Recent studies revealed trajectories of mutational events in early melanomagenesis, but the accompanying changes in gene expression are far less understood. Therefore, we performed a comprehensive RNA-seq analysis of laser-microdissected melanocytic nevi (n = 23) and primary melanoma samples (n = 57) and characterized the molecular mechanisms of early melanoma development. Using self-organizing maps, unsupervised clustering, and analysis of pseudotime (PT) dynamics to identify evolutionary trajectories, we describe here two transcriptomic types of melanocytic nevi (N1 and N2) and primary melanomas (M1 and M2). N1/M1 lesions are characterized by pigmentation-type and MITF gene signatures, and a high prevalence of NRAS mutations in M1 melanomas. N2/M2 lesions are characterized by inflammatory-type and AXL gene signatures with an equal distribution of wild-type and mutated BRAF and low prevalence of NRAS mutations in M2 melanomas. Interestingly, N1 nevi and M1 melanomas and N2 nevi and M2 melanomas, respectively, cluster together, but there is no clustering in a stage-dependent manner. Transcriptional signatures of M1 melanomas harbor signatures of BRAF/MEK inhibitor resistance and M2 melanomas harbor signatures of anti-PD-1 antibody treatment resistance. Pseudotime dynamics of nevus and melanoma samples are suggestive for a switch-like immune-escape mechanism in melanoma development with downregulation of immune genes paralleled by an increasing expression of a cell cycle signature in late-stage melanomas. Taken together, the transcriptome analysis identifies gene signatures and mechanisms underlying development of melanoma in early and late stages with relevance for diagnostics and therapy.

中文翻译：

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RNA-seq分析可识别原发性黑色素瘤的不同转录组类型和发育轨迹。

最近的研究揭示了早期黑色素瘤发生中突变事件的轨迹，但是对基因表达的伴随变化知之甚少。因此，我们对激光显微切割的黑素细胞痣（n = 23）和原发性黑色素瘤样品（n = 57）进行了全面的RNA序列分析，并表征了早期黑色素瘤发展的分子机制。使用自组织图，无监督聚类和伪时间（PT）动力学分析以识别进化轨迹，我们在这里描述黑素细胞痣（N1和N2）和原发性黑色素瘤（M1和M2）的两种转录组类型。N1 / M1病变的特征在于色素沉着型和MITF基因标记，以及M1黑色素瘤中NRAS突变的高患病率。N2 / M2病变的特征是具有炎症性和AXL基因特征，具有野生型和突变型BRAF的均等分布，并且在M2黑色素瘤中NRAS突变的患病率较低。有趣的是，N1痣和M1黑色素瘤和N2痣和M2黑色素瘤分别聚集在一起，但是没有阶段依赖性的聚集。M1黑色素瘤的转录标记具有BRAF / MEK抑制剂抗性的标记，而M2黑色素瘤则具有抗PD-1抗体治疗抗性的标记。痣和黑色素瘤样品的假时动态提示黑色素瘤发展中的开关样免疫逃逸机制，伴随着免疫基因的下调，同时在晚期黑色素瘤中细胞周期信号的表达增加。在一起