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New Advances in Proteomics in Disease

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Guest Editor
Department of Science and Technological Innovation, Universita' degli Studi del Piemonte Orientale "Amedeo Avogadro", Alessandria, Italy
Interests: patch-clamp on neuroblastoma cell line with PFAS agents on GABA_A receptors; morphological and physiological alterations on rat testis and pancreas upon exposure to hypergravity; proteomics and metabolomics of monocytes exposed to inflammatory cytokines

Special Issue Information

Dear Colleagues,

During the last thirty years, proteomics has proved to be a powerful tool to define the metabolic pathways and cellular mechanisms involved in the pathogenesis and development of human diseases. Besides the investigation of potential causes, the current interest in proteomics aims to identify new protein molecules as potential biomarkers, making proteomics a powerful prognostic and early diagnostic tool. Proteomics analysis enable the characterization of disease-associated proteins, their possible modifications, and reciprocal interactions contributing to understanding of human illnesses, including cancer, infectious, and autoimmune diseases. By comparing different protein profiles between healthy and sick individuals, it is possible to identify differentially expressed proteins which can change in pathological conditions, not only at single cell or tissue level, but also in intracellular organelles and body fluids. The different expression level can allow the fast detection of a disease, monitor its temporal course, and speed up the development of therapeutical agents, revealing altered cell signaling pathways and gaining insights into altered molecular interactions behind disease pathogenesis. Together with the discovery of new therapeutical agents, proteomics can lead to a personalized medicine tracing the patient profile, their probability of getting sick, and specific treatment strategies for specific patient populations. This Special Issue aims to focus on the molecular mechanisms of pathogenesis in order to identify specific pathways involved in diseases and proteins useful for fast and precise disease detection.

Dr. Valeria Magnelli
Guest Editor

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Keywords

  • proteomics
  • protein
  • profile
  • molecular mechanism
  • biomarker
  • therapeutical agent

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Published Papers (2 papers)

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Research

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17 pages, 3111 KiB  
Article
Proteomic Analysis Highlights the Impact of the Sphingolipid Metabolizing Enzyme β-Galactosylceramidase on Mitochondrial Plasticity in Human Melanoma
by Davide Capoferri, Luca Mignani, Marcello Manfredi and Marco Presta
Int. J. Mol. Sci. 2024, 25(5), 3062; https://doi.org/10.3390/ijms25053062 - 6 Mar 2024
Cited by 1 | Viewed by 1265
Abstract
Mitochondrial plasticity, marked by a dynamism between glycolysis and oxidative phosphorylation due to adaptation to genetic and microenvironmental alterations, represents a characteristic feature of melanoma progression. Sphingolipids play a significant role in various aspects of cancer cell biology, including metabolic reprogramming. Previous observations [...] Read more.
Mitochondrial plasticity, marked by a dynamism between glycolysis and oxidative phosphorylation due to adaptation to genetic and microenvironmental alterations, represents a characteristic feature of melanoma progression. Sphingolipids play a significant role in various aspects of cancer cell biology, including metabolic reprogramming. Previous observations have shown that the lysosomal sphingolipid-metabolizing enzyme β-galactosylceramidase (GALC) exerts pro-oncogenic functions in melanoma. Here, mining the cBioPortal for a Cancer Genomics data base identified the top 200 nuclear-encoded genes whose expression is negatively correlated with GALC expression in human melanoma. Their categorization indicated a significant enrichment in Gene Ontology terms and KEGG pathways related to mitochondrial proteins and function. In parallel, proteomic analysis by LC-MS/MS of two GALC overexpressing human melanoma cell lines identified 98 downregulated proteins when compared to control mock cells. Such downregulation was confirmed at a transcriptional level by a Gene Set Enrichment Analysis of the genome-wide expression profiling data obtained from the same cells. Among the GALC downregulated proteins, we identified a cluster of 42 proteins significantly associated with GO and KEGG categorizations related to mitochondrion and energetic metabolism. Overall, our data indicate that changes in GALC expression may exert a significant impact on mitochondrial plasticity in human melanoma cells. Full article
(This article belongs to the Special Issue New Advances in Proteomics in Disease)
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Review

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25 pages, 909 KiB  
Review
Phenotyping Tumor Heterogeneity through Proteogenomics: Study Models and Challenges
by Diletta Piana, Federica Iavarone, Elisa De Paolis, Gennaro Daniele, Federico Parisella, Angelo Minucci, Viviana Greco and Andrea Urbani
Int. J. Mol. Sci. 2024, 25(16), 8830; https://doi.org/10.3390/ijms25168830 - 14 Aug 2024
Cited by 1 | Viewed by 1571
Abstract
Tumor heterogeneity refers to the diversity observed among tumor cells: both between different tumors (inter-tumor heterogeneity) and within a single tumor (intra-tumor heterogeneity). These cells can display distinct morphological and phenotypic characteristics, including variations in cellular morphology, metastatic potential and variability treatment responses [...] Read more.
Tumor heterogeneity refers to the diversity observed among tumor cells: both between different tumors (inter-tumor heterogeneity) and within a single tumor (intra-tumor heterogeneity). These cells can display distinct morphological and phenotypic characteristics, including variations in cellular morphology, metastatic potential and variability treatment responses among patients. Therefore, a comprehensive understanding of such heterogeneity is necessary for deciphering tumor-specific mechanisms that may be diagnostically and therapeutically valuable. Innovative and multidisciplinary approaches are needed to understand this complex feature. In this context, proteogenomics has been emerging as a significant resource for integrating omics fields such as genomics and proteomics. By combining data obtained from both Next-Generation Sequencing (NGS) technologies and mass spectrometry (MS) analyses, proteogenomics aims to provide a comprehensive view of tumor heterogeneity. This approach reveals molecular alterations and phenotypic features related to tumor subtypes, potentially identifying therapeutic biomarkers. Many achievements have been made; however, despite continuous advances in proteogenomics-based methodologies, several challenges remain: in particular the limitations in sensitivity and specificity and the lack of optimal study models. This review highlights the impact of proteogenomics on characterizing tumor phenotypes, focusing on the critical challenges and current limitations of its use in different clinical and preclinical models for tumor phenotypic characterization. Full article
(This article belongs to the Special Issue New Advances in Proteomics in Disease)
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