Background/Purpose: SLE is an autoimmune disease heterogenous for symptoms, disease severity and therapeutic response. This heterogeneity makes stratifying patients difficult. B cells from SLE patients differ transcriptionally and epigenetically from healthy donors(HCD) even in mature resting naïve (rN) B cells (1). However, these studies were done on active disease patients and potentially, active and inactive patients may have still important transcriptional and epigenetic differences.
1. Scharer CD, Blalock EL, Mi T, Barwick BG, Jenks SA, Deguchi T, et al. Epigenetic programming underpins B cell dysfunction in human SLE. Nature Immunology. 2019;20(8):1071-82.

Methods: RNA-sequencing and ATAC-sequencing were performed on sorted rN and transitional 1 and 2 B cells (T1/2) from 6 HCD, 9 inactive SLE patient (SLEDAI < 5) and 8 active SLE patients (SLEDAI ≥ 5). A generalized linear model and edgeR were used to analyze differentially expressed genes (DEG) and differentially accessible region (DAR). GO biological process enrichment analysis of DEGs and DARs was performed using DAVID (2). Identification of motifs enriched in DARs was performed using the findMotifsGenome.pl function of HOMER (3). 2. Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature Protocols. 2009;4(1):44-57. 3. Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell. 2010;38(4):576-89.

Results: B cells from both active and inactive patients differed from HCD with 251 differentially expressed genes (DEG) in active and 186 DEG in inactive patients. Similarly, both active and inactive patients were epigenetically distinct from HCD and had differentially accessible regions (DAR). DEGs clearly separated patients by disease activity, while rN from both active and inactive patients had increased expression of interferon-stimulated genes, NFkB-, MAPK- and TNFSF-related genes were enriched specifically in the active group. Differences between HCD and inactive T1/2 B cells were minimal. DAR also differed between disease states, intriguingly, DAR with binding sites for basic leucine zipper (bZip) transcription factors (TF) were enriched inactive patients, while IRF and zinc finger TF binding DAR were more common in active patients.

Conclusion: In addition to validating the SLE-specific pathways previously reported this study establishes distinct signaling regulated activation states in naïve B cells depending on disease activity, suggesting that the combination of transcriptomic and epigenetic characteristics may be a useful marker to evaluate disease activity of lupus patients. Furthermore, considering that the inactive group contained 8 patients achieving extended clinical remission, DAR remained even in the absence of any activity. Permanently reversing these epigenetic changes suggests a new therapeutic target for prolonged remission.

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ACR Meeting Abstracts - https://acrabstracts.org/abstract/distinct-transcriptomic-and-epigenetic-profiles-mediated-by-disease-activity-in-sle/