Phosphoproteomics Modifications in Women with Rheumatoid ArthritisApplication of Web-Based Software to Enhance Data Visualization

Individuals with rheumatoid arthritis
(RA) are at increased risk
of functional disability, cardiovascular disease, and obesity, all
of which are influenced by dysregulated skeletal muscle. This pilot
study aims to identify phosphoproteomics changes in RA skeletal muscle
and visualize modifications through development of a web-based app
designed to promote user-friendly data interpretation and visualization.
NanoLC–MS/MS analysis was performed on vastus lateralis biopsies from three women with RA and matched healthy controls.
Differential analysis was performed using the Limma R package. Kinase
substrate enrichment analysis (KSEA) predicted changes in kinase activity.
RA muscle displayed 35 upregulated and 60 downregulated phosphosites,
including the cytoskeletal proteins TTN (Ser33201, Ser33013, Ser20925),
NEB (Ser2219, Thr254, Ser33013, Ser20925), FLNA (Ser1459), and LASP1
(Ser146). Compared to healthy controls, KSEA predicted decreased activity
of several kinases in RA muscle, including PRKACA and CDKs. All such
changes were visualized by use of our web-based app. Overall, phosphoproteome
analysis reveals signaling alterations in RA skeletal muscle linked
to cytoskeletal proteins, representing candidate disease biomarkers;
these modifications can be explored through use of our web-based software.