RNA sequencing of primary thymic, bone and skin mesenchymal cells. Mus musculus

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-adj1) 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. Overall design: 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，并系统评估胸腺、骨骼与皮肤来源的间充质细胞（mesenchymal cells, MCs）之间的功能重叠程度。
实验方法：采用高速细胞分选技术（high speed cell sorting），从小鼠胸腺、骨骼及皮肤组织中分离原代间充质细胞（primary MCs，即Lin⁻ SCA1+细胞）。提取各组细胞的总RNA，通过高通量RNA测序（high-throughput RNA-sequencing）比较其转录组表达谱差异。
研究结果：在三类间充质细胞群中，共鉴定出2036个差异表达基因（FC>5，p-adj1）。Ingenuity通路分析（IPA）显示，每一类间充质细胞群均显著富集于与吞噬细胞趋化相关的基因集。此外，我们还鉴定出2850个在三类间充质细胞群中共有表达的基因；对这些共有基因的IPA分析同样显示，其富集于影响吞噬细胞迁移、趋化及功能的基因集。最后，三类间充质细胞的转录组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：本研究整体揭示了胸腺间充质细胞的3项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（niche）。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测序数据可为科研共同体提供极具价值的公共资源，可用于挖掘与间充质细胞生物学相关的多类科学问题。
研究整体设计：不同来源间充质细胞群的转录组比较分析