Fairfax Group: Genomics of Inflammation and Cancer Immunology
We started at the WIMM in July 2017
Using genetic and epigenetic data to understand basic mechanisms of inflammation.
We are interested in the genetic and epigenetic determinants of inter-individual variation in immune responses. Our current projects are as detailed below:
Genetic and epigenetic determinants of immunity
The functional properties of a genetic polymorphism depend upon the cell type analysed and the state that the cell is in. Thus to understand the genetics of gene expression in immune cells we need to explore specific populations of cells in defined environmental contexts. We are using bulk and single cell RNA sequencing to explore the interplay between divergent immune stimuli and genetic variation across multiple cell types.
inflammation and methylation
We are exploring the effect of immune stimuli on DNA methylation in human primary immune cells with reference to underlying genetic variation.
genomics guided cancer treatment
We are using sequencing data from circulating plasma DNA, cell subset transcriptomics and germline genetics in samples from patients with metastatic melanoma who are undergoing treatment with checkpoint inhibitor therapy to identify peripheral predictors of clinical benefits and adverse responses.
Group Members
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Benjamin Fairfax
Associate Professor
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Bo Sun
NIHR Academic Clinical Lecturer in Neurology
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James Gilchrist
NIHR Academic Clinical Lecturer
Collaborators
Cancer Immunotherapy
We are collaborating with Anna & Dr Joe Sacco in Liverpool to understand the impact of toxicity to Immune Checkpoint Blockade on long-term cancer outcomes.
We are collaborating with Ricardo's team to help us identify the antigenic peptides partnering T cell receptors responsible for both clearing cancer and also causing immune related adverse events.
We are collaborating with members of Paul's team to explore MAIT cell function in health and disease, with a particular emphasis on cancer immunotherapy.
Immunogenetics
We are working with Yang who is based at the Kennedy Institute for Rheumatology to help us piece together the relationship between MHC alleles and T Cell Receptor Usage.
We work with Hélène, who is based at the MRC Biostatistics Group with Professor Sylvia Richardson in Cambridge, to further insights into trans regulatory master gene expression networks.
We have worked with Hussein & Professor Paul Bowness to explore the role of context specific regulatory polymorphisms at IL7R in autoimmune diseases.
Julian is a long-term collaborator with the group - we share interests in understanding the genetic and epigenetic determinants of gene expression in the immune system.
Lab alumni
Isar Nassiri - Former Postdoctoral Fellow with the group - now leading bioinformatic analysis at the Oxford Genomics Centre
Sara Danielli - Former research assistant now undertaking a DPhil with Jelena Mirkovic at the Kennedy
Gigi Lam - Gigi was an exchange student from the Chinese University of Hong Kong Medical School who worked in the lab over summer 2018.
DPhil Students
Piyush Kumar Sharma - Piyush was a DPhil student in the lab between 2019 and 2022 and is completing his thesis to viva in early 2023. He has returned to surgical training in Colorado focusing upon upper gastrointestinal cancers.
Ros Cooper - Ros was one of the first DPhil students in the group, working on circulating DNA and the effects of checkpoint immunotherapy on myeloid cells. Ros was awarded her doctrate at the beginning of 2022 and is now a Clinical Lecturer and trainee pathologist in Oxford.
Chelsea Taylor - Chelsea was one of the first DPhil students in the group, working on MAIT cells, IL-7 and T cell clonality. Chelsea was awarded her doctrate in 2022 and now works on CAR-T cells with Leucid Biotech.
Final Honours Students
Saarah Karim did her Final Honours reserach project with the group in 2021, working primarily with Piyush on a project titled: 'Exploring the relationship between peripheral NK cell transcriptomic response and immune checkpoint blockade therapy in a metastatic melanoma cohort'
Daisy Crisell - undertook her Final Honours research project in the lab (holding out so as to get wet-lab experience post COVID restrictions) in late 2021. Her topical research project had the title “Do patients with metastatic melanoma have autoantibodies to Type 1 interferons?”.
Bethan Storey - Bethan undertook her Final Honours research project working primarily with Rob in our group, studying changes in T cell clonality and clonal structure post-checkpoint immunotherapy. As well as leaning a lot of R, she had a poster at British Society for Immunology 2021 and won the BSI Prize for the best research project in an immunology-related area.
Amir Ahmed - undertook a research project with the lab 2020 titled 'Investigating the role of Gamma-Delta T cells in cancer'.
Harriet Taylor - Harriet undertook her Final Honours research project with Chelsea in our group, studying MAIT cell function in cancer.
Joe Morris - Joe did his Final Honours research project looking at CMV in plasma using droplet PCR
Funders
The Fairfax Group is funded by a Wellcome Intermediate Clinical Fellowship to Benjamin Fairfax as well as Wellcome Funding to Dr Robert Watson