Systemic lupus erythematosus and related autoimmune diseases are antigen-driven, epigenetic diseases

Polyamine patterns in plasma of patients with systemic lupus erythematosus and fever

Systemic lupus erythematosus (SLE) is a systemic autoimmune disease with various clinical manifestations and serologic markers. In this study, we analyzed nine polyamine (PA) profiles of plasma from patients with SLE and healthy controls (HCs), and the relationship between the PA profiles and disease activity. PA alterations in plasma of 44 patients with SLE and fever were investigated using gas chromatography mass spectrometry (GC-MS) in selected ion monitoring mode using N-ethoxycarbonyl/ N-pentafluoropropionyl derivatives, and compared with those of 43 HCs. Patients with SLE and HCs showed differences in five of nine PA profiles. Among five changed PA levels, four PAs, namely N¹-acetylcadaverine, spermidine, N¹-acetylspermidine, and spermine, were dramatically decreased. However, the level of cadaverine was increased in patients with SLE. In the partial correlation with PA profiles and disease activity markers of SLE, several disease activity markers and nutritional markers were correlated with cadaverine, spermidine, and N ⁸-acetylspermidine. Thus, our results provide a comprehensive understanding of the relationship between PA metabolomics and disease activity markers in patients with SLE.

Viral Impact in Autoimmune Diseases: Expanding the "X Chromosome-Nucleolus Nexus" Hypothesis

Viruses are suspected of significant roles in autoimmune diseases but the mechanisms are unclear. We get some insight by considering demands a virus places on host cells. Viruses not only require production of their own proteins, RNA and/or DNA, but also production of additional cellular machinery, such as ribosomes, to handle the increased demands. Since the nucleolus is a major site of RNA processing and ribonucleoprotein assembly, nucleoli are targeted by viruses, directly when viral RNA and proteins enter the nucleolus and indirectly when viruses induce increased expression of cellular polyamine genes. Polyamines are at high levels in nucleoli to assist in RNA folding. The size and activity of nucleoli increase directly with increases in polyamines. Nucleolar expansion due to abnormal increases in polyamines could disrupt nearby chromatin, such as the inactive X chromosome, leading to expression of previously sequestered DNA. Sudden expression of a large concentration of Alu elements from the disrupted inactive X can compete with RNA transcripts containing intronic Alu sequences that normally maintain nucleolar structural integrity. Such disruption of nucleolar activity can lead to misfolded RNAs, misassembled ribonucleoprotein complexes, and fragmentation of the nucleolus. Many autoantigens in lupus are, at least transiently, components of the nucleolus. Considering these effects of viruses, the “X chromosome–nucleolus nexus” hypothesis, which proposed disruption of the inactive X by the nucleolus during stress, is now expanded here to propose subsequent disruption of the nucleolus by previously sequestered Alu elements, which can fragment the nucleolus, leading to generation of autoantigens.

Epigenetics and autoimmune diseases: the X chromosome-nucleolus nexus

Autoimmune diseases occur more often in females, suggesting a key role for the X chromosome. X chromosome inactivation, a major epigenetic feature in female cells that provides dosage compensation of X-linked genes to avoid overexpression, presents special vulnerabilities that can contribute to the disease process. Disruption of X inactivation can result in loss of dosage compensation with expression from previously sequestered genes, imbalance of gene products, and altered endogenous material out of normal epigenetic context. In addition, the human X has significant differences compared to other species and these differences can contribute to the frequency and intensity of the autoimmune disease in humans as well as the types of autoantigens encountered. Here a link is demonstrated between autoimmune diseases, such as systemic lupus erythematosus, and the X chromosome by discussing cases in which typically non-autoimmune disorders complicated with X chromosome abnormalities also present lupus-like symptoms. The discussion is then extended to the reported spatial and temporal associations of the inactive X chromosome with the nucleolus. When frequent episodes of cellular stress occur, the inactive X chromosome may be disrupted and inadvertently become involved in the nucleolar stress response. Development of autoantigens, many of which are at least transiently components of the nucleolus, is then described. Polyamines, which aid in nucleoprotein complex assembly in the nucleolus, increase further during cell stress, and appear to have an important role in the autoimmune disease process. Autoantigenic endogenous material can potentially be stabilized by polyamines. This presents a new paradigm for autoimmune diseases: that many are antigen-driven and the autoantigens originate from altered endogenous material due to episodes of cellular stress that disrupt epigenetic control. This suggests that epigenetics and the X chromosome are important aspects of autoimmune diseases.

The X chromosome and the sex ratio of autoimmunity

The number of human conditions that are currently considered to be autoimmune diseases (AID) has been steadily growing over the past decades and it is now estimated that over 10 million people are affected in the United States. One of the major shared features among AID is the predominance in the female sex which in some cases changes with the age at disease diagnosis. Numerous hypotheses have been formulated based on intuitive scientific backgrounds to justify this sex imbalance, i.e. sex hormones and reproductive factors, fetal microchimerism, other sex-related environmental factors, a skewing of the X-chromosome inactivation patterns, and major defects in sex chromosomes. Nevertheless, none of these hypotheses has thus far gathered enough convincing evidence and in most cases data are conflicting, as well illustrated by the reports on fetal microchimerism in systemic sclerosis or primary biliary cirrhosis. The present article will critically discuss the main hypotheses (loss of mosaicism, reactivation, and haploinsufficiency) that have been proposed based on findings in female patients with specific AID along with two additional mechanisms (X-chromosome vulnerability and X-linked polyamine genes) that have been observed in AID models. Further, recent data have significantly shifted the paradigm of X chromosome inactivation by demonstrating that a large number of genes can variably escape silencing on one or both chromosomes. As a result we may hypothesize that more than one mechanism may contribute to the female susceptibility to tolerance breakdown while the possibility that unknown factors may indeed protect men from AID should not be overlooked.

X chromosome inactivation and autoimmunity

Autoimmune diseases appear to have multiple contributing factors including genetics, epigenetics, environmental factors, and aging. The predominance of females among patients with autoimmune diseases suggests possible involvement of the X chromosome and X chromosome inactivation. X chromosome inactivation is an epigenetic event resulting in multiple levels of control for modulation of the expression of X-linked genes in normal female cells such that there remains only one active X chromosome in the cell. The extent of this control is unique among the chromosomes and has the potential for problems when regulation is disrupted. Here we discuss the X chromosome inactivation process and how the X chromosome and X chromosome inactivation may be involved in development of autoimmune disorders.

Biomarker discovery and visualization in gene expression data with efficient generalized matrix approximations

In most real-world gene expression data sets, there are often multiple sample classes with ordinals, which are categorized into the normal or diseased type. The traditional feature or attribute selection methods consider multiple classes equally without paying attention to the up/down regulation across the normal and diseased types of classes, while the specific gene selection methods particularly consider the differential expressions across the normal and diseased, but ignore the existence of multiple classes. In this paper, to improve the biomarker discovery, we propose to make the best use of these two aspects: the differential expressions (that can be viewed as the domain knowledge of gene expression data) and the multiple classes (that can be viewed as a kind of data set characteristic). Therefore, we simultaneously take into account these two aspects by employing the 1-rank generalized matrix approximations (GMA). Our results show that GMA cannot only improve the accuracy of classifying the samples, but also provide a visualization method to effectively analyze the gene expression data on both genes and samples. Based on the mechanism of matrix approximation, we further propose an algorithm, CBiomarker, to discover compact biomarker by reducing the redundancy.

Targeting Toll-like receptor signaling in plasmacytoid dendritic cells and autoreactive B cells as a therapy for lupus

This review focuses on the role of Toll-like receptors (TLRs) in lupus and on possibilities to treat lupus using TLR modulating inhibitory oligodeoxynucleotides (INH-ODNs). TLRs bridge innate and adaptive immune responses and may play an important role in the pathogenesis of systemic lupus erythematosus. Of particular interest are TLR3, -7, -8, and -9, which are localized intracellularly. These TLRs recognize single-stranded or double-stranded RNA or hypomethylated CpG-DNA. Exposure to higher order CpG-DNA ligands or to immune complexed self-RNA triggers activation of autoreactive B cells and plasmacytoid dendritic cells. INH-ODNs were recently developed that block all downstream signaling events in TLR9-responsive cells. Some of these INH-ODNs can also target TLR7 signaling pathways. Based on their preferential cell reactivity, we classify INH-ODNs into class B and class R. Class B ('broadly reactive') INH-ODNs target a broad range of TLR-expressing cells. Class R ('restricted') INH-ODNs easily form DNA duplexes or higher order structures, and are preferentially recognized by autoreactive B cells and plasmacytoid dendritic cells, rather than by non-DNA specific follicular B cells. Both classes of INH-ODNs can block animal lupus. Hence, therapeutic application of these novel INH-ODNs in human lupus, particularly class R INH-ODNs, may result in more selective and disease-specific immunosuppression.

Toll-like receptors, endogenous ligands, and systemic autoimmune disease

The critical role of Toll-like receptors (TLRs) as mediators of pathogen recognition by the innate immune system is now firmly established. Such recognition results in the initiation of an inflammatory immune response and subsequent instruction of the adaptive immune system, both of which are designed to rid the host of the invading pathogen. More controversial is the potential role of TLRs in the recognition of endogenous ligands and what effect this might have on the consequent development of autoimmune or other chronic sterile inflammatory disorders. An increasing number of studies implicate TLRs as being involved in the immune response to self-molecules that have in some way been altered from their native state or accumulate in non-physiologic sites or amounts, although questions have been raised about possible contaminants in certain of these studies. In this review, we discuss the evidence for endogenous ligand-TLR interactions with particular emphasis on mammalian chromatin, systemic lupus erythematosus, and atherosclerosis. Overall, the data support the general concept of a role for TLRs in the recognition of endogenous ligands. However, the precise details of the interactions and the extent to which they may contribute to the pathogenesis of human disease remain to be clarified.

Autoimmune disorders result from loss of epigenetic control following chromosome damage

Multiple sclerosis, systemic lupus erythematosus, and rheumatoid arthritis share common features in typical cases such as: adult onset, central nervous system problems, female predominance, episodes triggered by a variety of stresses, and an autoimmune reaction. At times, the different disorders are found in the same patient or close relatives. These disorders are quite complex but they may share a common mechanism that results in different, tissue-specific consequences based on the cell types in which the mechanism occurs. Here, it is hypothesized that DNA damage can lead to loss of epigenetic control, particularly when the damaged chromatin is distributed unevenly to daughter cells. Expression of genes and pseudogenes that have lost their epigenetic restraints can lead to autoimmune disorders. Loss of control of genes on the X chromosome and loss of control of polyamine expression are discussed as examples of this mechanism.

The stimulation of Toll-like receptors by nuclear antigens: a link between apoptosis and autoimmunity

As immunologists have long understood, effective responses to foreign antigens require adjuvants. It is now apparent that the initiation of autoimmune disease is comparably facilitated by adjuvant activity. In the case of antinuclear antibodies, it seems that DNA itself can serve as an endogenous adjuvant. Similar to many of the microbial adjuvants, mammalian DNA mediates its effect through a Toll-like receptor--in this case, TLR9.

Calculating the etiology of systemic lupus erythematosus

Objective was to clarify the etiology and pathogenesis of systemic lupus erythematosus (SLE). Drug-induced lupus (DIL) and SLE are both found in humans, are exacerbated by the same viruses or drugs, and they are both more common in slow acetylators. Thus, DIL can be used as a model for SLE and the Adhami equation of DIL can be applied to SLE. Polyamines are the only possible link between the viral and amine hypotheses of SLE pathogenesis. Based on the Adhami equation, polyamines can explain the actual annual incidence of SLE in the general population. Putrescine is a very weak SLE-causing agent, while spermine and spermidine contribute equally in triggering SLE. The positively charged polyamines bind to negatively charged internucleosomal DNA and change its conformation from B (non-immunogenic) to Z (immunogenic). This is the major contribution of polyamines in triggering SLE. The other effects of polyamines are only secondary. Apoptosis is a necessary step in SLE pathogenesis, because it causes the internucleosomal fragmentation of DNA and exposes Z-DNA to the immune system (due to cell death). The next step is the production of anti-DNA antibodies, followed by other SLE phenomena. Polyamines not only cause SLE, but they are also important in sustaining the disease. Other endogenous and exogenous amines have additive effects with polyamines and may contribute in exacerbating SLE. When SLE is in the active phase, polyamine levels are higher as compared to remissions. Fluctuations in polyamine levels due to diet, metabolic factors, infections, intestinal flora, etc. or the presence of other amines may explain the course of SLE, characterized by remissions and exacerbations. Acetylcysteine is a drug that can be completely metabolized to acetyl groups. As such, this drug is proposed as the ideal acetyl donor for the acetylation of polyamines and other SLE-triggering compounds. Clinical trials will be necessary to test the role of acetylcysteine in the etiologic treatment of SLE.

CONCLUSIONS

Changes in DNA conformation by polyamines are the first step in SLE pathogenesis. Many genetic and environmental factors may increase or decrease the effects or levels of polyamines, causing SLE exacerbations or remissions. Viruses and other infectious agents may cause SLE by producing polyamines or by increasing the levels of endogenous polyamines. The major autoimmune diseases are characterized by remissions and exacerbations and not by a continuously progressive course, as commonly believed. Consequently, they are not sustained by internal vicious cycles, but by the initial triggering agent(s). While the conventional treatment of autoimmune disorders is important in minimizing tissue damage, the neutralization of their etiology may be important in curing and preventing autoimmunity.