Joint-specific rheumatoid arthritis fibroblast-like synoviocyte regulation identified by integration of chromatin access and transcriptional activity
Eunice Choi, Camilla R.L. Machado, Takaichi Okano, David Boyle, Wei Wang, Gary S. Firestein
Eunice Choi, Camilla R.L. Machado, Takaichi Okano, David Boyle, Wei Wang, Gary S. Firestein
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Research Article Inflammation

Joint-specific rheumatoid arthritis fibroblast-like synoviocyte regulation identified by integration of chromatin access and transcriptional activity

Abstract

The mechanisms responsible for the distribution and severity of joint involvement in rheumatoid arthritis (RA) are not known. To explore whether site-specific fibroblast-like synoviocyte (FLS) biology might be associated with location-specific synovitis and explain the predilection for hand (wrist/metacarpal phalangeal joints) involvement in RA, we generated transcriptomic and chromatin accessibility data from FLS to identify the transcription factors and pathways. Networks were constructed by integration of chromatin accessibility and gene expression data. Analysis revealed joint-specific patterns of FLS phenotype, with proliferative, migratory, proinflammatory, and matrix-degrading characteristics observed in resting FLS derived from the hand joints compared with hip or knee. TNF stimulation amplified these differences, with greater enrichment of proinflammatory and proliferative genes in hand FLS compared with hip and knee FLS. Hand FLS also had the greatest expression of markers associated with an “activated” state relative to the “resting” state, with the greatest cytokine and MMP expression in TNF-stimulated hand FLS. Predicted differences in proliferation and migration were biologically validated with hand FLS exhibiting greater migration and cell growth than hip or knee FLS. Distinctive joint-specific FLS biology associated with a more aggressive inflammatory response might contribute to the distribution and severity of joint involvement in RA.

Authors

Eunice Choi, Camilla R.L. Machado, Takaichi Okano, David Boyle, Wei Wang, Gary S. Firestein

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Figure 4

Validation of computational predictions.

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Validation of computational predictions. (A) Heatmap of differentially e...
(A) Heatmap of differentially expressed activated and resting marker expression in unstimulated FLS. Rows are activated/resting markers. While both hand and knee have increased expression of activated markers, knee also has increased expression of resting markers, indicating hand FLS have the greatest ratio of activated to resting marker expression. (B) Ratio of number of markers of maximum expression within each joint. Using either all markers or differentially expressed markers revealed hand FLS have a significantly increased “activated” to “resting” marker ratio (20). *P < 0.05, ***P < 0.005 by permutation test. The table indicates the number markers with greatest expression in that joint. For example, using all markers, hand FLS had the greatest expression of 66 activated and 42 resting markers. Hand FLS retain the greatest ratio when limiting markers to DEGs. (C) Heatmap of differentially expressed cytokines and MMPs in TNF-stimulated FLS. Rows indicates what joint has the greatest expression of that gene. TNF-stimulated hand FLS have the greatest number of cytokines and MMPs with greatest expression compared with the other joints. (D) Proliferation and migration biologic validation. Unstimulated and PDGF-stimulated hand FLS proliferate faster than hip or knee FLS. We also evaluated differences in unstimulated and PDGF-stimulated migration and found that hand FLS exhibited greater migration capacity than hip or knee FLS. *P < 0.05, **P < 0.01, ***P < 0.005 by 1-way ANOVA followed by Holm-Šidák multiple-comparison test.