Identifying quiescent satellite cells: a scoping review of transcriptomic markers and limitations

Skeletal muscle regeneration relies on the resident stem cell population, termed satellite cells. Mechanistically, understanding the quiescence and activation dynamics of muscle satellite cells is essential for regenerative therapies and emerging applications such as cellular agriculture. Quiescent satellite cells (QSCs) are typically identified by expression of paired box 7 (PAX7) and functional characteristics, including a lack of proliferation. However, with the rapidly growing body of transcriptomic data, there is a lack of consensus regarding what markers can be used to identify quiescent satellite cells across transcriptomic studies. The purpose of this review was to evaluate the transcripts currently used to identify QSCs using transcriptomics and to establish an evidence-based foundation that could be used for future analyses. After surveying published single-cell transcriptomic studies, we identified Pax7 and/or myogenic factor 5 (Myf5) as the most used markers of general satellite cell identity, whereas sprouty RTK signaling antagonist 1 (Spry1), cluster of differentiation 34 (Cd34), and calcitonin receptor (Calcr), together with the absence of myogenic differentiation 1 (Myod1), marker of proliferation Kiel 67 (Mki67), and cyclin-dependent kinase 1 (Cdk1), were most commonly used to identify QSC clusters in murine studies. In contrast, there is currently insufficient literature to make a confident conclusion on quiescence markers in larger mammals, including humans, pigs, and cattle. We also highlight the conceptual and technical challenges associated with transcriptomic analysis of satellite cell subpopulations, including continuum-based cell states, isolation-induced transcriptional changes, and inconsistent terminology. As a field, greater consistency in language, standardized analyses, and cross-species validation will be required to progress the study of satellite cell quiescence and its translational utility.