TYRP1 defines a proliferative melanoma cell subpopulation, driving malignant progression and therapy resistance via the GPNMB–Notch1–SOX10/MITF axis

BACKGROUND: Tumor cell heterogeneity contributes to melanoma progression, therapeutic resistance, and clinical outcome variability. However, the identity and functional role of specific proliferative subpopulations remain incompletely understood. This study aims to characterize TYRP1-positive melanoma cells and elucidate their role in tumor proliferation, signaling regulation, and treatment response. METHODS: We analyzed single-cell RNA sequencing (scRNA-seq) data from primary and metastatic melanoma samples to identify transcriptionally distinct tumor cell subtypes. Functional validation of TYRP1-positive cells was performed using patient-derived organoids, TYRP1-overexpressing melanoma cell lines (A375, SK-MEL-28), and xenograft mouse models. The downstream molecular mechanisms were investigated through gene expression profiling, siRNA-mediated knockdown, recombinant protein treatment, and pathway inhibition assays. Therapeutic responses were assessed using dabrafenib and pembrolizumab treatments. RESULTS: TYRP1 marked a transcriptionally distinct melanoma subpopulation associated with poor patient survival. TYRP1-high organoids and cell lines exhibited significantly enhanced proliferation in vitro and accelerated tumor growth in vivo, without increased metastatic capacity. Mechanistically, TYRP1 induced expression of GPNMB, which activated Notch1 signaling and subsequently upregulated SOX10 and MITF. These transcription factors formed a positive feedback loop with TYRP1 that maintained the proliferative phenotype. GPNMB or Notch1 inhibition disrupted this loop and suppressed tumor growth. Importantly, TYRP1-overexpressing tumors demonstrated resistance to immune checkpoint blockade but increased sensitivity to dabrafenib, suggesting distinct therapeutic vulnerabilities. CONCLUSIONS: Our findings identify TYRP1 as a marker of a highly proliferative melanoma subpopulation that promotes tumor progression through the GPNMB-Notch1-SOX10/MITF axis. The TYRP1-SOX10-MITF feedback loop represents a key driver of melanoma proliferation and a potential biomarker for stratifying therapeutic response, offering a novel avenue for precision treatment in melanoma.