Single-Cell Multiomics Analysis of Early Wound Response Programs in the Mouse Corneal Epithelium.

IF 5 2区 医学 Q1 OPHTHALMOLOGY
Zhao-Jing Lu, Jin-Guo Ye, Jing-Ni Li, Jiang-Bo Liang, Ming Zhou, Qiu-Ling Hu, Qi-Kai Zhang, Yu-Heng Lin, Ying-Feng Zheng
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引用次数: 0

Abstract

Purpose: Wound healing is crucial for restoring homeostasis in living organisms. Although wound response mechanisms have been studied extensively, the gene regulatory programs involved remain to be elucidated. Here, we used single-cell RNA sequencing (RNA-seq) and ATAC sequencing (ATAC-seq) analysis to profile the regulatory landscape of mouse corneal epithelium in early wound response.

Methods: We used our previously published single-cell data sets of homeostatic adult mouse corneal epithelium as the unwounded group. The wounded group data sets were obtained by sequencing the epithelium after an annular epithelial wound. Following the integration of the relevant data sets, the Seurat and ArchR packages were employed for single-cell RNA-seq and single-cell ATAC-seq data processing and downstream analysis, respectively. The Monocle 2 was used for pseudo-time analysis, CellChat for intercellular communication analysis, and pySCENIC for analyzing transcription factors. The expression of key genes was validated via immunofluorescence staining and quantitative real-time PCR.

Results: Our data show that the number of cell type-specific genes decreases and the number of common transcriptional responses increases in early wound response. Concurrently, we find that the chromatin accessibility landscape undergoes significant changes across all epithelial cell types and that the wound-induced open regions are similarly distributed across the genome. Motif enrichment analysis shows that Fosl1/AP-1 binding site is highly enriched among the opened regions. However, by assessing the correlation between changes in chromatin accessibility and gene expression, we observe that only a small subset of wound-induced genes shows a high correlation with the accessibility of nearby chromatin.

Conclusions: Our study provides a detailed single-cell landscape for transcriptomic and epigenetic changes in mouse corneal epithelium during early wound response, which improved our understanding of the mechanisms of wound healing.

小鼠角膜上皮早期创伤反应程序的单细胞多组学分析。
目的:伤口愈合是生物体恢复体内平衡的关键。虽然创伤反应机制已被广泛研究,但涉及的基因调控程序仍有待阐明。在这里,我们使用单细胞RNA测序(RNA-seq)和ATAC测序(ATAC-seq)分析来分析小鼠角膜上皮在早期伤口反应中的调控景观。方法:我们使用先前发表的稳态成年小鼠角膜上皮单细胞数据集作为未损伤组。损伤组数据集是通过对环形上皮损伤后的上皮进行测序获得的。在整合相关数据集后,分别使用Seurat和ArchR软件包进行单细胞RNA-seq和单细胞ATAC-seq数据处理和下游分析。Monocle 2用于伪时间分析,CellChat用于细胞间通讯分析,pySCENIC用于转录因子分析。通过免疫荧光染色和实时荧光定量PCR验证关键基因的表达。结果:我们的数据显示,在早期创伤反应中,细胞类型特异性基因的数量减少,共同转录反应的数量增加。同时,我们发现染色质可及性在所有上皮细胞类型中都经历了显著的变化,并且伤口诱导的开放区域在基因组中分布相似。Motif富集分析表明,Fosl1/AP-1结合位点在开放区域高度富集。然而,通过评估染色质可及性变化与基因表达之间的相关性,我们观察到只有一小部分伤口诱导基因与附近染色质的可及性表现出高度相关。结论:我们的研究提供了小鼠角膜上皮在早期创伤反应过程中转录组学和表观遗传学变化的详细单细胞景观,提高了我们对伤口愈合机制的理解。
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来源期刊
CiteScore
6.90
自引率
4.50%
发文量
339
审稿时长
1 months
期刊介绍: Investigative Ophthalmology & Visual Science (IOVS), published as ready online, is a peer-reviewed academic journal of the Association for Research in Vision and Ophthalmology (ARVO). IOVS features original research, mostly pertaining to clinical and laboratory ophthalmology and vision research in general.
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