Background/Purpose: Rheumatoid arthritis (RA), Systemic lupus erythematosus (SLE), and Systemic sclerosis (SSc) are all systemic rheumatic autoimmune diseases with a dysregulated myeloid compartment. Monocytes are poised to rapidly mobilise in large numbers to sites throughout the body, where they provide pro-inflammatory or pro-resolving roles. A key and unaddressed question is are circulating monocytes similarly perturbed on the transcriptional and epigenetic level across different rheumatic diseases. Despite the extensive research in the field, it is still poorly understood how these profiles influence the response to stimuli in disease environment. Understanding this may help understand how monocytes respond at disease sites and how this varies across different conditions. To comprehensively profile monocytes, we performed paired RNA-Seq and ChIP-Seq of activating histone 3 lysine 4 tri-methylation (H3K4me3), and repressive histone 3 lysine 27 tri-methylation (H3K27me3), modifications.

Methods: Fresh peripheral blood samples were collected from active RA patients (DAS28 > 2.7), SLE patients (1997 ACR criteria), SSc (ACR/EULAR 2013 criteria), as well as age- and gender-matched healthy controls (HC). SSc patients were subdivided into diffuse cutaneous (dcSSc), limited cutaneous SSc (lcSSc), and early SSc (eaSSc) subsets. CD14+ monocytes were isolated from peripheral blood and genome-wide profiling of RNA (HC, n=15; RA, n=9; SLE, n= 10; dcSSc, n=10; lcSSc, n=10; eaSSc, n=10), H3K4me3 (HC, n=20; RA, n=20; SLE, n=8; dcSSc, n=9; lcSSc, n=8; eaSSc, n=10), and H3K27me3 (HC, n=15; RA, n=10; SLE n=8, dcSSc, n=9 ; lcSSc, n=7; eaSSc, n=10) was performed. Statistical significance was determined using an adjusted p < 0.05 & absolute log2fold > 0.58 for RNA-Seq or an adjusted p < 0.05 for ChIP-Seq.

Results: We observed substantial differentially expressed genes (DEGs) in RA monocytes in comparison to HC (3,504 DEGs), whereas much fewer transcriptional changes were observed in SLE and SSc subsets. Similarly, much greater changes were seen in active H3K4me3 profiles in RA in comparison to HC (3,141 differential peaks), than those seen in SLE and SSc subsets (50 and 10, respectively). Moreover, the majority (~65%) of increased H3K4me3 peaks in RA were bivalent; contained a repressive H3K27me3 peak with either no or very low transcriptional expression. Notably, the H3K27me3 profile in RA was comparable to those seen in HC. This was also the case lcSSc and SLE. In contrast, numerous increases in repressive H3K27me3 peaks were identified in dcSSc and eaSSc (424 and 647, differential peaks respectively).

Conclusion: We found that systemic rheumatic diseases displayed a range of transcriptional and epigenetic profiles. Of note, we identified that in RA, there is an abundance of active H3K4me3 modifications that occur in repressed (H3K27me3) and transcriptionally inactive loci. We propose that the increased epigenetic activation of bivalent genes in RA could prime these monocytes for activation within the diseased joint microenvironment and could subsequently detrimentally contribute to disease pathogenesis.

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ACR Meeting Abstracts - https://acrabstracts.org/abstract/circulating-monocytes-in-ra-ssc-and-sle-have-radically-altered-and-unique-transcriptional-epigenetic-profiles/