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  • Project No: KIR-2023/17
  • Intake: 2023 KIR Non Clinical

Project overview 

Despite the importance of fibroblasts in human disease this is an unexploited area with no clinically approved therapies directly targeting stromal function. One of the key research foci of the group is understanding human fibroblast – macrophage cross talk in Immune Mediated Inflammatory Disease (IMID) and cancer using human culture systems, combing multiplex imaging with spatial genonomics, single cells RNA sequencing with functional assays. In this DPhil project, we will use multi-omics based approach (scRNAseq (10x) analysis, multiplex imaging (Cell Dive), high dimensional flow cytometry) to identify immunoreceptor tyrosine-based inhibitory motif (ITIM) domain expressing receptor expression in fibroblasts and then functionally determine how they regulate fibroblast function using CRISPR/Cas9 targetting of primary human fibroblasts using engineered 3D culture synovial joint system incorporating synovial primary human fibroblasts and macrophage systems that replicates key feature of arthritic disease and other IMIDs and 3D cancer spheroid model of human colorectal and prostate cancer combining transformed epithelium with cancer associated fibroblasts (CAFs) with tumour macrophages. These outcomes will be validated in human biopsies using multiplex immunohistochemistry and then using tissue specific mouse gene knock-out models. Together these datasets (in vitro and in vivo) will provide experimental validation of ITIM domain containing proteins in fibroblast function in human disease. 

Keywords 

Immunology, organoids, imaging, cancer, spatial genomics 

Training opportunities 

The successful candidate will be embedded within the Kennedy Institute of Rheumatology (KIR), Oxford. The KIR is a world-leading centre in the fields of tissue biology, inflammation, and repair, with a strong emphasis on clinical translation. They will receive supervision and training by an experienced team of scientists interested biology and genetics of inflammatory disease and cancer. They will work closely with collaborators withing the Institute and the wider community in Oxford.

Specific training opportunities/benefits include:

• Organoid culture systems
• Systems Immunology
• High dimensional imaging and image analysis

Highly collaborative environment with expertise ranging from translational immunology to computational biology. 

Key publications 

  1. Cross-tissue, single-cell stromal atlas identifies shared pathological fibroblast phenotypes in four chronic inflammatory diseases. Korsunsky I, Wei K, Pohin M, Kim EY, Barone F, Major T, Taylor E, Ravindran R, Kemble S, Watts GFM, Jonsson AH, Jeong Y, Athar H, Windell D, Kang JB, Friedrich M, Turner J, Nayar S, Fisher BA, Raza K, Marshall JL, Croft AP, Tamura T, Sholl LM, Vivero M, Rosas IO, Bowman SJ, Coles M, Frei AP, Lassen K, Filer A, Powrie F, Buckley CD, Brenner MB, Raychaudhuri S. Med . (2022) May 26:S2666-6340(22)00184-2
  2. Nayar S, Campos J, Smith CG, Iannizzotto V, Gardner DH, Mourcin F, Roulois D, Turner J, Sylvestre M, Asam S, Glaysher B, Bowman SJ, Fearon DT, Filer A, Tarte K, Luther SA, Fisher BA, Buckley CD, Coles MC*, Barone F*, Immunofibroblasts are pivotal drivers of tertiary lymphoid structure formation and local pathology. Proc Natl Acad Sci U S A. 2019 Jun 18. pii: 201905301. doi: 10.1073/pnas.1905301116. (*Co-corresponding author)
  3. 5. Croft AP, Campos J, Jansen K, Turner JD, Marshall J, Attar M, Savary L, Perlman H, Barone F, McGettrick HM, Fearon DT, Wei K, Raychaudhuri S, Lorsunsky I, Brenner MB, Coles M, Sansom SN, Filer A, Buckley CD, Pathologically distinct fibroblast subsets drive inflammation and tissue damage in arthritis, Nature. 2019
  4. Cosgrove J, Novkovic M, Albrecht S, Pikor NB, Zhou Z , Onder L, Mörbe U, Cupovic J, Miller H, Alden K, Thuery A, O'Toole P, Pinter R, Jarrett S, Taylor E, Venetz D, Heller M, Uguccioni M, Legler DF, Lacey CJ, Coatesworth A, Polak WG, Cupedo T, Manoury B, Thelen M, Stein JV, Wolf M, Leake MC, Timmis J, Ludewig B, Coles MC, B-cell Zone Reticular Cell Microenvironments Shape CXCL13 Gradient Formation, Nature Communications, 2020, Jul 22;11(1):3677. doi: 10.1038/s41467-020-17135-2
  5. Davidson S, Coles M, Thomas T, Kollias G, Ludewig B, Turley S, Brenner M, Buckley CD. Fibroblasts as immune regulators in infection, inflammation and cancer. Nat Rev Immunol. 2021 Nov;21(11):704-717. doi: 10.1038/s41577-021-00540-z.

Key themes 

Immunology, Systems Biology, Imaging, cancer