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Protein Interactions, Pathways, and Networks in Health and Disease
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Protein Interactions, Pathways, and Networks in Health and Disease

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (5 January 2023) | Viewed by 4341

Special Issue Editor

Dr. Panagiotis Katsonis

E-Mail Website
Guest Editor
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
Interests: genome interpretation; protein coding variants; pathogenic effects; disease driver genes
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Understanding the molecular mechanisms that underlie diseases is crucial in the design of preventive and therapeutic strategies. Genetic studies have associated single genes with phenotype and traits, but these associations are neither all causal nor complete. Genome-wide association studies (GWAS) may yield non-causal associations due to linkage disequilibrium, and rare disease driver genes may remain uncovered. However, genes associated with a phenotype often belong to the same molecular pathway, interact with each other, and/or share common protein functions. The gene networks that cover these relationships may help to refine and discover new gene-disease associations towards a better understanding of disease etiology. These networks may also help in the identification of the epistatic interactions that drive disease.

In this Special Issue, we welcome reviews, original articles, and short reports that cover different aspects of protein interactions, pathways, and networks. These may include works focused on a specific phenotype or on a gene network. We look forward to contributions on the construction of protein networks, evaluating the utility of networks, and predicting disease etiology based on gene networks or pathways.

Dr. Panagiotis Katsonis
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. Genes 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

  • gene networks
  • protein pathways
  • epistasis
  • pathogenic variants
  • disease genes
  • polygenic risk scores
  • molecular mechanism of disease
  • network-based disease classification

Published Papers (2 papers)

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Research

18 pages, 1943 KiB  
Article
Comparative Genetic Association Analysis of Human Genetic Susceptibility to Pulmonary and Lymph Node Tuberculosis
by Abhimanyu, Mridula Bose, Astha Giri and Mandira Varma-Basil
Genes 2023, 14(1), 207; https://doi.org/10.3390/genes14010207 - 13 Jan 2023
Cited by 1 | Viewed by 1763
Abstract
Background: Tuberculosis (TB) manifests itself primarily in the lungs as pulmonary disease (PTB) and sometimes disseminates to other organs to cause extra-pulmonary TB, such as lymph node TB (LNTB). This study aimed to investigate the role of host genetic polymorphism in immunity related [...] Read more.
Background: Tuberculosis (TB) manifests itself primarily in the lungs as pulmonary disease (PTB) and sometimes disseminates to other organs to cause extra-pulmonary TB, such as lymph node TB (LNTB). This study aimed to investigate the role of host genetic polymorphism in immunity related genes to find a genetic basis for such differences. Methods: Sixty-three, Single nucleotide polymorphisms (SNPs) in twenty-three, TB-immunity related genes including eleven innate immunity (SLCA11, VDR, TLR2, TLR4, TLR8, IRGM, P2RX7, LTA4H, SP110, DCSIGN and NOS2A) and twelve cytokine (TNFA, IFNG, IL2, Il12, IL18, IL1B, IL10, IL6, IL4, rs1794068, IL8 and TNFB) genes were investigated to find genetic associations in both PTB and LNTB as compared to healthy community controls. The serum cytokine levels were correlated for association with the genotypes. Results: PTB and LNTB showed differential genetic associations. The genetic variants in the cytokine genes (IFNG, IL12, IL4, TNFB and IL1RA and TLR2, 4 associated with PTB susceptibility and cytokine levels but not LNTB (p < 0.05). Similarly, genetic variants in LTA4H, P2RX7, DCSIGN and SP110 showed susceptibility to LNTB and not PTB. Pathway analysis showed abundance of cytokine related variants for PTB and apoptosis related variants for LNTB. Conclusions: PTB and LNTB outcomes of TB infection have a genetic component and should be considered for any future functional studies or studies on susceptibility to pulmonary and extra-pulmonary TB. Full article
(This article belongs to the Special Issue Protein Interactions, Pathways, and Networks in Health and Disease)
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15 pages, 2145 KiB  
Article
Pilot Study Showing Feasibility of Phosphoproteomic Profiling of Pathway-Level Molecular Alterations in Barrett’s Esophagus
by Jarrod Moore, Ryan Hekman, Benjamin C. Blum, Matthew Lawton, Sylvain Lehoux, Matthew Stachler, Douglas Pleskow, Mandeep S. Sawhney, Richard D. Cummings, Andrew Emili and Alia Qureshi
Genes 2022, 13(7), 1215; https://doi.org/10.3390/genes13071215 - 7 Jul 2022
Viewed by 1969
Abstract
(1) Background: Barrett’s esophagus is a major risk factor for esophageal adenocarcinoma. In this pilot study, we employed precision mass spectrometry to map global (phospho)protein perturbations in Barrett’s esophagus lesions and adjacent normal tissue to glean insights into disease progression. (2) Methods: Biopsies [...] Read more.
(1) Background: Barrett’s esophagus is a major risk factor for esophageal adenocarcinoma. In this pilot study, we employed precision mass spectrometry to map global (phospho)protein perturbations in Barrett’s esophagus lesions and adjacent normal tissue to glean insights into disease progression. (2) Methods: Biopsies were collected from two small but independent cohorts. Comparative analyses were performed between Barrett’s esophagus samples and adjacent matched (normal) tissues from patients with known pathology, while specimens from healthy patients served as additional controls. (3) Results: We identified and quantified 6810 proteins and 6395 phosphosites in the discovery cohort, revealing hundreds of statistically significant differences in protein abundances and phosphorylation states. We identified a robust proteomic signature that accurately classified the disease status of samples from the independent patient cohorts. Pathway-level analysis of the phosphoproteomic profiles revealed the dysregulation of specific cellular processes, including DNA repair, in Barrett’s esophagus relative to paired controls. Comparative analysis with previously published transcriptomic profiles provided independent evidence in support of these preliminary findings. (4) Conclusions: This pilot study establishes the feasibility of using unbiased quantitative phosphoproteomics to identify molecular perturbations associated with disease progression in Barrett’s esophagus to define potentially clinically actionable targets warranting further assessment. Full article
(This article belongs to the Special Issue Protein Interactions, Pathways, and Networks in Health and Disease)
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