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Biology
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Applications of Proteomics in Biological Fluids and Biopsies
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Applications of Proteomics in Biological Fluids and Biopsies

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

Deadline for manuscript submissions: 30 June 2025 | Viewed by 3002

Special Issue Editor

Prof. Dr. Youhe Gao

E-Mail Website
Guest Editor
Gene Engineering Drug and Biotechnology Beijing Key Laboratory, College of Life Sciences, Beijing Normal University, Beijing 100875, China
Interests: urinary biomarker; early diagnosis; proteomics; biochemistry; biobanking
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Samples from biological fluids and biopsies are very important for understanding the biology and pathophysiology of diseases. Proteomics is a tool that we can use for certain "disease-specific protein molecules" that could be molecular targets for new drug designs or provide molecular markers for the early diagnosis of diseases. The journal Biology is launching a Special Issue entitled "Applications of Proteomics in Biological Fluids and Biopsies”, which promotes basic research, translation, and clinical applications in the application of proteomics in samples including urine, blood, other biological fluids, and biopsies.

Prof. Dr. Youhe Gao
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
  • biological fluids
  • biomarkers
  • biopsies
  • disease
  • diagnosis
  • mechanisms

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Published Papers (2 papers)

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Research

11 pages, 706 KiB  
Article
Viral Fragments in the Urine Proteome: New Clues to the Cause of Fever
by Minhui Yang, Yan Su, Chenyang Zhao and Youhe Gao
Biology 2025, 14(4), 318; https://doi.org/10.3390/biology14040318 - 21 Mar 2025
Viewed by 246
Abstract
Background: To provide clues and a diagnostic basis for patients with fever of unknown origin through urinary proteomics analysis. Methods: For the first time, an attempt was made to conduct a full-library search for viruses in urine samples. Liquid chromatography–tandem mass spectrometry (LC-MS/MS) [...] Read more.
Background: To provide clues and a diagnostic basis for patients with fever of unknown origin through urinary proteomics analysis. Methods: For the first time, an attempt was made to conduct a full-library search for viruses in urine samples. Liquid chromatography–tandem mass spectrometry (LC-MS/MS) technology was employed to analyze the urinary proteomes of patients with fever of unknown origin, and to search for and identify viral protein fragments. In this study, there is no need to pre-determine the types of substances present in the samples. As long as the relevant sequences of viruses are available in the database, virus searches can be performed on the samples. Results: In the urine samples, multiple specific peptides from various viruses, such as the monkeypox virus, salivirus A, human herpesvirus 8 type P, Middle East respiratory syndrome-related coronavirus, rotavirus A, Orf virus (strain NZ2), human herpesvirus 2 (strain HG52), human adenovirus E serotype 4, influenza A virus, human coronavirus NL63, parainfluenza virus 5 (strain W3), Nipah virus, and hepatitis C virus genotype 2k (isolate VAT96), could be observed. It was found that the detection amounts of multiple viruses in febrile patients were much higher than those in the control group. Among them, the increase multiple of salivirus A was as high as more than 4200 times, and the increase multiples of multiple viral proteins were higher than 20 times. Conclusions: Viral fragments in urinary proteins can be reliably identified using mass spectrometry, which provides clues for the investigation of unexplained fever and may also be applied to the exploration of any unknown diseases. Full article
(This article belongs to the Special Issue Applications of Proteomics in Biological Fluids and Biopsies)
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15 pages, 4251 KiB  
Article
Proteomic Analysis Identifies Dysregulated Proteins in Albuminuria: A South African Pilot Study
by Siyabonga Khoza, Jaya A. George, Previn Naicker, Stoyan H. Stoychev, June Fabian and Ireshyn S. Govender
Biology 2024, 13(9), 680; https://doi.org/10.3390/biology13090680 - 30 Aug 2024
Cited by 1 | Viewed by 2032
Abstract
Albuminuria may precede decreases in the glomerular filtration rate (GFR) and both tests are insensitive predictors of early stages of kidney disease. Our aim was to characterise the urinary proteome in black African individuals with albuminuria and well-preserved GFR from South Africa. This [...] Read more.
Albuminuria may precede decreases in the glomerular filtration rate (GFR) and both tests are insensitive predictors of early stages of kidney disease. Our aim was to characterise the urinary proteome in black African individuals with albuminuria and well-preserved GFR from South Africa. This case-controlled study compared the urinary proteomes of 52 normoalbuminuric (urine albumin: creatinine ratio (uACR) < 3 mg/mmol) and 56 albuminuric (uACR ≥ 3 mg/mmol) adults of black African ethnicity. Urine proteins were precipitated, reduced, alkylated, digested, and analysed using an Evosep One LC (Evosep Biosystems, Odense, Denmark) coupled to a Sciex 5600 Triple-TOF (Sciex, Framingham, MA, USA) in data-independent acquisition mode. The data were searched on SpectronautTM 15. Differentially abundant proteins (DAPs) were filtered to include those with a ≥2.25-fold change and a false discovery rate ≤ 1%. Receiver–operating characteristic curves were used to assess the discriminating abilities of proteins of interest. Pathway analysis was performed using Enrichr software. As expected, the albuminuric group had higher uACR (7.9 vs. 0.55 mg/mmol, p < 0.001). The median eGFR (mL/min/1.73 m2) showed no difference between the groups (111 vs. 114, p = 0.707). We identified 80 DAPs in the albuminuria group compared to the normoalbuminuria group, of which 59 proteins were increased while 21 proteins were decreased in abundance. We found 12 urinary proteins with an AUC > 0.8 and a p < 0.001 in the multivariate analysis. Furthermore, an 80-protein model was developed that showed a high AUC ˃ 0.907 and a predictive accuracy of 91.3% between the two groups. Pathway analysis found that the DAPs were involved in insulin growth factor (IGF) functions, innate immunity, platelet degranulation, and extracellular matrix organization. In albuminuric individuals with a well-preserved eGFR, pathways involved in preventing the release and uptake of IGF by insulin growth factor binding protein were significantly enriched. These proteins are indicative of a homeostatic imbalance in a variety of cellular processes underlying renal dysfunction and are implicated in chronic kidney disease. Full article
(This article belongs to the Special Issue Applications of Proteomics in Biological Fluids and Biopsies)
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