DNA methylation and B-cell autoreactivity

EZH2: Its regulation and roles in immune disturbance of SLE

The pathogenesis of systemic lupus erythematosus (SLE) is related to immune homeostasis imbalance. Epigenetic mechanisms have played a significant role in breaking immune tolerance. Enhancer of zeste homolog 2 (EZH2), the specific methylation transferase of lysine at position 27 of histone 3, is currently found to participate in the pathogenesis of SLE through affecting multiple components of the immune system. This review mainly expounds the mechanisms underlying EZH2-mediated disruption of immune homeostasis in SLE patients, hoping to provide new ideas in the pathogenesis of SLE and new targets for future treatment.

B cell dysregulation in primary Sjögren's syndrome: A review

Primary Sjögren’s syndrome is a chronic autoimmune disorder of unknown etiology and is characterized by progressive focal lymphocytic infiltration of the lacrimal and salivary glands. Comparison of B cell subsets from the peripheral blood and salivary glands of patients with primary Sjögren’s syndrome and those from healthy individuals shows dysregulation and derangement of B cell subsets in both peripheral circulation and in inflamed glandular tissues. This dysregulation is expressed as a decrease in the percentage of CD27+ memory B cells in peripheral blood and an increase in the CD27+ memory B cells in the affected glands. Further, the overall percentage of long-lived autoantibodies-producing plasma cells within the affected glands is increased. In the last two decades, several studies have shown growing evidences that B cells play multiple roles in primary Sjögren’s syndrome pathophysiology, and that dysregulation of these cells may actually play a central role in the disease development.

Lymphocyte Disturbances in Primary Antiphospholipid Syndrome and Application to Venous Thromboembolism Follow-Up

Among patients with venous thromboembolism (VTE), the persistent detection of antiphospholipid (aPL) antibodies (Ab) represents an independent high risk factor for recurrence. However, oral anticoagulation vitamin K antagonist therapy, frequently used in these patients, is problematic in assessing and/or confirming a diagnosis of primary aPL syndrome (pAPS), suggesting use of alternative strategies. For this reason, and by analogy with other autoimmune diseases, a flow cytometer approach testing peripheral T cell subsets (CD3, CD4, and CD8), B cell subsets (B1, transitional, naive, and memory), and NK cells can be proposed. As an example and to validate the concept, pAPS patients selected from the monocentric VTE case-control EDITH's cohort were selected during their follow-up. As suspected and in contrast to non-APS VTE patients, other autoimmune diseases, and controls, pAPS VTE patients displayed specific lymphocyte disturbances. Quantitative and qualitative modifications were related to total CD4⁺ T cell reduction, a lower CD4/CD8 ratio, and disturbance in B cell homeostasis with increased proportions of B1 cells, transitional B cells (CD24⁺⁺CD38⁺⁺), and naive B cells (IgD⁺CD27^-), while memory B cells (IgD⁺CD27⁺ and IgD^-CD27⁺) were reduced. Interestingly, the absolute number of CD4⁺ T cells positively correlated with IgG anti-cardiolipin Ab levels. Altogether, disturbances of T and B cell homeostasis characterized pAPS VTE patients during their follow-up. This suggests a means of profiling that could be used in addition to existing criteria to characterize them.

Translating epigenetics into clinic: focus on lupus

Systemic lupus erythematosus (SLE) is a chronic relapsing–remitting autoimmune disease with highly heterogeneous phenotypes. Biomarkers with high sensitivity and specificity are useful for early diagnosis as well as monitoring disease activity and long-term complications. Epigenetics potentially provide novel biomarkers in autoimmune diseases. These may include DNA methylation changes in relevant lupus-prone genes or histone modifications and microRNAs to upregulate and downregulate relevant gene expression. The timing and nature of epigenetic modification provide such changes. In lupus, DNA methylation alterations in cytokine genes, such as IFN-related gene and retrovirus gene, have been found to offer biomarkers for lupus diagnosis. Histone modifications such as histone methylation and acetylation lead to transcriptional alterations of several genes such as PTPN22, LRP1B, and TNFSF70. There are varieties of microRNAs applied as lupus biomarkers, including DNMT1-related microRNAs, renal function-associated microRNAs, microRNAs involved in the immune system, and microRNAs for phenotype classification. Thus, we conclude a wide range of promising roles of epigenetic biomarkers aiding in the diagnosing and monitoring of lupus diseases and the risk of organ damage.

DNA methylation in systemic lupus erythematosus

Systemic lupus erythematosus (SLE) is a systemic autoimmune disease facilitated by aberrant immune responses directed against cells and tissues, resulting in inflammation and organ damage. In the majority of patients, genetic predisposition is accompanied by additional factors conferring disease expression. While the exact molecular mechanisms remain elusive, epigenetic alterations in immune cells have been demonstrated to play a key role in disease pathogenesis through the dysregulation of gene expression. Since epigenetic marks are dynamic, allowing cells and tissues to differentiate and adjust, they can be influenced by environmental factors and also be targeted in therapeutic interventions. Here, we summarize reports on DNA methylation patterns in SLE, underlying molecular defects and their effect on immune cell function. We discuss the potential of DNA methylation as biomarker or therapeutic target in SLE.

DNA methylation alterations in the pathogenesis of lupus

Although lupus is, by definition, associated with genetic and immunological factors, its molecular mechanisms remain unclear. The up-to-date research findings point out that various genetic and epigenetic factors, especially gene-specific and site-specific methylation, are believed to contribute to the initiation and development of systemic lupus erythematosus (SLE). This review presents and summarizes the association between abnormal DNA methylation of immune-related cells and lupus-like diseases, as well as the possible mechanisms of immune disorder caused by DNA methylation, aiming at a better understanding of the roles of aberrant DNA methylation in the initiation and development of certain forms of lupus and providing a new insight into promising therapeutic regimens in lupus-like diseases.

Human endogenous retrovirus group E and its involvement in diseases

Human endogenous retrovirus group E (HERV-E) elements are stably integrated into the human genome, transmitted vertically in a Mendelian manner, and are endowed with transcriptional activity as alternative promoters or enhancers. Such effects are under the control of the proviral long terminal repeats (LTR) that are organized into three HERV-E phylogenetic subgroups, namely LTR2, LTR2B, and LTR2C. Moreover, HERV-E expression is tissue-specific, and silenced by epigenetic constraints that may be disrupted in cancer, autoimmunity, and human placentation. Interest in HERV-E with regard to these conditions has been stimulated further by concerns regarding the capacity of HERV-E elements to modify the expression of neighboring genes and/or to produce retroviral proteins, including immunosuppressive env peptides, which in turn may induce (auto)-antibody (Ab) production. Finally, better understanding of HERV-E elements may have clinical applications for prevention, diagnosis, prognosis, and therapy.

Genome-wide DNA methylation profiling in rheumatoid arthritis identifies disease-associated methylation changes that are distinct to individual T- and B-lymphocyte populations

Changes to the DNA methylome have been described in patients with rheumatoid arthritis (RA). In previous work, we reported genome-wide methylation differences in T-lymphocyte and B-lymphocyte populations from healthy individuals. Now, using HumanMethylation450 BeadChips to interrogate genome-wide DNA methylation, we have determined disease-associated methylation changes in blood-derived T- and B-lymphocyte populations from 12 female patients with seropositive established RA, relative to 12 matched healthy individuals. Array data were analyzed using NIMBL software and bisulfite pyrosequencing was used to validate array candidates. Genome-wide DNA methylation, determined by analysis of LINE-1 sequences, revealed higher methylation in B-lymphocytes compared with T-lymphocytes (P ≤ 0.01), which is consistent with our findings in healthy individuals. Moreover, loci-specific methylation differences that distinguished T-lymphocytes from B-lymphocytes in healthy individuals were also apparent in RA patients. However, disease-associated methylation differences were also identified in RA. In these cases, we identified 509 and 252 CpGs in RA-derived T- and B-lymphocytes, respectively, that showed significant changes in methylation compared with their cognate healthy counterparts. Moreover, this included a restricted set of 32 CpGs in T-lymphocytes and 20 CpGs in B-lymphocytes (representing 15 and 10 genes, respectively, and including two, MGMT and CCS, that were common to both cell types) that displayed more substantial changes in methylation. These changes, apparent as hyper- or hypo-methylation, were independently confirmed by pyrosequencing analysis. Validation by pyrosequencing also revealed additional sites in some candidate genes that also displayed altered methylation in RA. In this first study of genome-wide DNA methylation in individual T- and B-lymphocyte populations in RA patients, we report disease-associated methylation changes that are distinct to each cell type and which support a role for discrete epigenetic regulation in this disease.

Epigenetic regulation of cytokine expression in systemic lupus erythematosus with special focus on T cells

Epigenetic events play a central role in the priming, differentiation and subset determination of T lymphocytes. Through their influence on chromatin conformation and DNA-accessibility to transcription factors and RNA polymerases, epigenetic marks allow or prevent gene expression and control cellular functions including cytokine expression. CpG-DNA methylation and post-translational modifications to histone tails are the two most well accepted epigenetic mechanisms. The involvement of epigenetic mechanisms in the pathogenesis of systemic lupus erythematosus (SLE) has been suggested by the development of lupus-like symptoms by individuals who received procainamide or hydralazine treatment resulting in a reduction of CpG-DNA methylation. To date, a growing body of literature indicates that the deregulation of cytokine expression through epigenetic disturbances can result in altered immune responses and autoimmune reactions. Over the past decade, various global and regional epigenetic alterations have been reported in immune cells from patients with SLE and other autoimmune disorders. More recently, the molecular mechanisms that result in epigenetic disturbances have been addressed, and deregulated transcription factor networks have been demonstrated to mediate epigenetic alterations in B and T lymphocytes from SLE patients. A better understanding of the molecular events that contribute to epigenetic alterations and subsequent immune imbalance is essential for the establishment of disease biomarkers and identification of potential therapeutic targets.

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.

Epigenetic dysregulation in systemic lupus erythematosus

Systemic lupus erythematosus (SLE) is a prototypical systemic autoimmune disease that affects multiple organs and is characterized by episodic flares and elevated morbidity. The etiology of SLE is only partly known. In this context, recent attention has been paid to the importance of environmentally induced epigenetic modifications as significant contributors to the disease pathogenesis in genetically predisposed individuals. Here we review what is currently known on the role of epigenetics in SLE, and the investigations aimed at possibly targeting epigenetic mechanisms and/or related biomarkers to improve the monitoring, management and, ultimately, the prognosis of SLE.

DNA methylation modulates HRES1/p28 expression in B cells from patients with Lupus

Systemic lupus erythematosus (SLE) disease is an autoimmune disease of unknown aetiology that affects predominantly women of child bearing age. Since previous studies, including ours, have demonstrated that CD4+ T cells and B cells from SLE patients are defective in their ability to methylate their DNA upon antigen stimulation, the aim of this study was to investigate whether DNA demethylation affects the transcription of HRES-1 in B cells. HRES-1 is the prototype of Human Endogenous Retrovirus (HERV) overexpressed in SLE. We have observed that SLE B cells were characterized by their incapacity to methylate the HRES-1 promoter, both in unstimulated and in anti-IgM stimulated B cells. In turn, HRES-1/p28 expression was increased in SLE B cells after B cell receptor engagement, but not in controls. In SLE B cells the Erk/DNMT1 pathway was defective. In addition, blocking the autocrine-loop of IL-6 in SLE B cells with an anti-IL-6 receptor monoclonal antibody restores DNA methylation and control of HRES-1/p28 expression became effective. As a consequence, a better understanding of HERV dysregulation in SLE reinforces our comprehension of the disease and opens new therapeutic perspectives.

Methylation--an uncommon modification of glycans

A methyl (Me) group on a sugar residue is a rarely reported event. Until now, this type of modification has been found in the animal kingdom only in worms and molluscs, whereas it is more frequently present in some species of bacteria, fungi, algae and plants, but not in mammals. The monosaccharides involved as well as the positions of the Me groups on the sugar vary with species. Methylation appears to play a role in some recognition events, but details are still unknown. This review summarises the current knowledge on methylation of sugars in all types of organism.

B cell tolerance and positive selection in lupus

Systemic lupus erythematosus is considered a prototype of systemic autoimmune diseases; however, despite considerable advances in recent years in the understanding of basic mechanisms in immunology, little progress has been made in elucidating the etiology and pathogenesis of this disease. This even holds for inbred mice, such as the lupus-prone New Zealand Black/New Zealand White F(1) mice, which are all genetically programmed to develop lupus at a predetermined age. This frustrating state of affairs calls for a fundamental change in our scientific thinking and the opening of new directions in lupus research. In this study, we suggest that intrinsic B cell tolerance mechanisms are not grossly impaired in lupus-prone mice, but that an unusually strong positive selection event recruits a small number of autoreactive B cells to the germinal centers. This event could be facilitated by nucleic acid-protein complexes that are created by somatic changes in the susceptible animal.

DNA methylation: a promising landscape for immune system-related diseases

During hematopoiesis, a unique hematopoietic stem cell (HSC) from the bone marrow gives rise to a subset of mature blood cells that directs all the immune responses. Recent studies have shown that this well-defined, hierarchical process is regulated in part by epigenetic mechanisms. Changes in the DNA methylation profile have a critical role in the division of these stem cells into the myeloid and lymphoid lineages and in the establishment of a specific phenotype and functionality in each terminally differentiated cell type. In this review, we describe how the DNA methylation patterns are modified during hematopoietic differentiation and what their role is in cell plasticity and immune function. An in-depth knowledge of these epigenetic mechanisms will help clarify how cell type-specific gene programs are established, and how they can be leveraged in the development of novel strategies for treating immune system-related pathologies.