Identifying therapeutic targets for human chronic wounds using single cell transcriptomics and digital spatial profiling

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Chronic skin wounds are a major and increasing clinical burden as a result of an aging population and increased prevalence of risk factors including diabetes and obesity. These wounds are physically and psychologically debilitating, have a high risk of infection and reoccurrence, are the commonest cause of limb amputation and have a 5 year mortality rate of 45% (equivalent to colon cancer). Despite this significant burden of disease there is a profound paucity of science-led therapeutics. This is in part due to the lack of a precision medicine-based approach, with a dearth of comparative data exploring the links between human disease and pre-clinical models. Macrophages (MFs) are phenotypically plastic cells implicated both in supporting the 'normal' repair process and in playing detrimental roles in aberrant healing scenarios. Previous studies indicate that MFs are dysfunctional, exhibiting unrestrained activation in the context of impaired skin healing in both mouse and human. MFs therefore represent an attractive therapeutic target for chronic wounds. However, MFs are highly heterogeneous and dynamic cells, making it challenging to identify specific pathogenic and pro-repair subpopulations. We aim to provide a more systematic view on the dynamic process of skin wound repair in both acute and chronic wounds, and in both human and the mouse model our lab established, centring the role of macrophages. To circumvent this, we are currently using an unbiased single-cell RNA-sequencing approach in two major projects: 1) defining the pro-repair MF population in murine acute skin wounds and 2) identifying pathogenic MF populations in our novel pre-clinical model of human chronic wounds. We have also performed Nanostring Digital Spatial Profiling (DSP) to define the immunological milieu of human chronic wounds and support the identification of "core" pathways in skin ulcer formation and persistence. The initial phase of the project will focus on resolving MFs subpopulations from human acute wounds and chronic skin ulcers by DSP, coupled with multiparameter flow cytometry, histology and imaging. MFs in rodent skin wounds mirror a number of features of those identified in human chronic wounds. However, the precise corollary subpopulations between mouse pre-clinical models and human chronic skin wounds have not yet been defined. We will establish a method to integrate data from human acute and chronic skin wounds, comprising single-cell RNA-sequencing and DSP, we will resolve the pro-repair and ulcerogenic MF subpopulations. We will proceed to map the transcriptomes of these cells to those currently being identified in our mouse acute and chronic wound models using cutting edge computational approaches. This project will enable the identification of 'core' pathways regulating skin ulcer formation and persistence versus effective wound healing across species and thus allow the definition of tractable therapeutic targets for chronic skin wounds. We will perform intervention studies on our mouse models to validate these anti-ulcerogenic therapeutic approaches at a later stage. This project will be a collaborative effort between University of Edinburgh and University of Glasgow. It will enable the training of both cutting-edge computational analysis skills as well as in-vivo and in-vitro wet lab techniques.