J. and Weischenfeldt, J., 2022. Rare Germline Variants Are Associated with Rapid Biochemical Recurrence After Radical Prostate Cancer Treatment: A Pan Prostate Cancer Group Study. European Urology.
• Oliver, T.R., Chappell, L., Sanghvi, R., Deighton, L., Ansari-Pour, N., Dentro, S.C., Young, M.D., Coorens, T.H., Jung, H., Butler, T. and Neville, M.D., 2022. Clonal diversification and histogenesis of malignant germ cell tumours. Nature Communications, 13(1), p.4272.
• Jaratlerdsiri, W., Jiang, J., Gong, T., Patrick, S.M., Willet, C., Chew, T., Lyons, R.J., Haynes, A.M., Pasqualim, G., Louw, M. and Kench, J.G., 2022. African-specific molecular taxonomy of prostate cancer. Nature, 609(7927), pp.552-559.
• Islam, S.A., Díaz-Gay, M., Wu, Y., Barnes, M., Vangara, R., Bergstrom, E.N., He, Y., Vella, M., Wang, J., Teague, J.W. and Clapham, P., 2022. Uncovering novel mutational signatures by de novo extraction with SigProfilerExtractor. Cell Genomics, 2(11), p.100179.
• Moreno Rueda, L.Y., Bryant, D., Tapper, W.J., Weston-Bell, N., Wedge, D.C., Ansari-Pour, N. and Sahota, S.S., 2022. Genomic Panorama and Clonal Evolutionary Trajectory of Classical Hairy Cell Leukemia. Blood, 140(Supplement 1), pp.8748-8749.
• Jakobsdottir, G.M., Brewer, D.S., Cooper, C., Green, C. and Wedge, D.C., 2022. APOBEC3 mutational signatures are associated with extensive and diverse genomic instability across multiple tumour types. BMC biology, 20(1), pp.1-12.
• Buhigas, C., Warren, A.Y., Leung, W.K., Whitaker, H.C., Luxton, H.J., Hawkins, S., Kay, J., Butler, A., Xu, Y., Woodcock, D.J. and Merson, S., 2022. The architecture of clonal expansions in morphologically normal tissue from cancerous and non-cancerous prostates. Molecular cancer, 21(1), pp.1-16.
• Garcia-Martin, N. et al. 2022 A Graph Based Neural Network Approach to Immune Profiling of Multiplexed Tissue Samples, in 2022 44th Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC), pp. 3063–3067.

Presentations

• Maria Jakobsdottir - Institut Curie - Computational Systems Biology of Cancer: Multimodal data integration
• Atef Sahli - PanProstate Cancer Group Meeting
• David Wedge - Systems genetics of Cancer (Cambridge)
• Natalia Garcia-Martin - 2022 44th Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC)

Pre-prints

• Salcedo, A., Tarabichi, M., Buchanan, A., Espiritu, S.M., Zhang, H., Zhu, K., Yang, T.H.O., Leshchiner, I., Anastassiou, D., Guan, Y. and Jang, G.H., 2022. Crowd-sourced benchmarking of single-sample tumour subclonal reconstruction. bioRxiv, pp.2022-06.
• Cornish, A., Gruber, A., Kinnersley, B., Chubb, D., Frangou, A., Caravagna, G., Noyvert, B., Lakatos, E., Wood, H., Arnedo-Pac, C. and Culliford, R., 2022. Whole genome sequencing of 2,023 colorectal cancers reveals mutational landscapes, new driver genes and immune interactions. bioRxiv, pp.2022-11.

Posters

• Maria Jakobsdottir - Institut Curie - Computational Systems Biology of Cancer: Multimodal data integration
• Parsa Pirhady - The British Association for Cancer Research 60th Anniversary Conference

Theses

• Haoqi Sun: Tracking the evolution of cancer genomes
• Noora Al-Muftah

New staff

• Sidi Yang: Research Assistant
• Samson Olofinsae: Post-doctoral Research Associate
• Marian Love: Post-doctoral Research Associate
• Chay Paterson: Post-doctoral Research Associate

New visiting reserchers

• Nadiah Zamri
• Vanessa Hayes
• Susanne Flach
• Asmau Usman

New PhD students

• Laura Woodhouse
• Diego Sanchez
• Lucy Barton

New Master’s students

PhDs completed

• Haoqi Sun

Grants awarded

• Manchester Biomedical Research Centre, Next Generation Phenotyping and Diagnostics theme (NIHR, £3.2M)
• ACED Project Award: Improving patient outcomes in oesophageal adenocarcinoma using cancer evolutionary trajectories (CRUK, £600K)
• ACED Pilot Award: Using HDGC to build a toolkit to distinguish indolent from consequential early cancer lesions (CRUK, £200K)

PhD vivas completed

• Haoqi Sun

Prizes received

• David Wedge - Highly commended UoM Making a Difference Awards Reducing inequalities in cancer tumour genetic screening, in the ‘Outstanding contribution to equality, diversity and inclusion’ category.
• Maria Jakobsdottir - Best Oral Presentation by a Post-doc - SysBioCancer2022

Master’s modules developed

• Transformative Oncology MSc Unit 2: Cancer is an Individualised Disease