Research on Proteomics and Its Applications in Disease

A special issue of Cells (ISSN 2073-4409).

Deadline for manuscript submissions: 31 May 2024 | Viewed by 1356

Special Issue Editor

Department of Life Sciences, University of Siena, 53100 Siena, Italy
Interests: proteomics; bioinformatics; melanoma; soft tissue sarcoma; interstitial lung diseases; extracellular vesicles; viral infections
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Proteomics has acquired a pivotal role in the comprehensive understanding of human biology, revealing biochemical processes involved in complex diseases. Over the last ten years, the main output of differential proteomics investigations evolved from long lists of proteins to the generation of new hypotheses and their functional verification. A bottom-up approach is well suited for the basic investigation and clinical diagnosis of human disease and enables a detailed functional characterization of pathogenic biochemical processes. On the other hand, top-down proteomics has been rapidly evolving and attracting new researchers and interest from different areas of biology, especially biomedicine, thanks to its ability to discriminate proteoforms to broaden the knowledge of the human proteome in health and diseases. Moreover, the topic of spatial proteomics has received increasing interest since protein subcellular localization is tightly controlled and intimately linked to the function.

This Special Issue seeks to provide articles on proteomics that focus on human diseases, comprising viral and bacterial infections, thus generating new hypotheses and providing functional verifications. New studies on spatial proteomics are welcome, since the localizations of molecules and their dynamics at the subcellular level are essential for a complete understanding of cell biology.

Dr. Claudia Landi
Guest Editor

Manuscript Submission Information

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Keywords

  • bottom-up proteomics
  • top-down proteomics
  • spatial proteomics
  • bioinformatics
  • human diseases
  • cancer
  • viral infections
  • bacterial infections
  • rare pathologies

Published Papers (1 paper)

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18 pages, 2048 KiB  
Article
Functional Characterization of Lysophospholipids by Proteomic and Lipidomic Analysis of Fibroblast-like Synoviocytes
Cells 2023, 12(13), 1743; https://doi.org/10.3390/cells12131743 - 29 Jun 2023
Viewed by 984
Abstract
Synovial fluid (SF) from human knee joints with osteoarthritis (OA) has elevated levels of lysophosphatidylcholine (LPC) species, but their functional role is not well understood. This in vitro study was designed to test the hypothesis that various LPCs found elevated in OA SF [...] Read more.
Synovial fluid (SF) from human knee joints with osteoarthritis (OA) has elevated levels of lysophosphatidylcholine (LPC) species, but their functional role is not well understood. This in vitro study was designed to test the hypothesis that various LPCs found elevated in OA SF and their metabolites, lysophosphatidic acids (LPAs), modulate the abundance of proteins and phospholipids (PLs) in human fibroblast-like synoviocytes (FLSs), with even minute chemical variations in lysophospholipids determining the extent of regulation. Cultured FLSs (n = 5–7) were treated with one of the LPC species, LPA species, IL-1β, or a vehicle. Tandem mass tag peptide labeling coupled with LC-MS/MS/MS was performed to quantify proteins. The expression of mRNA from regulated proteins was analyzed using RT-PCR. PL synthesis was determined via ESI-MS/MS, and the release of radiolabeled PLs was determined by means of liquid scintillation counting. In total, 3960 proteins were quantified using multiplexed MS, of which 119, 8, and 3 were significantly and reproducibly regulated by IL-1β, LPC 16:0, and LPC 18:0, respectively. LPC 16:0 significantly inhibited the release of PLs and the synthesis of phosphatidylcholine, LPC, and sphingomyelin. Neither LPC metabolite—LPA 16:0 nor LPA 18:0—had any reproducible effect on the levels of each protein. In conclusion, small chemical variations in LPC species can result in the significantly altered expression and secretion of proteins and PLs from FLSs. IL-1β influenced all proteins that were reproducibly regulated by LPC 16:0. LPC species are likely to modulate FLS protein expression only in more advanced OA stages with low IL-1β levels. None of the eight proteins being significantly regulated by LPC 16:0 have been previously reported in OA. However, our in vitro findings show that the CD81 antigen, calumenin, and B4E2C1 are promising candidates for further study, focusing in particular on their potential ability to modulate inflammatory and catabolic mechanisms. Full article
(This article belongs to the Special Issue Research on Proteomics and Its Applications in Disease)
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