Staff Profile

I am a Research Associate in the Cancer Prevention Group, led by Professor Sir John Burn, Dr Mike Jackson, and Dr Mauro Santibanez-Koref, within the Translational and Clinical Research Institute. I am funded by a Cancer Research UK Catalyst Award as part of the Aspirin for Cancer Prevention (AsCaP) network. I work in several projects developing diagnostic assays for clinical deployment, acting in a variety of roles. These include:

• molecular biologist developing assay protocols, typically using next generation sequencing technologies, and validating assay performance
• bioinformatician writing pipelines for the analysis of sequencing data and sample classification
• contact and support for local and national NHS partners, and research collaborators for assay training and deployment
• contact and support for business development and commercialisation partners
• outreach to initiate new collaborations
• laboratory manager

In addition to developing diagnostic assays, my research explores the mechanisms of chemo- or immuno-prevention of cancer, how genetic predisposition and the immune system influences tumour growth, and defining the true frequency of cancer predisposition syndromes associated with defects in mismatch repair genes. These projects are made possible through close collaboration with the Cancer Prevention Programme 3 (CaPP3) clinical trial, and invaluable collaborators, locally, nationally, and internationally.

Introduction

My research is driven by an interest in evolution by natural selection in the context of human genetics and cancer. I believe that by understanding the molecular pathways through which tumours develop, we can improve cancer prevention, with particular benefit to hereditary cancer syndromes.

Lynch syndrome (LS) is a hereditary predisposition to several cancer types, most commonly gastrointestinal, gynaecological, and urothelial cancers, caused by a pathogenic variant in one allele of the principle mismatch repair (MMR) genes: MLH1, MSH2, MSH6, and PMS2. LS is relatively common, with estimates suggesting that 1 in ~300 of the general population carry a pathogenic MMR gene variant, and that 3% of all colorectal cancers (CRC) are caused by it. Clinical management of LS carriers includes 1-3 yearly colonoscopy and polypectomy to reduce tumour burden. The CAPP2 clinical trial also showed that daily aspirin intake approximately halves the CRC-risk in LS.

Given LS carriers have a 75% lifetime risk of cancer overall, and due to the clinical interventions available, it has been recommended by the UK National Institute for Health and Care Excellence (NICE) that all CRCs are tested for microsatellite instability (MSI), a known feature of MMR deficient cancers, as part of a screening pipeline to identify LS. MSI testing also informs the use of immune checkpoint blockade therapy. However, existing assays are too costly or low throughput to meet the clinical need: more than 41,000 CRCs are diagnosed each year in the UK. Furthermore, the recommended prevention strategies, such as colonoscopy and polypectomy, or daily aspirin, do not prevent all CRCs, and a better understanding of how LS-associated tumours evolve is needed.

Related to LS is a childhood cancer predisposition syndrome caused by pathogenic MMR gene variants affecting both alleles of a MMR gene: Constitutional Mismatch Repair Deficiency (CMMRD). CMMRD is very rare, with estimates that one in a million are affected, but their exceptionally high tumour burden, mortality and distinct therapeutic-efficacy means their identification is critical. CMMRD patients may, like LS, also benefit from daily aspirin. Unfortunately, there are no diagnostic assays suitable for widespread screening of paediatric cancer patients for CMMRD. In addition, there are no national healthcare guidelines for the identification of CMMRD as its true frequency and phenotypic spectrum are unknown.

Previous Work

During my PhD in the Cancer Prevention Group, I developed a low cost and high throughput MSI assay for cancer diagnostics, based on next generation sequencing and a novel method of MSI classification. We showed that it was suitable for clinical practice according to professional guidelines, for example validating assay sensitivity and specificity across multiple independent cohorts, testing assay limits of detection, defining quantifiable quality control criteria, and showing the assay to be reproducible and portable. We also developed an alternative analysis and classification pipeline to diagnose CMMRD, using the same assay to sequence non-neoplastic peripheral blood leukocytes, in collaboration with Prof Katharina Wimmer (Medical University of Innsbruck).

In collaboration with Dr Matthias Kloor, Dr Aysel Ahadova, and Prof Magnus von Knebel Doeberitz (Heidelberg University Hospital), we used both histological and sequencing data to define three pathways of colorectal tumorigenesis in Lynch syndrome, which explain why some tumours are not prevented by colonoscopy and polypectomy. Also, we showed that increased anti-tumour antibodies could be detected in LS patients with a history of CRC, likely due to the high immunogenicity of their MMR deficient tumours. However, optimisation of the method and analysis is needed to show that the observed association could be a useful biomarker in the clinic. 

Current Research

The MSI assay developed during my PhD has now been deployed into local NHS laboratories, and we are working to deploy it in other NHS trusts throughout England and Wales. The assay is also being expanded to include other genetic markers, such as the DPYD SNPs that cause 5-FU therapeutic toxicity, making the assay into a single low cost test for the major clinical biomarkers that inform CRC management. The MSI assay is being further developed to show that it can be applied to cell free DNA, for cancer screening, and to extracolonic cancers, to show that LS screening could be expanded to other tumour types, by two PhD students, Peter Gawthorpe and Rachel Phelps. We are developing an assay to detect instability at tetranucleotide repeats, an alternative form of MSI.

The MSI assay has been deployed in the laboratory of Prof Wimmer to determine the frequency of CMMRD in high risk groups, specifically children without malignancy who have other clinical features of CMMRD. We are also working with Prof Anthony Moorman (Newcastle University), and others in the UK and Europe, to build a cohort of >1000 paediatric cancer patients for unselected screening to define the frequency and phenotype of CMMRD.

Having just started the second year of my five year post-doctoral position, I am initiating several projects to explore the influence of both the immune system and aspirin on CRC development in LS, using samples collected in the CaPP3 clinical trial, from the AsCaP network, and from collaborators throughout Europe. These projects will form the core of my research activity in the future.

Undergraduate genetics seminars BGM1004.

• Gallon R, Müglegger B, Wenzel S-S, Sheth H, Hayes C, Aretz S, Dahan K, Foulkes W, Kratz CP, Ripperger T, Azizi AA, Feldman HB, Chong AL, Demirsoy U, Florkin B, Imschweller T, Januskiewicz-Lewandowska D, Lobitz S, Nathrath M, Pander HJ, Perez-Alanso V, Perne C, Ragab I, Rosenbaum T, Rueda D, Seidel MG, Suerink M, Taeubner J, Zimmermann SY, Zschocke J, Borthwick GM, Burn J, Jackson MS, Santibanez-Koref M, Wimmer K. A sensitive and scalable microsatellite instability assay to diagnose constitutional mismatch repair deficiency by sequencing of peripheral blood leukocytes. Human Mutation 2019, 40(5), 649-655.
• Gallon R, Sheth H, Hayes C, Redford L, Alhilal G, O'Brien O, Spiewak H, Waltham A, McAnulty C, Izuogu OG, Arends MJ, Oniscu A, Alonso AM, Laguna SM, Borthwick GM, Santibanez-Koref M, Jackson MS, Burn J. Sequencing‐based microsatellite instability testing using as few as six markers for high‐throughput clinical diagnostics. Human Mutation 2020, 41(1), 332-341.
• Redford L, Alhilal G, Needham S, O'Brien O, Coaker J, Tyson J, Amorim LM, Middleton I, Izuogu O, Arends M, Oniscu A, Alonso AM, Laguna SM, Gallon R, Sheth H, Santibanez-Koref M, Jackson MS, Burn J. A novel panel of short mononucleotide repeats linked to informative polymorphisms enabling effective high volume low cost discrimination between mismatch repair deficient and proficient tumours. PLoS ONE 2018, 13(8), e0203052.
• Izuogu O, Alhasan AA, Mellough C, Collin J, Gallon R, Hyslop J, Mastrorosa FK, Ehrmann I, Lako M, Elliott DJ, Santibanez-Koref M, Jackson MS. Analysis of human ES cell differentiation establishes that the dominant isoforms of the lncRNAs RMST and FIRRE are circular. BMC Genomics 2018, 19(1), 276.
• Ahadova A, Gallon R, Gebert J, Ballhausen A, Endris V, Kirchner M, Stenzinger A, Burn J, von Knebel Doeberitz M, Bläker H, Kloor M. Three molecular pathways model colorectal carcinogenesis in Lynch syndrome. International Journal of Cancer 2018, 143(1), 139-150.