Background: Systemic lupus erythematosus (SLE) and systemic sclerosis (SSc) are autoimmune diseases with some overlapping clinical manifestations. SLE is characterized by systemic inflammation with vasculitis and multiple organ damage, whereas SSc manifests as low-grade inflammation with vasculopathy and tissue fibrosis. Recent studies have revealed that Toll-like receptors (TLRs) play essential roles in the pathogenesis of autoimmune diseases. This study investigated the expression of TLR genes in SLE and SSc to determine their roles in the pathogenesis of these diseases.Methods: Patients with SLE (n = 15) and SSc (n = 9) were recruited from a hospital in Taiwan from 2016 to 2017. RNA was extracted from peripheral blood cells of the patients for next-generation sequencing (NGS). Then, We identified differentially expressed genes and associated pathways to explore the association of TLRs with SLE and SSc pathogenesis. Several housekeeping genes, including ACTB, GAPDH, PGK1, PPIB, SDHA, and TBP, were used to normalize the expression levels of the TLR genes.Results: GAPDH, PGK1, PPIB and SDHA are significantly different (p < 0.05) in patients of SLE and SSc. The expression levels of TLR1 (p = 0.018) and TLR3 (p = 0.031) were significantly upregulated in the patients with SSc compared with those with SLE, normalized by GAPDH.Conclusions: TLR1 and TLR3 can serve as biomarkers to distinguish the gene expression between SLE and SSc, normalized with housekeeping genes such as ACTB, GADPH and TBP.

Objectives:Malar rash is one of clinical phenotypes seen in systemic lupus erythematosus (SLE). However, the pathogenesis of malar rash is not clear for each case of SLE patients. In this paper we endeavored to investigate the linking of clinical phenotype from the gene expression profiles between both patients with malar rash and without malar rash. Therefore we might perform better evaluation of the possible prognosis for different SLE patients in the future.Methods: This study utilizes transcriptome sequencing (RNA-Seq) technologies to discover underlying gene expression profile for systemic lupus erythematosus patients. We performed transcriptome sequencing experiments and analyzed differentially expressed genes (DEGs) and associated pathways.Results: From the analysis of gene expression profiling, we identified the gene DAAM2 is the most differentially expressed gene for patients with malar rash. Using a gene set enrichment analysis, we discuss the linkage between DAAM2 and the possible pathways for systemic lupus erythematosus with malar rash.Conclusions: We identified DAAM2 as a candidate biomarker for the clinical phenotype of malar rash for systemic lupus erythematosus.JRC and PWH did the analysis on the patient data. JRC, PWH, BJW, SIC, CMC, HHC and HTC discussed the project and jointly wrote the manuscript. HTC and HHC leaded the project. All authors read and approved the final manuscript.