Single-cell transcriptional profiles in human skeletal muscle

Abstract

Skeletal muscle is a heterogeneous tissue comprised of muscle fiber and mononuclear cell types that, in addition to movement, influences immunity, metabolism and cognition. We investigated the gene expression patterns of skeletal muscle cells using RNA-seq of subtype-pooled single human muscle fibers and single cell RNA-seq of mononuclear cells from human vastus lateralis, mouse quadriceps, and mouse diaphragm. We identified 11 human skeletal muscle mononuclear cell types, including two fibro-adipogenic progenitor (FAP) cell subtypes. The human FBN1+ FAP cell subtype is novel and a corresponding FBN1+ FAP cell type was also found in single cell RNA-seq analysis in mouse. Transcriptome exercise studies using bulk tissue analysis do not resolve changes in individual cell-type proportion or gene expression. The cell-type gene signatures provide the means to use computational methods to identify cell-type level changes in bulk studies. As an example, we analyzed public transcriptome data from an exercise training study and revealed significant changes in specific mononuclear cell-type proportions related to age, sex, acute exercise and training. Our single-cell expression map of skeletal muscle cell types will further the understanding of the diverse effects of exercise and the pathophysiology of muscle disease.Skeletal muscle is a complex heterogeneous tissue consisting of multinucleated muscle fibers, immune cells, endothelial cells, muscle stem cells (satellite cells), non-myogenic mesenchymal progenitors (e.g., fibro-adipogenic progenitors, or FAPs), and other mononuclear cells 1 . To improve the understanding of skeletal muscle cell types and their transcriptional signatures, we studied human and mouse skeletal muscle mononuclear cells by single-cell RNA-sequencing and single human muscle fiber subtypes by RNA-seq.The majority of skeletal muscle is composed of the multinucleated fibers that facilitate movement. These muscle fibers include several fiber types of differing metabolic and functional properties 2-4 . While slow-twitch (or Type I) muscle fibers possess high oxidative capacity, fast-twitch (or Type II) muscle fibers have a high glycolytic capacity and are capable of supplying more power than Type I fibers 2-4 . Fiber-type composition differs across individuals and can change by as much as 10-30% during exercise training regimens 5-7 . Furthermore, the transcriptomic response to physical activity is different in each fiber-type as each fiber-type responds differently to different modes of exercise 8,9 . Crucially, muscle fibers secrete myokines, which both act locally within muscle tissue as well as influence other organs and tissues via hormone-like signaling 10 . Myokines may be responsible for the immune-, metabolism-, and cognition-related benefits of physical activity, as well as the chronic diseases that are caused by lack of physical activity (insulin resistance, cardiovascular disease, etc.) 10 .Besides multinucleated fibers, skeletal muscle contains many mononuclear cells, such as immune cells,...

Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits

“…Discussion Here we present snATAC-seq and snRNA-seq for human skeletal muscle and snATAC-seq for rat skeletal muscle, which we use to map the transcriptomes and chromatin accessibility of cell types present in skeletal muscle samples. The cell types identified are consistent with known biology and with previous studies of human (13) and mouse (16,17,20) skeletal muscle tissue. However, our use of single-nucleus rather than single-cell techniques allows us to capture muscle fiber nuclei, cell types missing from previously published snRNA-seq datasets.…”

“…The majority of the nuclei were assigned as type I or type II muscle fibers. Genes previously discovered to be preferentially expressed in type I vs. type II muscle fibers (13) were usually similarly preferentially expressed in our snRNA-seq data ( Fig. S11), validating the quality of the data and accuracy of muscle fiber type assignments.…”

Skeletal Muscle Extracellular Matrix – What Do We Know About Its Composition, Regulation, and Physiological Roles? A Narrative Review

“…Given the complexity of human skeletal muscle tissue involving multinucleated muscle fibers, immune cells, endothelial cells, muscle stem cells, non-myogenic mesenchymal progenitors, and other mononuclear cell (Bentzinger et al, 2013a), future research would be needed to elucidate the contribution of each of these cells to the structure and remodeling of the IMCT. Gene signatures derived, e.g., from RNA-seq of isolated muscle fibers and other cell types comprise a promising tool in the deconvolution of bulk skeletal muscle tissue (Rubenstein et al, 2020).…”

Peer Review #2 of "Alveolar soft-part sarcoma (ASPS) resembles a mesenchymal stromal progenitor: evidence from meta-analysis of transcriptomic data (v0.2)"

“…MSC are found in most tissues, these cells are capable of multipotent differentiation into bone, muscle, cartilage, adipocytes, marrow stromal cells, tenocytes, fibroblasts, endothelial and neural cells (Caplan 2007;Pittenger et al 2019). Tissues maintain a pool of MSC, with varying degrees of specialization, ready to dynamically replenish differentiated cells in response to signals associated with growth, homeostasis or damage (Rubenstein et al 2020). Prior to this study, ASPL-TFE3 had already been shown to immortalize embryonic mesenchymal cells (Tanaka et al 2017).…”