Shaping intestinal inflammation by neutrophils: the host-diet-microbiome triad

The global incidence of ulcerative colitis (UC), a predominant form of inflammatory bowel disease, is on the rise worldwide. Neutrophils, as the most abundant circulating immune cell population, are recruited in high numbers to the colon in UC, and are associated with sites of deep ulceration (1). However, what drives neutrophil recruitment to the colon and what function the recruited neutrophils play in promoting intestinal inflammation has not been elucidated. Moreover, contrary to the long-held belief that neutrophils are transcriptionally inactive, recent research, including our own, has demonstrated that neutrophils undergo extensive chromatin remodelling, gene expression changes, and acquire specific effector functions en route to tissue (2,3). This results in a remarkable diversity of neutrophil states, but the contribution of distinct neutrophil subsets in immunopathology of UC is largely unknown. Understanding the functional roles of neutrophils in intestinal inflammation and the targeted modulation of neutrophil subset and/or activity would lead to a new yet untapped in window of therapeutic possibilities for reducing the burden of UC.

Based on our preliminary data that indicate a spatiotemporal recruitment of neutrophil subsets to the colon and associated pathology, we propose that this is driven by the altered cellular and microbiome composition along the length of the colon. In addition, neutrophil activation may itself alter the microbiome composition and cellular pathology. This project will address the hypothesis by applying single-cell and spatial transcriptomic approaches to experimental model of colitis (4) at different levels of resolution intended to capture changes in both the biogeography and local architecture of the colonic tissue and its associated microbiome. The primary objectives are:

1. Identify cellular and microbial signals controlling spatiotemporal recruitment of neutrophils along the colon. We will apply spatial transcriptomics analysis to the distal and proximal colon (niches) during colitis progression using the NanoString CoSMx Spatial Molecular Imaging platform in combination with a custom immune panel that incorporates degenerate 16S rRNA probes designed for universal detection of bacterial cells, as well as probes specific for bacterial pathogen.

2. Characterize spatiotemporal heterogeneity of neutrophils in inflamed colon. We will obtain single-cell RNA sequencing (scRNA-seq) data from neutrophils in different colon regions during colitis to define neutrophil subpopulations and their distribution across distinct sites. Subsequent biological pathway analyses will elucidate the functions of these subsets. The scRNA-seq results will be validated via immunofluorescence and integrated with spatial transcriptome data to visualize the distribution of neutrophil subsets along the colon. The contribution of neutrophil subsets to colitis progression will be further justified using in vivo models

3. Assess spatiotemporal reorganization of microbiota and metabolites in colitis. 16S rRNA gene sequencing of distal and proximal colon and lumen contents will be conducted to reveal the spatial composition of microbiota and its pathogenic features in colitis. The microbiota remodelling will subsequently be integrated with spatiotemporal metabolite analysis to map the metabolic and microbial niche-specific signals directing the recruitment, state and fate of neutrophils. The effector roles of diet on neutrophils, which modulate the outcome of colitis, will be measured using a model with a modified diet. Conversely, a model with deficient neutrophil activation will be used to understand the impact of neutrophils on microbiota, which modulates colitis progression.

KEYWORDS

Immunology, neutrophils, ulcerative colitis, scRNAseq, spatial transcriptomics

TRAINING OPPORTUNITIES

The Kennedy Institute is a world-renowned research centre housed in a state-of-the-art facility. The student will receive training in fundamental immunology techniques, including flow cytometry, tissue culture, and RT-qPCR, as well as imaging techniques such as immunohistochemistry, immunofluorescence, and microscopy. Additionally, the student will have access to advanced single-cell platforms (10X single cell gene expression, Visium spatial gene expression, Nanostring CosMx) and their corresponding computational analysis pipelines. The student will participate in weekly seminars within the department and those relevant across the broader University. They will regularly present their research to the department and the Genomics of Inflammation group, with opportunities to present at the Computational Genomics Forum. Furthermore, the student will attend external conferences to present their research to a global audience.

KEY PUBLICATIONS

1. Friedrich M,….., Powrie F. IL-1-driven stromal-neutrophil interactions define a subset of patients with inflammatory bowel disease that does not respond to therapies. Nat Med. 2021 Nov;27(11):1970-1981.
2. Ballesteros I, …, Udalova IA, Ng LG, Ostuni R, Hidalgo A. Co-option of Neutrophil Fates by Tissue Environments. Cell. 2020 Nov 25;183(5):1282-1297.e18.
3. Khoyratty TE, …, Udalova IA. Distinct transcription factor networks control neutrophil-driven inflammation. Nat Immunol. 2021 Sep;22(9):1093-1106.
4. Corbin AL, …, Udalova IA. IRF5 guides monocytes towards an inflammatory CD11c+ macrophage phenotype and promotes intestinal inflammation. Science Immunology, 2020 May 22;5(47):eaax6085.
5. Johnson JS, …., Weinstock. Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis. Nat Commun. 2019 Nov 6;10(1):5029.

THEMES

Immunity, Inflammation Bowel Disease, neutrophils, transcriptomes

CONTACT INFORMATION OF ALL SUPERVISORS

Prof Irina Udalova, irina.udalova@kennedy.ox.ac.uk 

Dr Linh Nguyen, linh.nguyen@kennedy.ox.ac.uk

The Kennedy Institute is a proud supporter of the Academic Futures scholarship programme, designed to address under-representation and help improve equality, diversity and inclusion in our graduate student body.  The Kennedy and the wider University rely on bringing the very best minds from across the world together, whatever their race, gender, religion or background to create new ideas, insights and innovations to change the world for the better. Up to 50 full awards are available across the three programme streams, and you can find further information on each stream on their individual tabs (Academic futures | Graduate access | University of Oxford).

How to Apply

Please contact the relevant supervisor(s), to register your interest in the project, and the departmental Education Team (graduate.studies@ndorms.ox.ac.uk), who will be able to advise you of the essential requirements for the programme and provide further information on how to make an official application. 

Interested applicants should have, or expect to obtain, a first or upper second-class BSc degree or equivalent in a relevant subject and will also need to provide evidence of English language competence (where applicable). The application guide and form is found online and the DPhil or MSc by research will commence in October 2025. 

Applications should be made to the following programme using the specified course code. 

D.Phil in Molecular and Cellular Medicine (course code: RD_MP1)

For further information, please visit http://www.ox.ac.uk/admissions/graduate/applying-to-oxford.

Interviews to be held week commencing 13^th January 2025.