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Proteomics and Its Applications in Disease 2.0

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

Deadline for manuscript submissions: closed (25 February 2024) | Viewed by 7156

Special Issue Editors

1. School of Optometry, Department of Applied Biology and Chemical Technology, Research Centre for SHARP Vision (RCSV), The Hong Kong Polytechnic University, Hong Kong 999077, China
2. Singapore Eye Research Institute, The Academia, 20 College Road, Singapore 169856, Singapore
Interests: mass spectrometry; proteomics; metabolomics; disease biomarker
Special Issues, Collections and Topics in MDPI journals
Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
Interests: proteomics; mass spectrometry; disease biomarker; drug target identification; aquaporin biomimetic membrane
Special Issues, Collections and Topics in MDPI journals
School of Optometry, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China
Interests: mass spectrometry; proteomics; post-translational modifications; disease biomarker
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue is a continuation of our previous successful Special Issue “Proteomics and Its Applications in Disease”.

Recent advances in mass spectrometry-based technologies, e.g., data-independent acquisition (DIA), ion mobility spectrometry (IMS), and multiple reaction monitoring (MRM), have provided superior sensitivity, reproducibility, and throughput in proteomics analysis. This allows researchers to explore diseases by assessing a deeper proteome in a relatively short time with high reproducibility and fewer missing data. No doubt, the applications of proteomics research in diseases not only provide new insights into disease mechanisms, but also novel disease biomarkers and therapeutic targets.

In this Special Issue, we invite you to contribute original research and review articles which focus on (but are not limited to) the following topics related to the applications of proteomics in diseases: disease biomarker (discovery and validation), molecular mechanisms (signaling pathway) of disease, new drug targets, the role of post-translational modifications in disease, targeted proteomics, multi-omics studies, proteomic studies on in vitro cell disease models, animal disease models, or patient cohort studies.

Prof. Dr. Lei Zhou
Dr. Qingsong Lin
Dr. Chuen Lam
Guest Editors

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
  • quantitative proteomics
  • biomarkers
  • signaling pathways
  • post-translational modifications
  • disease mechanism
  • novel therapeutic targets

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Published Papers (7 papers)

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Research

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37 pages, 24151 KiB  
Article
Nicotinamide Mononucleotide (NMN) Works in Type 2 Diabetes through Unexpected Effects in Adipose Tissue, Not by Mitochondrial Biogenesis
by Roua Gabriela Popescu, Anca Dinischiotu, Teodoru Soare, Ene Vlase and George Cătălin Marinescu
Int. J. Mol. Sci. 2024, 25(5), 2594; https://doi.org/10.3390/ijms25052594 - 23 Feb 2024
Viewed by 902
Abstract
Nicotinamide mononucleotide (NMN) has emerged as a promising therapeutic intervention for age-related disorders, including type 2 diabetes. In this study, we confirmed the previously observed effects of NMN treatment on glucose uptake and investigated its underlying mechanisms in various tissues and cell lines. [...] Read more.
Nicotinamide mononucleotide (NMN) has emerged as a promising therapeutic intervention for age-related disorders, including type 2 diabetes. In this study, we confirmed the previously observed effects of NMN treatment on glucose uptake and investigated its underlying mechanisms in various tissues and cell lines. Through the most comprehensive proteomic analysis to date, we discovered a series of novel organ-specific effects responsible for glucose uptake as measured by the IPGTT: adipose tissue growing (suggested by increased protein synthesis and degradation and mTOR proliferation signaling upregulation). Notably, we observed the upregulation of thermogenic UCP1, promoting enhanced glucose conversion to heat in intermuscular adipose tissue while showing a surprising repressive effect on mitochondrial biogenesis in muscle and the brain. Additionally, liver and muscle cells displayed a unique response, characterized by spliceosome downregulation and concurrent upregulation of chaperones, proteasomes, and ribosomes, leading to mildly impaired and energy-inefficient protein synthesis machinery. Furthermore, our findings revealed remarkable metabolic rewiring in the brain. This involved increased production of ketone bodies, downregulation of mitochondrial OXPHOS and TCA cycle components, as well as the induction of well-known fasting-associated effects. Collectively, our data elucidate the multifaceted nature of NMN action, highlighting its organ-specific effects and their role in improving glucose uptake. These findings deepen our understanding of NMN’s therapeutic potential and pave the way for novel strategies in managing metabolic disorders. Full article
(This article belongs to the Special Issue Proteomics and Its Applications in Disease 2.0)
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12 pages, 2013 KiB  
Communication
Variation of the 2D Pattern of Brain Proteins in Mice Infected with Taenia crassiceps ORF Strain
by Mariana Díaz-Zaragoza, Ricardo Hernández-Ávila, Abraham Landa and Pedro Ostoa-Saloma
Int. J. Mol. Sci. 2024, 25(3), 1460; https://doi.org/10.3390/ijms25031460 - 25 Jan 2024
Viewed by 418
Abstract
Some parasites are known to influence brain proteins or induce changes in the functioning of the nervous system. In this study, our objective is to demonstrate how the two-dimensional gel technique is valuable for detecting differences in protein expression and providing detailed information [...] Read more.
Some parasites are known to influence brain proteins or induce changes in the functioning of the nervous system. In this study, our objective is to demonstrate how the two-dimensional gel technique is valuable for detecting differences in protein expression and providing detailed information on changes in the brain proteome during a parasitic infection. Subsequently, we seek to understand how the parasitic infection affects the protein composition in the brain and how this may be related to changes in brain function. By analyzing de novo-expressed proteins at 2, 4, and 8 weeks post-infection compared to the brains of the control mice, we observed that proteins expressed at 2 weeks are primarily associated with neuroprotection or the initial response of the mouse brain to the infection. At 8 weeks, parasitic infection can induce oxidative stress in the brain, potentially activating signaling pathways related to the response to cellular damage. Proteins expressed at 8 weeks exhibit a pattern indicating that, as the host fails to balance the Neuro-Immuno-Endocrine network of the organism, the brain begins to undergo an apoptotic process and consequently experiences brain damage. Full article
(This article belongs to the Special Issue Proteomics and Its Applications in Disease 2.0)
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17 pages, 4066 KiB  
Article
Targeted Proteomics Reveals Quantitative Differences in Low-Abundance Glycosyltransferases of Patients with Congenital Disorders of Glycosylation
by Roman Sakson, Lars Beedgen, Patrick Bernhard, K. Merve Alp, Nicole Lübbehusen, Ralph Röth, Beate Niesler, Marcin Luzarowski, Olga Shevchuk, Matthias P. Mayer, Christian Thiel and Thomas Ruppert
Int. J. Mol. Sci. 2024, 25(2), 1191; https://doi.org/10.3390/ijms25021191 - 18 Jan 2024
Cited by 1 | Viewed by 761
Abstract
Protein glycosylation is an essential post-translational modification in all domains of life. Its impairment in humans can result in severe diseases named congenital disorders of glycosylation (CDGs). Most of the glycosyltransferases (GTs) responsible for proper glycosylation are polytopic membrane proteins that represent challenging [...] Read more.
Protein glycosylation is an essential post-translational modification in all domains of life. Its impairment in humans can result in severe diseases named congenital disorders of glycosylation (CDGs). Most of the glycosyltransferases (GTs) responsible for proper glycosylation are polytopic membrane proteins that represent challenging targets in proteomics. We established a multiple reaction monitoring (MRM) assay to comprehensively quantify GTs involved in the processes of N-glycosylation and O- and C-mannosylation in the endoplasmic reticulum. High robustness was achieved by using an enriched membrane protein fraction of isotopically labeled HEK 293T cells as an internal protein standard. The analysis of primary skin fibroblasts from eight CDG type I patients with impaired ALG1, ALG2, and ALG11 genes, respectively, revealed a substantial reduction in the corresponding protein levels. The abundance of the other GTs, however, remained unchanged at the transcript and protein levels, indicating that there is no fail-safe mechanism for the early steps of glycosylation in the endoplasmic reticulum. The established MRM assay was shared with the scientific community via the commonly used open source Skyline software environment, including Skyline Batch for automated data analysis. We demonstrate that another research group could easily reproduce all analysis steps, even while using different LC-MS hardware. Full article
(This article belongs to the Special Issue Proteomics and Its Applications in Disease 2.0)
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22 pages, 3713 KiB  
Article
Inhibition of HSP90 in Driver Oncogene-Defined Lung Adenocarcinoma Cell Lines: Key Proteins Underpinning Therapeutic Efficacy
by Ángela Marrugal, Irene Ferrer, Álvaro Quintanal-Villalonga, Laura Ojeda, María Dolores Pastor, Ricardo García-Luján, Amancio Carnero, Luis Paz-Ares and Sonia Molina-Pinelo
Int. J. Mol. Sci. 2023, 24(18), 13830; https://doi.org/10.3390/ijms241813830 - 07 Sep 2023
Viewed by 1037
Abstract
The use of 90 kDa heat shock protein (HSP90) inhibition as a therapy in lung adenocarcinoma remains limited due to moderate drug efficacy, the emergence of drug resistance, and early tumor recurrence. The main objective of this research is to maximize treatment efficacy [...] Read more.
The use of 90 kDa heat shock protein (HSP90) inhibition as a therapy in lung adenocarcinoma remains limited due to moderate drug efficacy, the emergence of drug resistance, and early tumor recurrence. The main objective of this research is to maximize treatment efficacy in lung adenocarcinoma by identifying key proteins underlying HSP90 inhibition according to molecular background, and to search for potential biomarkers of response to this therapeutic strategy. Inhibition of the HSP90 chaperone was evaluated in different lung adenocarcinoma cell lines representing the most relevant molecular alterations (EGFR mutations, KRAS mutations, or EML4-ALK translocation) and wild-type genes found in each tumor subtype. The proteomic technique iTRAQ was used to identify proteomic profiles and determine which biological pathways are involved in the response to HSP90 inhibition in lung adenocarcinoma. We corroborated the greater efficacy of HSP90 inhibition in EGFR mutated or EML4-ALK translocated cell lines. We identified proteins specifically and significantly deregulated after HSP90 inhibition for each molecular alteration. Two proteins, ADI1 and RRP1, showed independently deregulated molecular patterns. Functional annotation of the altered proteins suggested that apoptosis was the only pathway affected by HSP90 inhibition across all molecular subgroups. The expression of ADI1 and RRP1 could be used to monitor the correct inhibition of HSP90 in lung adenocarcinoma. In addition, proteins such as ASS1, ITCH, or UBE2L3 involved in pathways related to the inhibition of a particular molecular background could be used as potential response biomarkers, thereby improving the efficacy of this therapeutic approach to combat lung adenocarcinoma. Full article
(This article belongs to the Special Issue Proteomics and Its Applications in Disease 2.0)
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24 pages, 5257 KiB  
Article
Differential Responses of Retinal Neurons and Glia Revealed via Proteomic Analysis on Primary and Secondary Retinal Ganglion Cell Degeneration
by Jacky M. K. Kwong, Joseph Caprioli, Joanne C. Y. Lee, Yifan Song, Feng-Juan Yu, Jingfang Bian, Ying-Hon Sze, King-Kit Li, Chi-Wai Do, Chi-Ho To and Thomas Chuen Lam
Int. J. Mol. Sci. 2023, 24(15), 12109; https://doi.org/10.3390/ijms241512109 - 28 Jul 2023
Viewed by 941
Abstract
To explore the temporal profile of retinal proteomes specific to primary and secondary retinal ganglion cell (RGC) loss. Unilateral partial optic nerve transection (pONT) was performed on the temporal side of the rat optic nerve. Temporal and nasal retinal samples were collected at [...] Read more.
To explore the temporal profile of retinal proteomes specific to primary and secondary retinal ganglion cell (RGC) loss. Unilateral partial optic nerve transection (pONT) was performed on the temporal side of the rat optic nerve. Temporal and nasal retinal samples were collected at 1, 4 and 8 weeks after pONT (n = 4 each) for non-biased profiling with a high-resolution hybrid quadrupole time-of-flight mass spectrometry running on label-free SWATHTM acquisition (SCIEX). An information-dependent acquisition ion library was generated using ProteinPilot 5.0 and OneOmics cloud bioinformatics. Combined proteome analysis detected 2531 proteins with a false discovery rate of <1%. Compared to the nasal retina, 10, 25 and 61 significantly regulated proteins were found in the temporal retina at 1, 4, and 8 weeks, respectively (p < 0.05, FC ≥ 1.4 or ≤0.7). Eight proteins (ALDH1A1, TRY10, GFAP, HBB-B1, ALB, CDC42, SNCG, NEFL) were differentially expressed for at least two time points. The expressions of ALDH1A1 and SNCG at nerve fibers were decreased along with axonal loss. Increased ALDH1A1 localization in the inner nuclear layer suggested stress response. Increased GFAP expression demonstrated regional reactivity of astrocytes and Muller cells. Meta-analysis of gene ontology showed a pronounced difference in endopeptidase and peptidase inhibitor activity. Temporal proteomic profiling demonstrates established and novel protein targets associated with RGC damage. Full article
(This article belongs to the Special Issue Proteomics and Its Applications in Disease 2.0)
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Review

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37 pages, 1001 KiB  
Review
Circulating Proteins as Diagnostic Markers in Gastric Cancer
by Ombretta Repetto, Roberto Vettori, Agostino Steffan, Renato Cannizzaro and Valli De Re
Int. J. Mol. Sci. 2023, 24(23), 16931; https://doi.org/10.3390/ijms242316931 - 29 Nov 2023
Cited by 3 | Viewed by 1103
Abstract
Gastric cancer (GC) is a highly malignant disease affecting humans worldwide and has a poor prognosis. Most GC cases are detected at advanced stages due to the cancer lacking early detectable symptoms. Therefore, there is great interest in improving early diagnosis by implementing [...] Read more.
Gastric cancer (GC) is a highly malignant disease affecting humans worldwide and has a poor prognosis. Most GC cases are detected at advanced stages due to the cancer lacking early detectable symptoms. Therefore, there is great interest in improving early diagnosis by implementing targeted prevention strategies. Markers are necessary for early detection and to guide clinicians to the best personalized treatment. The current semi-invasive endoscopic methods to detect GC are invasive, costly, and time-consuming. Recent advances in proteomics technologies have enabled the screening of many samples and the detection of novel biomarkers and disease-related signature signaling networks. These biomarkers include circulating proteins from different fluids (e.g., plasma, serum, urine, and saliva) and extracellular vesicles. We review relevant published studies on circulating protein biomarkers in GC and detail their application as potential biomarkers for GC diagnosis. Identifying highly sensitive and highly specific diagnostic markers for GC may improve patient survival rates and contribute to advancing precision/personalized medicine. Full article
(This article belongs to the Special Issue Proteomics and Its Applications in Disease 2.0)
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34 pages, 2500 KiB  
Review
Searching for Atherosclerosis Biomarkers by Proteomics: A Focus on Lesion Pathogenesis and Vulnerability
by Gabriele Nieddu, Marilena Formato and Antonio Junior Lepedda
Int. J. Mol. Sci. 2023, 24(20), 15175; https://doi.org/10.3390/ijms242015175 - 14 Oct 2023
Cited by 1 | Viewed by 951
Abstract
Plaque rupture and thrombosis are the most important clinical complications in the pathogenesis of stroke, coronary arteries, and peripheral vascular diseases. The identification of early biomarkers of plaque presence and susceptibility to ulceration could be of primary importance in preventing such life-threatening events. [...] Read more.
Plaque rupture and thrombosis are the most important clinical complications in the pathogenesis of stroke, coronary arteries, and peripheral vascular diseases. The identification of early biomarkers of plaque presence and susceptibility to ulceration could be of primary importance in preventing such life-threatening events. With the improvement of proteomic tools, large-scale technologies have been proven valuable in attempting to unravel pathways of atherosclerotic degeneration and identifying new circulating markers to be utilized either as early diagnostic traits or as targets for new drug therapies. To address these issues, different matrices of human origin, such as vascular cells, arterial tissues, plasma, and urine, have been investigated. Besides, proteomics was also applied to experimental atherosclerosis in order to unveil significant insights into the mechanisms influencing atherogenesis. This narrative review provides an overview of the last twenty years of omics applications to the study of atherogenesis and lesion vulnerability, with particular emphasis on lipoproteomics and vascular tissue proteomics. Major issues of tissue analyses, such as plaque complexity, sampling, availability, choice of proper controls, and lipoproteins purification, will be raised, and future directions will be addressed. Full article
(This article belongs to the Special Issue Proteomics and Its Applications in Disease 2.0)
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