Bioinformatics identification of key candidate genes and pathways associated with systemic lupus erythematosus
Systemic lupus erythematosus (SLE) is a complex autoimmune disease characterized by autoantibody production and multi-system involvement, but the etiology is largely unclear. This study aimed to elucidate candidate genes and pathways involved in SLE.
Three original datasets GSE72509, GSE20864, and GSE39088 were downloaded from Gene Expression Omnibus (GEO) and the data were further integrated and analyzed. Subsequently, differentially expressed genes (DEGs) between SLE patients and healthy people were identified. And then we performed gene ontology (GO) function and pathway enrichment analyses of common DEGs, and constructed a protein-protein interaction (PPI) network with STRING database. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was carried out to validate the expression levels of candidate genes in blood samples from SLE patients and healthy controls.
In total, 321 common DEGs were identified in SLE patients compared with healthy controls, including 231 upregulated and 90 downregulated genes. GO function analysis revealed that 321 common DEGs were mainly enriched in innate immune response, defense response, cytokine-mediated signaling pathway, response to interferon-alpha, and I-kappaB kinase/NF-kappaB signaling. Additionally, pathway enrichment analysis indicated that DEGs were mainly enriched in several signaling pathways associated with immune system and apoptosis, including RIG-I-like receptor signaling pathway, antigen processing and presentation, and p53 signaling pathway. The expression levels of candidate genes RPL26L1, FBXW11, FOXO1, and SMAD7 were validated by RT-qPCR analysis.
• Integrated bioinformatics analysis of three profile datasets based on SLE patients and healthy controls was performed and 321 common DEGs were identified.
• The 321 common DEGs were mainly enriched in biological processes related to immune responses and inflammatory responses, including innate immune response, defense response, cytokine-mediated signaling pathway, response to interferon-alpha, I-kappaB kinase/NF-kappaB signaling, whereas the three most significant cellular components were oxidoreductase complex, AIM2 inflammasome complex, and ubiquitin ligase complex.
• KEGG pathway enrichment analysis indicated that common DEGs were mainly enriched in several signaling pathways associated with immune system and apoptosis, including RIG-I-like receptor signaling pathway, antigen processing and presentation, and p53 signaling pathway.
• Candidate genes RPL26L1, FBXW11, FOXO1, and SMAD7 may be closely involved in the pathogenesis and development of SLE and may provide valuable novel markers or targets for the diagnosis and treatment of SLE.
KeywordsBioinformatics analysis Interferon signaling pathway NF-κB signaling pathway RIG-I-like receptor signaling pathway Systemic lupus erythematosus
We gratefully thank many researchers for providing technical assistance and all the patients who were enrolled in the study.
This work was supported by grants from National Natural Science Foundation of China (No. 81501417, No. 81671623) and Science and Technology Planning Project of Guangdong Province, China (2014B020212024).
Compliance with ethical standards
Declaration of conflicting interests
The authors declare that there is no conflict of interest.
Ethics approval and consent to participate
The study was approved by the Ethics Committee of The Third Affiliated Hospital of Southern Medical University. Informed consent has been obtained from the patients’ legal guardians.
- 6.Baechler EC, Batliwalla FM, Karypis G, Gaffney PM, Ortmann WA, Espe KJ, Shark KB, Grande WJ, Hughes KM, Kapur V, Gregersen PK, Behrens TW (2003) Interferon-inducible gene expression signature in peripheral blood cells of patients with severe lupus. Proc Natl Acad Sci U S A 100:2610–2615. https://doi.org/10.1073/pnas.0337679100 CrossRefPubMedPubMedCentralGoogle Scholar
- 9.Xu HC, Grusdat M, Pandyra AA, Polz R, Huang J, Sharma P, Deenen R, Köhrer K, Rahbar R, Diefenbach A, Gibbert K, Löhning M, Höcker L, Waibler Z, Häussinger D, Mak TW, Ohashi PS, Lang KS, Lang PA (2014) Type I interferon protects antiviral CD8+ T cells from NK cell cytotoxicity. IMMUNITY. 40:949–960. https://doi.org/10.1016/j.immuni.2014.05.004 CrossRefPubMedGoogle Scholar
- 10.Donnelly S, Roake W, Brown S, Young P, Naik H, Wordsworth P, Isenberg DA, Reid KBM, Eggleton P (2006) Impaired recognition of apoptotic neutrophils by the C1q/calreticulin and CD91 pathway in systemic lupus erythematosus. Arthritis Rheum 54:1543–1556. https://doi.org/10.1002/art.21783 CrossRefPubMedGoogle Scholar
- 12.Hung T, Pratt GA, Sundararaman B, Townsend MJ, Chaivorapol C, Bhangale T, Graham RR, Ortmann W, Criswell LA, Yeo GW, Behrens TW (2015) The Ro60 autoantigen binds endogenous retroelements and regulates inflammatory gene expression. SCIENCE. 350:455–459. https://doi.org/10.1126/science.aac7442 CrossRefPubMedPubMedCentralGoogle Scholar
- 14.Lauwerys BR, Hachulla E, Spertini F, Lazaro E, Jorgensen C, Mariette X, Haelterman E, Grouard-Vogel G, Fanget B, Dhellin O, Vandepapelière P, Houssiau FA (2013) Down-regulation of interferon signature in systemic lupus erythematosus patients by active immunization with interferon alpha-kinoid. Arthritis Rheum 65:447–456. https://doi.org/10.1002/art.37785 CrossRefPubMedGoogle Scholar
- 15.Ducreux J, Houssiau FA, Vandepapeliere P, Jorgensen C, Lazaro E, Spertini F et al (2016) Interferon alpha kinoid induces neutralizing anti-interferon alpha antibodies that decrease the expression of interferon-induced and B cell activation associated transcripts: analysis of extended follow-up data from the interferon alpha kinoid phase I/II study. Rheumatology (Oxford) 55:1901–1905. https://doi.org/10.1093/rheumatology/kew262 CrossRefGoogle Scholar
- 17.Li J, Wang F, Wang G, Sun Y, Cai J, Liu X, Zhang J, Lu X, Li Y, Chen M, Chen L, Jiang C (2017) Combination epidermal growth factor receptor variant III peptide-pulsed dendritic cell vaccine with miR-326 results in enhanced killing on EGFRvIII-positive cells. Oncotarget. 8:26256–26268. https://doi.org/10.18632/oncotarget.15445 CrossRefPubMedPubMedCentralGoogle Scholar
- 19.Labonte AC, Kegerreis B, Geraci NS, Bachali P, Madamanchi S, Robl R, Catalina MD, Lipsky PE, Grammer AC (2018) Identification of alterations in macrophage activation associated with disease activity in systemic lupus erythematosus. PLoS One 13:e208132. https://doi.org/10.1371/journal.pone.0208132 CrossRefGoogle Scholar
- 21.Feng X, Wu H, Grossman JM, Hanvivadhanakul P, FitzGerald JD, Park GS et al (2006) Association of increased interferon-inducible gene expression with disease activity and lupus nephritis in patients with systemic lupus erythematosus. Arthritis Rheum 54:2951–2962. https://doi.org/10.1002/art.22044 CrossRefPubMedGoogle Scholar
- 23.Dixit E, Kagan JC (2013) Intracellular pathogen detection by RIG-I-like receptors. Adv Immunol 117:99–125. https://doi.org/10.1016/B978-0-12-410524-9.00004-9 CrossRefPubMedPubMedCentralGoogle Scholar
- 25.Wu C, Zhao Y, Lin Y, Yang X, Yan M, Min Y, Pan Z, Xia S, Shao Q (2017) Bioinformatics analysis of differentially expressed gene profiles associated with systemic lupus erythematosus. Mol Med Rep. https://doi.org/10.3892/mmr.2017.8293
- 27.Enzler T, Bonizzi G, Silverman GJ, Otero DC, Widhopf GF, Anzelon-Mills A, Rickert RC, Karin M (2006) Alternative and classical NF-kappa B signaling retain autoreactive B cells in the splenic marginal zone and result in lupus-like disease. Immunity 25:403–415. https://doi.org/10.1016/j.immuni.2006.07.010 CrossRefPubMedGoogle Scholar
- 30.Gross JA, Johnston J, Mudri S, Enselman R, Dillon SR, Madden K, Xu W, Parrish-Novak J, Foster D, Lofton-Day C, Moore M, Littau A, Grossman A, Haugen H, Foley K, Blumberg H, Harrison K, Kindsvogel W, Clegg CH (2000) TACI and BCMA are receptors for a TNF homologue implicated in B-cell autoimmune disease. NATURE. 404:995–999. https://doi.org/10.1038/35010115 CrossRefPubMedGoogle Scholar
- 31.You Y, Qin Y, Lin X, Yang F, Li J, Sooranna SR, Pinhu L (2015) Methylprednisolone attenuates lipopolysaccharide-induced Fractalkine expression in kidney of Lupus-prone MRL/lpr mice through the NF-kappaB pathway. BMC Nephrol 16:148. https://doi.org/10.1186/s12882-015-0145-y CrossRefPubMedPubMedCentralGoogle Scholar
- 34.Winston JT, Strack P, Beer-Romero P, Chu CY, Elledge SJ, Harper JW (1999) The SCFbeta-TRCP-ubiquitin ligase complex associates specifically with phosphorylated destruction motifs in IkappaBalpha and beta-catenin and stimulates IkappaBalpha ubiquitination in vitro. Genes Dev 13:270–283CrossRefGoogle Scholar
- 42.Omori SA, Cato MH, Anzelon-Mills A, Puri KD, Shapiro-Shelef M, Calame K, Rickert RC (2006) Regulation of class-switch recombination and plasma cell differentiation by phosphatidylinositol 3-kinase signaling. Immunity 25:545–557. https://doi.org/10.1016/j.immuni.2006.08.015 CrossRefPubMedGoogle Scholar
- 46.Liu L, Liu Y, Yuan M, Xu L, Sun H (2017) Elevated expression of microRNA-873 facilitates Th17 differentiation by targeting forkhead box O1 (Foxo1) in the pathogenesis of systemic lupus erythematosus. Biochem Biophys Res Commun 492:453–460. https://doi.org/10.1016/j.bbrc.2017.08.075 CrossRefPubMedGoogle Scholar
- 50.Towers CG, Guarnieri AL, Micalizzi DS, Harrell JC, Gillen AE, Kim J, Wang CA, Oliphant MUJ, Drasin DJ, Guney MA, Kabos P, Sartorius CA, Tan AC, Perou CM, Espinosa JM, Ford HL (2015) The Six1 oncoprotein downregulates p53 via concomitant regulation of RPL26 and microRNA-27a-3p. Nat Commun 6:10077. https://doi.org/10.1038/ncomms10077 CrossRefPubMedPubMedCentralGoogle Scholar