Multi-omic analysis reveals retinoic acid molecular drivers for fibrosis and regenerative repair in skin fibrosis [Spatial transcriptomics]

In the skin, tissue injury results in fibrosis in the form of scars composed of dense extracellular matrix deposited by fibroblasts. The therapeutic goal of regenerative wound healing has remained elusive, in part because principles of fibroblast programming and adaptive response to injury remain incompletely understood. Here, we present a multimodal -omics platform for the comprehensive study of cell populations in complex tissue, which has allowed us to characterize the cells involved in wound healing using a bleomycin induced ifibrosis model. We employ a bleomycin skin models that recapitulates human tissue repair kinetics. Through integrated analysis of single cell chromatin landscapes and gene expression states, coupled with spatial transcriptomic profiling, we are able to impute fibroblast epigenomes with temporospatial resolution. This has allowed us to reveal potential mechanisms controlling fibroblast fate during migration, proliferation, and differentiation following skin injury, and thereby reexamine the canonical phases of wound healing. These findings have broad implications for the study of tissue repair in complex organ systems. Overall design: Mouse wound tissue transcriptomes were profiles using single cell RNA sequencing, single cell ATAC sequencing, and Visium spatial transcriptomics. For single-cell RNA sequencing, wound cells were harvested at 3 timepoints over the course of wound healing (POD 12, 21, 28) and normal skin as a control. For single-cell ATAC sequencing and visium similiar time points were harvested. For single cell RNA sequencing, cells treated with a cyp26b1 inhibitor were also assessed referred to as POD 12 + TREATMENT.