Multiparameter tissue landscapes: shaping neutrophil functional states

PROJECT OVERVIEW

Neutrophils represent a major arm of the innate immune defence system, with a long- held view of them being transcriptionally inactive, fast responders, mobilised in response to microbial and tissue insults. Recent developments in the field have changed this perception and firmly positioned neutrophils as transcriptionally active cells with the ability to adapt their transcriptional program. Our recent findings demonstrate that, despite limited residence times in tissues, neutrophils can tailor their properties to support organ homeostasis and mount tissue specific and transcriptionally regulated inflammatory response1. Importantly, in inflammation neutrophils are presented as functionally, morphologically and behaviourally heterogeneous cells in circulation and tissue2. Our central research question is: How do distinct tissue niches shape neutrophil functional states, and can this be leveraged to ameliorate immunopathology?

This project aims to uncover how distinct tissue environments shape neutrophil gene expression programs and functional states, with a particular focus on immunopathology. Building on our recently generated single-cell RNA sequencing (scRNA-seq) datasets from inflamed joint and colon tissues (unpublished), we will define common and tissue-specific neutrophil signatures and identify the transcriptional networks underlying their adaptation to regional niches. By integrating these datasets with spatial transcriptomic and high-resolution imaging data, both in mouse models and human tissue biopsies, we will explore how the geography of inflammation, including the spatial distribution of neutrophils and their interactions with tissue-resident immune and stromal cells3, orchestrates neutrophil functional heterogeneity.

A key component of the project is to map the temporal and spatial dynamics of neutrophil recruitment and adaptation in tissue. We will apply advanced mathematical and spatial modelling to analyse multiparameter tissue landscapes and infer how spatially constrained signals influence transcriptional regulatory networks using the recently developed Multiscale Spatial Analysis toolbox (MuSpAn). Lattice Light Sheet (LLS) microscopy will be used to visualise neutrophil morphology and behaviour in three dimensions, enabling the integration of morphological features with transcriptomic identity using machine learning and topological data analysis4. This multimodal approach will allow us to identify spatially restricted transcriptional states and how these relate to disease-driving or resolving neutrophil phenotypes.

This work will capitalise on our extensive transcriptomic and imaging datasets, as well as unique genetic models2. The results will enhance our understanding of the spatial and transcriptional logic of neutrophil plasticity and contribute to identifying new therapeutic strategies targeting pathogenic neutrophil states in tissue-specific inflammatory diseases5.

DISEASE RELEVANCE

Our proposed research focuses on the rapidly developing new field of neutrophil function in tissue, which has the potential to bring about a new class of therapeutics that target immune-pathogenic neutrophil states without the devastating effects of total neutrophil depletion. This is particularly relevant to diseases in which neutrophil presence correlates with heightened clinical disease activity, such as of the gut-joint axis. A new Biopsy Investigation of Oxford Synovial Cohort (BIOPSICO) for ultrasound-guided synovial biopsies of people with all forms of arthritis, as well as synovial and colonic biopsies of IBD patients with arthritis, just before the start of their standard of care treatment and then 3 and 6 months, has already allowed us to categorise forms of arthritis, where myeloid cells dominate vs those with a lymphpid pathotype. As a part of this project, we will capture diversity and cellular heterogeneity of these arthritis patients and examine our hypothesis that patients presented with co-morbidities, such as inflammatory bowel disease may be characterised by a distinct inflammatory neutrophil signature.

KEYWORDS

Neutrophils, transcriptional regulators, computational genomics/epigenomics, spatial transcriptomics, mathematical modelling

TRAINING OPPORTUNITIES

The Kennedy Institute is a world-renowned research centre and is housed in a state-of-the-art research facility. Training will be provided in a wide range of functional genomics approaches, cutting edge single cell platforms and computational pipelines. A core curriculum of lectures will be taken in the first term to provide a strong foundation across a broad range of subjects, including musculoskeletal biology, inflammation, epigenetics, translational immunology and data analysis. The student will attend weekly seminars within the department and those relevant in the wider University. They will present their research regularly to the department and the Genomics of Inflammation group, and at the Computational Genomics Forum. They will also attend external conferences at which they will present their research to a global audience. The student will also have the opportunity to work closely with members of the Wolfson Centre for Mathematical Biology at the Mathematical Institute, University of Oxford, and to further broaden their theoretical knowledge by attending lecture courses in mathematical biology, statistics and related subjects.

KEY PUBLICATIONS

1. Khoyratty T*, Ai Z*, Ballesteros I, Mathie S, … Udalova IA. Distinct transcription factor networks control neutrophil-driven inflammation. Nature Immunology, 2021 Sep;22(9):1093-1106.
2. Wang L, Luqmani R, Udalova IA. The role of neutrophils in rheumatic disease-associated vascular inflammation. Nature Reviews Rheumatology. 2022 Mar;18(3):158-170.
3. Thomas T, Friedrich M, Rich-Griffin C, Pohin M,…. Buckley CD. A longitudinal single-cell atlas of anti-tumour necrosis factor treatment in inflammatory bowel disease. Nat Immunol. 2024 Nov;25(11):2152-2165.
4. L Marsh, FY. Zhou, X Qin, X Lu, HM Byrne, HA Harrington (2024). Detecting Temporal shape changes with the Euler Characteristic Transform. Transactions of Mathematics and Its Applications 2024, 8(2): tnae002.
5. Devaprasad A, Ai Z, Mukherjee AK,…. Udalova IA (2024). Zfp263 is a transcriptional checkpoint of neutrophil development. BioRxiv. 2024.08.22.609132

THEMES

Immunology; Computational Genomics; Spatial transcriptomics; Mathematical modelling

CONTACT INFORMATION OF ALL SUPERVISORS

Prof Irina Udalova

Prof Helen Byrne

Dr Abhinandan Devaprasad