Application of single cell omics to dissect tissue-immune cell crosstalk and identify targetable mediators of tissue fibrosis
- Project No: #OxKEN-2021/14
- Intake: OxKEN
Advances in single cell technologies have revolutionized our ability to dissect cellular and molecular heterogeneity and identify the key cell-cell interactions in healthy and diseased tissues. This is a cross-disciplinary project that brings together scientific and clinical expertise in musculo-skleletal, bone marrow, cardiac and lung fibrosis. The goal is to develop and interrogate parallel single cell genomic datasets of samples from tissue fibrosis and to perform comprehensive analysis of a shared pathological pathway, to facilitate discovery of novel anti-fibrosis targets and to develop pre-clincial models to validate these ‘hits’. We believe that a multi-organ and cross-disciplinary approach greatly increases the likelihood of identifying clinically-relevant targets, with potential for identifying a universal fibrosis ‘hit’ amenable to small molecule or antibody targeting.
Fibrosis is a pathological process in which healthy tissue is replaced by excessive, abnormal extracellular matrix proteins leading to loss of tissue architecture and function, and consequential morbidity and mortality1. This can occur secondary to repair from mechanical or chemical injury, in response to autoimmune reactions, or in association with malignant transformation (cancer-associated fibrosis). The overall burden of tissue fibrosis is substantial, and has been estimated as affecting 1 in 4 people globally2. There is major unmet clinical need for effective strategies to reverse or prevent tissue fibrosis, and the potential clinical and commercial impact of a successful anti-fibrosis therapy is great, given the relevance to many common disorders affecting different body organs, including the musculoskeletal system (e.g. Dupytren’s Disease, keloid scarring, scleroderma, frozen shoulder), heart, lungs, skin, liver, kidneys and bone marrow. Many studies have implicated a key role for interactions between inflammatory myeloid cells and stromal cells in fibrotic disorders. Advances in single cell technologies now offer an opportunity to conduct a more comprehensive and unbiased assessment of the cellular and molecular pathways involved than has previously been possible using studies of tissue samples in ‘bulk’. In this project, we propose applying state-of-the-art single cell transcriptomic and proteomic assays and in-house computational pipelines to perform parallel studies of pulmonary, cardiac and bone marrow fibrosis.
METHODS/TECHNIQUES TO BE USED
- Single cell multi-omic analysis of primary tissue biopsies from patients and appropriate controls, including biopsies from Dupytren’s Disease, Frozen Shoulder, human myocardium3,4, lung tissue from patients with idiopathic pulmonary fibrosis5-7 and bone marrow biopsies from patients with bone marrow fibrosis8,9. All ethical approvals are in place and extensive tissue banks collated.
- With support from an experienced computational biologist, you would apply computational pipelines to analyse the data and identify disease-specific cell types and cell-cell interactions. The ability to compare multiple distinct tissue types and in malignant and non-malignant pathologies would greatly increase the power of the study and likelihood of identifying a clinically relevant, tractable target.
- Validate targets using in vitro fibrosis deposition assays3,10 and animal models.
Example data from cardiac biopsy: Fig. 1. Trascriptional clusters of scRNAseq of human cardiac fibrobalsts (A) and differentially expressed genes (B-C) assessed by SMART-seq2 scRNAseq in matched patients with fibrosis and controls; assessmen of collagen-1 accumulation (by scar-in-a-jar, top, D) and cell migration (by wound healing assay, bottom, D) in human cardiac fibroblasts.
- Eckes B, Eming SA. Tissue fibrosis: a pathomechanistically unresolved challenge and scary clinical problem. Exp Dermatol. 2017;26(2):135-136.
- Zhao X, Kwan JYY, Yip K, Liu PP, Liu FF. Targeting metabolic dysregulation for fibrosis therapy. Nat Rev Drug Discov. 2020;19(1):57-75.
- Moreira L, Takawale A, Hulsurkar M, et al. Calcitonin paracrine signaling controls atrial fibrogenesis and arrhythmia. . Nature. 2020;In press.
- Reilly SN, Liu X, Carnicer R, et al. Up-regulation of miR-31 in human atrial fibrillation begets the arrhythmia by depleting dystrophin and neuronal nitric oxide synthase. Sci Transl Med. 2016;8(340):340ra374.
- Mann E, Menon M, Knight S, et al. Longitudinal immune profiling reveals distinct features of COVID-19 pathogenesis. Science Immunology (in press). 2020.
- E Fraser, L Denney, K Blirando, et al. Type-1 IFN primed monocytes in pathogenesis of idiopathic pulmonary fibrosis. BioRxiv 2020;doi 10.1101/2020.01.16.908749.
- Peng Y, Mentzer AJ, Liu G, et al. Broad and strong memory CD4(+) and CD8(+) T cells induced by SARS-CoV-2 in UK convalescent individuals following COVID-19. Nat Immunol. 2020.
- Psaila B, Wang G, Rodriguez-Meira A, et al. Single-Cell Analyses Reveal Megakaryocyte-Biased Hematopoiesis in Myelofibrosis and Identify Mutant Clone-Specific Targets. Mol Cell. 2020;78(3):477-492 e478.
- Rodriguez-Meira A, Buck G, Clark SA, et al. Unravelling Intratumoral Heterogeneity through High-Sensitivity Single-Cell Mutational Analysis and Parallel RNA Sequencing. Mol Cell. 2019;73(6):1292-1305 e1298.
- Colombo M, Brierley C, Wang G, et al. A novel tissue-specific platform for prioritisation and validation of novel inhibitors of bone marrow fibrosis using human bone marrow stromal cells. European Haematology Association Annual Meeting Abstract 2020.
CONTACT INFORMATION OF ALL SUPERVISORS
NDORMS (Furniss), MRC Weatherall Institute of Molecular Medicine (Psaila, Mead, Ho groups) and Division of Cardiovascular Medicine (Reilly).