The new era of autoimmune disease research

Recent genome-wide association studies have advanced our understanding of genetic factors that underlie systemic lupus erythematosus (SLE), a multifactorial autoimmune disease characterized by various clinical manifestations. SLE also has an environmental component, which can trigger or exacerbate the disease. Despite extensive efforts aimed at elucidating the cellular and biological abnormalities that arise in the immune system of patients with SLE, its pathology remains unclear. Lee and colleagues recently carried out gene expression profiling of patients with SLE followed by bioinformatics analysis and discovered the existence of abnormal regulatory networks and potential key molecules. The authors found that ATP synthesis and DNA repair pathways may be involved in the pathogenesis, providing a potential explanation for photosensitivity experienced by patients with SLE.

Microarray analysis and gene expression profi ling allow patterns of gene expression in diseases and developmental processes to be assessed. Advances in biological databases have enabled the large-scale expression profi ling data to be processed and the foundation for biological interpretation to be laid. Despite this, a major limitation involves the interpretation of massive amounts of microarray data. In microarray analysis, which is often used to identify diff erentially expressed genes, genes that are expressed at higher or lower levels than controls are of interest. In the previous issue of Arthritis Research & Th erapy, Lee and colleagues [1] conducted gene expression and bioinformatics analyses between healthy individuals and patients with systemic lupus erythematosus (SLE) and provided insights into biological and functional abnormalities in SLE as well as abnormal regulatory networks. Such analyses -that is, gene ontology analysis, which is used to classify genes into functionally related gene groups, and network pathway analysis, which identifi es relationships among these genes -provide an additional layer of insight that cannot be achieved by focusing on individual molecules [1].

Interferon signature
Lee and colleagues [2] previously demonstrated, by DNA microarray and bioinformatics analyses, that genes related to the immune response were diff erentially expressed in patients with SLE compared with healthy controls. Other studies have also reported increased expres sion of IFNinducible genes (that is, the 'IFN signature') in peripheral blood cells from patients with SLE [2][3][4]. Many groups are currently looking into patho logical roles of plasmacytoid dendritic cells (pDCs) and IFN-inducible genes in SLE since pDCs are major producers of IFN-α [4][5][6][7]. Given that SLE is a systemic disease that infl uences multiple organs, Lee and colleagues [1] emphasized the importance of assessing biological and cellular abnormalities associated with SLE other than those related to the immune response. To this end, the authors revealed not only that apoptosis-related genes are up regulated but also that genes related to sensory perception and response to radiation/light were down regulated.

Abnormalities in DNA repair and ATP synthesis
Downregulated genes associated with sensory perception and response to radiation/light included ATPase/ATPase domain-containing genes, two excision repair crosscomplementing genes (ERCC2 and ERCC5), and six mito chon drial DNA (mtDNA) encoded genes: ATP synthase 6 (ATP6), cytochrome c oxidases 1 (COX1) and 3 (COX3), cytochrome b (CYTB), and NADH dehydrogenase sub units 1 (ND1) and 2 (ND2). ERCC2/XPD and ERCC5/XPG are both involved in excision repair of UVinduced DNA damage. Patients with Xeroderma pigmentosum, Cockayne syndrome, or trichothiodystrophy harbor mutations in ERCC genes, and such patients exhibit photo sensitivity. Th e process of UV-induced DNA damage repair is known to require ATP, and the main function of mitochondria is to generate ATP Abstract Recent genome-wide association studies have advanced our understanding of genetic factors that underlie systemic lupus erythematosus (SLE), a multifactorial autoimmune disease characterized by various clinical manifestations. SLE also has an environmental component, which can trigger or exacerbate the disease. Despite extensive eff orts aimed at elucidating the cellular and biological abnormalities that arise in the immune system of patients with SLE, its pathology remains unclear. Lee and colleagues recently carried out gene expression profi ling of patients with SLE followed by bioinformatics analysis and discovered the existence of abnormal regulatory networks and potential key molecules. The authors found that ATP synthesis and DNA repair pathways may be involved in the pathogenesis, providing a potential explanation for photosensitivity experienced by patients with SLE.

E D I TO R I A L
*Correspondence: tkoike@med.hokudai.ac.jp Hokkaido University Graduate School of Medicine, N-15 W-7, Kita-ku, Sapporo, Japan through oxidative phosphorylation. Accordingly, downregulation of ATP-dependent ERCC genes and mtDNAencoded genes implies that impaired DNA repair and ATP synthesis, or increased apoptosis, may contribute to the various manifestations of SLE. Consistent with this, a study by Fernandez and Perl [8] showed that mito chondrial hyperpolarization and ATP depletion predispose lupus T cells to necrosis. Via network pathway analysis, Lee and colleagues [1] demon strated that cytokines IL-6, transforming growth factor-beta (TGF-β), and TNF play central roles as ATP synthesis-related molecules. Patients with SLE had signifi cantly higher levels of TNF and IL-6, which are proinfl ammatory, whereas levels of the antiinfl ammatory cytokine TGF-β were lower [9]. Furthermore, Pfl egerl and colleagues [10] reported that epidermal loss of Jun B, which is linked to increased epidermal IL-6 secretion, is suffi cient to induce an SLE phenotype in mice, and this suggests that defects in skin function may lead to systemic autoimmune diseases.

Conclusions
Lee and colleagues [1] revealed func tional abnormalities in ATP synthesis and DNA repair in peripheral blood cells from patients with SLE. Further DNA microarray and bioinformatics analyses should provide interesting insights into the pathophysiology of autoimmune diseases.