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Recent Advances of Proteomics in Human Health and Disease
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Recent Advances of Proteomics in Human Health and Disease

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Informatics".

Deadline for manuscript submissions: closed (20 February 2025) | Viewed by 9795

Special Issue Editor

Dr. Ekaterina Poverennaya

E-Mail Website
Guest Editor
Institute of Biomedical Chemistry, 119121 Moscow, Russia
Interests: human proteome; proteoforms; interactomics; bioinformatics

Special Issue Information

Dear Colleagues,

With the accumulation of omics data, the request for a healthy molecular profile of a person is increasingly emerging. As the final chord in the realization of genomic information, the proteome reflects the complete picture of molecular processes in the body. Nevertheless, despite the significant and encouraging progress in developing proteomic technologies, there are still many difficulties with a complete inventory of all molecules. Low-copy proteins, as well as aberrant forms, are still difficult to detect. This limitation complicates the decoding of biological processes and further identification of predictive, diagnostic, and therapeutic biomarkers of diseases.

This Special Issue focuses on (but is not limited to) the application of proteomics solo and in integration with other omics in disease, with emphasis on biomarkers, molecular mechanisms of disease, new drug targets, aberrant proteoforms, proteins functional annotation, proteomic studies on the disease model or patient cohort studies, and novel proteomics methodologies and strategies.

Dr. Ekaterina Poverennaya
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • proteomics
  • biomarkers
  • drug target
  • disease mechanism
  • signalling pathways
  • interactomics
  • omics
  • proteoforms
  • bioinformatics
  • technology development

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Published Papers (6 papers)

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Research

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18 pages, 492 KiB  
Article
GTPLM-GO: Enhancing Protein Function Prediction Through Dual-Branch Graph Transformer and Protein Language Model Fusing Sequence and Local–Global PPI Information
by Haotian Zhang, Yundong Sun, Yansong Wang, Xiaoling Luo, Yumeng Liu, Bin Chen, Xiaopeng Jin and Dongjie Zhu
Int. J. Mol. Sci. 2025, 26(9), 4088; https://doi.org/10.3390/ijms26094088 - 25 Apr 2025
Viewed by 130
Abstract
Currently, protein–protein interaction (PPI) networks have become an essential data source for protein function prediction. However, methods utilizing graph neural networks (GNNs) face significant challenges in modeling PPI networks. A primary issue is over-smoothing, which occurs when multiple GNN layers are stacked to [...] Read more.
Currently, protein–protein interaction (PPI) networks have become an essential data source for protein function prediction. However, methods utilizing graph neural networks (GNNs) face significant challenges in modeling PPI networks. A primary issue is over-smoothing, which occurs when multiple GNN layers are stacked to capture global information. This architectural limitation inherently impairs the integration of local and global information within PPI networks, thereby limiting the accuracy of protein function prediction. To effectively utilize information within PPI networks, we propose GTPLM-GO, a protein function prediction method based on a dual-branch Graph Transformer and protein language model. The dual-branch Graph Transformer achieves the collaborative modeling of local and global information in PPI networks through two branches: a graph neural network and a linear attention-based Transformer encoder. GTPLM-GO integrates local–global PPI information with the functional semantic encoding constructed by the protein language model, overcoming the issue of inadequate information extraction in existing methods. Experimental results demonstrate that GTPLM-GO outperforms advanced network-based and sequence-based methods on PPI network datasets of varying scales. Full article
(This article belongs to the Special Issue Recent Advances of Proteomics in Human Health and Disease)
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16 pages, 3000 KiB  
Article
IQGAP3 Is an Important Mediator of Skin Inflammatory Diseases
by Alena Zolotarenko and Sergey Bruskin
Int. J. Mol. Sci. 2024, 25(8), 4545; https://doi.org/10.3390/ijms25084545 - 21 Apr 2024
Viewed by 1883
Abstract
IQGAP3 (IQ Motif Containing GTPase Activating Protein 3) is member of the IQGAP family of scaffold proteins, which are essential for assembling multiprotein complexes that coordinate various intracellular signaling pathways. Previous research has shown that IQGAP3 is overexpressed in psoriatic skin lesions. Given [...] Read more.
IQGAP3 (IQ Motif Containing GTPase Activating Protein 3) is member of the IQGAP family of scaffold proteins, which are essential for assembling multiprotein complexes that coordinate various intracellular signaling pathways. Previous research has shown that IQGAP3 is overexpressed in psoriatic skin lesions. Given its involvement in processes like cell proliferation and chemokine signaling, we sought to explore its molecular role in driving the psoriatic phenotype of keratinocytes. By conducting transcriptome profiling of HaCaT keratinocytes, we identified numerous psoriasis-associated pathways that were affected when IQGAP3 was knocked down. These included alterations in NFkB signaling, EGFR signaling, activation of p38/MAPK and ERK1/ERK2, lipid metabolism, cytokine production, and the response to inflammatory cytokine stimulation. Real-time analysis further revealed changes in cell growth dynamics, including proliferation and wound healing. The balance between cell proliferation and apoptosis was altered, as were skin barrier functions and the production of IL-6 and IFNγ. Despite these significant findings, the diversity of the alterations observed in the knockdown cells led us to conclude that IQGAP3 may not be the best target for the therapeutic inhibition to normalize the phenotype of keratinocytes in psoriasis. Full article
(This article belongs to the Special Issue Recent Advances of Proteomics in Human Health and Disease)
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23 pages, 8253 KiB  
Article
Exploring the Molecular Tapestry: Organ-Specific Peptide and Protein Ultrafiltrates and Their Role in Therapeutics
by Jakub Peter Slivka, Chris Bauer, Alexander Younsi, Michelle B. F. Wong, Mike K. S. Chan and Thomas Skutella
Int. J. Mol. Sci. 2024, 25(5), 2863; https://doi.org/10.3390/ijms25052863 - 1 Mar 2024
Viewed by 2026
Abstract
This study aims to characterize the proteome composition of organ-derived protein extracts from rabbits. Protein isolation was performed using soft homogenization and size exclusion via ultrafiltration. The proteome analysis of the ultrafiltrates was conducted using gel electrophoresis, and the mass spectrometry data were [...] Read more.
This study aims to characterize the proteome composition of organ-derived protein extracts from rabbits. Protein isolation was performed using soft homogenization and size exclusion via ultrafiltration. The proteome analysis of the ultrafiltrates was conducted using gel electrophoresis, and the mass spectrometry data were subjected to gene ontology analysis. Proteomic profiling revealed comprehensive protein profiles associated with RNA regulation, fatty acid binding, inflammatory response, oxidative stress, and metabolism. Additionally, our results demonstrate the presence of abundant small proteins, as observed in the mass spectrometry datasets. Small proteins and peptides are crucial in transcription modulation and various biological processes. The protein networks identified in the ultrafiltrates have the potential to enhance and complement biological therapeutic interventions. Data are available via ProteomeXchange with identifier PXD050039. Full article
(This article belongs to the Special Issue Recent Advances of Proteomics in Human Health and Disease)
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Review

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19 pages, 906 KiB  
Review
Dried Spot Paradigm: Problems and Prospects in Proteomics
by Olga I. Kiseleva, Yuriy A. Ikhalaynen, Ilya Y. Kurbatov, Viktoriia A. Arzumanian, Polina A. Kryukova and Ekaterina V. Poverennaya
Int. J. Mol. Sci. 2025, 26(8), 3857; https://doi.org/10.3390/ijms26083857 - 18 Apr 2025
Viewed by 278
Abstract
The analysis of biological fluids plays a crucial role in biomarker discovery, disease diagnostics, and precision medicine. Dried sample carriers—such as dried blood spots, dried plasma, serum, saliva, tears, and urine—have emerged as powerful tools, offering advantages in sample collection, storage, and transport, [...] Read more.
The analysis of biological fluids plays a crucial role in biomarker discovery, disease diagnostics, and precision medicine. Dried sample carriers—such as dried blood spots, dried plasma, serum, saliva, tears, and urine—have emerged as powerful tools, offering advantages in sample collection, storage, and transport, particularly in remote and resource-limited settings. Recent advances in proteomic methodologies have expanded the potential of these dried matrices, yet challenges related to protein stability, sensitivity, and standardization persist. This review critically examines the current state of proteomic investigations using dried biological fluids. Furthermore, we compare proteomics’ progress in this field with other omics approaches, such as metabolomics, to contextualize its development and integration potential. While dried fluid proteomics is promising for non-invasive diagnostics and large-scale epidemiological studies, addressing technical limitations will be essential for its broader adoption in clinical and translational research. Full article
(This article belongs to the Special Issue Recent Advances of Proteomics in Human Health and Disease)
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13 pages, 1408 KiB  
Review
Proteomic Markers of Aging and Longevity: A Systematic Review
by Anna A. Kliuchnikova, Ekaterina V. Ilgisonis, Alexander I. Archakov, Elena A. Ponomarenko and Alexey A. Moskalev
Int. J. Mol. Sci. 2024, 25(23), 12634; https://doi.org/10.3390/ijms252312634 - 25 Nov 2024
Cited by 2 | Viewed by 2145
Abstract
This article provides a systematic review of research conducted on the proteomic composition of blood as part of a complex biological age estimation. We performed a comprehensive analysis of 17 publicly available datasets and compiled an integral list of proteins. These proteins were [...] Read more.
This article provides a systematic review of research conducted on the proteomic composition of blood as part of a complex biological age estimation. We performed a comprehensive analysis of 17 publicly available datasets and compiled an integral list of proteins. These proteins were sorted based on their detection probability using mass spectrometry in human plasma. We propose this list as a basis for creating a panel of peptides and quantifying the content of selected proteins in the format of a proteomic aging clock. The selected proteins are especially notable for their roles in inflammatory processes and lipid metabolism. Our findings suggest, for the first time, that proteins associated with systemic disorders, including those approved by the FDA for clinical use, could serve as potential markers of aging. Full article
(This article belongs to the Special Issue Recent Advances of Proteomics in Human Health and Disease)
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17 pages, 1363 KiB  
Review
Low-Abundance Protein Enrichment for Medical Applications: The Involvement of Combinatorial Peptide Library Technique
by Egisto Boschetti and Pier Giorgio Righetti
Int. J. Mol. Sci. 2023, 24(12), 10329; https://doi.org/10.3390/ijms241210329 - 19 Jun 2023
Cited by 6 | Viewed by 2535
Abstract
The discovery of low- and very low-abundance proteins in medical applications is considered a key success factor in various important domains. To reach this category of proteins, it is essential to adopt procedures consisting of the selective enrichment of species that are present [...] Read more.
The discovery of low- and very low-abundance proteins in medical applications is considered a key success factor in various important domains. To reach this category of proteins, it is essential to adopt procedures consisting of the selective enrichment of species that are present at extremely low concentrations. In the past few years pathways towards this objective have been proposed. In this review, a general landscape of the enrichment technology situation is made first with the presentation and the use of combinatorial peptide libraries. Then, a description of this peculiar technology for the identification of early-stage biomarkers for well-known pathologies with concrete examples is given. In another field of medical applications, the determination of host cell protein traces potentially present in recombinant therapeutic proteins, such as antibodies, is discussed along with their potentially deleterious effects on the health of patients on the one hand, and on the stability of these biodrugs on the other hand. Various additional applications of medical interest are disclosed for biological fluids investigations where the target proteins are present at very low concentrations (e.g., protein allergens). Full article
(This article belongs to the Special Issue Recent Advances of Proteomics in Human Health and Disease)
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