Associations between the expression of epigenetically regulated genes and the expression of DNMTs and MBDs in systemic lupus erythematosus

Exposome: Epigenetics and autoimmune diseases

Systemic autoimmune diseases are complex conditions characterized by an immune system dysregulation and an aberrant activation against self-antigens, leading to tissue and organ damage. Even though genetic predisposition plays a role, it cannot fully explain the onset of these diseases, highlighting the significant impact of non-heritable influences such as environment, hormones and infections. The exposome represents all those factors, ranging from chemical pollutants and dietary components to psychological stressors and infectious agents. Epigenetics, which studies changes in gene expression without altering the DNA sequence, is a crucial link between exposome and the development of autoimmune diseases. Key epigenetic mechanisms include DNA methylation, histone modifications, and non-coding RNAs. These epigenetic modifications could provide a potential piece of the puzzle in understanding systemic autoimmune diseases and their connection with the exposome. In this work we have collected the most important and recent evidence in epigenetic changes linked to systemic autoimmune diseases (systemic lupus erythematosus, idiopathic inflammatory myopathies, ANCA-associated vasculitis, and rheumatoid arthritis), emphasizing the roles these changes may play in disease pathogenesis, their potential as diagnostic biomarkers and their prospective in the development of targeted therapies.

The Killer's Web: Interconnection between Inflammation, Epigenetics and Nutrition in Cancer

Inflammation is a key contributor to both the initiation and progression of tumors, and it can be triggered by genetic instability within tumors, as well as by lifestyle and dietary factors. The inflammatory response plays a critical role in the genetic and epigenetic reprogramming of tumor cells, as well as in the cells that comprise the tumor microenvironment. Cells in the microenvironment acquire a phenotype that promotes immune evasion, progression, and metastasis. We will review the mechanisms and pathways involved in the interaction between tumors, inflammation, and nutrition, the limitations of current therapies, and discuss potential future therapeutic approaches.

Application of epigenetics in dermatological research and skin management

BACKGROUND

Epigenetics has recently evolved from a collection of diverse phenomena to a defined and far-reaching field of study. Epigenetic modifications of the genome, such as DNA methylation and histone modifications, have been reported to play a role in some skin diseases or cancer.

AIMS

The purpose of this article was to review the development of epigenetic in recent decades and their applications in dermatological research.

METHODS

An extensive literature search was conducted on epigenetic modifications since the first research on epigenetic.

RESULTS

This article summarizes the concept and development of epigenetics, as well as the process and principle of epigenetic modifications such as DNA methylation, histone modification, and non-coding RNA. Their application in some skin diseases and cosmetic research and development is also summarized.

CONCLUSIONS

This information will help to understand the mechanisms of epigenetics and some non-coding RNA, the discovery of the related drugs, and provide new insights for skin health management and cosmetic research and development.

Bioinformatics analysis of epigenetic and SNP-related molecular markers in systemic lupus erythematosus

We analyzed gene expression in peripheral blood mononuclear cells (PBMCs) from patients with systemic lupus erythematosus (SLE) using public databases. The goal was to identify lupus biomarkers by determining whether differentially expressed genes are mediated by methylation, miRNA, or SNP. Two cDNA microarrays were subjected to integration analysis, and we calculated the mutually differentially expressed genes (|log2fold change (FC)| > 1, P < 0.05). These genes were analyzed using gene otology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and protein-protein interaction (PPI) networks. The differences in methylation sites for two methylation chips were calculated and the differentially methylated sites were annotated. These genes were compared to the differentially expressed genes. We obtained 135 differentially expressed microRNAs from the microRNA-chip results using PBMCs from SLE and healthy individuals. Predictive microRNA target genes were identified using GO, KEGG pathways, and PPI networks. The target genes identified were compared to the differentially expressed genes. We downloaded Chinese SLE genome-wide association study data from SLE-related literature, analyzed the loci with a P value < 0.05, and used annotated SLE-associated SNPs. We selected the genes corresponding to an SNP located on an exon and determined the intersection with the differentially expressed genes. We found 18 differentially expressed genes in both cDNA microarrays. The methylation chips had 50 corresponding methylation sites. On the basis of these results, we identified two genes, IFI44 and IFI44L. We further identified 135 differentially expressed microRNAs predicted to affect 5766 target genes. Two identified genes were in common with the differentially expressed genes. Finally, SNP annotated genes and cDNA chip genes overlap with identified MX1. Therefore, we used existing data to analyze the causes of differential gene expression in SLE, introducing new methods for determining biomarkers and therapeutic targets.

Epigenetics in Non-tumor Immune-Mediated Skin Diseases

Epigenetics is the study of the mechanisms that regulate gene expression without modifying DNA sequences. Knowledge of and evidence about how epigenetics plays a causative role in the pathogenesis of many skin diseases is increasing. Since the epigenetic changes present in tumor diseases have been thoroughly reviewed, we believe that knowledge of the new epigenetic findings in non-tumor immune-mediated dermatological diseases should be of interest to the general dermatologist. Hence, the purpose of this review is to summarize the recent literature on epigenetics in most non-tumor dermatological pathologies, focusing on psoriasis. Hyper- and hypomethylation of DNA methyltransferases and methyl-DNA binding domain proteins are the most common and studied methylation mechanisms. The acetylation and methylation of histones H3 and H4 are the most frequent and well-characterized histone modifications and may be associated with disease severity parameters and serve as therapeutic response markers. Many specific microRNAs dysregulated in non-tumor dermatological disease have been reviewed. Deepening the study of how epigenetic mechanisms influence non-tumor immune-mediated dermatological diseases might help us better understand the role of interactions between the environment and the genome in the physiopathogenesis of these diseases.

Base Excision Repair in the Immune System: Small DNA Lesions With Big Consequences

The integrity of the genome is under constant threat of environmental and endogenous agents that cause DNA damage. Endogenous damage is particularly pervasive, occurring at an estimated rate of 10,000–30,000 per cell/per day, and mostly involves chemical DNA base lesions caused by oxidation, depurination, alkylation, and deamination. The base excision repair (BER) pathway is primary responsible for removing and repairing these small base lesions that would otherwise lead to mutations or DNA breaks during replication. Next to preventing DNA mutations and damage, the BER pathway is also involved in mutagenic processes in B cells during immunoglobulin (Ig) class switch recombination (CSR) and somatic hypermutation (SHM), which are instigated by uracil (U) lesions derived from activation-induced cytidine deaminase (AID) activity. BER is required for the processing of AID-induced lesions into DNA double strand breaks (DSB) that are required for CSR, and is of pivotal importance for determining the mutagenic outcome of uracil lesions during SHM. Although uracils are generally efficiently repaired by error-free BER, this process is surprisingly error-prone at the Ig loci in proliferating B cells. Breakdown of this high-fidelity process outside of the Ig loci has been linked to mutations observed in B-cell tumors and DNA breaks and chromosomal translocations in activated B cells. Next to its role in preventing cancer, BER has also been implicated in immune tolerance. Several defects in BER components have been associated with autoimmune diseases, and animal models have shown that BER defects can cause autoimmunity in a B-cell intrinsic and extrinsic fashion. In this review we discuss the contribution of BER to genomic integrity in the context of immune receptor diversification, cancer and autoimmune diseases.

Uncovering potential lncRNAs and nearby mRNAs in systemic lupus erythematosus from the Gene Expression Omnibus dataset

Aim: The aim of this study was to find potential differentially expressed long noncoding RNAs (lncRNAs) and mRNAs in systemic lupus erythematosus. Materials & methods: Differentially expressed lncRNAs and mRNAs were obtained in the Gene Expression Omnibus dataset. Functional annotation of differentially expressed mRNAs was performed, followed by protein-protein interaction network analysis. Then, the interaction network of lncRNA-nearby targeted mRNA was built. Results: Several interaction pairs of lncRNA-nearby targeted mRNA including NRIR-RSAD2, RP11-153M7.5-TLR2, RP4-758J18.2-CCNL2, RP11-69E11.4-PABPC4 and RP11-496I9.1-IRF7/HRAS/PHRF1 were identified. Measles and MAPK were significantly enriched signaling pathways of differentially expressed mRNAs. Conclusion: Our study identified several differentially expressed lncRNAs and mRNAs. And their interactions may play a crucial role in the process of systemic lupus erythematosus.

Circular RNAS: novel biomarkers of disease activity in systemic lupus erythematosus?

Circular RNAs (circRNAs) are a class of non-coding RNAs that regulate gene expression by acting as competitive endogenous RNAs (ceRNAs) and modulating gene transcription. Several studies support the implication of circRNAs in a variety of human diseases, but research on the role of circRNAs in systemic lupus erythematosus (SLE) is lacking. In a study recently published in Clinical Science (2018), Zhang et al. identified hsa_circ_0012919 as a potential biomarker of disease activity in SLE patients. The authors observed different circRNA expression between SLE patients and healthy controls, an association with clinical variables and with the abnormal DNA methylation present in SLE CD4⁺ T cells. Finally, Zhang et al. demonstrated that hsa_circ_0012919 acts as a miRNA sponge for miR-125a-3p, regulating the gene expression of targets RANTES and KLF13 that are involved in the physiology and pathophysiology of acute and chronic inflammatory processes. These findings support the role of circRNAs in the pathophysiology of SLE.

Environmental triggers in systemic lupus erythematosus

Systemic lupus erythematosus (SLE) is an autoimmune disease that can affect almost any organ in the human body. Despite significant advancements in our understanding of SLE over the recent years, its exact mode of onset and disease progression remains elusive. Low concordance rates among monozygotic twins with SLE (as low as 24%), clustering of disease prevalence around polluted regions and an urban-rural difference in prevalence all highlight the importance of environmental influences in SLE. Experimental data strongly suggests a complex interaction between the exposome (or environmental influences) and genome (genetic material) to produce epigenetic changes (epigenome) that can alter the expression of genetic material and lead to development of disease in the susceptible individual. In this review, we focus on the available literature to explore the role of environmental factors in SLE disease onset and progression and to better understand the role of exposome-epigenome-genome interactions in this dreaded disease.

Decreased mRNA expression levels of DNA methyltransferases type 1 and 3A in systemic lupus erythematosus

OBJECTIVES

Systemic lupus erythematosus (SLE) is a chronic relapsing autoimmune disease characterized by the presence of autoantibodies directed against nuclear antigens and by chronic inflammation. Although the etiology of SLE remains unclear, the influence of environment factors, which is largely reflected by the epigenetic mechanisms, with DNA methylation changes in particular, is generally considered as main players in the pathogenesis of SLE. We studied DNA methyltransferases' (DNMTs) type 1, 3A and 3B transcript levels in peripheral blood mononuclear cells from patients diagnosed with systemic lupus erythematosus and from the healthy control subjects. Furthermore, the association of DNMT1, DNMT3A, and DNMT3B mRNA levels with gender, age, and major clinical manifestations was analyzed.

METHODS

Peripheral blood mononuclear cells (PBMCs) were isolated from 32 SLE patients and 40 healthy controls. Reverse transcription and real-time quantitative polymerase chain reaction (RT-qPCR) analyses were used to determine DNMT1, DNMT3A, and DNMT3B mRNA expression levels.

RESULTS

Significantly lower DNMT1 (p = 0.015543) and DNMT3A (p = 0.003652) transcript levels in SLE patients were observed compared with healthy controls. Nevertheless, the DNMT3B mRNA expression levels were markedly lower compared with DNMT1 and DNMT3A, both in PBMCs from affected patients and those from control subjects. Furthermore, the DNMT1 transcript levels were positively correlated with SLE disease activity index (SLEDAI) (r s = 0.4087, p = 0.020224), while the DNMT3A transcript levels were negatively correlated with patients age (r s = -0.3765, p = 0.03369).

CONCLUSIONS

Our analyses confirmed the importance of epigenetic alterations in SLE etiology. Moreover, our results suggest that the presence of some clinical manifestations, such as phototosensitivity and arthritis, might be associated with the dysregulation of DNA methyltransferases' mRNA expression levels.

The role of IFI35 in lupus nephritis and related mechanisms

OBJECTIVES

It's reported that multiple genes in the IFN-γ/STAT1 pathway were hypomethylated and associated with the pathogenesis of lupus nephritis (LN). Our previous study using microarray analysis suggested that interferon induced 35-kDa protein (IFI35) was hypomethylated and increased in LN. However, the role of IFI35 in LN and related mechanism remains to be elucidate.

METHODS

The expressions of IFNγR, STAT1, IFI35 and MBD2 in the human kidneys tissues was detected by real-time PCR and Western blot. The protein levels of IFI35 in the human kidney tissues were detected by immunohistochemistry. The methylation status of IFNγR, STAT1 and IFI35 were detected by methylation specific PCR. Cell proliferation assay was evaluated using cell counting kit 8; pcDNA-IFI35 (pcDNA-MBD2) or IFI35 RNAi (MBD2 RNAi) was used to upregulated or downregulated the expression of the IFI35 and MBD2.

RESULTS

The expressions of IFNγR, STAT1 and IFI35 in the LN kidneys were significantly higher than controls. IFI35 was expressed in mesangial cells, and positively correlated with the proliferation of mesangial cells. IFNγR, STAT1and IFI35 was hypomethylated and MBD2 was increased in LN kidneys. In vitro data confirmed those findings: after stimulating with the serum from LN patients, the proliferation of human renal mesangial cells (HRMCs) was increased. The expressions of the three members of IFNγ signal pathway were hypomethylated and upregulated. However, this effect was reversed by MBD2 knockdown. IFI35 promoted the proliferation of HRMCs and was regulated by MBD2.

CONCLUSION

Our results demonstrated that IFI35 enhances the proliferation of mesangial cells and was regulated by MBD2 in LN.

DUSP23 is over-expressed and linked to the expression of DNMTs in CD4+ T cells from systemic lupus erythematosus patients

We evaluated the transcriptional expression of dual-specificity protein phosphatase 23 (DUSP23) in CD4⁺ T cells from 30 systemic lupus erythematosus (SLE) patients and 30 healthy controls. DUSP23 mRNA levels were considerably higher in the patient group: 1490 ± 1713 versus 294·1 ± 204·2. No association was found between DUSP23 mRNA expression and the presence of typical serological and clinical parameters associated with SLE. Meaningful statistical values were obtained in the patient group between the levels of DUSP23 and integrin subunit alpha L (ITGAL), perforin 1 (PRF1) and CD40L. Similarly, transcript levels of different DNA methylation-related enzymes [DNA methylation-related enzymes (DNMT1, DNMT3A, DNMT3B, MBD2, and MBD4)] were also correlated positively with the expression of DUSP23. In an attempt to counteract the hypomethylation status of the promoters of certain genes known to be over-expressed in SLE, it is possible that DUSP23 acts as a negative regulatory mechanism which ultimately silences the transcription of these epigenetically regulated genes by triggering an increase in the expression of different DNMTs.

Association of DNA Methyltransferase 3B Promotor Polymorphism With Childhood Chronic Immune Thrombocytopenia

BACKGROUND

DNA methylation is an epigenetic process that refers to chromatin-based mechanisms in the regulation of gene expression without DNA alternation. It is mediated by DNA methyltransferases (DNMTs). The DNA methyltransferase 3B (DNMT3B) gene contains a C-to-T single nucleotide polymorphism (SNP; rs2424913) in the Promotor region, 149 base pairs from the transcription start site, which is reported to significantly increase the Promotor activity.

OBJECTIVE

To investigate the prevalance of rs2424913 single nucleotide polymorphism located in the DNMT3B gene Promotor.

METHODS

In the present study, we investigated the prevalence of rs2424913 single nucleotide polymorphism located in DNMT3B gene Promotor by restriction fragment length polymorphism (PCR-RFLP) in Egyptian pediatric chronic immune thrombocytopenia (ITP) patients and controls.

RESULTS

The homozygous genotype (TT) was significantly higher in our patient and conferred almost 3-fold increased risk of chronic ITP when compared to controls.

CONCLUSION

The present study shows that DNMT3B rs2424913 promotor polymorphism represents a genetic risk factor that may play an important role in understanding the pathogenesis of chronic ITP.

Epigenetic Aspects of Systemic Lupus Erythematosus

Autoimmune diseases such as systemic lupus erythematosus (SLE), rheumatoid arthritis, multiple sclerosis, autoimmune hepatitis, and inflammatory bowel disease have complex pathogeneses and the courses of events leading to these diseases are not well understood. The immune surveillance is a delicate balance between self and foreign as well as between tolerance and immune response. Exposure to certain environmental factors may impair this equilibrium, leading to autoimmune diseases, cancer, and the so-called “lifestyle diseases” such as atherosclerosis, heart attack, stroke, and obesity, among others. These external stimuli may also alter the epigenetic status quo and may trigger autoimmune diseases such as SLE in genetically susceptible individuals. This review aims to highlight the role of epigenetic (dys-)regulation in the pathogenesis of SLE.

The danger model approach to the pathogenesis of the rheumatic diseases

The danger model was proposed by Polly Matzinger as complement to the traditional self-non-self- (SNS-) model to explain the immunoreactivity. The danger model proposes a central role of the tissular cells' discomfort as an element to prime the immune response processes in opposition to the traditional SNS-model where foreignness is a prerequisite. However recent insights in the proteomics of diverse tissular cells have revealed that under stressful conditions they have a significant potential to initiate, coordinate, and perpetuate autoimmune processes, in many cases, ruling over the adaptive immune response cells; this ruling potential can also be confirmed by observations in several genetically manipulated animal models. Here, we review the pathogenesis of rheumatic diseases such as systemic lupus erythematous, rheumatoid arthritis, spondyloarthritis including ankylosing spondylitis, psoriasis, and Crohn's disease and provide realistic approaches based on the logic of the danger model. We assume that tissular dysfunction is a prerequisite for chronic autoimmunity and propose two genetically conferred hypothetical roles for the tissular cells causing the disease: (A) the Impaired cell and (B) the paranoid cell. Both roles are not mutually exclusive. Some examples in human disease and in animal models are provided based on current evidence.

Natural antisense RNAs are involved in the regulation of CD45 expression in autoimmune diseases

CD45 is a transmembrane protein tyrosine phosphatase that is specifically expressed in hematopoietic cells and can initiate signal transduction via the dephosphorylation of tyrosine. Alternatively spliced transcript variants of this gene encode distinct isoforms, which indicate different functional states of CD45. Among these variants, CD45RO, which contains neither exon 4, 5, or 6, is over-expressed in lymphocytes in autoimmune diseases, including systemic lupus erythematosus, rheumatoid arthritis, multiple sclerosis, and type I diabetes. The CD45 RO serves as a marker of the immune response activity and lymphocyte development. Previous studies have indicated that exon splicing is generally correlated with local hypermethylated DNA and acetylated histone modification, while autoimmune diseases are commonly associated with global hypomethylation and histone deacetylation in lymphocytes. Thus, the question arises of how exons 4, 5, and 6 of CD45RO are excluded under the status of global DNA hypomethylation and histone deacetylation in these autoimmune diseases. On the basis of the analyses of the context sequence of CD45 and its natural antisense RNA in GenBank, we proposed that the long noncoding RNA encoded by the natural antisense gene of CD45 contributes to the expressional regulation of the CD45RO splicing variant via recruitment of DNA methyltransferase and histone modification modulators specific to the sense gene CD45; thus, it is associated with the over-expression of CD45RO and the functional regulation of lymphocytes in the pathogenic development of autoimmune diseases.

MS risk allele rs1883832T is associated with decreased mRNA expression of CD40

CD40-CD40L interactions mediate T-dependent B cell response and efficient T cell priming. Therefore, genes encoding these molecules are attractive candidates for studies on autoimmune diseases, such as multiple sclerosis (MS), in which activated T and B cells are involved. Thus, we analyzed CD40 and CD40L mRNA expression in whole blood samples from MS patients and controls. Additionally, we examined the effect of three SNPs of CD40 (rs1883832C>T, rs11569343C>G, and rs752118C>T) and two SNPs of CD40L (rs3092923T>C and rs3092952A>G) on their mRNA expression. Our results showed that the rs1883832C>T SNP affects CD40 gene expression. Our analysis revealed that individuals possessing CT and TT genotypes (predisposing to MS) had decreased level of CD40 mRNA in comparison to those with CC. Moreover, we demonstrated the potential role of impaired CD40-CD40L interaction in developing of multiple sclerosis.

Epigenetics in the treatment of systemic lupus erythematosus: potential clinical application

The current treatments of systemic lupus erythematosus (SLE) have been based on the use of immunosuppressive drugs which are linked to serious side effects. The more effective therapeutic approaches with minimal or no side effects for SLE patients are hard to develop, mainly due to the complexity of the disease. The discovery of pharmacoepigenetics provides a new way to solve this problem. Epigenetic modifications can influence drug efficacy by altering gene expression via changing chromatin structure. Although still in early development, epigenetic studies in SLE are expected to reveal novel therapeutic targets and disease biomarkers in autoimmunity. For example, miRNAs, which have been identified to govern many genes including drug targets, are altered in disease development and after drug administration. This review aims to present an overview of current epigenetic mechanisms involved in the pathogenesis of SLE, and discuss their potential roles in clinical and pharmacological applications.

Critical role of DNA methylation in the pathogenesis of systemic lupus erythematosus: new advances and future challenges

Systemic lupus erythematosus (SLE) is a systemic multi-organ autoimmune disease with different immunological characteristics and clinical manifestations characterized by an autoantibody response to nuclear and cytoplasmic antigens; the etiology of this disease remains largely unknown. Most recent genome-wide association studies demonstrate that genetics significantly predispose to SLE onset, but the incomplete disease concordance rates between monozygotic twins indicates a role for other complementary factors in SLE pathogenesis. Recently, much evidence strongly supports other molecular mechanisms involved in the regulation of gene expression ultimately causing autoimmune disease, and several studies, both in clinical settings and experimental models, have demonstrated that epigenetic modifications may hold the key to a better understanding of SLE initiation and development. DNA methylation changes the structure of chromatin, being typically able to modulate the fine interactions between promoter-transcription factors and encoding genes within the transcription machinery. Alteration in DNA methylation has been confirmed as a major epigenetic mechanism that may potentially cause a breakdown of immune tolerance and perpetuation of SLE. Based on recent findings, DNA methylation treatments already being used in oncology may soon prove beneficial to patients with SLE. We herein discuss what we currently know, and what we expect in the future.

The Interaction Between Allelic Variants of CD86 and CD40LG: A Common Risk Factor of Allergic Asthma and Rheumatoid Arthritis

PURPOSE

Allergic asthma (AA) and rheumatoid arthritis (RA) are immune tolerance-related diseases, and immune tolerance is known to be influenced by costimulatory molecules. In this study, we sought to identify common genetic susceptibility in AA and RA.

METHODS

Two hundred cases of AA, 184 cases of RA, and 182 healthy controls were recruited at the Seoul National University Hospital, Seoul, Korea. Eight single nucleotide polymorphisms (SNPs) in five genes coding costimulatory molecules, namely, -318C>T, +49A>G, and 6230G>A in CTLA4, IVS3+17T>C in CD28, -3479T>G and I179V in CD86, -1C>T in CD40, and -3458A>G in CD40LG were scored, and genetic interactions were evaluated by multifactor dimensionality reduction (MDR) analysis.

RESULTS

MDR analysis revealed a significant gene-gene interaction between -3479T>G CD86 and -3458A>G CD40LG for AA. Subjects with the T/T genotype of -3479T>G CD86 and the A/A genotype of -3458A>G CD40LG were found to be significantly more likely to develop AA than those with the T/T genotype of -3479T>G CD86 and A/- genotype of -3458A>G CD40LG (adjusted OR, 6.09; 95% CI, 2.89-12.98; logistic regression analysis controlled by age). Similarly those subjects showed a significant risk of developing RA (adjusted OR, 39.35; 95% CI, 15.01-107.00, logistic regression analysis controlled by age).

CONCLUSIONS

Our findings suggest that a genetic interaction between CD86 and CD40LG favors the development of both AA and RA.

Systemic lupus erythematosus diagnostics in the 'omics' era

Systemic lupus erythematosus is a complex autoimmune disease affecting multiple organ systems. Currently, diagnosis relies upon meeting at least four out of eleven criteria outlined by the ACR. The scientific community actively pursues discovery of novel diagnostics in the hope of better identifying susceptible individuals in early stages of disease. Comprehensive studies have been conducted at multiple biological levels including: DNA (or genomics), mRNA (or transcriptomics), protein (or proteomics) and metabolites (or metabolomics). The 'omics' platforms allow us to re-examine systemic lupus erythematosus at a greater degree of molecular resolution. More importantly, one is hopeful that these 'omics' platforms may yield newer biomarkers for systemic lupus erythematosus that can help clinicians track the disease course with greater sensitivity and specificity.

Gene expression and regulation in systemic lupus erythematosus

BACKGROUND

Systemic lupus erythematosus (SLE) is the prototypic systemic autoimmune disease. Genome-wide (GW) association studies have identified more than 40 disease-associated loci, together accounting for only 10-20% of disease heritability. Gene expression represents the intermediate phenotype between DNA and disease phenotypic variation, and provides insights regarding genetic and epigenetic effects. We review data on gene expression and regulation in SLE by our group and other investigators.

MATERIALS AND METHODS

Systematic PubMed search for GW expression studies in SLE published since the year 2000.

RESULTS

Deregulation of genes involved in type I interferon signaling is a consistent finding in the peripheral blood of active and severe SLE patients. Upregulation of granulocyte-specific transcripts especially in bone marrow mononuclear cells (BMMCs), and of myeloid lineage transcripts in lupus nephritis, provide evidence for pathogenic role of these cells. Gene network analysis in BMMCs identified central gene regulators which could represent therapeutic targets and a high similarity between SLE and non-Hodgkin lymphoma providing a molecular basis for the reported association of the two diseases. Gene expression abnormalities driven by deregulated expression of certain microRNAs in SLE contribute to interferon production, T- and B-cell hyperactivity, DNA hypomethylation, and defective tissue response to injury. Methylation arrays have revealed alterations in white blood cell DNA methylation in SLE suggesting an important role of epigenetics and the environment.

CONCLUSIONS

Gene expression studies have contributed to the characterization of pathogenic processes in SLE. Integrated approaches utilizing genetic variation, transcriptome and epigenome profiling will facilitate efforts towards a molecular-based disease taxonomy.