Single-cell transcriptional profiles in human skeletal muscle
Open accessAbstract
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.
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In vivo measurement of ribosomal turnover in humans frequently forces researchers to rely on bulk total RNA quantification from percutaneous biopsies.
“In vivo measurement of ribosomal turnover in humans frequently forces researchers to rely on bulk total RNA quantification from percutaneous biopsies”
From Ribosome Biogenesis as a Putative Bottleneck to Skeletal Muscle Hypertrophy: Mechanisms, Human Evidence, and Practical Modulators (2026) · cites this paper as [49]
The Methods (Microarray dataset for deconvolution; page unavailable) describe extracting and quantifying total RNA from homogenized muscle samples, and the Methods (Mononuclear cell scRNA-seq; page unavailable) describe a human muscle biopsy. Neither passage links that quantification to in vivo ribosomal turnover or says researchers frequently must rely on it; the biopsy is not described as percutaneous. (LLM, conf=0.76)
Experimental — accuracy not yet measuredIn human clinical and sports science trials, total bulk RNA from muscle homogenates serves as the ubiquitous primary proxy for cellular ribosomal density.
“In human clinical and sports science trials, the quantification of total bulk RNA extracted from muscle homogenates serves as the ubiquitous primary proxy for cellular ribosomal density [36,49].”
From Ribosome Biogenesis as a Putative Bottleneck to Skeletal Muscle Hypertrophy: Mechanisms, Human Evidence, and Practical Modulators (2026) · cites this paper as [49]
The Methods section (“Microarray dataset for deconvolution”; page unavailable) describes extracting and quantifying total RNA from homogenized muscle samples. It does not say that total RNA is a proxy for cellular ribosomal density or that this is the ubiquitous primary measure in human clinical and sports science trials. (LLM, conf=0.83)
Experimental — accuracy not yet measuredsnRNA-seq permits high-resolution isolation of nucleolar output from myofiber-derived myonuclei, decoupling analysis from non-muscle cellular noise.
“The definitive frontier lies in single-nucleus RNA sequencing (snRNA-seq), which permits the high-resolution isolation of nucleolar output specifically from myofiber-derived myonuclei, effectively decoupling the analysis from non-muscle cellular noise, such as infiltrating immune cells and fibroblasts [49].”
From Ribosome Biogenesis as a Putative Bottleneck to Skeletal Muscle Hypertrophy: Mechanisms, Human Evidence, and Practical Modulators (2026) · cites this paper as [49]
The Methods section describes single-cell RNA sequencing of dissociated mononuclear cells and separate RNA sequencing of manually isolated muscle fibers. Our copy does not address single-nucleus RNA sequencing, isolation of myofiber-derived myonuclei, or measurement of nucleolar output; searches for snRNA-seq and myonuclei found no supporting passage. The methods described do not establish the claimed decoupling from non-muscle cells. (LLM, conf=0.76)
Experimental — accuracy not yet measuredKey angiogenic regulators and endothelial cell content in skeletal muscle are reduced during aging.
“Key angiogenic regulators and endothelial cell content in skeletal muscle are reduced during aging.”
From Skeletal muscle aging, cellular senescence, and senotherapeutics: current knowledge and future directions (2021) · cites this paper as Rubenstein et al., 2020
Declines in skeletal muscle perfusion may directly influence anabolic resistance and contribute to sarcopenia.
“Corresponding declines in skeletal muscle perfusion may directly influence anabolic resistance and contribute to sarcopenia”
From Skeletal muscle aging, cellular senescence, and senotherapeutics: current knowledge and future directions (2021) · cites this paper as Rubenstein et al., 2020
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Hargreaves, M. (2021) · Journal of Applied Physiology · doi:10.1152/japplphysiol.00242.2021 · Cited by 25 · see citing works
Endothelial Reactive Oxygen Species: Key Players in Cardiovascular Health and Disease
Craige, S. M., Kaur, G., Bond, J. M., Caliz, A. D., Kant, S., & Keaney, J. F. (2024) · Antioxidants and Redox Signaling · doi:10.1089/ars.2024.0706 · Cited by 23 · see citing works
- Authors
- Rubenstein, A. B., Smith, G. R., Raue, U., Begue, G., Minchev, K., Ruf-Zamojski, F., Nair, V. D., Wang, X., Zhou, L., Zaslavsky, E., Trappe, T. A., Trappe, S., & Sealfon, S. C.
- Affiliations
- Icahn School of Medicine at Mount Sinai (US)
- Ball State University (US)
- Boston University (US)
- Corresponding author
- Sealfon, Stuart C.
- ORCID
- Venue
- Scientific Reports
- Published
- 2020-01-14
- Volume
- 10
- Issue
- 1
- Pages
- 229-229
- ISSN
- 2045-2322 (ISSN-L)
- PMC
- PMC6959232
- OpenAlex
- W2999612022
- Cited by
- 323
- References
- 72
- Citations by year
- 2026: 41 · 2025: 53 · 2024: 57 · 2023: 59 · 2022: 52 · 2021: 37 · 2020: 24
- FWCI
- 13.94
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Scientific Reports (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Funders
- U.S. Department of Health & Human Services | NIH | National Institute of Arthritis and Musculoskeletal and Skin Diseases (1R01AR074428)
- U.S. Department of Health & Human Services | National Institutes of Health (AG038576, AG184809, U24 DK112331)
- Ball State University (Academic Excellence Award)
- Empire State Development's Division of Science, Technology and Innovation
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Muscle Physiology and Disorders
- Health Sciences › Medicine › Physiology › Adipose Tissue and Metabolism
- Keywords
- skeletal muscle, muscle fiber heterogeneity, fibro-adipogenic progenitor cells, exercise training, vastus lateralis, quadriceps, diaphragm, single-cell transcriptomics, cell type proportions
- MeSH terms
- Animals, Diaphragm, Female, Humans, Male, Biomarkers, Muscle, Skeletal, Adipogenesis, Mice, Quadriceps Muscle, Single-Cell Analysis, Transcriptome
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