TY - JOUR
T1 - Melanoma Proteomics Unveiled
T2 - Harmonizing Diverse Data Sets for Biomarker Discovery and Clinical Insights via MEL-PLOT
AU - Bartha, Áron
AU - Weltz, Boglárka
AU - Betancourt, Lazaro Hiram
AU - Gil, Jeovanis
AU - Pinto de Almeida, Natália
AU - Bianchini, Giampaolo
AU - Szeitz, Beáta
AU - Szadai, Leticia
AU - Pla, Indira
AU - Kemény, Lajos V
AU - Jánosi, Ágnes Judit
AU - Hong, Runyu
AU - Rajeh, Ahmad
AU - Nogueira, Fábio
AU - Doma, Viktória
AU - Woldmar, Nicole
AU - Guedes, Jéssica
AU - Újfaludi, Zsuzsanna
AU - Kim, Yonghyo
AU - Szarvas, Tibor
AU - Pahi, Zoltan
AU - Pankotai, Tibor
AU - Szasz, A Marcell
AU - Sanchez, Aniel
AU - Baldetorp, Bo
AU - Tímár, József
AU - Németh, István Balázs
AU - Kárpáti, Sarolta
AU - Appelqvist, Roger
AU - Domont, Gilberto Barbosa
AU - Pawlowski, Krzysztof
AU - Wieslander, Elisabet
AU - Malm, Johan
AU - Fenyo, David
AU - Horvatovich, Peter
AU - Marko-Varga, György
AU - Győrffy, Balázs
PY - 2025/5/5
Y1 - 2025/5/5
N2 - 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.
AB - 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.
U2 - 10.1021/acs.jproteome.4c00749
DO - 10.1021/acs.jproteome.4c00749
M3 - Article
C2 - 40322912
SN - 1535-3893
JO - Journal of Proteome Research
JF - Journal of Proteome Research
ER -