Integrative transcriptomic analysis of SLE reveals IFN-driven cross-talk between immune cells

Abstract

The systemic lupus erythematosus (SLE) is an incurable autoimmune disease disproportionately affecting women and may lead to damage in multiple different organs. The marked heterogeneity in its clinical manifestations is a major obstacle in finding targeted treatments and involvement of multiple immune cell types further increases this complexity. Thus, identifying molecular subtypes that best correlate with disease heterogeneity and severity as well as deducing molecular cross-talk among major immune cell types that lead to disease progression are critical steps in the development of more informed therapies for SLE. Here we profile and analyze gene expression of six major circulating immune cell types from patients with well-characterized SLE (classical monocytes (n=64), T cells (n=24), neutrophils (n=24), B cells (n=20), conventional (n=20) and plasmacytoid (n=22) dendritic cells) and from healthy control subjects. Our results show that the interferon (IFN) response signature was the major molecular feature that classified SLE patients into two distinct groups: IFN-signature negative (IFNneg) and positive (IFNpos). We show that the gene expression signature of IFN response was consistent (i) across all immune cell types, (ii) all single cells profiled from three IFNpos donors using single-cell RNA-seq, and (iii) longitudinal samples of the same patient. For a better understanding of molecular differences of IFNpos versus IFNneg patients, we combined differential gene expression analysis with differential Weighted Gene Co-expression Network Analysis (WGCNA), which revealed a relatively small list of genes from classical monocytes including two known immune modulators, one the target of an approved therapeutic for SLE (TNFSF13B/BAFF: belimumab) and one itself a therapeutic for Rheumatoid Arthritis (IL1RN: anakinra). For a more integrative understanding of the cross-talk among different cell types and to identify potentially novel gene or pathway connections, we also developed a novel gene coexpression analysis method for joint analysis of multiple cell types named integrated WGNCA (iWGCNA). This method revealed an interesting cross-talk between T and B cells highlighted by a significant enrichment in the expression of known markers of T follicular helper cells (Tfh), which also correlate with disease severity in the context of IFNpos patients. Interestingly, higher expression of BAFF from all myeloid cells also shows a strong correlation with enrichment in the expression of genes in T cells that may mark circulating Tfh cells or related memory cell populations. These cell types have been shown to promote B cell class-switching and antibody production, which are well-characterized in SLE patients. In summary, we generated a large-scale gene expression dataset from sorted immune cell populations and present a novel computational approach to analyze such data in an integrative fashion in the context of an autoimmune disease. Our results reveal the power of a hypothesis-free and datadriven approach to discover drug t...

The shared biomarkers and pathways of systemic lupus erythematosus and metabolic syndrome analyzed by bioinformatics combining machine learning algorithm and single-cell sequencing analysis

“…BAFF has been shown to be commonly overexpressed in SLE, which plays a vital role in the proliferation and differentiation of B cells and is strongly involved in the pathogenesis of SLE (34). A recent study revealed that TNFSF13B expression was elevated in SLE and highly positively correlated with monocytes (31), which was consistent with our results of CIBERSORT and scRNA analyses. Belimumab, the only effective biological therapy that targets BAFF, has been authorized for clinical use in SLE (35).…”

“…In addition, clinical data indicated that the main obstacle to target treatment of SLE patients is its heterogeneity in the involvement of different cell types. The clinical heterogeneity of SLE and its related involvement of different cell types has made it challenging to design accurate therapy (31). Therefore, finding the major cell types involved in the pathogenesis of SLE and MetS comorbidity and exploring a cell-specific molecular program is of vital importance.…”

Unique monocyte transcriptomic profiles are associated with preclinical atherosclerosis in women with systemic lupus erythematosus (SLE)

“…Differential expression analysis was performed using DESeq2-3.5 in RNA Flow, via Wald hypothesis testing and parametric fit typing and using the Benjamin-Hochberg method for multiple testing correction (see Robinson et al, 2019). IFN signature gene lists were obtained from published reports (IFN-GSEA (Panwar et al, 2020), IFN-Vital (El-Sherbiny et al, 2018). Publicly available differential gene expression datasets from atherosclerotic plaque macrophages were also obtained (Chai et al, 2018; Fernandez et al, 2019).…”

Variant to Gene Mapping to Discover New Targets for Immune Tolerance

“…A transcriptomic study conducted in SLE patients showed that gene signatures associated with interferon signaling is significantly dysregulated ( 38 ), although current efforts targeting IFN in SLE have not been successful. A more recent study in this field profiled six major immune types in SLE patients by single-cell RNAseq and found a unique set of genes in monocytes, including two well-known immune modulators for SLE and RA therapeutics ( TNFSF13B/BAFF : belimumab and IL1RN : anakinra, respectively) ( 39 ). A single cell transcriptomic study in Crohn’s patients revealed a gene program associated with inflamed tissue, consisting of genes expressed by plasma cells, inflammatory mononuclear phagocytes, and activated T cells ( 40 ).…”