PhD opportunities
We are excited to announce that we are recruiting our first cohort of six Exposome Immunology PhD students, to begin in October 2026.
How to apply
Details of the programme and how to apply can be found on our Fully funded PhD studentship page.
Supervisor selection
Applicants are asked to list three supervisors from the institution they may wish to develop PhD projects with. Please see below for a summary of each lab’s interests.
Manchester supervisors
David Brough
The Brough lab (Manchester) investigates inflammasome-dependent inflammation in the brain and how it contributes to brain injury and disease such as stroke, Alzheimer's disease, and brain tumours. Using spatially resolved single cell approaches combined with unique reporter systems we will discover the danger sensing pathways driving inflammation in brain disease. We will validate key pathways identified in models using clinical tissue. Use genetic and pharmacological approaches in disease relevant preclinical models will define new therapeutic approaches.
Kevin Couper
The Couper lab (Manchester) is interested in investigating the immune landscape within tissues, identifying how spatial immune determinants (i.e. the compartmentalisation and interactomes of immune cell populations) within tissues shape the trajectory of disease. Utilising established imaging mass cytometry antibody panels and spatial transcriptomics analysis workflows, we are able to collaborate with researchers in Manchester and Oxford to study how exposome factors remodel barrier tissue landscapes (including neuro-immune interactions), predisposing towards chronic disease.
Kat Coyte
The Coyte lab (Manchester) combines next-generation -omics, machine learning, and classical microbiology to explore the interplay between the gut microbiome and the immune system. We study how different immune components shape the ecological and evolutionary dynamics of the microbiome, and how members of the microbiome in turn shape immune development. Potential PhD projects range from targeted studies of how specific microbes shape immune responses during chronic infections, to “big data” driven explorations of how the microbiome-immune system interactions drive the devastating inflammatory disease Necrotizing Enterocolitis (NEC) in preterm infants.
Sheena Cruickshank
The Cruickshank lab (Manchester) examines how barrier resident cells in tissues such as the respiratory tract respond to damage from airborne pollutants and infections and how these impact the immune system. We want to understand how sustained exposure to pollutants alters the immune response to viral infection, amongst others, and whether this enhances susceptibility to disease. We will address this using in vivo and in vitro model systems combined with different ‘omic approaches in collaboration with the Udalova lab (Oxford), with a goal of identifying novel targets for treatments for infections and lung disease.
Giuseppe D’Agostino
By integrating circuit neuroscience and immunology, we seek to understand how the nervous system senses and decodes environmental exposures (the exposome) to control immunity at key barrier sites and how the host's internal state - such as previous disease or metabolic condition - alters this cross-tissue interplay. In collaboration with colleagues at Manchester and Oxford, we aim to visualize and functionally interrogate the brain-body circuits coordinating these responses. Research projects will employ cutting-edge genetic technologies, including chemo/optogenetics and genome editing, and also involve the development of novel tools and approaches.
View Giuseppe's research profile
Doug Dyer
The glycocalyx is a thick, hydrated and adhesion resistant cell-matrix barrier that surrounds all cells of the body, particularly endothelial and immune cells. It is the first structure to interact with environmental exposures at barrier surfaces, but very little is known about how it regulates subsequent immune responses and disease. We will use a multi-disciplinary approach, including high-end imaging, in collaboration with Prof. Tracy Hussell to understand how the glycocalyx on different cells regulates the immune response to common exposome factors, such as infectious agents (e.g. viruses) and air pollution.
Alex Frangi
The Frangi lab (Manchester) develops multimodal foundation models and generative AI methods to create virtual populations from vast NHS real-world datasets and high-throughput experimental data. Using spatially-resolved computational mechanistic modelling approaches to interrogate exposome challenges across populations of individuals, organs, tissues, and cells, we will collaborate with Oxford and Manchester colleagues to explore how environmental and lifestyle exposures regulate immune responses using digital twins and digital chimaeras. Through strong methodological expertise and by harnessing synthetic populations and in-silico data integration within the Data Foundation pillar, we aim to understand exposome-immune interactions and develop new computational approaches for personalised medicine interventions.
Andrew Greenhalgh
The Greenhalgh lab (Manchester) investigates how the immune response shapes brain function. We have projects exploring how early-life allergy affects neurodevelopmental trajectories and why allergy is a risk factor for conditions like Attention-Deficit-Hyperactivity-Disorder (ADHD). Using in vivo models, we want to understand how tissue-resident immune cells in the brain and its meningeal borders control neuronal circuit development after allergy. Using patient cohorts, we can assess how multifactorial factors such as birthplace, diet, exposure to pollutants and allergens contribute to burden of disease and inflammation. Examining the exposome-immune-brain axis will be critical to understanding brain function in health and disease.
Matt Hepworth
The Hepworth lab (Manchester) is focused on understanding how innate and adaptive lymphocyte populations resident with mucosal barrier tissues, such as the gut and the lung, sense environmental challenges. These cells provide critical immune mediators in response to pollution, smoking, diet and the microbiota to ensure tissue repair, or when dysregulated – to drive disease. The lab utilizes animal models of disease, mechanistic and transgenic approaches, and cutting edge ‘omics technologies to understand the immune networks that underpin health and disease.
Tracy Hussell
The Hussell (Manchester) and Arnon (Oxford) groups share an interest in how environmental disruptors cause lasting changes in the respiratory tree. This project addresses a major knowledge gap: the impact of pollutants and viral infection on the multi-layered tracheal ecosystem. Preliminary data show that influenza induces persistent alterations in tracheal immune cells and the epithelial basement membrane, while germ-free mice exhibit a different tracheal environment. The student will apply spatial proteomics and 16S rRNA sequencing to map these changes, with emphasis on exposome responses at the epithelium. Results will be integrated with datasets analysing the same pollutants across other sites.
Gloria Lopez-Castejon
The Lopez-Castejon lab investigates how macrophages sense and decode danger signals provided by infection or injury, like toxins and extracellular ATP, and translate them into an inflammatory response. Our constant exposure to environmental factors including pollutants and infection agents contribute to chronic inflammatory diseases. We will explore the impact that danger signals generated after exposure to environmental factors has on the airways in collaboration with Prof Midwood (University of Oxford). Using in vitro and in vivo models paired with transcriptomics and proteomic approaches we will generate a new understanding on how pollutants impact the immune system and its ability to function properly when exposed to a new threat.
Magnus Rattray
The Rattray lab (Manchester) develops machine learning methods for analysis of high-resolution omics data. We are interested in developing computational approaches to uncover how environmental exposures and genetic effects interact via the immune system to cause or protect against disease. The Grainger lab (Manchester) are planning highly multiplexed genetic and environmental perturbation experiments to understand the role of macrophages in this process. We will collaborate with the Yau lab (Oxford) to develop AI-driven approaches to the optimal design of perturbation experiments that can infer causal gene-environment-immune cell effects.
Mark Travis
Infection to respiratory viruses is a major crucial facet of our exposome, and a major international health issue. As well as damaging tissues locally, respiratory infections, such as influenza, can have important detrimental systemic effects. Using pre-clinical mouse models, the Travis lab (Manchester), in collaboration with the Powrie lab (Oxford), is studying how respiratory viral infection causes immune-mediated damage to the intestine. Additionally, with Thornton (Manchester), effects of respiratory infection on the intestinal mucus layer and extracellular matrix are being investigated, and how this regulates immunity in the intestine.
Fiona Whelan
Research in the Whelan lab (Manchester) focusses on understanding how the composition and interactions within the human microbiome contribute to human health and disease. The lab uses a combination of bioinformatic and microbiology techniques to study strain-level microbe-microbe and microbe-host interactions. As part of the MRC CoRE, we are interested in studying how particular exposures affect changes in the respiratory (e.g. nasal, oral, airway) microbiome and how this contributes to the likelihood of developing respiratory disease later in life.
Oxford supervisors
Mark Coles
The Coles group uses poly-omics approaches to analyse human immune microenvironment integrating spatial proteomics and genomics with clinical data. All people are exposed to a myriad of exposome (chemical, biological), however most of our understanding comes western European populations. The healthy aging of individuals in Vietnam varies significantly from that in western Europe with high rates of chronic unhealthy aging. This might result from differences in ancestry and exposome, with extremely high rates of airborne pollution and high rates of smoking. In this project compare populations in Vietnam with the UK to explore exposome effects on tissue inflammation.
Ana Domingos
The Domingos lab (Oxford) examines how crosstalk between sympathetic neurons and resident immune cells maintains tissue health and integrity. Using transcriptomic and tissue clearing volumetric imaging approaches to interrogate disease mouse models, we will collaborate with the Progatzky lab (Oxford) to investigate how these neuroimmune pathways are shaped across the life course and by environmental (exposome) challenges, with the goal of identifying strategies to translate this knowledge into new therapies for lung disease.
Michael Dustin
The Dustin lab (Oxford) is focused on the immunological synapse and integrating this into the 3D tissue context. Using high-resolution imaging, we aim to define how representative nanoplastics alter dendritic cell–T cell interactions, antigen processing, and intracellular stress pathways that may predispose to allergy and autoimmunity. In collaboration with Cyrill Bussy (Manchester) and researchers at the Henry Royce Institute @Manchester, who are developing true-to-life nanoplastics (fragments and fibres) and advanced analytical platforms, we will link reproducible materials science with cutting-edge immunology. Together, this project will establish how environmentally relevant nanoplastics shape immune responses and contribute to exposome-driven human disease.
View Michaels research profile
Paul Klenerman
The Klenerman lab (Oxford) examines how populations of CD8+ T cells serve to protect tissues and repair epithelia. This includes innate-like T cells especially MAIT cells, as well as responses triggered by persistent viruses such as CMV. We use in vivo models and studies of patient cohorts combined with transcriptomic and spatial approaches to address the functional impact of such cells and work out how they impact their local microenvironment in a steady state and in disease. Together with Ben Fairfax (Oxford) we are exploring how such cell populations vary and the impact this has on responses to vaccines, cancer and tissue inflammation.
Kim Midwood
The Midwood lab (Oxford) examines how crosstalk between the extracellular matrix and barrier resident cells in the lung maintains tissue health and integrity. Using spatially-resolved transcriptomic and proteomic approaches to interrogate disease models and patient cohorts, we will collaborate with the Hussell lab (Manchester) to explore how these protective pathways are regulated in a sex-specific manner, and lost over the life course, during exposome challenge, to understand how to harness this information to develop new treatment approaches for people with lung disease.
Claudia Monaco
The Monaco lab (Oxford) studies how perivascular macrophages and their diverse transcriptional programming within barrier organs contribute to human health and disease. By integrating spatial and single-cell biology platforms with preclinical and human models, we will collaborate with the Hussell lab (Manchester) and other PIs to explore how environmental exposures to agents such as viruses and air pollution impacts the functions of perivascular macrophages and their cellular interactions within the niches of barrier organs. Elucidation of the underlying pathways will help identify new therapeutic targets for chronic inflammatory diseases.
View Claudia's research profile
Franze Progatzky
The Progatzky lab (Oxford) investigates how the peripheral nervous system, particularly through glial cells, regulates immunity and tissue repair in the lung. Using spatially resolved transcriptomics, tissue clearing, 3D imaging, and functional perturbations in disease models and patient cohorts, we aim to understand how neuro-immune interactions are shaped by and influence responses to environmental (exposome) challenges. By integrating these advanced approaches, we seek to uncover the cellular and molecular circuits that govern lung homeostasis and inflammatory responses, with the ultimate goal of translating this knowledge into novel, targeted therapies for inflammatory lung disorders.
View Franze's research profile
Stephen Sansom
Immune-mediated diseases such as rheumatoid and spondyloarthritis can be triggered by antigens from the exposome. The Sansom lab (Oxford) is investigating how the exposome alters gut microbes to induce pathogenic T cells that drive joint inflammation in arthritis. Working with the Travis lab (Manchester) we will use single-cell and spatial omic approaches to study clonally expanded T-cells in patient tissues. In parallel, with the Powrie group (Oxford), mechanistic hypotheses relating to inflammation of the gut-joint axis will be tested using mouse models with defined microbial communities. This research will inform novel treatment strategies targeting the exposome-related causes of inflammatory diseases.
View Stephen's research profile
Jack Satsangi
The Satsangi team investigates the genetic and epigenetic contribution to inflammatory bowel disease pathogenesis, and the clinical translation of genetics and epigenetic markers in diagnosis and personalisation of care. The team has demonstrated that epigenetic alterations of specific pathways in response to smoking and air pollution may represent key gene-environmental interactions in intestinal inflammation. These data implicate the HLA region for both smoking (AHRR & DNMT3A) and air pollution (CXCLR5). The findings may have implications widely across complex and immune-mediated diseases and provide a paradigm for the exploration of the epigenome in characterising gene-environmental interactions.
Irina Udalova
The Udalova lab (Oxford) studies how the inflammatory response is controlled on the molecular level. Using an integrated approach of genomic, molecular and in vivo models, human cell and tissue samples we aim to provide novel insights into the key regulators of myeloid cell development and functional states in response to exposome challenge and whether these can be targeted to ameliorate tissue and vascular immunopathology in disease. We also investigate the role of mechanical stimulation provided by the microenvironments of tissue niches in the immune cell function.
Holm Uhlig
Using advanced technologies, such as single cell transcriptomics and spatial transcriptomics, this project will investigate how the cellular landscape in inflammatory bowel disease is shaped by acute and chronic CMV and EBV infection. This project will integrate patient genetics, treatment history, peripheral blood cell and intestinal tissue transcriptomic signatures. To understand complex signatures, we will apply machine learning methods for feature recognition of inflammation (e.g. immune cells, epithelial damage and matrix composition) to understand the cellular ecosystem. This multiomic analysis and deconvolution of signatures will subsequently allow screening of very large patient cohorts for IBD for relevant virus exposome analysis.
Chris Yau
Chris Yau works on the development of Artificial Intelligence approaches for the analysis of biomedical and health data. Principled approaches for integration and analysis of data arising from complex experimental designs is a fundamental challenge for many areas of exposome immunology. Models must adopt multimodal molecular readouts as well as environmental exposures against a backdrop of potential spatial and temporal dimensions in addition to perturbation effects. We will collaborate with the Rattray lab (Manchester) to develop AI-based frameworks for automating model design, selection, and implementation to address these challenges. We will work with other MOXIE investigators to apply these techniques to a variety of experimental settings.