Table_1_Single-Cell RNA-seq Analysis Reveals Cellular Functional Heterogeneity in Dermis Between Fibrotic and Regenerative Wound Healing Fates.xlsx

BackgroundFibrotic scars are common in both human and mouse skin wounds. However, wound-induced hair neogenesis in the murine wounding models often results in regenerative repair response. Herein, we aimed to uncover cellular functional heterogeneity in dermis between fibrotic and regenerative wound healing fates.MethodsThe expression matrix of single-cell RNA sequencing (scRNA-seq) data of fibrotic and regenerative wound dermal cells was filtered, normalized, and scaled; underwent principal components analysis; and further analyzed by Uniform Manifold Approximation and Projection (UMAP) for dimension reduction with the Seurat package. Cell types were annotated, and cell–cell communications were analyzed. The core cell population myofibroblast was identified and the biological functions of ligand and receptor genes between myofibroblast and macrophage were evaluated. Specific genes between fibrotic and regenerative myofibroblast and macrophage were identified. Temporal dynamics of myofibroblast and macrophage were reconstructed with the Monocle tool.ResultsAcross dermal cells, there were six cell types, namely, EN1-negative myofibroblasts, EN1-positive myofibroblasts, hematopoietic cells, macrophages, pericytes, and endothelial cells. Ligand and receptor genes between myofibroblasts and macrophages mainly modulated cell proliferation and migration, tube development, and the TGF-β pathway. Specific genes that were differentially expressed in fibrotic compared to regenerative myofibroblasts or macrophages were separately identified. Specific genes between fibrotic and regenerative myofibroblasts were involved in the mRNA metabolic process and organelle organization. Specific genes between fibrotic and regenerative macrophages participated in regulating immunity and phagocytosis. We then observed the underlying evolution of myofibroblasts or macrophages.ConclusionCollectively, our findings reveal that myofibroblasts and macrophages may alter the skin wound healing fate through modulating critical signaling pathways.

背景：纤维化疤痕在人类和鼠类皮肤伤口中均较为常见。然而，在鼠类伤口模型中诱发的伤口诱导性毛发生成往往导致再生修复反应。本研究旨在揭示真皮中纤维化与再生伤口愈合命运之间的细胞功能异质性。方法：对纤维化和再生伤口真皮细胞的单细胞RNA测序（scRNA-seq）数据表达矩阵进行筛选、归一化和缩放；进行主成分分析；并使用Seurat软件包进行均匀流形近似与投影（UMAP）降维分析。对细胞类型进行注释，并分析细胞间通讯。确定了核心细胞群体肌成纤维细胞，并评估了肌成纤维细胞与巨噬细胞之间配体和受体基因的生物功能。识别了纤维化和再生肌成纤维细胞与巨噬细胞之间的特异性基因。利用Monocle工具重建了肌成纤维细胞和巨噬细胞的时序动态。结果：在真皮细胞中，共存在六种细胞类型，即EN1阴性肌成纤维细胞、EN1阳性肌成纤维细胞、造血细胞、巨噬细胞、周细胞和内皮细胞。肌成纤维细胞与巨噬细胞之间的配体和受体基因主要调节细胞增殖和迁移、管状结构发育和TGF-β通路。分别识别了纤维化与再生肌成纤维细胞或巨噬细胞中差异表达的特异性基因。纤维化和再生肌成纤维细胞之间的特异性基因参与mRNA代谢过程和细胞器组织。纤维化和再生巨噬细胞之间的特异性基因参与调节免疫和吞噬作用。随后，我们观察了肌成纤维细胞或巨噬细胞的潜在进化过程。结论：综合来看，我们的研究揭示了肌成纤维细胞和巨噬细胞可能通过调节关键信号通路来改变皮肤伤口愈合的命运。