RT Journal Article
SR Electronic
T1 B lymphocytes in treatment-naive paediatric patients with lupus are epigenetically distinct from healthy children
JF Lupus Science & Medicine
JO Lupus Sci Med
FD Lupus Foundation of America
SP e000921
DO 10.1136/lupus-2023-000921
VO 10
IS 1
A1 Joyce Hui-Yuen
A1 Kaiyu Jiang
A1 Susan Malkiel
A1 Barbara Anne Eberhard
A1 Heather Walters
A1 Betty Diamond
A1 James Jarvis
YR 2023
UL http://lupus.bmj.com/content/10/1/e000921.abstract
AB Background SLE is likely triggered by gene–environment interactions. We have shown that most SLE-associated haplotypes encompass genomic regions enriched for epigenetic marks associated with enhancer function in lymphocytes, suggesting genetic risk is exerted through altered gene regulation. Data remain scarce on how epigenetic variance contributes to disease risk in paediatric SLE (pSLE). We aim to identify differences in epigenetically regulated chromatin architecture in treatment-naive patients with pSLE compared with healthy children.Methods Using the assay for transposase-accessible chromatin with sequencing (ATACseq), we surveyed open chromatin in 10 treatment-naive patients with pSLE, with at least moderate disease severity, and 5 healthy children. We investigated whether regions of open chromatin unique to patients with pSLE demonstrate enrichment for specific transcriptional regulators, using standard computational approaches to identify unique peaks and a false discovery rate of <0.05. Further analyses for histone modification enrichment and variant calling were performed using bioinformatics packages in R and Linux.Results We identified 30 139 differentially accessible regions (DAR) unique to pSLE B cells; 64.3% are more accessible in pSLE than healthy children. Many DAR are found in distal, intergenic regions and enriched for enhancer histone marks (p=0.027). B cells from adult patients with SLE contain more regions of inaccessible chromatin than those in pSLE. In pSLE B cells, 65.2% of the DAR are located within or near known SLE haplotypes. Further analysis revealed enrichment of transcription factor binding motifs within these DAR that may regulate genes involved in pro-inflammatory responses and cellular adhesion.Conclusions We demonstrate an epigenetically distinct profile in pSLE B cells when compared with healthy children and adults with lupus, indicating that pSLE B cells are predisposed for disease onset/development. Increased chromatin accessibility in non-coding genomic regions controlling activation of inflammation suggest that transcriptional dysregulation by regulatory elements controlling B cell activation plays an important role in pSLE pathogenesis.Data are available in a public, open access repository. ATACseq data sets generated and analysed for this manuscript are uploaded into Sequence Read Archive, per protocol, accession number PRJNA884097 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA884097). Adult ATACseq data set is publicly available at Sequence Read Archive, accession number PRJNA290920 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA290920).