Senescent skeletal muscle fibroadipogenic progenitors recruit and promote M2 polarization of macrophages

Senescent cells compromise tissue structure and function in older organisms. We recently identified senescent fibroadipogenic progenitors (FAPs) with activated chemokine signaling pathways in the skeletal muscle of old mice, and hypothesized these cells may contribute to the age-associated accumulation of immune cells in skeletal muscle. In this study, through cell-cell communication analysis of skeletal muscle single-cell RNA-sequencing data, we identified unique interactions between senescent FAPs and macrophages, including those mediated by Ccl2 and Spp1. Using mouse primary FAPs in vitro, we verified increased expression of Ccl2 and Spp1 and secretion of their respective proteins in the context of both irradiation- and etoposide-induced senescence. Compared to non-senescent FAPs, the medium of senescent FAPs markedly increased the recruitment of macrophages in an in vitro migration assay, an effect that was mitigated by preincubation with antibodies to either CCL2 or osteopontin (encoded by Spp1). Further studies demonstrated that the secretome of senescent FAPs promotes polarization of macrophages toward an M2 subtype. These data suggest the unique secretome of senescent FAPs may compromise skeletal muscle homeostasis by recruiting and directing the behavior of macrophages.

Single-cell Mayo Map (scMayoMap): an easy-to-use tool for cell type annotation in single-cell RNA-sequencing data analysis

BACKGROUND

Single-cell RNA-sequencing (scRNA-seq) has become a widely used tool for both basic and translational biomedical research. In scRNA-seq data analysis, cell type annotation is an essential but challenging step. In the past few years, several annotation tools have been developed. These methods require either labeled training/reference datasets, which are not always available, or a list of predefined cell subset markers, which are subject to biases. Thus, a user-friendly and precise annotation tool is still critically needed.

RESULTS

We curated a comprehensive cell marker database named scMayoMapDatabase and developed a companion R package scMayoMap, an easy-to-use single-cell annotation tool, to provide fast and accurate cell type annotation. The effectiveness of scMayoMap was demonstrated in 48 independent scRNA-seq datasets across different platforms and tissues. Additionally, the scMayoMapDatabase can be integrated with other tools and further improve their performance.

CONCLUSIONS

scMayoMap and scMayoMapDatabase will help investigators to define the cell types in their scRNA-seq data in a streamlined and user-friendly way.

Single-cell Mayo Map ( scMayoMap ): an easy-to-use tool for cell type annotation in single-cell RNA-sequencing data analysis

Single-cell RNA-sequencing (scRNA-seq) has become a widely used tool for both basic and translational biomedical research. In scRNA-seq data analysis, cell type annotation is an essential but challenging step. In the past few years, several annotation tools have been developed. These methods require either labeled training/reference datasets, which are not always available, or a list of predefined cell subset markers, which are subject to biases. Thus, a user-friendly and precise annotation tool is still critically needed. We curated a comprehensive cell marker database named scMayoMapDatabase and developed a companion R package scMayoMap , an easy-to-use single cell annotation tool, to provide fast and accurate cell type annotation. The effectiveness of scMayoMap was demonstrated in 48 independent scRNA-seq datasets across different platforms and tissues. scMayoMap performs better than the currently available annotation tools on all the datasets tested. Additionally, the scMayoMapDatabase can be integrated with other tools and further improve their performance. scMayoMap and scMayoMapDatabase will help investigators to define the cell types in their scRNA-seq data in a streamlined and user-friendly way.

IDENTIFICATION AND INVESTIGATION OF SENESCENT CELLS IN SKELETAL MUSCLE AGING

Skeletal muscle aging is marked by the loss and atrophy of resident fibers, and the accumulation of functionally diverse cell types including fibroblasts, adipocytes, and immune cells. Senescent cells amass in multiple tissues with advancing age where they contribute to aging, chronic disease, and physical decline. The role of senescence in mediating muscle aging has become a popular and sometimes contentious topic. However, to date, this concept has not been methodically tested. In this study, we characterized the changes in cell abundance and, importantly, cell-specific transcriptional profiles with skeletal muscle aging using scRNAseq. Interestingly, we identified a small population of p16 positive fibro-adipogenic progenitors (FAPs) which, upon further investigation using immunohistochemical methods, were found to express other senescence markers. This subpopulation of FAPs did not exhibit elevation in p21 levels with age. Instead, terminally differentiated myofibers were the source of the p21 increase. Myofibers with high p21 expression exhibit a strong inflammatory phenotype, which includes activated p53 signaling pathways together with strong cytokine-cytokine receptor interactions. We further identified large amounts of cross-talk between different cell types, suggesting that senescent FAPs and myofibers could contribute to skeletal muscle aging in a paracrine manner. Importantly, these observations in mice were confirmed in human samples, suggesting the strong translational power of these findings.

IDENTIFICATION AND INVESTIGATION OF SENESCENT CELLS IN SKELETAL MUSCLE AGING

Skeletal muscle aging is marked by the loss and atrophy of resident fibers, and the accumulation of functionally diverse cell types including fibroblasts, adipocytes, and immune cells. Senescent cells amass in multiple tissues with advancing age where they contribute to aging, chronic disease, and physical decline. The role of senescence in mediating muscle aging has become a popular and sometimes contentious topic. However, to date, this concept has not been methodically tested. In this study, we characterized the changes in cell abundance and, importantly, cell-specific transcriptional profiles with skeletal muscle aging using scRNAseq. Interestingly, we identified a small population of p16 positive fibro-adipogenic progenitors (FAPs) which, upon further investigation using immunohistochemical methods, were found to express other senescence markers. This subpopulation of FAPs did not exhibit elevation in p21 levels with age. Instead, terminally differentiated myofibers were the source of the p21 increase. Myofibers with high p21 expression exhibit a strong inflammatory phenotype, which includes activated p53 signaling pathways together with strong cytokine-cytokine receptor interactions. We further identified large amounts of cross-talk between different cell types, suggesting that senescent FAPs and myofibers could contribute to skeletal muscle aging in a paracrine manner. Importantly, these observations in mice were confirmed in human samples, suggesting the strong translational power of these findings.

IDENTIFICATION AND INVESTIGATION OF SENESCENT CELLS IN SKELETAL MUSCLE AGING

Skeletal muscle aging is marked by the loss and atrophy of resident fibers, and the accumulation of functionally diverse cell types including fibroblasts, adipocytes, and immune cells. Senescent cells amass in multiple tissues with advancing age where they contribute to aging, chronic disease, and physical decline. The role of senescence in mediating muscle aging has become a popular and sometimes contentious topic. However, to date, this concept has not been methodically tested. In this study, we characterized the changes in cell abundance and, importantly, cell-specific transcriptional profiles with skeletal muscle aging using scRNAseq. Interestingly, we identified a small population of p16 positive fibro-adipogenic progenitors (FAPs) which, upon further investigation using immunohistochemical methods, were found to express other senescence markers. This subpopulation of FAPs did not exhibit elevation in p21 levels with age. Instead, terminally differentiated myofibers were the source of the p21 increase. Myofibers with high p21 expression exhibit a strong inflammatory phenotype, which includes activated p53 signaling pathways together with strong cytokine-cytokine receptor interactions. We further identified large amounts of cross-talk between different cell types, suggesting that senescent FAPs and myofibers could contribute to skeletal muscle aging in a paracrine manner. Importantly, these observations in mice were confirmed in human samples, suggesting the strong translational power of these findings.