Objective:Cellular heterogeneity is regarded as a major factor affecting treatment response and resistance in malignant melanoma.Recent developments in single-cell sequencing technology have provided deeper insights i...Objective:Cellular heterogeneity is regarded as a major factor affecting treatment response and resistance in malignant melanoma.Recent developments in single-cell sequencing technology have provided deeper insights into these mechanisms.Methods:Here,we analyzed a BRAFV600 E-mutant melanoma cell line by single-cell RNA-seq under various conditions:cells sensitive to BRAF inhibition with BRAF inhibitor vemurafenib and cells resistant to BRAF inhibition with vemurafenib alone or vemurafenib in combination with the MEK1/2 inhibitors cobimetinib or trametinib.Dimensionality reduction by t-distributed stochastic neighbor embedding and self-organizing maps identified distinct trajectories of resistance development clearly separating the 4 treatment conditions in cell and gene state space.Results:Trajectories associated with resistance to single-agent treatment involved cell cycle,extracellular matrix,and de-differentiation programs.In contrast,shifts detected in double-resistant cells primarily affected translation and mitogen-activated protein kinase pathway reactivation,with a small subpopulation showing markers of pluripotency.These findings were validated in pseudotime analyses and RNA velocity measurements.Conclusions:The single-cell transcriptomic analyses reported here employed a spectrum of bioinformatics methods to identify mechanisms of melanoma resistance to single-and double-agent treatments.This study deepens our understanding of treatmentinduced cellular reprogramming and plasticity in melanoma cells and identifies targets of potential relevance to the management of treatment resistance.展开更多
基金supported by the German Research Foundation(Deutsche Forschungsgemeinschaft,Grant Nos.KU 1320/10-1 and HO 6586/1-1)。
文摘Objective:Cellular heterogeneity is regarded as a major factor affecting treatment response and resistance in malignant melanoma.Recent developments in single-cell sequencing technology have provided deeper insights into these mechanisms.Methods:Here,we analyzed a BRAFV600 E-mutant melanoma cell line by single-cell RNA-seq under various conditions:cells sensitive to BRAF inhibition with BRAF inhibitor vemurafenib and cells resistant to BRAF inhibition with vemurafenib alone or vemurafenib in combination with the MEK1/2 inhibitors cobimetinib or trametinib.Dimensionality reduction by t-distributed stochastic neighbor embedding and self-organizing maps identified distinct trajectories of resistance development clearly separating the 4 treatment conditions in cell and gene state space.Results:Trajectories associated with resistance to single-agent treatment involved cell cycle,extracellular matrix,and de-differentiation programs.In contrast,shifts detected in double-resistant cells primarily affected translation and mitogen-activated protein kinase pathway reactivation,with a small subpopulation showing markers of pluripotency.These findings were validated in pseudotime analyses and RNA velocity measurements.Conclusions:The single-cell transcriptomic analyses reported here employed a spectrum of bioinformatics methods to identify mechanisms of melanoma resistance to single-and double-agent treatments.This study deepens our understanding of treatmentinduced cellular reprogramming and plasticity in melanoma cells and identifies targets of potential relevance to the management of treatment resistance.
