Proteomics and Metabolomics in Biomedicine, 2nd Volume

Topic Information

Dear Colleagues,

After the great success of the last edition, with fresh enthusiasm and energy, we are pleased to invite you to take part in the 2nd version of our topic. The pivotal role of omics technologies and their applications in every field of medical research, and in the diagnostic context, has already been established. During the omics revolution, which has taken place over the last decade, each omics has established an independent branch of knowledge, and many applications have been developed in this time, providing crucial insights into the most disparate fields of science. Nowadays, it has become even more common to integrate different omics data types to magnify the evidence related to various diseases with the aim of discovering their molecular bases or finding potential treatments. Among the omics disciplines, proteomics and metabolomics strategies, in particular, can provide a precise fingerprint of a biochemical status and can rapidly identify the responses of an organism, even when subtle fluctuations occur. As well as taking the aforementioned considerations into account, this topic aims to collect papers that particularly focus on the application of proteomics and metabolomics strategies in the context of biomedicine or related fields. The interplay among proteins, metabolites, lipids, interactors, and molecule modifications makes it possible to finely regulate a plethora of cellular processes, including metabolic pathways, growth processes, etc. Therefore, a broad range of proteomics- and metabolomics-derived disciplines will also be considered. These disciplines include but are not limited to the following: interactomics, the analysis of post-translational modifications (PTMs), proteogenomics, lipidomics, fluxomics, data analysis, bioinformatics, and single-cell omics. Furthermore, papers describing the development of strategies for sample preparation, mass spectrometry analysis, and computational elaboration are welcome in order to provide further knowledge of proteomics and metabolomics to a wider audience. All the work brought together by this topic will certainly provide new insights into the molecular aspects of pathophysiology and biochemistry in health and disease and will have important implications in systems biology, with the insights that are provided being useful for basic science and clinical applications.

Dr. Lucia Santorelli
Dr. Marianna Caterino
Dr. Michele Costanzo
Topic Editors

Keywords

Participating Journals

Journal Name	Impact Factor	CiteScore	Launched Year	First Decision (median)	APC
Biomedicines biomedicines	4.7	3.7	2013	15.4 Days	CHF 2600	Submit
International Journal of Molecular Sciences ijms	5.6	7.8	2000	16.3 Days	CHF 2900	Submit
Metabolites metabolites	4.1	5.3	2011	13.2 Days	CHF 2700	Submit
Molecules molecules	4.6	6.7	1996	14.6 Days	CHF 2700	Submit
Proteomes proteomes	3.3	5.7	2013	28.3 Days	CHF 1800	Submit

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Published Papers (5 papers)

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All Biomedicines IJMS Metabolites Molecules Proteomes

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15 pages, 2633 KiB  

Open AccessArticle

Lipidomics Analysis Unravels Aberrant Lipid Species and Pathways Induced by Zinc Oxide Nanoparticles in Kidney Cells

by Boyun Kim, Gaeun Kim, Hyun Pyo Jeon and Jewon Jung

Int. J. Mol. Sci. 2024, 25(8), 4285; https://doi.org/10.3390/ijms25084285 - 12 Apr 2024

Viewed by 373

Abstract

Zinc oxide nanoparticles (ZnO NPs) are widely used in versatile applications, from high technology to household products. While numerous studies have examined the toxic gene profile of ZnO NPs across various tissues, the specific lipid species associated with adverse effects and potential biomarkers [...] Read more.

Zinc oxide nanoparticles (ZnO NPs) are widely used in versatile applications, from high technology to household products. While numerous studies have examined the toxic gene profile of ZnO NPs across various tissues, the specific lipid species associated with adverse effects and potential biomarkers remain elusive. In this study, we conducted a liquid chromatography-mass spectrometry based lipidomics analysis to uncover potential lipid biomarkers in human kidney cells following treatment with ZnO NPs. Furthermore, we employed lipid pathway enrichment analysis (LIPEA) to elucidate altered lipid-related signaling pathways. Our results demonstrate that ZnO NPs induce cytotoxicity in renal epithelial cells and modulate lipid species; we identified 64 lipids with a fold change (FC) > 2 and p < 0.01 with corrected p < 0.05 in HK2 cells post-treatment with ZnO NPs. Notably, the altered lipids between control HK2 cells and those treated with ZnO NPs were associated with the sphingolipid, autophagy, and glycerophospholipid pathways. This study unveils novel potential lipid biomarkers of ZnO NP nanotoxicity, representing the first lipidomic profiling of ZnO NPs in human renal epithelial cells. Full article

(This article belongs to the Topic Proteomics and Metabolomics in Biomedicine, 2nd Volume)

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14 pages, 768 KiB  

Open AccessReview

Proteoform Analysis of the Human Olfactory System: A Window into Neurodegenerative Diseases

by Eqrem Rusi, Fiorenza Pennacchia, Wael Abu Ruqa, Giuseppina Talarico, Giuseppe Bruno, Antonio Minni and Christian Barbato

Proteomes 2024, 12(1), 9; https://doi.org/10.3390/proteomes12010009 - 21 Mar 2024

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Abstract

Background: Very little is known about the proteome of the human olfactory system and how diseases associated with olfactory dysfunctions can affect it. With this review, we try to summarize the existing literature on the use of this technique for a better [...] Read more.

Background: Very little is known about the proteome of the human olfactory system and how diseases associated with olfactory dysfunctions can affect it. With this review, we try to summarize the existing literature on the use of this technique for a better understanding of the neurodegenerative disease process. Methods: We used the PubMed database and found different articles which were then selected independently by three authors. Results: We found 157 articles, of which, after careful selection, only 30 were analyzed in this review. We presented all the associations identified between the protein/pathway alterations neurodegenerative diseases and SARS-CoV-2 infection. Conclusions: We think that the proteome of the olfactory system through blood, saliva, and mucus analysis could be a new way to better understand, diagnose, and finally treat neurodegenerative diseases. Full article

(This article belongs to the Topic Proteomics and Metabolomics in Biomedicine, 2nd Volume)

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14 pages, 6239 KiB  

Open AccessArticle

Proteomic Profiling of Early Secreted Proteins in Response to Lipopolysaccharide-Induced Vascular Endothelial Cell EA.hy926 Injury

by Worawat Songjang, Nitchawat Paiyabhroma, Noppadon Jumroon, Arunya Jiraviriyakul, Nitirut Nernpermpisooth, Porrnthanate Seenak, Sarawut Kumphune, Siriwan Thaisakun, Narumon Phaonakrop, Sittiruk Roytrakul and Panyupa Pankhong

Biomedicines 2023, 11(11), 3065; https://doi.org/10.3390/biomedicines11113065 - 15 Nov 2023

Cited by 2 | Viewed by 1726

Abstract

Sepsis is a crucial public health problem with a high mortality rate caused by a dysregulated host immune response to infection. Vascular endothelial cell injury is an important hallmark of sepsis, which leads to multiple organ failure and death. Early biomarkers to diagnose [...] Read more.

Sepsis is a crucial public health problem with a high mortality rate caused by a dysregulated host immune response to infection. Vascular endothelial cell injury is an important hallmark of sepsis, which leads to multiple organ failure and death. Early biomarkers to diagnose sepsis may provide early intervention and reduce risk of death. Damage-associated molecular patterns (DAMPs) are host nuclear or cytoplasmic molecules released from cells following tissue damage. We postulated that DAMPs could potentially be a novel sepsis biomarker. We used an in vitro model to determine suitable protein–DAMPs biomarkers for early sepsis diagnosis. Low and high lipopolysaccharide (LPS) doses were used to stimulate the human umbilical vein endothelial cell line EA.hy926 for 24, 48, and 72 h. Results showed that cell viability was reduced in both dose-dependent and time-dependent manners. Cell injury was corroborated by a significant increase in lactate dehydrogenase (LDH) activity within 24 h in cell-conditioned medium. Secreted protein–DAMPs in the supernatant, collected at different time points within 24 h, were characterized using shotgun proteomics LC-MS/MS analysis. Results showed that there were 2233 proteins. Among these, 181 proteins from the LPS-stimulated EA.hy926 at 1, 12, and 24 h were significantly different from those of the control. Twelve proteins were up-regulated at all three time points. Furthermore, a potential interaction analysis of predominant DAMPs-related proteins using STITCH 5.0 revealed the following associations with pathways: response to stress; bacterium; and LPS (GO:0080134; 0009617; 0032496). Markedly, alpha-2-HS-glycoprotein (AHSG or fetuin-A) and lactotransferrin (LTF) potentially presented since the first hour of LPS stimulation, and were highly up-regulated at 24 h. Taken together, we reported proteomic profiling of vascular endothelial cell-specific DAMPs in response to early an in vitro LPS stimulation, suggesting that these early damage-response protein candidates could be novel early biomarkers associated with sepsis. Full article

(This article belongs to the Topic Proteomics and Metabolomics in Biomedicine, 2nd Volume)

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17 pages, 3059 KiB  

Open AccessArticle

Metabolic Fingerprints of Effective Fluoxetine Treatment in the Prefrontal Cortex of Chronically Socially Isolated Rats: Marker Candidates and Predictive Metabolites

by Dragana Filipović, Julica Inderhees, Alexandra Korda, Predrag Tadić, Markus Schwaninger, Dragoš Inta and Stefan Borgwardt

Int. J. Mol. Sci. 2023, 24(13), 10957; https://doi.org/10.3390/ijms241310957 - 30 Jun 2023

Cited by 2 | Viewed by 1114

Abstract

The increasing prevalence of depression requires more effective therapy and the understanding of antidepressants’ mode of action. We carried out untargeted metabolomics of the prefrontal cortex of rats exposed to chronic social isolation (CSIS), a rat model of depression, and/or fluoxetine treatment using [...] Read more.

The increasing prevalence of depression requires more effective therapy and the understanding of antidepressants’ mode of action. We carried out untargeted metabolomics of the prefrontal cortex of rats exposed to chronic social isolation (CSIS), a rat model of depression, and/or fluoxetine treatment using liquid chromatography–high resolution mass spectrometry. The behavioral phenotype was assessed by the forced swim test. To analyze the metabolomics data, we employed univariate and multivariate analysis and biomarker capacity assessment using the receiver operating characteristic (ROC) curve. We also identified the most predictive biomarkers using a support vector machine with linear kernel (SVM-LK). Upregulated myo-inositol following CSIS may represent a potential marker of depressive phenotype. Effective fluoxetine treatment reversed depressive-like behavior and increased sedoheptulose 7-phosphate, hypotaurine, and acetyl-L-carnitine contents, which were identified as marker candidates for fluoxetine efficacy. ROC analysis revealed 4 significant marker candidates for CSIS group discrimination, and 10 for fluoxetine efficacy. SVM-LK with accuracies of 61.50% or 93.30% identified a panel of 7 or 25 predictive metabolites for depressive-like behavior or fluoxetine effectiveness, respectively. Overall, metabolic fingerprints combined with the ROC curve and SVM-LK may represent a new approach to identifying marker candidates or predictive metabolites for ongoing disease or disease risk and treatment outcome. Full article

(This article belongs to the Topic Proteomics and Metabolomics in Biomedicine, 2nd Volume)

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12 pages, 1162 KiB  

Open AccessArticle

LC/MS-Based Untargeted Metabolomics Study in Women with Nonalcoholic Steatohepatitis Associated with Morbid Obesity

by Laia Bertran, Jordi Capellades, Sonia Abelló, Joan Durán-Bertran, Carmen Aguilar, Salomé Martinez, Fàtima Sabench, Xavier Correig, Oscar Yanes, Teresa Auguet and Cristóbal Richart

Int. J. Mol. Sci. 2023, 24(12), 9789; https://doi.org/10.3390/ijms24129789 - 06 Jun 2023

Cited by 1 | Viewed by 1432

Abstract

This study investigated the importance of a metabolomic analysis in a complex disease such as nonalcoholic steatohepatitis (NASH) associated with obesity. Using an untargeted metabolomics technique, we studied blood metabolites in 216 morbidly obese women with liver histological diagnosis. A total of 172 [...] Read more.

This study investigated the importance of a metabolomic analysis in a complex disease such as nonalcoholic steatohepatitis (NASH) associated with obesity. Using an untargeted metabolomics technique, we studied blood metabolites in 216 morbidly obese women with liver histological diagnosis. A total of 172 patients were diagnosed with nonalcoholic fatty liver disease (NAFLD), and 44 were diagnosed with normal liver (NL). Patients with NAFLD were classified into simple steatosis (n = 66) and NASH (n = 106) categories. A comparative analysis of metabolites levels between NASH and NL demonstrated significant differences in lipid metabolites and derivatives, mainly from the phospholipid group. In NASH, there were increased levels of several phosphatidylinositols and phosphatidylethanolamines, as well as isolated metabolites such as diacylglycerol 34:1, lyso-phosphatidylethanolamine 20:3 and sphingomyelin 38:1. By contrast, there were decreased levels of acylcarnitines, sphingomyelins and linoleic acid. These findings may facilitate identification studies of the main pathogenic metabolic pathways related to NASH and may also have a possible applicability in a panel of metabolites to be used as biomarkers in future algorithms of the disease diagnosis and its follow-up. Further confirmatory studies in groups with different ages and sexes are necessary. Full article

(This article belongs to the Topic Proteomics and Metabolomics in Biomedicine, 2nd Volume)

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