sc-RNA sequencing of skeletal muscle macrophages during T. gondii infection and injury

The proper coordination of macrophages is essential for skeletal muscle repair. However, the full heterogenity of macrophages responding to injury has yet to be elucidated on the single-cell level. Furthermore, chronic inflammation may shift macrophage heterogeneity at steady-state and affect the generation of heterogeneity necessary for tissue repair. We use scRNA-sequencing to determine the heterogeneity of skeletal muscle macrophages during infection and wound repair (uninfected and infected). We identify multiple transcriptionally distinct macrophage subsets during injury in uninfected mice as well as during infection at steady-state. Interestingly, in response to injury, infected skeletal muscle macrophages fail to generate certain subsets of reparative macrophages in a timely fashion. 8-12 week old C57BL/6 mice were orally infected with 5 ME49 T.gondii cysts and allowed to reach d24 post-infection to establish chronicity. Age and sex-matched uninfected and infected mice were given cardiotoxin naja pallida i.m. in one leg at 24 days post-infection. Contralateral leg was used as an uninjured control. Muscles were harvested at 4 days-post injury and prepared into a single cell suspension. Single cell suspensions were bulk sorted for macrophages by 7AAD-CD45+CD64+MerTK+ cells. Sorted cells from each group was individually assessed for and loaded onto the 10X Genomics Chromium platform for single-cell capture. cDNA libraries were constructed and subsequently sequenced on the Illumina platform. Experimental groups were performed in duplicate.