The Human Proteinomics in Disease, Diagnostics and Translation into Precision Medicine: Current Status and Future Prospects—2nd Edition

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

Deadline for manuscript submissions: 31 May 2026 | Viewed by 886

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Guest Editor
1. Q3 Research Institute (QRI), Research & Policy Division, Ann Arbor, MI 48197, USA
2. Consulting Services Department, 21 HealthStreet Ltd., London SW16 3JY, UK
Interests: precision medicine; drug discovery; biotechnology; functional genomics; proteomics; biomarkers; companion diagnostics
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Special Issue Information

Dear Colleagues,

It gives us great pleasure to invite researchers and scientists to contribute 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 in diversity, and deciphering their structure and function is critical to both basic and translational research. The launch of this Special Issue is particularly timely, as we celebrate more than 20 years of human proteome accomplishments and look forward to the next generation of proteomics advancements.

Since the inception of the Human Proteome Organization (HUPO) and its first World Congress in November 2002, its visionary goal has been the translation of 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 both the cellular and molecular levels but will also establish a foundation for the development of diagnostic, prognostic, therapeutic and preventive medical applications.

The HPP effort today 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 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.

To mark the continued achievements in human proteomics, this second edition Special Issue of Biomedicines aims to expand and 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 target 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;
  • Human proteome and proteomics translational research.

Dr. M. Walid Qoronfleh
Guest Editor

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Keywords

  • proteomics
  • human proteome
  • systems biology
  • precision medicine
  • biomarker(s)
  • disease pathogenesis
  • diagnostics
  • mass spectrometry
  • tandem mass spectrometry
  • LC-MS/MS
  • peptides and proteins
  • multiplex protein analysis
  • protein network
  • protein–protein interaction
  • splice variants
  • post-translational modifications
  • omics analysis
  • data integration
  • bioinformatics
  • artificial intelligence
  • deep learning

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Published Papers (1 paper)

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Research

37 pages, 4989 KB  
Article
Genomic and Structural Investigation of Mutations in Biotinidase (BTD) Gene Deficiency in Greater Middle Eastern Cohort: Insights from Molecular Dynamics Study
by Faisal E. Ibrahim, BalaSubramani Gattu Linga, Muthanna Samara, Jameela Roshanuddin, Salma Younes, Gheyath K. Nasrallah, Hatem Zayed, M. Walid Qoronfleh, Sawsan G. A. A. Mohammed, Dalia El Khoury, Dinesh Velayutham, Ghassan Abdoh, Hilal Al Rifai and Nader Al-Dewik
Biomedicines 2025, 13(9), 2210; https://doi.org/10.3390/biomedicines13092210 - 9 Sep 2025
Viewed by 428
Abstract
Background: Biotinidase deficiency (BD) is a common autosomal recessive metabolic disorder in Qatar and the Arab world. It is treatable if detected early, making it essential to understand the genetic variants involved. This study aimed to investigate the carrier frequency of BD-related [...] Read more.
Background: Biotinidase deficiency (BD) is a common autosomal recessive metabolic disorder in Qatar and the Arab world. It is treatable if detected early, making it essential to understand the genetic variants involved. This study aimed to investigate the carrier frequency of BD-related variants in a healthy Qatari population, reflecting the genetic landscape of the broader Middle Eastern region; classify them using bioinformatics tools; and compare findings with global datasets. Methods: Whole-genome sequencing data from 14,669 participants in the Qatar Genome Program (QGP), a multiethnic cohort including Qatari nationals and long-term residents (≥15 years), were analyzed to identify BTD variants. A total of 723, including 653 single-nucleotide polymorphisms (SNPs) and 70 structural variants (SVs) in BTD associated with BD, were screened against the Qatari cohort and compared with international data. In silico tools were used to assess variant pathogenicity, conservation, and protein stability. Molecular dynamics (MD) simulations were performed to evaluate structural and functional changes in the BTD. Results: A total of 80 SNPs and 3 SVs were identified, among which 21 variants (19 SNPs and 2 SVs) were classified as pathogenic or likely pathogenic, according to ClinVar. The carrier frequency of BTD-related variants in Qatar was 1:20, primarily driven by rs13078881 (D444H). Molecular dynamics (MD) simulations revealed significant conformational changes with H323R, D444H, and P497S, which demonstrated increased flexibility (higher RMSD/RMSF and PCA trace values). Additionally, R209C and D444H showed reduced compactness (higher Rg) and distinct energy minima, suggesting altered conformational states. Conclusions: This study demonstrates a high carrier frequency of pathogenic BTD variants in the Qatari population, underscoring the need to integrate these SNPs and SVs into the national genomic neonatal screening program (gNBS) for enhanced early detection and treatment strategies. The mild structural deviations observed in the D444H mutant through MD simulations may explain its association with milder clinical phenotypes of BTD, offering valuable insights for personalized therapeutic approaches. Full article
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