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 BRAFV600E-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 treatment-induced cellular reprogramming and plasticity in melanoma cells and identifies targets of potential relevance to the management of treatment resistance.

Maria Schmidt;Lena Sünke Mortensen;Henry Loeffler-Wirth;Corinna Kosnopfel;Knut Krohn;Hans Binder;Manfred Kunz

Interdisciplinary Centre for Bioinformatics,University of Leipzig,Leipzig 04107,Germany;Department of Dermatology,Venereology and Allergology,University of Würzburg,Würzburg 97074,Germany;Core Unit DNA Technologies,Medical Faculty,University of Leipzig,Leipzig 04103,Germany;Department of Dermatology,Venereology and Allergology,University of Leipzig Medical Center,Leipzig 04103,Germany

癌症生物学与医学（英文版）

[1]Maria Schmidt;Lena Sünke Mortensen;Henry Loeffler-Wirth;Corinna Kosnopfel;Knut Krohn;Hans Binder;Manfred Kunz-.Single-cell trajectories of melanoma cell resistance to targeted treatment)[J].癌症生物学与医学（英文版）,2022(01):56-73

cobimetinib,trametinib,pseudotime

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