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Single cell RNA sequencing time-course of mesenchymal progenitors during regeneration after notexin induced muscle injury

ABSTRACT: After tissue injury mesenchymal progenitors undergo a transient proliferative expansion, morphological transition and migration from their perivascular niche. To gain transcriptomic insights into the MP function in regeneration, a muscle-injury model was employed to activate MPs and follow their contribution to tissue regeneration. To compliment the population RNA seq profile previously obtained and to uncover the suspected heterogeneity of MPs in this context, tdTomato positive cells from selected timepoints were profiled by single cell RNA sequencing.

ORGANISM(S): Mus musculus

PROVIDER: GSE110037 | GEO | 2019/12/05

REPOSITORIES: GEO

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Project description:Tissue macrophages (MPs) develop distinctive functions due to unique transcriptional programs driven by local environmental ques. In the intestine, it is known that MPs are heterogeneous cells that differentiate from blood monocytes and embryonic precursors, and are essential for homeostasis with the vast microbiome through their ability to kill invading microbes, clear apoptotic cells, and produce regulatory cytokines. However, the full extent of MP heterogeneity, their developmental relationships, and how the intestinal microbiota affects MP generation is not known. Here, we performed single cell RNA sequencing of colonic myeloid cells from specific pathogen free (SPF) and germ free (GF) C57BL/6 mice and found extensive heterogeneity of colon MP, with at least six different identifiable populations, with less heterogeneity of dendritic cells (DCs). Unsupervised modeling of developmental pathways combined with inference of gene regulatory networks suggested two major trajectories from common CCR2+ precursors resulting in CD11c+CD9+MMRintCD121b+ and CD11c-CD9intMMRhiCD121b- MP populations with unique transcription factors activities to coordinate downstream target molecules. The generation of both mature populations of colon MPs was impaired in germ-free mice, which coincided with the appearance of a dominant unique population of MPs, whereas the generation of DC populations in GF mice were unaffected or increased. Furthermore, the two major MP populations were clearly distinct from other populations regarding their gene expression profile, localization within the lamina propria, and ability to phagocytose macromolecules from the blood. These data uncover the diversity of intestinal myeloid cell populations, highlight the importance of microbiota on the unique developmental as well as anatomical and functional fates of colon MPs. We anticipate that these findings will form the basis for future studies on how tissue myeloid cell development is influenced either directly or indirectly by signals from endogenous microbiota in the intestine, as well as other tissues.

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Single cell RNA sequencing time-course of mesenchymal progenitors during regeneration after notexin induced muscle injury

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