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Genome\u2010wide (<jats:styled-content style=\"fixed-case\">GW<\/jats:styled-content>) association studies have identified more than 40 disease\u2010associated loci, together accounting for only 10\u201320% of disease heritability. Gene expression represents the intermediate phenotype between <jats:styled-content style=\"fixed-case\">DNA<\/jats:styled-content> and disease phenotypic variation, and provides insights regarding genetic and epigenetic effects. We review data on gene expression and regulation in <jats:styled-content style=\"fixed-case\">SLE<\/jats:styled-content> by our group and other investigators.<\/jats:p><\/jats:sec><jats:sec><jats:title>Materials and methods<\/jats:title><jats:p>Systematic <jats:styled-content style=\"fixed-case\">P<\/jats:styled-content>ub<jats:styled-content style=\"fixed-case\">M<\/jats:styled-content>ed search for <jats:styled-content style=\"fixed-case\">GW<\/jats:styled-content> expression studies in <jats:styled-content style=\"fixed-case\">SLE<\/jats:styled-content> published since the year 2000.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Deregulation of genes involved in type I interferon signaling is a consistent finding in the peripheral blood of active and severe <jats:styled-content style=\"fixed-case\">SLE<\/jats:styled-content> patients. Upregulation of granulocyte\u2010specific transcripts especially in bone marrow mononuclear cells (<jats:styled-content style=\"fixed-case\">BMMC<\/jats:styled-content>s), and of myeloid lineage transcripts in lupus nephritis, provide evidence for pathogenic role of these cells. Gene network analysis in <jats:styled-content style=\"fixed-case\">BMMC<\/jats:styled-content>s identified central gene regulators which could represent therapeutic targets and a high similarity between <jats:styled-content style=\"fixed-case\">SLE<\/jats:styled-content> and non\u2010<jats:styled-content style=\"fixed-case\">H<\/jats:styled-content>odgkin lymphoma providing a molecular basis for the reported association of the two diseases. Gene expression abnormalities driven by deregulated expression of certain micro<jats:styled-content style=\"fixed-case\">RNA<\/jats:styled-content>s in <jats:styled-content style=\"fixed-case\">SLE<\/jats:styled-content> contribute to interferon production, <jats:styled-content style=\"fixed-case\">T<\/jats:styled-content>\u2010 and <jats:styled-content style=\"fixed-case\">B<\/jats:styled-content>\u2010cell hyperactivity, <jats:styled-content style=\"fixed-case\">DNA<\/jats:styled-content> hypomethylation, and defective tissue response to injury. Methylation arrays have revealed alterations in white blood cell <jats:styled-content style=\"fixed-case\">DNA<\/jats:styled-content> methylation in <jats:styled-content style=\"fixed-case\">SLE<\/jats:styled-content> suggesting an important role of epigenetics and the environment.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>Gene expression studies have contributed to the characterization of pathogenic processes in <jats:styled-content style=\"fixed-case\">SLE<\/jats:styled-content>. Integrated approaches utilizing genetic variation, transcriptome and epigenome profiling will facilitate efforts towards a molecular\u2010based disease taxonomy.<\/jats:p><\/jats:sec>","DOI":"10.1111\/eci.12130","type":"journal-article","created":{"date-parts":[[2013,6,26]],"date-time":"2013-06-26T18:12:06Z","timestamp":1372270326000},"page":"1084-1096","source":"Crossref","is-referenced-by-count":51,"title":["Gene expression and regulation in systemic lupus erythematosus"],"prefix":"10.1111","volume":"43","author":[{"given":"Eleni A.","family":"Frangou","sequence":"first","affiliation":[{"name":"Biomedical Research Foundation of the Academy of Athens Medical School of National and Kapodistrian University of Athens Athens Greece"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"George K.","family":"Bertsias","sequence":"additional","affiliation":[{"name":"Institute of Molecular Biology and Biotechnology Foundation of Research and Technology\u2010Heraklion Crete and 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