目的 研究颌骨和长骨全骨髓细胞组成并比较下颌骨来源间充质干细胞（M-MSC）与股骨来源间充质干细胞（F-MSC）异质性，探讨不同谱系来源骨间充质干细胞（MSC）的功能特性差异。 方法 对文献中下颌骨与股骨全骨髓单细胞RNA测序（scRNA-seq）数据集，使用R语言的Seurat包进行数据处理，参考既往文献报道标记基因对亚群进行细胞注释。计算M-MSC与F-MSC的差异表达基因，并对MSC与其他亚群间的相互作用进行细胞通讯分析。分别对上下调差异基因进行基因本体功能注释（GO）和京都基因与基因组百科全书（KEGG）富集分析，并对M-MSC和F-MSC的所有基因进行基因集富集分析（GSEA）。 结果 scRNA-seq分析显示下颌骨与股骨骨髓细胞组成相同，但特定细胞亚群所占比例存在差异。差异基因计算显示M-MSC和F-MSC间存在显著差异基因。细胞通讯分析显示M-MSC和F-MSC与骨髓其他细胞亚群相互作用的配受体对数存在差异。进一步GO、KEGG、GSEA分析显示相比于F-MSC，M-MSC具有更高的细胞外基质生成潜能，但对骨髓其他细胞，尤其是免疫细胞的调控能力较低。 结论 M-MSC和F-MSC在基因表达模式与上调信号通路上存在较大差异，这些差异可能与颌骨和长骨发育来源以及功能特性不同密切相关。 Objective To study the whole bone marrow cellular composition of jaw and long bones, and further analyze the heterogeneity of mesenchymal stem cells (MSCs) derived from these two tissue, aiming at exploring the differences in functional characteristics of bone MSCs from different lineage sources. Methods The Seurat package of R language was used to analyze the mandibular and femur whole bone marrow single-cell RNA-sequencing (scRNA-seq) datasets in the literature, and the subpopulations were annotated by reference to the marker genes reported by previous studies. The differentially expressed genes between mandible-derived MSCs (M-MSCs) and femur-derived MSCs (F-MSCs) were calculated, and cell-cell communication analysis between M-MSCs or F-MSCs with other cell populations was performed. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed on up-regulated and down-regulated differentially expressed genes of M-MSCs, and Gene Set Enrichment Analysis (GSEA) was performed on M-MSCs or F-MSCs. Results cRNA-seq analysis showed that the mandible and femur had the same bone marrow cell composition, but there were differences in the proportion of specific cell populations. Also, there were significantly differentially expressed genes between M-MSCs and F-MSCs. In addition, cell-cell communication analysis revealed differences in numbers of ligand-receptor pairs between M-MSCs or F-MSCs with other cell populations. Furthermore, GO, KEGG and GSEA analysis showed that M-MSCs had higher extracellular matrix production potential than F-MSCs, but had lower ability to regulate other cells in the bone marrow, especially immune cells. Conclusions M-MSCs and F-MSCs showed distinct differences in the gene expression pattern and up-regulated signaling pathways, which may be closely related to the developmental sources and functional characteristics of jaw and long bones.
Abstract
Objective To study the whole bone marrow cellular composition of jaw and long bones, and further analyze the heterogeneity of mesenchymal stem cells (MSCs) derived from these two tissue, aiming at exploring the differences in functional characteristics of bone MSCs from different lineage sources. Methods The Seurat package of R language was used to analyze the mandibular and femur whole bone marrow single-cell RNA-sequencing (scRNA-seq) datasets in the literature, and the subpopulations were annotated by reference to the marker genes reported by previous studies. The differentially expressed genes between mandible-derived MSCs (M-MSCs) and femur-derived MSCs (F-MSCs) were calculated, and cell-cell communication analysis between M-MSCs or F-MSCs with other cell populations was performed. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed on up-regulated and down-regulated differentially expressed genes of M-MSCs, and Gene Set Enrichment Analysis (GSEA) was performed on M-MSCs or F-MSCs. Results cRNA-seq analysis showed that the mandible and femur had the same bone marrow cell composition, but there were differences in the proportion of specific cell populations. Also, there were significantly differentially expressed genes between M-MSCs and F-MSCs. In addition, cell-cell communication analysis revealed differences in numbers of ligand-receptor pairs between M-MSCs or F-MSCs with other cell populations. Furthermore, GO, KEGG and GSEA analysis showed that M-MSCs had higher extracellular matrix production potential than F-MSCs, but had lower ability to regulate other cells in the bone marrow, especially immune cells. Conclusions M-MSCs and F-MSCs showed distinct differences in the gene expression pattern and up-regulated signaling pathways, which may be closely related to the developmental sources and functional characteristics of jaw and long bones.
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