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Self funded BMS Project: Tissue-specific roles of human endogenous retroviruses in urothelial carcinoma

   York Biomedical Research Institute

  Dr Andrew Mason,  Applications accepted all year round  Self-Funded PhD Students Only

About the Project

Applications accepted for PhD Only

Human endogenous retroviruses (HERVs) are the remnants of retroviral infections in our evolutionary past that contribute 8% of our genome. Whilst HERVs have lost the ability to produce and shed retroviral particles, many have open reading frames and intact regulatory regions. HERV transcripts are readily detected by RNA-sequencing (and typically elevated in cancer), and there are many examples of tissue-specific transcript regulation driven by HERV long terminal repeats.

In this bioinformatics-driven project, you will generate and analyse whole-genome and long-read transcriptome sequencing data from healthy urothelium to identify donor-specific integrations and tissue-specific transcription. The project will then address the role for HERVs in urothelial carcinoma, by 1) identifying novel integrations using whole-genome data from the bladder cancer cohort of the Genomics England 100,000 Genomes Project, and 2) interpreting RNA-sequencing cohort data (such as The Cancer Genome Atlas) based on initial work with normal urothelium. This project will functionally annotate HERVs in urothelium for the first time, and inform our understanding of HERV dysregulation in urothelial carcinoma; cancers where high-burden mutational profiles are largely attributable to APOBEC-mediated antiviral defence. This project offers training in the analysis and interpretation of large datasets from multiple sequencing technologies, and has the scope to expand to consider the pan-cancer relevance of the results.

The York Biomedical Research Institute at the University of York is committed to recruiting extraordinary future scientists regardless of age, ethnicity, gender, gender identity, disability, sexual orientation or career pathway to date. We understand that commitment and excellence can be shown in many ways and have built our recruitment process to reflect this. We welcome applicants from all backgrounds, particularly those underrepresented in science, who have curiosity, creativity and a drive to learn new skills.

Entry Requirements: Students with, or expecting to gain, at least an upper second class honours degree, or equivalent, are invited to apply. The interdisciplinary nature of this programme means that we welcome applications from students with backgrounds in any biological, chemical, and/or physical science, or students with mathematical backgrounds who are interested in using their skills in addressing biological questions. 

Programme: PhD in Biomedical Science (3 years)

Start Date: 1st October 2022


Funding Notes

This is a self funded research project. Applicants need to have adequate funds to meet the costs of a self-funded research project including tuition fees and living expenses for the duration of the research programme.

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