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Proteogenomic of postmortem melanoma metastases from preimmuno

ABSTRACT: Proteomic analysis of postmortem melanoma metastases from pre-immunonotherapy era

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Lazaro H. Betancourt Nunez

LAB HEAD: Prof. Gyorgy Marko-Varga

PROVIDER: PXD058546 | Pride | 2025-06-16

REPOSITORIES: Pride

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			Action	DRS
	MF13B_R1.htrms	Other
	MF13C_R1.htrms	Other
	MF13C_R4.htrms	Other
	MF13D_R3.htrms	Other
	MF13D_R4.htrms	Other

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Publications

Melanoma Proteomics Unveiled: Harmonizing Diverse Data Sets for Biomarker Discovery and Clinical Insights via MEL-PLOT.

Bartha Áron Á Weltz Boglárka B Betancourt Lazaro Hiram LH Gil Jeovanis J Pinto de Almeida Natália N Bianchini Giampaolo G Szeitz Beáta B Szadai Leticia L Pla Indira I Kemény Lajos V LV Jánosi Ágnes Judit ÁJ Hong Runyu R Rajeh Ahmad A Nogueira Fábio F Doma Viktória V Woldmar Nicole N Guedes Jéssica J Újfaludi Zsuzsanna Z Kim Yonghyo Y Szarvas Tibor T Pahi Zoltan Z Pankotai Tibor T Szasz A Marcell AM Sanchez Aniel A Baldetorp Bo B Tímár József J Németh István Balázs IB Kárpáti Sarolta S Appelqvist Roger R Domont Gilberto Barbosa GB Pawlowski Krzysztof K Wieslander Elisabet E Malm Johan J Fenyo David D Horvatovich Peter P Marko-Varga György G Győrffy Balázs B

Journal of proteome research 20250505 6

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 ...[more]

PMID: 40322912

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Transgelin contributes to a poor response of metastatic renal cell carcinoma to sunitinib treatment

Project description:Renal cell carcinoma (RCC) represents about 2-3% of all cancers with over 400,000 new cases per year. Sunitinib, a vascular endothelial growth factor tyrosine kinase receptor inhibitor, has been used mainly for first-line treatment of metastatic clear-cell RCC with good or intermediate prognosis. However, about one third of metastatic RCC patients do not respond to sunitinib, leading to disease progression. Here we aim to find and characterize proteins associated with poor sunitinib response in a pilot proteomics study. 16 RCC tumors from patients responding (8) vs. non-responding (8) to sunitinib in 3 months after treatment initiation, together with their adjacent non-cancerous tissues, were analyzed using data independent acquisition mass spectrometry. Proteomics analysis quantified 1996 protein groups (q<0.01) and revealed 27 proteins deregulated between tumors non-responding vs. responding to sunitinib, representing a pattern of deregulated proteins potentially contributing to sunitinib resistance. Gene set enrichment analysis showed up-regulation of epithelial-to-mesenchymal transition with transgelin as one of the most significantly abundant protein. Transgelin expression was silenced by CRISPR/Cas9 and RNA interference, and the cells with reduced transgelin level exhibited significantly slower proliferation. Our data indicate that transgelin is an essential protein supporting RCC cell proliferation which could contribute to intrinsic sunitinib resistance.

2021-11-03 | PXD027065 | Pride

Plasma Proteomic Analysis Based on 4D-DIA Evaluates the Clinical Response to Imrecoxib in the Early Treatment of Osteoarthritis

Project description:Nonsteroidal anti-inflammatory drugs (NSAIDs) are the primary treatment for osteoarthritis (OA), but prolonged use has adverse effects and varying efficacy. Among NSAIDs, imrecoxib, a selective cyclooxygenase-2 (COX-2) inhibitor, reduces side effects yet remains ineffective for half the patient population. This study aims to identify biomarkers for early imrecoxib efficacy evaluation in OA for personalized therapy optimization. From September 2021 to January 2022, imrecoxib was administered to patients with OA at Nanjing Drum Tower Hospital. Plasma samples from these patients underwent proteomic analysis through the four-dimensional data-independent acquisition (4D-DIA) method, followed by bioinformatics analysis. Potential differentially expressed proteins (DEPs) were validated using enzyme-linked immunosorbent assay (ELISA). Sixty-six patients with knee OA were included and divided into responders (n=35) and non-responders (n=31). Proteomic analysis was conducted on 15 patients from each group, and ELISA validation was performed for every patient. We found 140 DEPs between the two groups after administering imrecoxib treatment, characterized by 29 proteins showing up-regulation and 111 displaying down-regulation (p < 0.05, fold change > ±1.2). Galectin-1 (LGALS1), galectin-3 (LGALS3), and the cluster of differentiation 44 (CD44) could be utilized to evaluate the clinical response to imrecoxib in the treatment of OA after ELISA validation.This study successfully identified biomarkers for evaluating imrecoxib's clinical response in OA patients using 4D-DIA technology. These biomarkers may play a vital role in future personalized OA treatment strategies, pending further confirmation.

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The V-ATPase complex component RNAseK is required for lysosomal hydrolase delivery and autophagosome degradation

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The DIALib-QC software tool for the systematic assessment of spectral library quality in data-independent acquisition proteomics

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SWATH mass spectrometry as a tool for quantitative profiling of the matrisome

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An Amphipathic Helix in Brl1 is Required for Nuclear Pore Complex Biogenesis in S. cerevisiae - Lysate intermixing text (DIA)

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An Amphipathic Helix in Brl1 is Required for Nuclear Pore Complex Biogenesis in S. cerevisiae - KARMA analysis of Nup170 with/without Brl1 degradation (DIA)

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