Proteomics Data Suggest Diagnostic, Therapeutic Targets for RA Patients With Interstitial Lung Disease

Doctor examing ct scan images of lungs at desk, lung disease concept

About 40% of patients with rheumatoid arthritis have varying degrees of interstitial lung disease (RA-ILD), as published in Chest, but the latter frequently goes undetected until the advanced stages.

Yunju Jeong, PhD, a research fellow, and Tracy J. Doyle, MD, a physician in the Division of Pulmonary and Critical Care Medicine at Brigham and Women’s Hospital, collaborated with Paul F. Dellaripa, MD, and others in the Brigham’s Division of Rheumatology, Inflammation and Immunity to complete the first proteomic analysis in RA-ILD, simultaneously analyzing over a thousand molecular markers and mapping groups of proteins to common biological pathways. In Thorax, they identify molecular signatures strongly associated with the presence and severity of RA-ILD, and they provide insight into unexplored disease pathways.


The team quantified 1,321 proteins in serum from:

  • 39 subjects who had RA-ILD
  • 36 subjects who had RA without ILD (RA-noILD)
  • 42 subjects with idiopathic pulmonary fibrosis (IPF)
  • 42 healthy control (HC) subjects

Subjects in the latter two groups were matched by age, gender, and smoking history to those in the RA-ILD group.

Differential Expression

The SomaScan assay (Somalogic, Boulder, CO) revealed:

  • 234 proteins differentially expressed between RA-ILD and RA-noILD
  • 98 proteins differentially expressed between IPF and HC
  • 25 proteins differentially expressed in both the RA-ILD to RA-noILD comparison and the IPF to HC comparisons
  • 16 proteins overexpressed in both RA-ILD and IPF, perhaps reflecting shared disease mechanisms

Hierarchical Clustering

The team further explored the top five proteins differentially expressed between RA-ILD and RA-noILD. Independent of gender, age, and smoking, two proteins were associated with percent predicted carbon monoxide diffusing capacity (P<0.00001 for both):

  • PIANP (paired immunoglobulin-like type two receptor-associated neural protein), which is moderately expressed in respiratory epithelial cells and appears to be necessary for regulation of tissue damage in response to neutrophil-mediated inflammation—mean difference, 1.34; fold change, 2.53
  • SLPI (secretory leukocyte peptidase inhibitor), a major defense against the destruction of lung tissue by neutrophil elastase—mean difference, 1.36; fold change, 2.57

Neither protein was associated with percent predicted forced vital capacity or percent predicted total lung capacity.

Important Gene Sets in RA-ILD vs. RA-noILD

Gene set enrichment analysis detected 50 significantly enriched functional groups in RA-ILD compared with RA-noILD. Some of the strongest associations with RA-ILD were:

  • Signaling receptor binding—normalized enrichment score (NES), 3.06 (adjusted P=0.0077)
  • G protein–coupled receptor binding—NES, 2.70 (P=0.0077)
  • Negative regulation of proteolysis—NES, 2.62 (P=0.0113)
  • Extracellular matrix—NES, 2.61 (P=0.0077)
  • Cell–cell signaling—NES, 2.56 (P=0.0077)

The leading-edge proteins driving these gene sets in RA-ILD included several proteins implicated in pulmonary fibrosis:

  • The cytokines CCL18 and interleukin-17
  • The chemokines CXCL12 and CCL5
  • Fibroblast growth factor family members FGF4 and FGF7
  • Galectin-3, which helps regulate myofibroblast proliferation, fibrogenesis, and tissue repair

Based on encouraging results from human and mouse studies, some of those proteins are already considered new therapeutic targets for IPF or RA-ILD.

Important Gene Sets in Fibrotic vs. Nonfibrotic RA-ILD

Gene set enrichment analysis also demonstrated enrichment of fibrotic RA-ILD for extracellular matrix and receptor signaling compared with nonfibrotic RA-ILD. The leading-edge gene sets driving this enrichment included proteins, such as matrix metalloproteinase-7 and galectin-3, that were also enriched in the comparison of all RA-ILD with RA-noILD.

This finding suggests differences between the pathogenesis of fibrotic and nonfibrotic ILD subtypes. This may have implications for clinical trials of antifibrotic or anti-inflammatory treatments for RA-ILD.

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