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Biology
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Proteomics and Human Diseases
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Proteomics and Human Diseases

A special issue of Biology (ISSN 2079-7737). This special issue belongs to the section "Medical Biology".

Deadline for manuscript submissions: 31 March 2026 | Viewed by 3039

Special Issue Editor

Prof. Dr. Lei Fang

E-Mail Website
Guest Editor
The State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Center, Medical School of Nanjing University, Nanjing 210093, China
Interests: proteomics; clinical proteomics; disease diagnosis; biomarker identification; therapeutic target; drug discovery; precision medicine; personalized medicine; metabolic diseases; molecular mechanism

Special Issue Information

Dear Colleagues,

Proteins are vital biomolecules regulating most biological processes and molecular functions in the human body. The alteration in protein abundance, its post-translational modifications, cellular localization, and protein–protein interaction are closely related to the pathologies of human diseases. In the past two decades, proteomics has gradually developed into a cutting-edge technology in life science and medical research in the post-genomic era. In the field of medicine, proteomics assists in disease diagnosis, drug discovery, and personalized medicine. On the one hand, traditional functional proteomics strategies have been extensively used to characterize the abundance, localization, and post-translational modification of proteins in clinical samples and disease animal models, elucidate the molecular mechanisms of disease occurrence and development, and discover new disease treatment targets for innovative drug development. On the other hand, interactions between biomolecules can be screened through chemical proteomics and protein–protein interactomics to identify the direct protein targets of small-molecule compounds (including marketed drugs, endogenous metabolites, food-derived small molecules, and environmental pollutant small molecules), accelerating drug development.

In this Special Issue, we aim to showcase the most recent advances in proteomics-driven precision medicine, and it mainly includes, but is not limited to, the following topics of interest:

  1. Development of new high-throughout and high-sensitivity methodologies and technologies for the quantitative proteomics of clinical samples, including tissues/organs, body fluids, and exosomes.
  2. Identification of potential protein biomarkers for various human diseases including cancers, metabolic diseases, cardiovascular diseases, neurodegeneration diseases, etc.
  3. Chemical proteomics to identify novel protein targets of small-molecule drugs, endogenous metabolites, and new environmental pollutants and to further elucidate biological function of their interaction.
  4. Proteomics-based investigation of molecular mechanisms regulating the occurrence and development of human diseases.
  5. Artificial Intelligence (AI)-assisted proteomics in therapeutic target identification and drug discovery.

This Special Issue focuses on the application of proteomics in precision medicine and human disease research and bridges the gap between proteomics and medical research in the current field, thus promoting the interdisciplinarity and communication among researchers in life sciences, proteomics, and clinical medicine, and accelerating proteomics to better serve human disease research.

Prof. Dr. Lei Fang
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. Biology 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 2700 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
  • clinical proteomics
  • human diseases
  • biomarker identification
  • therapeutic target
  • molecular mechanism
  • cancers
  • metabolic diseases
  • cardiovascular diseases
  • neurodegeneration diseases

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Published Papers (4 papers)

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Research

24 pages, 3544 KiB  
Article
Significant Changes in Low-Abundance Protein Content Detected by Proteomic Analysis of Urine from Patients with Renal Stones After Extracorporeal Shock Wave Lithotripsy
by Elena Carestia, Fabrizio Di Giuseppe, Mohammad Kazemi, Massoumeh Ramahi, Uditanshu Priyadarshi, Patricia Giuliani, Piergustavo De Francesco, Luigi Schips, Carmine Di Ilio, Renata Ciccarelli, Patrizia Di Iorio and Stefania Angelucci
Biology 2025, 14(5), 482; https://doi.org/10.3390/biology14050482 - 27 Apr 2025
Viewed by 137
Abstract
Extracorporeal shock wave lithotripsy (ESWL), although a highly effective method for the treatment of kidney stones, can cause significant kidney damage. Since urinary protein composition directly reflects kidney function, proteomic analysis of this fluid may be useful to identify changes in protein levels [...] Read more.
Extracorporeal shock wave lithotripsy (ESWL), although a highly effective method for the treatment of kidney stones, can cause significant kidney damage. Since urinary protein composition directly reflects kidney function, proteomic analysis of this fluid may be useful to identify changes in protein levels induced by patient exposure to ESWL as a sign of kidney damage. To this end, we collected urine samples from 80 patients with nephrolithiasis 2 h before and 24 h after exposure to ESWL, which were concentrated and subsequently processed with a commercially available enrichment method to extract low-abundance urinary proteins. These were then separated by 2D electrophoresis and subsequently analyzed by a proteomic approach. A large number of proteins were identified as being related to inflammatory, fibrotic, and antioxidant processes and changes in the levels of some of them were confirmed by Western blot analysis. Therefore, although further experimental confirmation is needed, our results demonstrate that ESWL significantly influences the low urinary protein profile of patients with nephrolithiasis. Notably, among the identified proteins, matrix metalloproteinase 7, alpha1-antitrypsin, and clusterin, as well as dimethyl arginine dimethyl amino hydrolase 2 and ab-hydrolase, may play an important role as putative biomarkers in the monitoring and management of ESWL-induced renal damage. Full article
(This article belongs to the Special Issue Proteomics and Human Diseases)
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18 pages, 6470 KiB  
Article
Mapping the Interactome of KRAS and Its G12C/D/V Mutants by Integrating TurboID Proximity Labeling with Quantitative Proteomics
by Jiangwei Song, Busong Wang, Mingjie Zou, Haiyuan Zhou, Yibing Ding, Wei Ren, Lei Fang and Jingzi Zhang
Biology 2025, 14(5), 477; https://doi.org/10.3390/biology14050477 - 26 Apr 2025
Viewed by 143
Abstract
KRAS mutations are major drivers of human cancers, yet how distinct mutations rewire protein interactions and metabolic pathways to promote tumorigenesis remains poorly understood. To address this, we systematically mapped the protein interaction networks of wild-type KRAS and three high-frequency oncogenic mutants (G12C, [...] Read more.
KRAS mutations are major drivers of human cancers, yet how distinct mutations rewire protein interactions and metabolic pathways to promote tumorigenesis remains poorly understood. To address this, we systematically mapped the protein interaction networks of wild-type KRAS and three high-frequency oncogenic mutants (G12C, G12D, and G12V) using TurboID proximity labeling coupled with quantitative proteomics. Bioinformatic analysis revealed mutant-specific binding partners and metabolic pathway alterations, including significant enrichment in insulin signaling, reactive oxygen species regulation, and glucose/lipid metabolism. These changes collectively drive tumor proliferation and immune evasion. Comparative analysis identified shared interactome shifts across all mutants: reduced binding to LZTR1, an adaptor for KRAS degradation, and enhanced recruitment of LAMTOR1, a regulator of mTORC1-mediated growth signaling. Our multi-dimensional profiling establishes the first comprehensive map of KRAS-mutant interactomes and links specific mutations to metabolic reprogramming. These findings provide mechanistic insights into KRAS-driven malignancy and highlight LZTR1 and LAMTOR1 as potential therapeutic targets. The study further lays a foundation for developing mutation-specific strategies to counteract KRAS oncogenic signaling. Full article
(This article belongs to the Special Issue Proteomics and Human Diseases)
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18 pages, 6262 KiB  
Article
Label-Free Quantitative Proteomics Analysis of Nasal Lavage Fluid in Chronic Rhinosinusitis with Nasal Polyposis
by Musallam Kashoob, Afshan Masood, Assim A. Alfadda, Salini Scaria Joy, Wed Alluhaim, Shahid Nawaz, Mashal Abaalkhail, Omar Alotaibi, Saad Alsaleh and Hicham Benabdelkamel
Biology 2024, 13(11), 887; https://doi.org/10.3390/biology13110887 - 30 Oct 2024
Viewed by 1374
Abstract
(1) Background: Chronic rhinosinusitis (CRS) is a common chronic inflammation of the nasal mucosa and the paranasal sinuses. The pathogenesis of chronic rhinosinusitis (CRS) is multifactorial and, as of yet, not well understood. (2) Methods: Nasal lavage fluid samples were collected from patients [...] Read more.
(1) Background: Chronic rhinosinusitis (CRS) is a common chronic inflammation of the nasal mucosa and the paranasal sinuses. The pathogenesis of chronic rhinosinusitis (CRS) is multifactorial and, as of yet, not well understood. (2) Methods: Nasal lavage fluid samples were collected from patients diagnosed with chronic sinusitis with nasal polyposis (CRSwNP) (n = 10) and individuals without sinusitis (control group) (n = 10) who had no nasal complaints. In the present study, we used an untargeted label-free LC-MS/MS mass spectrometric approach combined with bioinformatics and network pathway analysis to compare the changes in the proteomic profiles of the CRSwNP group and the control group. Data from LC-MS/MS underwent univariate and multivariate analyses. (3) Results: The proteomic analyses revealed distinct differences in the abundances of nasal lavage fluid proteins between the CRSwNP and control groups: a total of 234 proteins, 151 up- and 83 down-regulated in CRSwNP. Functional Gene Ontology (GO) analysis showed that dysregulated proteins were involved in airway inflammatory reaction, immune response, and oxidative stress. The biomarkers were evaluated using the Receiver Operating Characteristic (ROC) curve; an Area Under the Curve (AUC) of 0.999 (95% CI) identified potential biomarkers between the CRSwNP and control group. EMILIN-3 and RAB11-binding protein RELCH were down-regulated, and Macrophage migration inhibitory factor and deoxyribonuclease-1 were up-regulated, in CRSwNP compared to the control group. (4) Conclusions: These differentially expressed proteins identified in CRSwNP are involved in airway inflammatory reaction, immune response, and oxidative stress. In particular, the identification of increased interleukin-36 gamma (IL-36γ), which contributes to inflammatory response, and a decrease in SOD, in this group are notable findings. In the future, several of these proteins may prove useful for exploring the pathogenesis of nasal polyps and chronic sinusitis or as objective biomarkers for quantitatively monitoring disease progression or response to therapy. Full article
(This article belongs to the Special Issue Proteomics and Human Diseases)
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13 pages, 4853 KiB  
Article
Effects of 4.9 GHz Radiofrequency Field Exposure on Brain Metabolomic and Proteomic Characterization in Mice
by Xing Wang, Guiqiang Zhou, Jiajin Lin, Zhaowen Zhang, Tongzhou Qin, Ling Guo, Haonan Wang, Zhifei Huang and Guirong Ding
Biology 2024, 13(10), 806; https://doi.org/10.3390/biology13100806 - 10 Oct 2024
Viewed by 1201
Abstract
Electromagnetic exposure has become increasingly widespread, and its biological effects have received extensive attention. The purpose of this study was to explore changes in the metabolism profile of the brain and serum and to identify differentially expressed proteins in the brain after exposure [...] Read more.
Electromagnetic exposure has become increasingly widespread, and its biological effects have received extensive attention. The purpose of this study was to explore changes in the metabolism profile of the brain and serum and to identify differentially expressed proteins in the brain after exposure to the 4.9 GHz radiofrequency (RF) field. C57BL/6 mice were randomly divided into a Sham group and an RF group, which were sham-exposed and continuously exposed to a 4.9 RF field for 35 d, 1 h/d, at an average power density (PD) of 50 W/m2. After exposure, untargeted metabolomics and Tandem Mass Tags (TMT) quantitative proteomics were performed. We found 104 and 153 up- and down-regulated differentially expressed metabolites (DEMs) in the RF_Brain group and RF_Serum group, and the DEMs were significantly enriched in glycerophospholipid metabolism. Moreover, 10 up-regulated and 51 down-regulated differentially expressed proteins (DEPs) were discovered in the RF group. Functional correlation analysis showed that most DEMs and DEPs showed a significant correlation. These results suggested that 4.9 GHz exposure induced disturbance of metabolism in the brain and serum, and caused deregulation of proteins in the brain. Full article
(This article belongs to the Special Issue Proteomics and Human Diseases)
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