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Proteomes
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Human Proteomics
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Human Proteomics

A special issue of Proteomes (ISSN 2227-7382).

Deadline for manuscript submissions: closed (15 October 2020) | Viewed by 38480

Special Issue Editors

Dr. Daniele Vergara

E-Mail Website
Guest Editor
Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy
Interests: cellular physiology; proteomics; cell plasticity; epithelial to mesenchymal transition; signal transduction
Special Issues, Collections and Topics in MDPI journals
Prof. Piero Del Boccio

E-Mail Website1 Website2
Guest Editor
Department of Pharmacy, University of G. d'Annunzio Chieti-Pescara, Chieti, Italy
Interests: proteomics; metabolomics, mass spectrometry; extracellular vesicles; neurological diseases
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

A number of physiological and pathological conditions in people are characterized by dynamic and profound remodeling of the proteome. A functional consequence of this is the significant alteration of cellular pathways and networks with different nodes of interaction and crossregulation. This is evident from critical differences between normal and cancer tissues, and other conditions, including neurological disorders. In this scenario, understanding global proteome modifications will require the application of innovative qualitative and quantitative approaches, and their integration with novel methods for tissue/cell analysis. This will lead to further definition of the regulatory phenomena at the basis of human diseases, providing a functional link between the complex molecular heterogeneity within human samples and the observed proteome changes.

For this Special Issue, we invite authors to contribute original research articles, method papers, as well as review articles that will address recent development in the area of human proteomics.

Potential topics include, but are not limited to, the following:

  • Proteomics of normal and diseased tissues
  • Clinical proteomics
  • Novel methods for the detection and analysis of proteins
  • Bioinformatics for the analysis of proteomic data
  • Integration of proteomics with other omics approaches

Dr. Daniele Vergara
Prof. Piero Del Boccio
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. Proteomes is an international peer-reviewed open access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs). 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

  • proteome
  • PTMs
  • protein signaling
  • biomarker discovery
  • mass spectrometry
  • molecular heterogeneity

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Published Papers (7 papers)

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Research

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18 pages, 4349 KiB  
Article
The Constitutive Proteome of Human Aqueous Humor and Race Specific Alterations
by Sai Karthik Kodeboyina, Tae Jin Lee, Lara Churchwell, Lane Ulrich, Kathryn Bollinger, David Bogorad, Amy Estes, Wenbo Zhi, Shruti Sharma and Ashok Sharma
Proteomes 2020, 8(4), 34; https://doi.org/10.3390/proteomes8040034 - 18 Nov 2020
Cited by 12 | Viewed by 4435
Abstract
Aqueous humor (AH) is the fluid in the anterior and posterior chambers of the eye that contains proteins regulating ocular homeostasis. Analysis of aqueous humor proteome is challenging, mainly due to low sample volume and protein concentration. In this study, by utilizing state [...] Read more.
Aqueous humor (AH) is the fluid in the anterior and posterior chambers of the eye that contains proteins regulating ocular homeostasis. Analysis of aqueous humor proteome is challenging, mainly due to low sample volume and protein concentration. In this study, by utilizing state of the art technology, we performed Liquid-Chromatography Mass spectrometry (LC-MS/MS) analysis of 88 aqueous humor samples from subjects undergoing cataract surgery. A total of 2263 unique proteins were identified, which were sub-divided into four categories that were based on their detection in the number of samples: High (n = 152), Medium (n = 91), Low (n = 128), and Rare (n = 1892). A total of 243 proteins detected in at least 50% of the samples were considered as the constitutive proteome of human aqueous humor. The biological processes and pathways enriched in the AH proteins mainly include vesicle mediated transport, acute phase response signaling, LXR/RXR activation, complement system, and secretion. The enriched molecular functions are endopeptidase activity, and various binding functions, such as protein binding, lipid binding, and ion binding. Additionally, this study provides a novel insight into race specific differences in the AH proteome. A total of six proteins were upregulated, and five proteins were downregulated in African American subjects as compared to Caucasians. Full article
(This article belongs to the Special Issue Human Proteomics)
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16 pages, 5249 KiB  
Article
Serum Glycoproteomic Alterations in Patients with Diabetic Retinopathy
by Ashok Sharma, James Cox, Joshua Glass, Tae Jin Lee, Sai Karthik Kodeboyina, Wenbo Zhi, Lane Ulrich, Zachary Lukowski and Shruti Sharma
Proteomes 2020, 8(3), 25; https://doi.org/10.3390/proteomes8030025 - 13 Sep 2020
Cited by 8 | Viewed by 4010
Abstract
The precise molecular mechanisms of diabetic retinopathy (DR) pathogenesis are unclear, and treatment options are limited. There is an urgent need to discover and develop novel therapeutic targets for the treatment of this disease. Glycosylation is a post-translational modification that plays a critical [...] Read more.
The precise molecular mechanisms of diabetic retinopathy (DR) pathogenesis are unclear, and treatment options are limited. There is an urgent need to discover and develop novel therapeutic targets for the treatment of this disease. Glycosylation is a post-translational modification that plays a critical role in determining protein structure, function, and stability. Recent studies have found that serum glycoproteomic changes are associated with the presence or progression of several inflammatory diseases. However, very little is known about the glycoproteomic changes associated with DR. In this study, glycoproteomic profiling of the serum of diabetic patients with and without DR was performed. A total of 15 glycopeptides from 11 glycoproteins were found to be significantly altered (5 upregulated and 10 downregulated) within the serum glycoproteome of DR patients. These glycoproteins are known to be involved in the maintenance of the extracellular matrix and complement system through peptidolytic activity or regulation. Full article
(This article belongs to the Special Issue Human Proteomics)
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15 pages, 1610 KiB  
Article
Is It Possible to Find Needles in a Haystack? Meta-Analysis of 1000+ MS/MS Files Provided by the Russian Proteomic Consortium for Mining Missing Proteins
by Ekaterina Poverennaya, Olga Kiseleva, Ekaterina Ilgisonis, Svetlana Novikova, Arthur Kopylov, Yuri Ivanov, Alexei Kononikhin, Mikhail Gorshkov, Nikolay Kushlinskii, Alexander Archakov and Elena Ponomarenko
Proteomes 2020, 8(2), 12; https://doi.org/10.3390/proteomes8020012 - 23 May 2020
Cited by 4 | Viewed by 4154
Abstract
Despite direct or indirect efforts of the proteomic community, the fraction of blind spots on the protein map is still significant. Almost 11% of human genes encode missing proteins; the existence of which proteins is still in doubt. Apparently, proteomics has reached a [...] Read more.
Despite direct or indirect efforts of the proteomic community, the fraction of blind spots on the protein map is still significant. Almost 11% of human genes encode missing proteins; the existence of which proteins is still in doubt. Apparently, proteomics has reached a stage when more attention and curiosity need to be exerted in the identification of every novel protein in order to expand the unusual types of biomaterials and/or conditions. It seems that we have exhausted the current conventional approaches to the discovery of missing proteins and may need to investigate alternatives. Here, we present an approach to deciphering missing proteins based on the use of non-standard methodological solutions and encompassing diverse MS/MS data, obtained for rare types of biological samples by members of the Russian Proteomic community in the last five years. These data were re-analyzed in a uniform manner by three search engines, which are part of the SearchGUI package. The study resulted in the identification of two missing and five uncertain proteins detected with two peptides. Moreover, 149 proteins were detected with a single proteotypic peptide. Finally, we analyzed the gene expression levels to suggest feasible targets for further validation of missing and uncertain protein observations, which will fully meet the requirements of the international consortium. The MS data are available on the ProteomeXchange platform (PXD014300). Full article
(This article belongs to the Special Issue Human Proteomics)
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18 pages, 2056 KiB  
Article
Urinary Extracellular Vesicles and Salt-Losing Tubulopathies: A Proteomic Approach
by Francesca Raimondo, Clizia Chinello, Luigi Porcaro, Fulvio Magni and Marina Pitto
Proteomes 2020, 8(2), 9; https://doi.org/10.3390/proteomes8020009 - 9 May 2020
Cited by 6 | Viewed by 3885
Abstract
Renal tubular cells release urinary extracellular vesicles (uEV) that are considered a promising source of molecular markers for renal dysfunction and injury. We investigated uEV proteomes of patients with hereditary salt-losing tubulopathies (SLTs), focusing on those caused by Gitelman and Bartter (BS) syndromes, [...] Read more.
Renal tubular cells release urinary extracellular vesicles (uEV) that are considered a promising source of molecular markers for renal dysfunction and injury. We investigated uEV proteomes of patients with hereditary salt-losing tubulopathies (SLTs), focusing on those caused by Gitelman and Bartter (BS) syndromes, to provide potential markers for differential diagnosis. Second morning urine was collected from patients with genetically proven SLTs and uEV were isolated by the ultracentrifugation-based protocol. The uEV proteome was run through a diagonal bidimensional electrophoresis (16BAC/SDS-PAGE), to improve hydrophobic protein resolution. Sixteen differential spots from the proteome of two variants (BS2 and BS3) were analysed by nLC-ESI-MS/MS after in-gel tryptic digestion. A total of 167 protein species were identified from 7 BS2 spots and 9 BS3 spot. Most of these proteins were membrane-associated proteins, in particular transmembrane proteins, and were related to typical renal functions. The differential content of some uEV was then validated by immunoblotting. Our work suggests that uEV proteomics represents a promising strategy for the identification of differential SLT proteins. This could play a role in understanding the pathophysiological disease mechanisms and may support the recognition of different syndromes. Full article
(This article belongs to the Special Issue Human Proteomics)
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10 pages, 858 KiB  
Article
Analysis of Reference Ranges of Total Serum Protein in Namibia: Clinical Implications
by Josephine N. Henok, Benjamin I. Okeleye, Elizabeth I. Omodanisi, Seteno K. O. Ntwampe and Yapo G. Aboua
Proteomes 2020, 8(2), 7; https://doi.org/10.3390/proteomes8020007 - 15 Apr 2020
Cited by 6 | Viewed by 4421
Abstract
A reference range is an essential part of clinical laboratory test interpretation and patient care. The levels of total serum protein (TSP) are measured in sera to assess nutritional, liver, and kidney disorders. This study determined the TSP reference range with respect to [...] Read more.
A reference range is an essential part of clinical laboratory test interpretation and patient care. The levels of total serum protein (TSP) are measured in sera to assess nutritional, liver, and kidney disorders. This study determined the TSP reference range with respect to gender, age, and region in Namibia. A retrospective cross-sectional study was conducted to determine the TSP reference range among 78,477 healthy participants within the ages of less than one year to more than 65 yrs in 14 regions of Namibia. The reference range of TSP was 51–91 g/L for females and 51–92 g/L for males. A reduced TSP range of 48.00–85.55 g/L (2.5–97.5 percentiles) was established at <1–5 years and increased towards adolescence. An uttermost range of 54–93 g/L was observed from 36–65 years of age. At the age >65 years; a steady decline in the reference range (51.00–89 g/L) was recorded. An upper TSP range of 53–92 g/L (2.5–97.5 percentiles) was detected in Erongo, Zambezi, Hardap, Kavango East, and a comparable trend was also seen in Omusati with a 54–91 g/L range. Meanwhile; a reduced TSP range of 50–89 g/L was identified in Ohangwena. This study showed that gender, age, and geographical location can impact TSP levels with a significant clinical difference (p < 0.05) between each category. Full article
(This article belongs to the Special Issue Human Proteomics)
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17 pages, 2225 KiB  
Article
Proteomics-Based Detection of Immune Dysfunction in an Elite Adventure Athlete Trekking Across the Antarctica
by David C. Nieman, Arnoud J. Groen, Artyom Pugachev, Andrew J. Simonson, Kristine Polley, Karma James, Bassem F. El-Khodor, Saradhadevi Varadharaj and Claudia Hernández-Armenta
Proteomes 2020, 8(1), 4; https://doi.org/10.3390/proteomes8010004 - 3 Mar 2020
Cited by 12 | Viewed by 9284
Abstract
Proteomics monitoring of an elite adventure athlete (age 33 years) was conducted over a 28-week period that culminated in the successful, solo, unassisted, and unsupported two month trek across the Antarctica (1500 km). Training distress was monitored weekly using a 19-item, validated training [...] Read more.
Proteomics monitoring of an elite adventure athlete (age 33 years) was conducted over a 28-week period that culminated in the successful, solo, unassisted, and unsupported two month trek across the Antarctica (1500 km). Training distress was monitored weekly using a 19-item, validated training distress scale (TDS). Weekly dried blood spot (DBS) specimens were collected via fingerprick blood drops onto standard blood spot cards. DBS proteins were measured with nano-electrospray ionization liquid chromatography tandem mass spectrometry (nanoLC-MS/MS) in data-independent acquisition (DIA) mode, and 712 proteins were identified and quantified. The 28-week period was divided into time segments based on TDS scores, and a contrast analysis between weeks five and eight (low TDS) and between weeks 20 and 23 (high TDS, last month of Antarctica trek) showed that 31 proteins (n = 20 immune related) were upregulated and 35 (n = 17 immune related) were downregulated. Protein–protein interaction (PPI) networks supported a dichotomous immune response. Gene ontology (GO) biological process terms for the upregulated immune proteins showed an increase in regulation of the immune system process, especially inflammation, complement activation, and leukocyte mediated immunity. At the same time, GO terms for the downregulated immune-related proteins indicated a decrease in several aspects of the overall immune system process including neutrophil degranulation and the antimicrobial humoral response. These proteomics data support a dysfunctional immune response in an elite adventure athlete during a sustained period of mental and physical distress while trekking solo across the Antarctica. Full article
(This article belongs to the Special Issue Human Proteomics)
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16 pages, 955 KiB  
Review
New Insights into Inflammatory Bowel Diseases from Proteomic and Lipidomic Studies
by Serena Longo, Marcello Chieppa, Luca G. Cossa, Chiara C. Spinelli, Marco Greco, Michele Maffia and Anna M. Giudetti
Proteomes 2020, 8(3), 18; https://doi.org/10.3390/proteomes8030018 - 10 Aug 2020
Cited by 9 | Viewed by 7392
Abstract
Ulcerative colitis (UC) and Crohn’s disease (CD) represent the two main forms of chronic inflammatory bowel diseases (IBD). The exact IBD etiology is not yet revealed but CD and UC are likely induced by an excessive immune response against normal constituents of the [...] Read more.
Ulcerative colitis (UC) and Crohn’s disease (CD) represent the two main forms of chronic inflammatory bowel diseases (IBD). The exact IBD etiology is not yet revealed but CD and UC are likely induced by an excessive immune response against normal constituents of the intestinal microbial flora. IBD diagnosis is based on clinical symptoms often combined with invasive and costly procedures. Thus, the need for more non-invasive markers is urgent. Several routine laboratory investigations have been explored as indicators of intestinal inflammation in IBD, including blood testing for C-reactive protein, erythrocyte sedimentation rate, and specific antibodies, in addition to stool testing for calprotectin and lactoferrin. However, none has been universally adopted, some have been well-characterized, and others hold great promise. In recent years, the technological developments within the field of mass spectrometry (MS) and bioinformatics have greatly enhanced the ability to retrieve, characterize, and analyze large amounts of data. High-throughput research allowed enhancing the understanding of the biology of IBD permitting a more accurate biomarker discovery than ever before. In this review, we summarize currently used IBD serological and stool biomarkers and how proteomics and lipidomics are contributing to the identification of IBD biomarkers. Full article
(This article belongs to the Special Issue Human Proteomics)
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