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Author Spotlight: Enhancing Rheumatoid Arthritis Research Through HR-pQCT Imaging Analysis
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Phosphoproteomics Modifications in Women with Rheumatoid Arthritis─Application of Web-Based Software to Enhance Data

Grace Kim1, Akshay Bareja2,3, Melissa Orenduff2

  • 1Duke University School of Medicine, Durham, North Carolina 27701, USA.

Journal of Proteome Research
|August 22, 2025
PubMed
Summary

Rheumatoid arthritis (RA) alters skeletal muscle phosphoproteomics, particularly affecting cytoskeletal proteins. A new web app visualizes these changes, aiding biomarker discovery for RA-related muscle dysfunction.

Keywords:
phosphoproteomicsproteomic visualization softwarerheumatoid arthritisskeletal muscle

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Systems Biology

Background:

  • Rheumatoid arthritis (RA) is linked to skeletal muscle dysfunction, increasing risks of disability and cardiovascular disease.
  • Understanding molecular changes in skeletal muscle is crucial for RA management.

Purpose of the Study:

  • To identify phosphoproteomic alterations in skeletal muscle of individuals with RA.
  • To develop a user-friendly web application for visualizing these phosphoproteomic changes.

Main Methods:

  • NanoLC-MS/MS analysis of vastus lateralis muscle biopsies from RA patients and healthy controls.
  • Differential phosphosite analysis using Limma R package and kinase activity prediction via KSEA.
  • Development of a web-based application for data visualization.

Main Results:

  • Identified 35 upregulated and 60 downregulated phosphosites in RA skeletal muscle.
  • Key affected proteins include cytoskeletal components like TTN, NEB, FLNA, and LASP1.
  • Predicted decreased activity of kinases such as PRKACA and CDKs in RA muscle.

Conclusions:

  • Phosphoproteome analysis reveals significant signaling alterations in RA skeletal muscle, particularly involving cytoskeletal proteins.
  • These altered phosphosites represent potential biomarkers for RA.
  • The developed web app facilitates exploration of these molecular changes.