Proietti, D. | bioRxiv Science

bioRxiv2022

Spatially resolved transcriptomics reveals innervation-responsive functional clusters in skeletal muscle

Striated muscle is a highly organized structure composed by well-defined anatomical domains with integrated but distinct assignments. So far, the lack of a direct correlation between tissue architecture and gene expression has limited our understanding of how each unit responds to physio-pathologic contexts. Here, we show how the combined use of spatially resolved transcriptomics and immunofluorescence can bridge this gap by enabling the unbiased identification of such domains and the characterization of their response to external perturbations. Using a spatiotemporal analysis, we followed the changes in the transcriptomics profile of specific domains in muscle in a model of denervation. Furthermore, our approach allowed us to identify the spatial distribution and nerve dependence of atrophic signalling pathway and polyamine metabolism to glycolytic fibers. Indeed, we demonstrate a pronounced alteration of polyamine homeostasis upon denervation. Our dataset will serve as a resource for future studies of the mechanisms underlying skeletal muscle homeostasis and innervation. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=188 HEIGHT=200 SRC="FIGDIR/small/486563v1_ufig1.gif" ALT="Figure 1"> View larger version (59K): org.highwire.dtl.DTLVardef@6ee767org.highwire.dtl.DTLVardef@11a4eb4org.highwire.dtl.DTLVardef@25228eorg.highwire.dtl.DTLVardef@1ffa60a_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2020

scRNA-seq-based analysis of skeletal muscle response to denervation reveals selective activation of muscle-resident glial cells and fibroblasts

Developmental synaptogenesis toward formation of neuromuscular junctions (NMJs) is regulated by the reciprocal exchange of signals derived from nerve or muscle ends, respectively. These signals are re-deployed in adult life to repair NMJ lesions. The emerging heterogeneity of skeletal muscle cellular composition and the functional interplay between different muscle-resident cell types activated in response to homeostatic perturbations challenge the traditional notion that muscle-derived signals uniquely derive from myofibers. We have used single cell RNA sequencing (scRNA-seq) for a longitudinal analysis of gene expression profiles in cells isolated from skeletal muscles subjected to denervation by complete sciatic nerve transection. Our data show that, unlike muscle injury, which massively activates multiple muscle-resident cell types, denervation selectively induced the expansion of two cell types - muscle glial cells and activated fibroblasts. These cells were also identified as putative sources of muscle-derived signals implicated in NMJ repair and extracellular matrix (ECM) remodelling. Pseudo-time analysis of gene expression in muscle glial-derived cells at sequential timepoints post-denervation revealed an initial bifurcation into distinct processes related to either cellular de-differentiation and commitment to specialized cell types, such as Schwann cells, or ECM remodeling. However, at later time points muscle glial-derived cells appear to adopt a more uniform pattern of gene expression, dominated by a reduction of neurogenic signals. Consensual activation of pro-fibrotic and pro-atrophic genes from fibroblasts and other muscle-resident cell types suggests a global conversion of denervated muscles into an environment hostile for NMJ repair, while conductive for progressive development of fibrosis and myofiber atrophy.

cell biology↗