Multi-omics Study Reveals The Pathogenesis Of SLE And Its Heterogeneity Between Male And Female

Background: Systemic lupus erythematosus(SLE,OMIM #152700)is a complex autoimmune disease involved in both genetic and environmental factors,feature production of autoantibodies,immune complex deposition,complement activation,and multiple organ damage.The global prevalence of SLE is about 12-39/100,000,and there are great differences among different races.The incidence of SLE is the highest in black women,which is about 2-4 times than that of white women.The white women have the lowest incidence of SLE,while Asian and Hispanic women are in the middle.There are also significant differences in the incidence and severity of SLE among gender and age groups.Studies have shown that SLE is particularly prevalent in women of childbearing age,with a male-to-female incidence ratio of about 1:9.Male SLE progresses more rapidly than female SLE and is more likely to involve other organs,such as the kidneys,cardiovascular and neuropsychiatric systems.The pathogenesis of SLE is not fully understood.Early genetic studies found that SLE susceptibility genes were involved in the type I interferon pathway.Transcriptomic and proteomic studies have suggested that type I interferon and neutrophilic activation play an important role in the pathogenesis of SLE,and found that these pathways have a positive correlation with disease severity.Metabonomics studies revealed that the risk of SLE was significantly related to energy metabolism pathways such as oxidative phosphorylation and glycolysis.However,the correlation between these pathways and disease phenotypes as well as the specific mechanisms and key biomarkers of these pathways still need to be further clarified.Objective: To integrate genetic and transcriptome data with a large sample size to search for functionally relevant genes of SLE and reveal the pathologic pathways of the disease.Furthermore,proteomics studies of peripheral blood monouclear cells(PBMC)were conducted to reveal the pathogenesis of SLE,and to reveal the heterogeneity in the pathogenesis of SLE between male and female.Methods:(1)Genome-wide association study(GWAS)data and expression quantitative trait Loci(eQTL)data with large sample size were integrated by Mendelian randomization to identify functional susceptibility genes of SLE,and gene expression data from GEO database and q PCR were used to verify functional relavent genes identified above.(2)We first included 26 SLE cases and 22 healthy controls according to the inclusion criteria and exclusion criteria.After quality control,15 SLE(7 male SLE and 8 female SLE)and 15 healthy controls(7 male controls and 8 female controls)were remained for the following label-free protein quantification.Then,we performed a differentially expressed protein analysis of four binary phenotypes: 1)female SLE vs female control;2)Male SLE vs male control;3)Male SLE vs female SLE.Subsequently,the differentially expressed proteins were used to perfrom GO(Gene Ontology)and KEGG(Kyoto Encyclopedia of Genes and Genomes)enrichment analysis.Last,we conducted a weighted correlation network analysis to construct protein modules,and evaluated the associations of modules with SLE gender,24-hour proteinuria,lupus encephalopathy,complement C3,anti-DS-DNA,anti-SSA,anti-SSB,anti-SM and SLEDAI scores.(3)We inclueded 44 SLE(9 male SLE and 35 female)and 8 controls(4male control and 4 female control),markers of calprotectin,circulating free DNA(cf DNA),neutrophil elastase(NE)and Glutathione(GSH)in plasma were detected.Results:(1)Mendelian randomization has identified 5 potential SLE functionally relavent genes,among which IRF3 gene had not been reported in previous SLE GWAS.Further differential expression analysis of GEO data and q PCR study confirmed the 5genes.Among the 5 functional genes,3 genes(IRF7,IRF3 and BLK)were involved in the regulation of type I interferon.(2)Male SLE and female SLE had more abundant proteins comparing to healthy control.Proteins more abundant in male SLE related to male control mapped to type I interferon pathway and neutrophil activation,and proteins more abundant in female SLE related to female control mapped to type I interferon pathway,neutrophil activation,cellular respiration,and oxidative phosphorylation.(3)Proteins more abundant in male SLE related to female were mapped to neutrophil activation,while proteins more abundant in female SLE related to male SLE were mapped to cellular respiration and oxidative phosphorylation.(4)The modules that associated with both male SLE and female SLE were mapped to type I interferon pathway;(5)Association analysis of modules with SLE phenotypes showed that 24 h proteinuria was associated with neutrophils activation.Lupus encephalopathy was associated with type I interferon.Anti-ds DNA was associated with type I interferon and neutrophils activation.SLEDAI score was associated with type I interferon pathway and neutrophil activation.(6)Detection of plasma markers showed that the levels of neutrophil activation marker(calprotectin)and cell death markers(cf DNA and NE)were significantly increased in SLE patients,while the levels of oxidative stress negative markers(GSH)were significantly decreased.In contrast to female SLE,male SLE has a higher level of calprotectin and a lower level of GSH,suggesting a higher level of Neutrophil activation and oxidative stress in male SLE than female SLE.Conclusion: Based on GWAS,eQTL and proteomic data with a large sample size,this study is the first to conduct a systematic multi-omics study of SLE.Genomic,transcriptomic and proteomic studies all support the involvement of type I interferon pathway in the pathogenesis of SLE.Proteomic study further revealed the heterogeneity of male SLE and female SLE.Direct comparison of male and female SLE indicated that proteins enriched in neutrophil activation were more significantly up-regulated in male SLE,while cell respiration and oxidative phosphorylation may be the specific pathogenetic pathways of female SLE.Further detection of plasma markers confirmed that male SLE had higher levels of neutrophil activation than female SLE.Moreover,type I interferon pathway and neutrophilic activation were also associated with various phenotypes of SLE.