Department of Dermatology, The Third Affiliated Hospital of Soochow University, Changzhou, China.
Department of Dermatology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China.
Cell Biol Int. 2022 Sep;46(9):1480-1494. doi: 10.1002/cbin.11834. Epub 2022 Jun 8.
The aim of this study is to characterize the molecular properties of multilineage differentiating stress-enduring (Muse) cells compared with dermal fibroblasts (FBs) and to characterize differences in their transcriptomes and open chromatin regions that are involved in cellular plasticity. Assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) and RNA sequencing (RNA-seq) analyses was then performed on FBs and Muse cells. Subsequently, cell type-selective gene regulatory regions were identified by coalition analysis. Expression patterns of transcription factors (TFs) and signaling pathways intermediates were verified using quantitative real-time polymerase chain reaction and Western blot analyses. RNA-seq identified 2355 significantly differentially expressed genes (DEGs) that regulate the transcriptome, including 1222 upregulated and 1133 downregulated DEGs. The general panorama of RNA-seq and ATAC-seq analyses confirmed the differences in TFs and open chromatin regions between FBs and Muse cells. ATAC-seq analysis showed that Muse cells had more reproducible and meaningful peaks than FBs, and the peak signals were concentrated near promoter-transcription start site areas. In genomic regions that can be preferentially accessed in FBs and Muse cells, more than 200 TFs had binding motif sequences. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and coalition analyses identified differences in factors involved in the cell cycle and the protein kinase B (AKT) signaling pathway of FBs and Muse cells. The results of RNA-seq and ATAC-seq analyses clarified the genetic basis of the different biological properties of Muse cells and FBs. These results suggest that the cell cycle transition and the AKT signaling pathway may affect the morphology and biological characteristics of Muse cells.
本研究旨在比较多谱系分化应激耐受（Muse）细胞与真皮成纤维细胞（FB）的分子特性，并分析其参与细胞可塑性的转录组和开放染色质区域的差异。然后对 FB 和 Muse 细胞进行转座酶可及染色质高通量测序（ATAC-seq）和 RNA 测序（RNA-seq）分析。随后，通过联合分析鉴定细胞类型选择性基因调控区域。使用定量实时聚合酶链反应和 Western blot 分析验证转录因子（TFs）和信号通路中间产物的表达模式。RNA-seq 鉴定了 2355 个显著差异表达基因（DEGs），这些基因调控着转录组，包括 1222 个上调和 1133 个下调的 DEGs。RNA-seq 和 ATAC-seq 分析的总体情况证实了 FB 和 Muse 细胞之间 TF 和开放染色质区域的差异。ATAC-seq 分析表明，Muse 细胞的峰更具可重复性和意义，且峰信号集中在启动子-转录起始位点区域附近。在 FB 和 Muse 细胞中可优先访问的基因组区域中，有超过 200 个 TF 具有结合基序序列。基因本体论、京都基因与基因组百科全书和联合分析确定了 FB 和 Muse 细胞中参与细胞周期和蛋白激酶 B（AKT）信号通路的因子的差异。RNA-seq 和 ATAC-seq 分析的结果阐明了 Muse 细胞和 FB 不同生物学特性的遗传基础。这些结果表明，细胞周期转换和 AKT 信号通路可能影响 Muse 细胞的形态和生物学特征。
