Distant metastases of melanoma exhibit varying extent of intrapatient proteogenomic heterogeneity

Szeitz, Beáta and Hagemeijer, Yanick Paco and Páhi, Zoltán Gábor and Újfaludi, Zsuzsanna and Kuras, Magdalena and Rodriguez, Jimmy and Doma, Viktória and Mohácsi, Réka and Herold, Magdolna and Herold, Zoltán and Horvath, Zsolt and Pla, Indira and Sugihara, Yutaka and Baldetorp, Bo and Lindberg, Henrik and Oskolas, Henriett and Rezeli, Melinda and Gil, Jeovanis and Appelqvist, Roger and Kemény, Lajos Vince and Guedes, Jessica and Malm, Johan and Sanchez, Aniel and Boros, Imre Miklós and Németh, István Balázs and Guryev, Victor and Pankotai, Tibor and Pawłowski, Krzysztof and Wieslander, Elisabet and Szász, Attila Marcell and Tímár, József (2025) Distant metastases of melanoma exhibit varying extent of intrapatient proteogenomic heterogeneity. CLINICAL AND TRANSLATIONAL MEDICINE, 15 (10). No. e70477. ISSN 2001-1326

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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 vesiclemediated 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.

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