Tracing the origin of regenerative and scarring fibroblasts during wound healing with single-cell technologies

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PROJECT SUMMARY Wound fibroblasts play a crucial role during wound healing by producing extracellular matrix (ECM), providing a physical framework for cell repopulation, replenishing the skin's structural strength. While wound fibroblasts promote skin healing, in adults this process is associated with changes that lead to scarring and can result in non-functional repair. Here, we hypothesize that the comparison of wound fibroblast differentiation during regeneration and scarring conditions will identify novel molecular mechanisms to diminish scarring. Contrasting the differentiation paths of wound fibroblasts in regenerative and scarring processes will increase our understanding of the molecular mechanisms that drive these processes and could highlight new targets for therapeutic approaches. In this proposal, we aim to overcome previous technical limitations surrounding wound fibroblast heterogeneity and a lack of specific markers by adapting and deploying novel single-cell genomic technologies in an established wound healing model. This approach will enable the high-resolution deconstruction of the intrinsic and extrinsic components driving wound fibroblast differentiation to heterogeneous states during regeneration and scarring. First, in Aim 1, we will adapt a single-cell tracking tool developed in our laboratory, CellTagging, for deployment in the context of regenerative and scarring in vivo wound healing. CellTagging is the unique labeling of cells using virus-delivered barcodes that are expressed as transcripts, enabling capture of lineage information in parallel with cell identity and function. We will adapt our CellTagging technology to track the wound fibroblast origins and differentiation during wound regenerative and scarring healing. This strategy will consist of labeling fibroblasts recovered from embryonic (promote regeneration) and adult (promote scarring) uninjured skin, followed by their transplant into a host and subsequent wounding. Here, we aim to characterize heterogeneity and origin of wound fibroblasts tracing their lineage back to fibroblast populations in uninjured skin. We will use our proprietary gene regulatory network reconstruction algorithm, CellOracle, to identify key regulatory factors driving wound fibroblast differentiation during regeneration and scarring conditions. In our complementary Aim 2, we propose to investigate wound fibroblast interactions with their cellular microenvironment in situ. To achieve this, we will perform multiplex error-robust fluorescence in situ hybridization (MERFISH) on sections from wounds transplanted with embryonic (regenerative) or adult (scarring) fibroblasts to identify cell populations based on the expression of specific markers in the wound bed. Using established computational tools, we will assign cell identities and states to individual cells within the tissue, creating a map of gene expression projected onto wound bed histology. This will allow us to identify key interacting partners for regenerative and scarring fibroblasts. Together, the success of the aims proposed here will support unprecedented quantitation of wound fibroblast differentiation and origins. This knowledge will enable the identification of key molecular mechanisms that could be used to promote regeneration and diminish scarring during wound healing.