肌源性细胞分化的单细胞转录谱变化及细胞间通讯分析

Change of Single-cell Transcription Profile and Analysis of Intercellular Communication in Myogenic Cell Differentiation

【目的】基于单细胞转录组测序(single-cell RNA sequencing,scRNA-seq)揭示牛肌源性细胞分化中的基因表达谱变化,并探究介导细胞间通讯的配体-受体互作机制,为构建成肌分化的动态调控网络奠定基础。【方法】利用Seurat、ClusterProfiler、STRING、Cytoscape、CellChatDB和Monocle2等数据库或软件,对NCBI-GEO公共数据库中牛肌源性细胞单细胞转录组测序的原始数据进行了深入分析,包括细胞分群鉴定及差异基因表达谱、相关性、GO富集、PPI、细胞间通讯和拟时序分析等。【结果】根据基因表达相关性及标志性基因共鉴定出4个具有独特转录特征的细胞群Myoblasts、Myocytes、Fibroblasts和FAPs,通过Myoblasts亚群的基因表达谱比较及拟时序分化轨迹分析发现,各亚群之间异质性很强,其中Myoblasts_1为分化轨迹起点,Myoblasts_0和3处于分化早期阶段,而Myoblasts_2是肌肉特征表现最为明显的亚群,可能是临近形成Myocytes的后期阶段的Myoblasts;Myoblasts_2和Myocytes差异基因富集的肌肉相关GO term存在差异,各基因间存在复杂的蛋白互作关系;Myoblasts_0-5、Myocytes、Fibroblasts和FAPs同型或异型细胞间的通讯机制,涉及到PTN-NCL、IGF2-IGF2R和ANGPTL2-(ITGA5+ITGB1)等多种不同的配体-受体作用。【结论】肌源性细胞在分化过程中存在不断变化的基因表达谱和细胞间通讯,反映了复杂的动态异质性及分子调控机制。

【Objective】Based on single-cell RNA sequencing(scRNA-seq),the changes of gene expression profile during bovine myogenic cell differentiation were revealed,and the mechanisms of ligand-receptor interaction mediating intercellular communication were explored,which lays the foundation for the construction of dynamic regulatory network in myogenic differentiation.【Method】The scRNAseq raw data of bovine myogenic cells in NCBI-GEO public database were deeply analyzed,including the identification of cell cluster and the analyses of differential gene expression profile,correlation,GO enrichment,PPI,intercellular communication,and pseudotime,by using databases or softwares such as Seurat,ClusterProfiler,STRING,Cytoscape,CellChatDB,and Monocle2.【Result】Four cell clusters with unique transcriptional characteristics,including Myoblasts,Myocytes,Fibroblasts,and FAPs,were identified based on the gene expression correlations and marker genes.By comparing the gene expression profiles and analyzing the pseudotime differentiation trajectory of myoblast subclusters,it was found that there was strong heterogeneity among subclusters,of which Myoblasts_1 was the starting point of differentiation,Myoblasts_0 and 3 were in the early stage of differentiation,while Myoblasts_2 was the most obvious subcluster with muscle characteristics and they might be the late-stage Myoblasts adjacent to forming Myocytes.There were differences in muscle-related GO terms enriched by differential genes between Myoblasts_2 and Myocytes,and there were complex protein interactions among these genes.The communication mechanisms between homotypic or heterotypic cells of Myoblasts_0-5,Myocytes,Fibroblasts,and FAPs involved various ligand-receptor interactions,such as PTN-NCL,IGF2-IGF2R,and ANGPTL2-(ITGA5+ITGB1).【Conclusion】There are gradually changing of gene expression profiles and intercellular communication during the differentiation of myogenic cells,reflecting the complex dynamic heterogeneity and molecular regulatory mechanisms.