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 1

Experimental overview and stratification of RA FLS based on joint location.

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Experimental overview and stratification of RA FLS based on joint locati...
(A) Experimental workflow. Synovial tissue was obtained from RA patients at the time of clinically indicated arthroplasty at 3 joint locations: knee, hip, and hand (metacarpal phalangeal joint and wrist). Cells were cultured in medium or TNF-stimulated conditions and harvested for whole-genome RNA-seq and ATAC-seq. Amber, blue, and yellow represent hand, hip, and knee, respectively. Green and red represent medium and TNF-stimulated conditions, respectively. The color palette is maintained throughout all figures. (B) PCA of all gene expression and chromatin accessibility profiles within medium and TNF-stimulated conditions. PCA using the chromatin accessibility profiles revealed greater stratification between the joints compared to gene expression. (C) Gene expression profiles of differentially expressed interleukins and homeobox (HOX) genes. RA FLS have distinct cytokine expression in medium. Similarly, RA FLS have distinct patterns of cytokine induction after TNF stimulation. Several proinflammatory cytokines like IL-6 had marked induction in hand in response to TNF. Limb-patterning HOX gene expression was evaluated for medium and TNF-stimulated conditions. Hand FLS had the most distinct expression compared with hip and knee within both medium and TNF-stimulated conditions for several HOX features like HOXD10. See Supplemental Data Set 1 for DEGs, P values, and fold changes.