TCF3-mediated lysosomal function contributes to muscle stem cell quiescence

Abstract Muscle stem cells (MuSCs) preserve skeletal muscle homeostasis and regeneration by entering a reversible quiescent state. Importantly, quiescence is not a state of transcriptional inactivity but an actively maintained cellular state governed by specialized transcriptional programs. However, the transcription factors that coordinate these programs with intracellular homeostasis remain incompletely understood. Here, we identify the transcription factor 3 (TCF3) as a previously unrecognized regulator of MuSC quiescence and long-term regenerative potential. TCF3 was enriched in quiescent MuSCs and rapidly downregulated upon activation. TCF3 overexpression suppressed proliferation and differentiation and reinforced a quiescence-associated transcriptional program, whereas MuSC-specific TCF3 deletion increased activation propensity. Although acute TCF3 loss accelerated MuSC activation and early repair after a single injury, prolonged deficiency or repeated injury progressively depleted the stem cell pool and compromised regeneration, demonstrating that transient enhancement of activation occurs at the expense of long-term regenerative capacity. Transcriptomic, ATAC-seq, and ChIP-seq analyses further revealed that TCF3 shapes chromatin accessibility and regulates genes involved in stem cell maintenance and lysosomal function. Mechanistically, TCF3 enhanced lysosomal biogenesis and degradative activity, while pharmacological inhibition of lysosomal function partially relieved TCF3-mediated suppression of proliferation. Conversely, upregulation of lysosomal regulator TFEB reduced proliferative and activation-associated features while promoting a quiescence-associated state. Together, these findings establish a TCF3-lysosome regulatory axis that actively safeguards MuSC quiescence, prevents premature stem cell exhaustion, and sustains regenerative competence across repeated tissue injuries. This work provides a framework linking transcriptional control, chromatin state, and organelle homeostasis in quiescent adult stem cells, with potential relevance to muscle aging and regenerative medicine.