Background/Purpose: RA FLS display a unique aggressive phenotype with a distinctive DNA methylation profile that marks genes involved with cytokine signaling, cell recruitment, and matrix regulation. In this study, the epigenetic and transcriptomic signature was expanded by adding multiple omics technologies to the integrative analysis. Patterns that distinguish RA and osteoarthritis (OA) FLS lines were identified using RNA-seq, ChIP-seq and DNA methylation datasets from the same cell lines. This analysis allowed us to create the first high-resolution functional genomic map of aggressive RA FLS.

Methods: Genome-wide data were collected from 11 RA and 11 OA FLS lines: (i) gene expression using RNA-seq for differentially expressed genes (DEGs); (ii) epigenetic modifications of six histone marks by ChIP-seq for differentially modified histone regions (DMHR) (H3K4me1, H3K4me3, H3K27ac, H3K27me3, H3K36me3, H3K9me3); (iii) DNA methylation by Illumina chip for differentially methylated genes (DMGs) previously reported on the same FLS lines (Genome Medicine, 2013). One RA and one OA FLS were filtered because they overlapped in principle component analyses (PCAs). Unbiased hierarchical clustering and PCA assessed the relationships between RA and OA. Integrative analysis was performed with overlapping gene sets and identified multi-evidence genes (MEGs), i.e., found in more than one dataset. Enriched pathways were determined with Ingenuity Pathway Analysis.

Results: 997 DEGs for RA compared with OA were identified by RNA-seq, with 43 enriched pathways including RA-specific pathways “Osteoblasts, Osteoclasts and Chondrocytes in RA” and “Macrophages, Fibroblasts and Endothelial Cells in RA”. Hierarchical clustering and PCA showed that RA and OA FLS transcriptomes significantly separated. For histone marks, 18,642 DMHRs between RA and OA were identified for six histone marks; H3K27ac, H3K4me1 and H3K4me3 showed far more DMHRs than the other marks. Multiple histone mark-enriched pathways were identified in inflammation, immune response and cell migration processes. When combined with the previously identified 2375 DMGs, integrative analysis of the 3 datasets revealed MEGs with overlapping DEGs, DMGs with H3K27ac, H3K4me1 and H3K4me3 histone marks. 19 biological pathways among the MEGS were enriched including “Macrophages, Fibroblasts and Endothelial Cells in RA”, “JAK family kinases in IL-6-type Cytokine Signaling”, “Cytokine Regulation in Macrophages and Th Cells by IL-17A/F”.

Conclusion:  This is the first genome-wide analysis of the RA FLS transcriptome, methylome and histone marks. Pathogenic gene expression and epigenetic marks identify a distinctive RA signature that sheds light on the pathogenesis RA. The MEGs participate in immune networks, which enables strategies to modulate the unique aggressive phenotype of RA FLS. The data also permit development of in silico models that prioritize non-obvious targets for drug discovery.

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ACR Meeting Abstracts - https://acrabstracts.org/abstract/complete-whole-genome-transcriptome-dna-methylation-and-histone-mark-analysis-of-rheumatoid-arthritis-ra-fibroblast-like-synoviocytes-fls-reveals-a-distinctive-epigenetic-landscape-and-critical/