Submit to Special Issue Submit Abstract to Special Issue Review for Biomedicines Propose a Special Issue

Journal Browser

The Human Proteome in Disease, Diagnostics and Translation into Precision Medicine: Current Status and Future Prospects

Print Special Issue Flyer
Special Issue Editors
Special Issue Information
Keywords
Published Papers

A special issue of Biomedicines (ISSN 2227-9059). This special issue belongs to the section "Molecular Genetics and Genetic Diseases".

Deadline for manuscript submissions: 31 October 2024 | Viewed by 5128

Share This Special Issue

Special Issue Editor

Dr. M. Walid Qoronfleh

E-Mail Website
Guest Editor

1. Q3 Research Institute (QRI), Research & Policy Division, Ann Arbor, MI 48197, USA
2. Consulting Services Department, 21 HealthStreet, London SW16 3JY, UK
Interests: precision medicine; drug discovery; biotechnology; functional genomics; proteomics; biomarkers; companion diagnostics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

It gives us great pleasure to invite researchers and scientists to this MDPI Special Issue by Biomedicines, which focuses on the human proteome in health, disease and therapy. Proteins are the primary functional effectors in human biology and are involved in health and diseases. The human proteoforms are rich and deciphering their structure/function is critical to both basic and translational research. It is very fitting and timely to launch this Special Issue as we celebrate 20 years of human proteome accomplishments and prepare for the next generation of advancements.

Since the inception of the Human Proteome organization (HUPO) and its first World Congress in November 2002, the stated visionary goal has been translating the code of life. The HUPO international, collaborative initiative ‘The Human Proteome Project (HPP)’ (a Grand Challenge Project, “A Function for Each Protein”) aims to transform our knowledge of the human proteome and map it in its entirety, systematically utilizing state-of-the-art proteomics methods and software, available platform technologies and emerging techniques. Undoubtedly, this will not only enhance our holistic understanding of human biology at the cellular/molecular levels but will also establish a foundation for the development of diagnostic, prognostic, therapeutic, and preventive medical applications.

The HPP is better coordinated and more focused. Nowadays, the HPP comprises two strategic initiatives—chromosome-centric (C-HPP) and biology/disease-centric (B/D-HPP). To date, protein expression has now been credibly detected for 93.2% of the predicted proteins encoded in the human genome. Conversely, the number of proteins in existence (missing proteins) has been reduced.

For marking the human proteome achievements, this Biomedicines’ Special Issue aims to contribute to the knowledge of the human proteome and will describe the following:

Application of proteomics in a variety of biological and clinical studies;
Cutting-edge technologies, techniques and analytical tools in proteomics;
Integration with other ‘omics’ platforms;
Recent progress in biology and disease-driven proteome knowledge;
Emergence of translational activities from protein profiling;
Discerning protein structure/function and molecular processes;
Protein expression including sequence variants and splice variants, post-translational modification, sub-cellular localization, physiology and pathologies;
Protein–protein interactions, molecular pathways and networks (interactomics);
Protein therapeutic targets discovery, validation, drug discovery, biomarkers and companion diagnostics ;
Current trends in computational biology, bioinformatics and databases associated with the human proteome;
Precision and translational medicine of human proteome.

Dr. M. Walid Qoronfleh
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. Biomedicines is an international peer-reviewed open access monthly 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 2600 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

proteomics
human proteome
systems biology
precision medicine
biomarker
disease pathogenesis
diagnostics
mass spectrometry
multiplex protein analysis
protein network
splice variants
post-translational modifications
omics analysis
data integration

Published Papers (4 papers)

Download All Papers

Research

Jump to: Review

17 pages, 2641 KiB

Open AccessArticle

Plasma Proteomics Elucidated a Protein Signature in COVID-19 Patients with Comorbidities and Early-Diagnosis Biomarkers

by Víctor Urbiola-Salvador, Suiane Lima de Souza, Katarzyna Macur, Paulina Czaplewska and Zhi Chen

Biomedicines 2024, 12(4), 840; https://doi.org/10.3390/biomedicines12040840 - 10 Apr 2024

Viewed by 500

Abstract

Despite great scientific efforts, deep understanding of coronavirus-19 disease (COVID-19) immunopathology and clinical biomarkers remains a challenge. Pre-existing comorbidities increase the mortality rate and aggravate the exacerbated immune response against the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection, which can result in more severe symptoms as well as long-COVID and post-COVID complications. In this study, we applied proteomics analysis of plasma samples from 28 patients with SARS-CoV-2, with and without pre-existing comorbidities, as well as their corresponding controls to determine the systemic protein changes caused by the SARS-CoV-2 infection. As a result, the protein signature shared amongst COVID-19 patients with comorbidities was revealed to be characterized by alterations in the coagulation and complement pathways, acute-phase response proteins, tissue damage and remodeling, as well as cholesterol metabolism. These altered proteins may play a relevant role in COVID-19 pathophysiology. Moreover, several novel potential biomarkers for early diagnosis of the SARS-CoV-2 infection were detected, such as increased levels of keratin K22E, extracellular matrix protein-1 (ECM1), and acute-phase response protein α-2-antiplasmin (A2AP). Importantly, elevated A2AP may contribute to persistent clotting complications associated with the long-COVID syndrome in patients with comorbidities. This study provides new insights into COVID-19 pathogenesis and proposes novel potential biomarkers for early diagnosis that could be facilitated for clinical application by further validation studies. Full article

(This article belongs to the Special Issue The Human Proteome in Disease, Diagnostics and Translation into Precision Medicine: Current Status and Future Prospects)

► Show Figures

Figure 1

16 pages, 4559 KiB

Open AccessArticle

Comparative Efficacy of Metformin and Glimepiride in Modulating Pharmacological Network to Increase BDNF Levels and Benefit Type 2 Diabetes-Related Cognitive Impairment

by Athira Anirudhan, Sheikh F. Ahmad, Talha Bin Emran, Paola Isabel Angulo-Bejarano, Ashutosh Sharma and Shiek S. S. J. Ahmed

Biomedicines 2023, 11(11), 2939; https://doi.org/10.3390/biomedicines11112939 - 31 Oct 2023

Cited by 2 | Viewed by 1585

Abstract

Cognitive impairment is anotable complication of type 2 diabetes (T2DM), accompanied by reduced brain-derived neurotrophic factor (BDNF) in the brain and blood. Anti-diabetic drugs reduce hyperglycemia, yet their effect on cognitive improvement is unknown. We aimed to investigate the effect of anti-diabetic drugs regulating BDNF in T2DM through computational and case-control study design. We obtained T2DMproteins viatext-mining to construct a T2DMprotein network. From the T2DMnetwork, the metformin and glimepiride interactomes and their crucial shortest-path-stimulating BDNF were identified. Using qRTPCR, the genes encoding the shortest-path proteins were assessed in four groups (untreated-T2DM, metformin-treated, glimepiride-treated, and healthy controls). Finally, ELISA was used to assess serum BDNF levels to validate drug efficacy. As a result of this investigation, aT2DMnetwork was constructed with 3683 text-mined proteins. Then, the T2DMnetwork was explored to generate a metformin and glimepiride interactome that establishes the critical shortest-path for BDNF stimulation. Metformin stimulates BDNF via APP binding to the PRKAB1 receptor. Whereas, glimepiride increases BDNF by binding to KCNJ11 via AP2M1 and ESR1 proteins. Both drug shortest-path encoding genes differed significantly between the groups. Unlike metformin, BDNF gene and protein expression rise significantly with glimepiride. Overall, glimepiride can effectively increase BDNF, which could benefit T2DM patients with cognitive deterioration. Full article

(This article belongs to the Special Issue The Human Proteome in Disease, Diagnostics and Translation into Precision Medicine: Current Status and Future Prospects)

► Show Figures

Figure 1

14 pages, 1676 KiB

Open AccessArticle

Pharmacometabolomic Approach to Investigate the Response to Metformin in Patients with Type 2 Diabetes: A Cross-Sectional Study

by Khaled Naja, Najeha Anwardeen, Moustafa Al-Hariri, Asmaa A. Al Thani and Mohamed A. Elrayess

Biomedicines 2023, 11(8), 2164; https://doi.org/10.3390/biomedicines11082164 - 1 Aug 2023

Viewed by 1262

Abstract

Metformin constitutes the foundation therapy in type 2 diabetes (T2D). Despite its multiple beneficial effects and widespread use, there is considerable inter-individual variability in response to metformin. Our objective is to identify metabolic signatures associated with poor and good responses to metformin, which may improve our ability to predict outcomes for metformin treatment. In this cross-sectional study, clinical and metabolic data for 119 patients with type 2 diabetes taking metformin were collected from the Qatar Biobank. Patients were empirically dichotomized according to their HbA_1C levels into good and poor responders. Differences in the level of metabolites between these two groups were compared using orthogonal partial least square discriminate analysis (OPLS-DA) and linear models. Good responders showed increased levels of sphingomyelins, acylcholines, and glutathione metabolites. On the other hand, poor responders showed increased levels of metabolites resulting from glucose metabolism and gut microbiota metabolites. The results of this study have the potential to increase our knowledge of patient response variability to metformin and carry significant implications for enabling personalized medicine. Full article

(This article belongs to the Special Issue The Human Proteome in Disease, Diagnostics and Translation into Precision Medicine: Current Status and Future Prospects)

► Show Figures

Figure 1

Review

Jump to: Research

16 pages, 675 KiB

Open AccessReview

Chronic Pelvic Pain, Vulvar Pain Disorders, and Proteomics Profiles: New Discoveries, New Hopes

by Chiara Di Tucci and Ludovico Muzii

Biomedicines 2024, 12(1), 1; https://doi.org/10.3390/biomedicines12010001 - 19 Dec 2023

Viewed by 1140

Abstract

Chronic pelvic pain (CPP) is generally defined as non-cyclic pain perceived in the pelvic area that has persisted from three to six months or longer and is unrelated to pregnancy. The etiology of CPP is complex, multifactorial, with heterogeneous presentation, and includes several diseases such as endometriosis, adenomyosis, and interstitial cystitis/bladder pain syndrome. It may also be associated with sexual dysfunction, musculoskeletal disorders, and comorbid psychiatric symptoms. Vulvar pain disorders (VPDs) are typically categorized separately from chronic pelvic pain; among all VPDs, vulvodynia is a chronic vulvar pain of unknown etiology, lasting at least 3 months and that might be associated with other potentially linked factors. Proteomics represents a useful approach to study the proteome profiles of clinical samples. In this review, we have considered a selection of articles that have analyzed the protein abundance and novel protein species from various biological samples, including eutopic/ectopic endometrium, urine, serum, follicular, peritoneal fluid, and cervical mucus, potentially involved in the pathogenesis and progression of CPP and VPDs. These findings could represent valuable targets for paving the way for the differential diagnosis and therapeutic management of CPP and VDPs, thereby optimizing both the prevention and treatment of these conditions. Full article

(This article belongs to the Special Issue The Human Proteome in Disease, Diagnostics and Translation into Precision Medicine: Current Status and Future Prospects)

► Show Figures