Clonal dynamics shaped by diverse drug-tolerant persister states in melanoma resistance

Area of Science:

• Oncology
• Cancer Biology
• Genomics

Background:

• Advanced melanomas often relapse after initial response to targeted therapy.
• Therapy resistance in melanoma is frequently driven by drug-tolerant persister cells, not new mutations.
• These persister cells enter a reversible, drug-refractory state, complicating treatment outcomes.

Purpose of the Study:

• To develop and utilize a high-resolution platform, MeRLin, for tracking melanoma clonal and transcriptional dynamics during therapy.
• To investigate the mechanisms of adaptive resistance and identify key cellular states in persister melanoma populations.
• To spatially map clonal evolution and gene expression within melanoma models under prolonged treatment.

Main Methods:

• Development of MeRLin: a platform integrating cellular barcoding, single-cell transcriptomics, and RNA fluorescence in situ hybridization (FISH).
• Application of MeRLin to patient-derived melanoma models undergoing prolonged targeted therapy.
• Computational analysis of clonal dynamics, transcriptional states, and spatial organization of persister cells.

Main Results:

• Persister subpopulations initially responded to treatment but persisted and expanded, leading to tumor recurrence.
• Pre-treatment melanoma cells diversified into four conserved persister states linked to adaptive resistance (stress, lipid metabolism, PI3K signaling, ECM remodeling).
• Spatial transcriptomics and barcoded RNA-FISH revealed in situ organization of adaptive programs and co-localization of resistant clones with SLC2A1 expression.

Conclusions:

• MeRLin provides a powerful framework for dissecting cancer cell heterogeneity and adaptive resistance mechanisms.
• Understanding persister cell dynamics and their associated transcriptional states is crucial for overcoming melanoma treatment failure.
• Identification of specific persister states and signaling networks offers potential therapeutic vulnerabilities for targeting melanoma recurrence.