RNA sequencing of primary thymic, bone and skin mesenchymal cells

Purpose : Elucidate post-natal role of SCA1+ thymic mesenchymal cells (tMCs) and evaluate the functional overlap between thymic, bone and skin MCs. Method : By high speed cell sorting, we isolated primary MCs (Lin- SCA1+ cells) from mouse thymus, bone and skin. We extracted their respective total RNA and compared their transcriptome by high-throughput RNA-sequencing. Results : We found a total of 2036 differentially expressed genes (FC>5, p-adj<0.1 and RPKM>1) between the 3 MC populations. IPA analyses revealed that each MC population was enriched for genes associated to phagocyte chemotaxis. We also denoted 2850 genes with shared expression across MC populations. IPA analysis of those shared genes also revealed an enrichment for genes influencing phagocyte migration, chemotaxis and function. Finally, MC transcriptomes showed that all 3 MC populations were expressing genes associated with hematopoietic stem and progenitor cell (HSPC) support, strongly suggesting that MCs from thymic, bone and skin all possess the ability to support HSPCs. Conclusion : Overall, our study highlighted 3 potential novel roles for tMCs : 1) Promoting macrophage/monocyte chemotaxis, 2) Enhacing the apoptotic cell clearance process and 3) setting an inviting niche for hematopoietic progenitors. These novel biological roles for tMCs could have substantial effets on thymic biology. Finally, our RNA-seq data offer a valuable resource to the community that can be mined to explore multiple questions related mesenchymal cell biology. Transcriptome comparison between MC populations研究目的：阐明SCA1+胸腺间充质细胞（thymic mesenchymal cells, tMCs）的产后生物学功能，并评估胸腺、骨骼与皮肤来源间充质细胞之间的功能重叠情况。实验方法：本研究通过高速细胞分选技术，从小鼠胸腺、骨骼及皮肤组织中分离原代间充质细胞（Lin⁻ SCA1+细胞）；提取各组细胞的总RNA，采用高通量RNA测序技术比较其转录组差异。实验结果：本研究在3组间充质细胞群体中共鉴定出2036个差异表达基因（倍数变化>5、校正后P值<0.1且RPKM>1）。Ingenuity通路分析（Ingenuity Pathway Analysis, IPA）显示，各组间充质细胞均富集于吞噬细胞趋化相关基因集。此外，本研究还鉴定出2850个在3组间充质细胞中共有表达的基因，对该部分基因的IPA分析同样揭示其富集于影响吞噬细胞迁移、趋化及功能的基因集。最后，转录组分析显示，3组间充质细胞均表达与造血干祖细胞（hematopoietic stem and progenitor cell, HSPC）支持功能相关的基因，强烈提示胸腺、骨骼及皮肤来源的间充质细胞均具备支持造血干祖细胞的能力。研究结论：综上，本研究揭示了胸腺间充质细胞的3种潜在全新生物学功能：1）促进巨噬细胞/单核细胞趋化；2）增强凋亡细胞清除过程；3）为造血祖细胞构建适宜的造血微环境。上述胸腺间充质细胞的全新生物学功能可能对胸腺生物学特性产生显著影响。此外，本研究产生的RNA测序数据可为学界提供宝贵的公共资源，可用于探索与间充质细胞生物学相关的诸多科学问题。间充质细胞群体转录组比较