Distant metastases of melanoma exhibit varying extent of intrapatient proteogenomic heterogeneity

Beata Szeitz; Yanick Paco Hagemeijer; Zoltan Gabor Pahi; Zsuzsanna Ujfaludi; Magdalena Kuras; Jimmy Rodriguez; Viktoria Doma; Reka Mohacsi; Magdolna Herold; Zoltan Herold; Zsolt Horvath; Indira Pla; Yutaka Sugihara; Bo Baldetorp; Henrik Lindberg; Henriett Oskolas; Melinda Rezeli; Jeovanis Gil; Roger Appelqvist; Lajos V. Kemeny; Jessica Guedes; Johan Malm; Aniel Sanchez; Imre Miklos Boros; Istvan Balazs Nemeth; Victor Guryev; Tibor Pankotai; Krzysztof Pawłowski; Elisabet Wieslander; Attila Marcell Szasz; David Fenyö; Peter Horvatovich; Jozsef Timar; György Marko-Varga; Lazaro Hiram Betancourt

doi:10.1002/ctm2.70477

Clinical and Translational Medicine ›› 2025, Vol. 15 ›› Issue (10) : e70477 DOI: 10.1002/ctm2.70477

RESEARCH ARTICLE

Distant metastases of melanoma exhibit varying extent of intrapatient proteogenomic heterogeneity

Author information +

¹. Division of Oncology, Department of Internal Medicine and Oncology, Semmelweis University, Budapest, Hungary

². Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands

³. European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands

⁴. Department of Pathology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary

⁵. Genome Integrity and DNA Repair Core Group, Hungarian Centre of Excellence for Molecular Medicine (HCEMM), University of Szeged, Szeged, Hungary

⁶. Competence Centre of the Life Sciences Cluster of the Centre of Excellence for Interdisciplinary Research, Development and Innovation, University of Szeged, Szeged, Hungary

⁷. Division of Clinical Protein Science & Imaging, Department of Biomedical Engineering, Lund University, Lund, Sweden

⁸. Department of Translational Medicine, Skåne University Hospital Malmö, Lund University, Malmö, Sweden

⁹. Department of Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden

¹⁰. Department of Dermatology, Venerology and Dermatooncology, Faculty of Medicine, Semmelweis University, Budapest, Hungary

¹¹. European Cancer Moonshot Lund Center, Lund, Sweden

¹². Section of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden

¹³. BioMS−Swedish National Infrastructure for Biological Mass Spectrometry, Lund University, Lund, Sweden

¹⁴. HCEMM-SU Translational Dermatology Research Group, Semmelweis University, Budapest, Hungary

¹⁵. Department of Physiology, Semmelweis University, Budapest, Hungary

¹⁶. Chemistry Institute, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil

¹⁷. Department of Biochemistry and Molecular Biology, University of Szeged, Szeged, Hungary

¹⁸. Hungarian Research Network Biological Research Center, Institute of Biochemistry, Szeged, Hungary

¹⁹. Department of Dermatology and Allergology, University of Szeged, Szeged, Hungary

²⁰. Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA

²¹. Howard Hughes Medical Institute, Dallas, Texas, USA

²². Institute for Systems Genetics, NYU Grossman School of Medicine, New York, New York, USA

²³. Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, New York, USA

²⁴. Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, Budapest, Hungary

gyorgy.marko-varga@bme.lth.se

lazaro_hiram.betancourt_nunez@med.lu.se

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Abstract

Background: Metastatic melanoma is a highly aggressive disease with poor survival rates despite recent therapeutic advancements with immunotherapy. The proteomic landscape of advanced melanoma remains poorly understood, especially regarding proteomic heterogeneity across metastases within patients.

Methods: We collected 83 melanoma metastases from 19 different metastatic sites in 24 patients with advanced metastatic melanoma almost exclusively from the pre-immunotherapy era, using semi-rapid autopsies. The metastases were subjected to histopathological evaluation, RNA-sequencing and mass spectrometry-based proteomics for protein quantitation and non-reference peptide (NRP) sequence detection using a proteogenomic data integration approach.

Results: NRPs associated with mutations frequently occurred in proteins related to focal adhesion, vesicle-mediated transport, MAPK signalling and immune response pathways across the cohort. Intrapatient heterogeneity was negligible when considering morphology and driver gene mutation status but was substantial at the proteogenomic level. This heterogeneity was not driven by metastasis location, albeit liver metastases exhibited distinct proteogenomic patterns, including upregulation of metabolic pathways. Cluster analysis outlined four proteomic clusters (C1–4) of the metastases, characterised by the upregulation of cell cycle and RNA-splicing (C1), mitochondrial processes (C3), extracellular matrix (ECM) and immune pathways (C2) and ECM and vesicle-mediated transport pathways (C4). Around two-thirds of patients had metastases that had strongly distinct phenotypes. Patients in our cohort whose metastases were primarily assigned to clusters C1 and C3 exhibited shorter overall survival than patients whose metastases were categorised mainly into the C2 and C4 clusters.

Conclusion: Our unique multi-metastasis cohort captured the proteogenomic heterogeneity of immunotherapy-naïve melanoma distant metastases, establishing a foundation for future studies aimed at identifying novel therapeutic targets to complement current immunotherapies.

Keywords

distant metastasis / histopathology / mass spectrometry-based proteomics / melanoma / post mortem / proteogenomics / RNA-sequencing

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Beata Szeitz, Yanick Paco Hagemeijer, Zoltan Gabor Pahi, Zsuzsanna Ujfaludi, Magdalena Kuras, Jimmy Rodriguez, Viktoria Doma, Reka Mohacsi, Magdolna Herold, Zoltan Herold, Zsolt Horvath, Indira Pla, Yutaka Sugihara, Bo Baldetorp, Henrik Lindberg, Henriett Oskolas, Melinda Rezeli, Jeovanis Gil, Roger Appelqvist, Lajos V. Kemeny, Jessica Guedes, Johan Malm, Aniel Sanchez, Imre Miklos Boros, Istvan Balazs Nemeth, Victor Guryev, Tibor Pankotai, Krzysztof Pawłowski, Elisabet Wieslander, Attila Marcell Szasz, David Fenyö, Peter Horvatovich, Jozsef Timar, György Marko-Varga, Lazaro Hiram Betancourt. Distant metastases of melanoma exhibit varying extent of intrapatient proteogenomic heterogeneity. Clinical and Translational Medicine, 2025, 15(10): e70477 DOI:10.1002/ctm2.70477

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