Melanoma Proteomics Unveiled: Harmonizing Diverse Data Sets for Biomarker Discovery and Clinical Insights via MEL-PLOT
Using several melanoma proteomics data sets we created a single analysis platform that enables the discovery, knowledge build, and validation of diagnostic, predictive, and prognostic biomarkers at the protein level. Quantitative mass-spectrometry-based proteomic data was obtained from five independent cohorts, including 489 tissue samples from 394 patients with accompanying clinical metadata. We established an interactive R-based web platform that enables the comparison of protein levels across diverse cohorts, and supports correlation analysis between proteins and clinical metadata including survival outcomes. By comparing differential protein levels between metastatic, primary tumor, and nonmalignant samples in two of the cohorts, we identified 274 proteins showing significant differences among the sample types. Further analysis of these 274 proteins in lymph node metastatic samples from a third cohort revealed that 45 proteins exhibited a significant effect on patient survival. The three most significant proteins were HP (HR = 4.67, p = 2.8e-06), LGALS7 (HR = 3.83, p = 2.9e-05), and UBQLN1 (HR = 3.2, p = 4.8e-05). The user-friendly interactive web platform, accessible at https://www.tnmplot.com/melanoma, provides an interactive interface for the analysis of proteomic and clinical data. The MEL-PLOT platform, through its interactive capabilities, streamlines the creation of a comprehensive knowledge base, empowering hypothesis formulation and diligent monitoring of the most recent advancements in the domains of biomedical research and drug development.
Authors
- Aniel Sánchez (ORCID: https://orcid.org/0000-0002-0278-8802)
- Sarolta Kárpáti
- Bo Baldetorp
- Beáta Szeitz (ORCID: https://orcid.org/0000-0001-6414-0537)
- Jeovanis Gil (ORCID: https://orcid.org/0000-0003-3601-3893)
- Indira Plá (ORCID: https://orcid.org/0000-0002-0839-7829)
- Balázs Győrffy (ORCID: https://orcid.org/0000-0002-5772-3766)
- György Marko‐Varga (ORCID: https://orcid.org/0000-0001-7140-8925)
- Letícia Szadai
- Lazaro Hiram Betancourt (ORCID: https://orcid.org/0000-0001-8207-7041)
- Zoltán G. Páhi (ORCID: https://orcid.org/0000-0002-3428-553X)
- Ágnes Judit Jánosi
- Natália Pinto de Almeida (ORCID: https://orcid.org/0000-0002-8851-8669)
- Gilberto B. Domont (ORCID: https://orcid.org/0000-0002-1329-6483)
- Johan Malm (ORCID: https://orcid.org/0000-0002-9365-7313)
- Tibor Szarvas (ORCID: https://orcid.org/0000-0002-6321-0799)
- Fábio César Sousa Nogueira (ORCID: https://orcid.org/0000-0001-5507-7142)
- Yonghyo Kim (ORCID: https://orcid.org/0000-0002-4447-9864)
- Giampaolo Bianchini (ORCID: https://orcid.org/0000-0002-6790-6267)
- Tibor Pankotai (ORCID: https://orcid.org/0000-0001-9810-5465)
- Elisabet Wieslander
- Boglárka Weltz
- Áron Bartha (ORCID: https://orcid.org/0000-0003-0395-243X)
- David Fenyö (ORCID: https://orcid.org/0000-0001-5049-3825)
- József Tı́már (ORCID: https://orcid.org/0000-0001-9183-0859)
- Nicole Woldmar (ORCID: https://orcid.org/0000-0002-5387-1059)
- Roger Appelqvist (ORCID: https://orcid.org/0000-0001-7450-7216)
- Ahmad Rajeh (ORCID: https://orcid.org/0000-0002-8916-6845)
- Krzysztof Pawłowski (ORCID: https://orcid.org/0000-0002-5367-0935)
- Attila Marcell Szász (ORCID: https://orcid.org/0000-0003-2739-4196)
- Zsuzsanna Újfaludi (ORCID: https://orcid.org/0000-0003-4738-0963)
- Viktória Doma
- Péter Horvatovich (ORCID: https://orcid.org/0000-0003-2218-1140)
- Jéssica de Siqueira Guedes (ORCID: https://orcid.org/0000-0002-8061-1623)
- Runyu Hong (ORCID: https://orcid.org/0000-0002-0941-351X)
- István Balázs Németh (ORCID: https://orcid.org/0000-0003-0161-4277)
- Lajos V. Kemény
Institutions
- Semmelweis University (HU)
- Universidade Federal do Rio de Janeiro (BR)
- Harvard University (US)
- Vita-Salute San Raffaele University (IT)
- University of Groningen (NL)
- Warsaw University of Life Sciences (PL)
- Lund University (SE)
- University of Szeged (HU)
- Universidade do Estado do Rio de Janeiro (BR)
- Massachusetts General Hospital (US)
- Czech Academy of Sciences, Institute of Biophysics (CZ)
- Institute of Dermatology (TH)
- Drug Discovery Laboratory (Norway) (NO)
- Skåne University Hospital (SE)
- Korea Research Institute of Chemical Technology (KR)
- Southwestern Medical Center (US)
- New York University (US)
- University of Duisburg-Essen (DE)
- University of Pecs (HU)
- HUN-REN Research Centre for Natural Sciences (HU)
- The University of Texas Southwestern Medical Center (US)
Publication Details
- Journal
- Journal of Proteome Research
- Published
- 2025-05-05
- DOI
- https://doi.org/10.1021/acs.jproteome.4c00749
- Citations
- 3
- Primary Topic
- vaccines and immunoinformatics approaches
- Type
- article
- Field-Weighted Citation Impact
- 2.42
Funders
- Massachusetts General Hospital
- Rijksuniversiteit Groningen
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
- Semmelweis Egyetem
- Lunds Universitet
- Hungarian Scientific Research Fund
- Conselho Nacional de Desenvolvimento Científico e Tecnológico
- Korea Research Institute of Chemical Technology
- Fru Berta Kamprads Stiftelse
- Universidade Federal do Rio de Janeiro
- Universität Duisburg-Essen
- Nemzeti Kutatási Fejlesztési és Innovációs Hivatal
- Szkola Glówna Gospodarstwa Wiejskiego w Warszawie
- Szegedi Tudományegyetem
- NYU Grossman School of Medicine
- Lunds Tekniska Högskola, Lunds universitet
- National Research, Development and Innovation Office
- National Cancer Institute
- Moonshot Research and Development Program
- Cancer Moonshot