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.

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MK, MD, AB, SM, and MS were supported by funding of the Deutsche Krebshilfe, Melanomverbund, grant number 109716.

Author contributions

MK, HL-W, MD, EW, GD, JK, TK, BN, JL, PZ, CM, HJS, LH, HB, SM, AB, and MS conceived and designed the work that led to the submission, acquired data, and played an important role in interpreting the results and approved the final version. SH, TT, JU, MZ, SK, MH, and AR supported the interpretation of the results and approved the final version.

Author information

Author notes

  1. These authors contributed equally: Hans Binder, Manfred Schartl.


  1. Department of Dermatology, Venereology and Allergology, University of Leipzig, Philipp-Rosenthal-Str. 23-25, 04103, Leipzig, Germany

    • Manfred Kunz
    • , Tina Kottek
    •  & Mirjana Ziemer
  2. Interdisciplinary Centre for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, 04107, Leipzig, Germany

    • Henry Löffler-Wirth
    • , Edith Willscher
    • , Gero Doose
    • , Lydia Hopp
    • , Steve Hoffmann
    •  & Hans Binder
  3. Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany

    • Michael Dannemann
    • , Janet Kelso
    •  & Birgit Nickel
  4. Bioinformatics Group, Faculty for Mathematics and Computer Science, University of Leipzig, Härtelstrasse 16-18, 04107, Leipzig, Germany

    • Gero Doose
    •  & Steve Hoffmann
  5. Department of Dermatology and Allergy, University of Bonn, Sigmund-Freud-Strasse 25, 53127, Bonn, Germany

    • Jenny Landsberg
  6. Department of Dermatology, University of Magdeburg, Leipziger Strasse 44, 39120, Magdeburg, Germany

    • Thomas Tüting
  7. Department of Dermatology, Venereology and Allergology, University of Köln, 50937 Köln, Germany

    • Paola Zigrino
    •  & Cornelia Mauch
  8. Skin Cancer Unit, German Cancer Research Center (DKFZ), Heidelberg, and Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Ruprecht-Karl University of Heidelberg, 68167 Mannheim, Germany

    • Jochen Utikal
  9. Department of Dermatology, Fachklinik Hornheide, Dorbaumstrasse 300, 48157, Münster, Germany

    • Hans-Joachim Schulze
  10. Unit for RNA Biology, Department of Clinical Chemistry and Clinical Pharmacology, University of Bonn, 53127 Bonn, Germany

    • Michael Hölzel
  11. Department of Dermatology, University Hospital Essen, West German Cancer Center, University Duisburg-Essen and the German Cancer Consortium (DKTK), University of Duisburg-Essen, 45122 Essen, Germany

    • Alexander Roesch
  12. Department of Physiological Chemistry, University of Würzburg, Biozentrum, Am Hubland, 97074, Würzburg, Germany

    • Susanne Kneitz
    • , Svenja Meierjohann
    •  & Manfred Schartl
  13. Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, 97080, Würzburg, Germany

    • Susanne Kneitz
    • , Svenja Meierjohann
    •  & Manfred Schartl
  14. Institute of Biochemistry, Emil-Fischer Zentrum, University of Erlangen, Fahrstraße 17, 91054, Erlangen, Germany

    • Anja Bosserhoff
  15. Hagler Institute for Advanced Study and Department of Biology, Texas A&M University, College Station, TX, 77843-3572, USA

    • Manfred Schartl


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Conflict of interest

MK has received honoraria from the Speakers Bureau of Roche Pharma AG and travel support from Novartis Pharma GmbH and Bristol-Myers Squibb GmbH (BMS). MZ has received speakers honoraria and honoraria for Medical Advisory Boards from BMS, Roche Pharma AG, MSD Sharp & Dohme GmbH (MSD), Amgen GmbH, Novartis Pharma GmbH, Pfizer Pharma GmbH, and Merck Serono GmbH as well as financial support for travel support from BMS and Amgen GmbH. TT has received honoraria from the Speakers Bureau of Roche Pharma AG and travel support from Novartis Pharma GmbH and BMS. CM has received travel support from MSD and Pfizer GmbH and Roche Pharma AG and received honoraria from Novartis Pharma GmbH. JU is on the advisory board or has received honoraria and travel support from Amgen, BMS, GlaxoSmithKline GmbH &nCo, LeoPharma, MSD, Novartis, Roche Pharma AG. AR received travel grants and honoraria from Roche Pharma AG, TEVA, MMS, MSD, Amgen, and Novartis Pharma GmbH and a research grant from Novartis Pharma GmbH. JL, HL-W, MD, EW, GD, JK, LH, SH, PZ, HJS, MH, SK, SM, AB, HB and MS declare that they have no conflict of interest.

Corresponding author

Correspondence to Manfred Kunz.

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