Abstract

Background

   Systemic lupus erythematosus (SLE) is an autoimmune condition that
   impacts various organs. Given the intricate clinical progression of
   SLE, it is imperative to explore novel avenues for precise diagnosis
   and treatment.

Methods

   Peripheral blood mononuclear cells (PBMC) were isolated from 6 SLE
   patients before and after treatment, 7 healthy controls and 7 disease
   controls. Assay for Transposase Accessible Chromatin with high
   throughput Sequencing (ATAC-seq) was used to analyze the chromatin
   accessibility signatures and RNA-seq was used to identify the
   differentially expressed genes, mRNA, lncRNA, circRNA, miRNA. Then
   ATAC-seq and RNA-seq were integrated to further analyze hub genes and
   pathways. Finally, we validated gene expression levels and examined
   changes in key genes after treatment through in vitro experiments.

Results

   Our analysis reveals dynamic changes in chromatin accessibility during
   the course of disease progression in SLE. Significantly higher numbers
   of differentially accessible regions, transcripts, genes, mRNA, lncRNA,
   circRNA, and miRNA were observed in SLE patients compared to other
   cohorts, with these variances markedly reduced post-treatment. Two gene
   clusters associated with SLE disease improvement were identified, with
   a total of 140 genes intersecting with ATAC results. Pathway analysis
   revealed that NK cell mediated cytotoxicity was the most differentiated
   and therapeutically altered pathway in SLE patients. Independent sample
   validation confirmed that the gene expression of this pathway was
   reduced in SLE patients and associated with disease activity, whereas
   hydroxychloroquine (HCQ) effectively elevated their expression in
   vitro.

Conclusion

   Our findings suggest that these NK cell signature genes may be
   associated with the complex pathogenesis of SLE. The restoration of NK
   cell-mediated cytotoxicity may serve as a useful marker of improvement
   following SLE treatment.

   Keywords: systemic lupus erythematosus, ATAC-seq, RNA-Seq, NK cells,
   open chromatin

Graphical Abstract

   [37]graphic file with name fimmu-16-1580540-g007.jpg

1. Introduction

   Systemic lupus erythematosus (SLE), a complex autoimmune disease
   character-ized by diverse clinical manifestations and multi-organ
   involvement, poses significant challenges to effective patient
   management. Despite advancements in treatment, a substantial proportion
   of SLE patients, particularly those with high disease activity,
   continue to face unfavorable prognoses, and long-term medication often
   results in detrimental side effects ([38]1, [39]2) These clinical
   limitations underscore the urgent need for innovative diagnostic and
   therapeutic strategies. Given the heterogeneous nature of SLE and the
   elusive nature of its clinical progression ([40]3), personalized
   approaches based on precision medicine technologies, notably
   transcriptomics, hold great promise for improving disease management.

   While several studies have identified distinctive transcriptome
   signatures in SLE patients that can differentiate them from healthy
   individuals ([41]4), as well as reflecting clinical variations in
   disease severity and antibody profiles ([42]5, [43]6), our
   understanding of the dynamic changes in gene expression throughout the
   course of SLE, especially in response to treatment, remains incomplete.
   Epigenetic modifications, operating independently of DNA sequences,
   play a crucial role in regulating gene ex-pression, including DNA
   methylation, histone modifications, chromatin accessibility, and
   non-coding RNAs ([44]7). Of these, chromatin accessibility, which
   governs the binding of regulatory elements and transcription factors,
   is particularly pivotal in transcriptional control ([45]8). The assay
   for Transposase Accessible Chromatin using sequencing (ATAC-seq)
   provides a straightforward and scalable approach to explore open
   chromatin regions.

   When integrated with RNA-seq, ATAC-seq helps identify regulatory
   changes that impact gene expression crucial for understanding disease’s
   pathogenesis. There have been several successful applications of
   combining ATAC-seq with RNA-seq, such as the discovery of candidate
   genes and transcriptional factors associated with hemangiomas ([46]9).
   These findings offer new perspectives on understanding the pathogenesis
   of complex diseases. There have been attempts to explore the
   pathogenesis of SLE in conjunction with the application of ATAC-seq
   combined with transcriptome analysis ([47]10, [48]11), but to date no
   dynamic changes in these multi-omics before and after treatment have
   been reported. In this study, we conducted integrated analysis of
   ATAC-seq and RNA-seq to explain the epigenetic and transcriptional
   landscape of SLE, focusing on gene clusters that underwent changes
   after treatment. The research results may provide new references for