Expression of long non-coding RNAs in autoimmunity and linkage to enhancer function and autoimmune disease risk genetic variants.

Genome-wide association studies have identified numerous genetic variants conferring autoimmune disease risk. Most of these genetic variants lie outside protein-coding genes hampering mechanistic explorations. Numerous mRNAs are also differentially expressed in autoimmune disease but their regulation is also unclear. The majority of the human genome is transcribed yet its biologic significance is incompletely understood. We performed whole genome RNA-sequencing [RNA-seq] to categorize expression of mRNAs, known and novel long non-coding RNAs [lncRNAs] in leukocytes from subjects with autoimmune disease and identified annotated and novel lncRNAs differentially expressed across multiple disorders. We found that loci transcribing novel lncRNAs were not randomly distributed across the genome but co-localized with leukocyte transcriptional enhancers, especially super-enhancers, and near genetic variants associated with autoimmune disease risk. We propose that alterations in enhancer function, including lncRNA expression, produced by genetics and environment, change cellular phenotypes contributing to disease risk and pathogenesis and represent attractive therapeutic targets.

Reciprocal regulation of Rag expression in thymocytes by the zinc-finger proteins, Zfp608 and Zfp609.

Recombination-activating gene 1 (Rag1) and Rag2 enzymes are required for T cell receptor assembly and thymocyte development. The mechanisms underlying the transcriptional activation and repression of Rag1 and Rag2 are incompletely understood. The zinc-finger protein, Zfp608, represses Rag1 and Rag2 expression when expressed in thymocytes blocking T-cell maturation. Here we show that the related zinc-finger protein, Zfp609, is necessary for Rag1 and Rag2 expression in developing thymocytes. Zfp608 represses Rag1 and Rag2 expression indirectly by repressing the expression of Zfp609. Thus, the balance of Zfp608 and Zfp609 plays a critical role in regulating Rag1 and Rag2 expression, which may manifest itself not only during development of immature thymocytes into mature T cells but also in generation of the T-cell arm of the adaptive immune system, which does not fully develop until after birth.

Lineage-specific adjacent IFNG and IL26 genes share a common distal enhancer element.

Certain groups of physically linked genes remain linked over long periods of evolutionary time. The general view is that such evolutionary conservation confers 'fitness' to the species. Why gene order confers 'fitness' to the species is incompletely understood. For example, linkage of IL26 and IFNG is preserved over evolutionary time yet Th17 lineages express IL26 and Th1 lineages express IFNG. We considered the hypothesis that distal enhancer elements may be shared between adjacent genes, which would require linkage be maintained in evolution. We test this hypothesis using a bacterial artificial chromosome transgenic model with deletions of specific conserved non-coding sequences. We identify one enhancer element uniquely required for IL26 expression but not for IFNG expression. We identify a second enhancer element positioned between IL26 and IFNG required for both IL26 and IFNG expression. One function of this enhancer is to facilitate recruitment of RNA polymerase II to promoters of both genes. Thus, sharing of distal enhancers between adjacent genes may contribute to evolutionary preservation of gene order.

Gene-expression signatures: biomarkers toward diagnosing multiple sclerosis.

Identification of biomarkers contributing to disease diagnosis, classification or prognosis could be of considerable utility. For example, primary methods to diagnose multiple sclerosis (MS) include magnetic resonance imaging and detection of immunological abnormalities in cerebrospinal fluid. We determined whether gene-expression differences in blood discriminated MS subjects from comparator groups, and identified panels of ratios that performed with varying degrees of accuracy depending upon complexity of comparator groups. High levels of overall accuracy were achieved by comparing MS with homogeneous comparator groups. Overall accuracy was compromised when MS was compared with a heterogeneous comparator group. Results, validated in independent cohorts, indicate that gene-expression differences in blood accurately exclude or include a diagnosis of MS and suggest that these approaches may provide clinically useful prediction of MS.

Peripheral blood gene expression profiles in metabolic syndrome, coronary artery disease and type 2 diabetes.

To determine if individuals with metabolic disorders possess unique gene expression profiles, we compared transcript levels in peripheral blood from patients with coronary artery disease (CAD), type 2 diabetes (T2D) and their precursor state, metabolic syndrome to those of control (CTRL) subjects and subjects with rheumatoid arthritis (RA). The gene expression profile of each metabolic state was distinguishable from CTRLs and correlated with other metabolic states more than with RA. Of note, subjects in the metabolic cohorts overexpressed gene sets that participate in the innate immune response. Genes involved in activation of the pro-inflammatory transcription factor, NF-κB, were overexpressed in CAD whereas genes differentially expressed in T2D have key roles in T-cell activation and signaling. Reverse transcriptase PCR validation confirmed microarray results. Furthermore, several genes differentially expressed in human metabolic disorders have been previously shown to participate in inflammatory responses in murine models of obesity and T2D. Taken together, these data demonstrate that peripheral blood from individuals with metabolic disorders display overlapping and non-overlapping patterns of gene expression indicative of unique, underlying immune processes.

Inhibition of tumor cell growth by interferon-gamma is mediated by two distinct mechanisms dependent upon oxygen tension: induction of tryptophan degradation and depletion of intracellular nicotinamide adenine dinucleotide.

Growth of a variety of human tumor cell lines is inhibited by interferon-gamma (IFN-gamma) in vitro. This mechanism is not well understood. The present experiments identify two separate mechanisms which account for the growth inhibitory activity of IFN-gamma. Cell lines most sensitive to IFN-gamma (inhibited by 10-30 U/ml IFN-gamma in 3 d) were stimulated by IFN-gamma to oxidize tryptophan in media to kynurenine and completely eliminated tryptophan from the culture media after 48-72 h. Addition of L-tryptophan, but not other aromatic amino acids, other essential amino acids, or D-tryptophan, prevented inhibition of cell growth by IFN-gamma. The amount of IFN-gamma required to yield 50% inhibition of cell growth was directly related to the concentration of L-tryptophan in culture media and increased from approximately 3 to 600 U/ml as the concentration of tryptophan in the media was increased from 25 to 1,000 microM. By contrast, inhibition of growth of the cell lines, BT20 and HT29, was not prevented by addition of tryptophan. Inhibition by IFN-gamma (100-300 U/ml after 5-6 d) was, however, completely prevented by addition of two inhibitors of adenosine diphosphate-ribosyl transferase (ADP-RT), 3-aminobenzamide or nicotinamide. Activity of ADP-RT was increased in these cell lines after addition of IFN-gamma. ADP-RT catalyzes the incorporation of the ADP moiety of nicotinamide adenine dinucleotide (NAD) into proteins and causes depletion of intracellular NAD. All tumor cell lines tested had reduced levels of intracellular NAD after treatment with IFN-gamma and loss of NAD preceded inhibition of cell growth by 12-24 h. Inhibitors of IFN-gamma-mediated inhibition of cell growth prevented loss of levels of intracellular NAD. Generation of reactive oxygen species lead to DNA strand breaks which result in activation of ADP-RT. Increased DNA strand breaks were induced in BT20 and HT29 cells but not ME180 and A549 cells after culture with IFN-gamma. The two enzymes known to catalyze the decyclization of tryptophan to kynurenine require superoxide anion for activity. Increased amounts of superoxide anion were released from ME180 and A549 cells after culture with IFN-gamma. Reduced oxygen concentration decreased the ability of IFN-gamma to inhibit tumor cell growth in vitro. Intracellular glutathione has been shown to protect cells against oxidative damage by various agents. Elevation or reduction of intracellular glutathione concentrations lowered or raised sensitivity of cell lines to IFN-gamma, respectively. These data indicate that at least two distinct mechanisms can account for IFN-gamma-madiated inhibition of tumor cell growth. Both mechanisms appear to be sensitive to oxygen tension and to changes in intracellular glutathione concentrations, and both mechanisms lead to loss of intracellular NAD.

Steroid-sensitive mechanism of soluble immune response suppressor production in steroid-responsive nephrotic syndrome.

Soluble immune response suppressor (SIRS), a lymphokine that suppresses antibody production and delayed type hypersensitivity in vivo, has been detected in urine and serum from certain patients with nephrotic syndrome. In the present paper, the relationship between SIRS production and nephrotic syndrome is further characterized. A striking correlation was found between detection of SIRS and the presence of steroid-responsive nephrotic syndrome (SRNS). A potential mechanism of SIRS production in SRNS patients was identified, in that lymphocytes from patients produced SIRS without requiring activation by exogenous agents, and incubation of normal lymphocytes with serum from patients activated the cells to secrete SIRS in culture. Although SIRS disappears rapidly from urine or serum after initiation of corticosteroid therapy, hydrocortisone (10(-6)-10(-7) M) did not block secretion of SIRS by activated suppressor cells. It did, however, inhibit in vitro activation of lymphocytes to produce SIRS by concanavalin A, interferon, or SRNS patient serum. The association of suppressor cell activation with SRNS and the sensitivity of both to steroids suggest that the pathogeneses of albuminuria and SIRS production are related.

Identification of the lymphokine soluble immune response suppressor in urine of nephrotic children.

Patients with minimal change nephrotic syndrome (MCNS) frequently have suppressed in vivo and in vitro immune responsiveness of uncertain etiology. Because increased suppressor cell activity has been associated with this disease, urines from MCNS patients were screened for activity of the lymphokine soluble immune response suppressor (SIRS), a product of concanavalin A- or interferon-activated suppressor T cells. Urines from untreated MCNS patients suppressed polyclonal plaque-forming cell responses of cultured splenocytes. This suppressive activity was identified as human SIRS by the following functional and physical criteria: molecular weight estimated by gel filtration; kinetics of suppression; inhibition of suppression by catalase, levamisole, and 2-mercaptoethanol; abrogation of activity by acid or protease treatment; elution pattern on high performance liquid chromatography; and cross-reactivity with monoclonal antimurine SIRS antibodies. Suppressive activity disappeared from urine after initiation of treatment but before remission of symptoms. Urines were tested from 11 patients with MCNS, all of whom excreted SIRS. In addition, two nephrotic patients with acute glomerulonephritis and three nephrotic patients with membranoproliferative disease excreted SIRS, but other nephrotics and all nonnephrotic patients did not. These results indicate that excretion of SIRS occurs in certain cases of nephrotic syndrome and that the presence of SIRS in the urine is not accounted for solely by the presence of proteinuria or nephrosis. Serum from four nephrotic patients also contained SIRS, whereas neither serum nor urine from six normal subjects contained SIRS activity. The systemic presence of SIRS in these four patients, and the identification of SIRS in urines from a larger group of patients, suggest a possible role for SIRS in the suppressed immune responses often found in nephrotic syndrome.

Differential transcription directed by discrete gamma interferon promoter elements in naive and memory (effector) CD4 T cells and CD8 T cells.

Acquisition of the ability to produce gamma interferon (IFN-gamma) is a fundamental property of memory T cells and enables one subset (T helper 1 [TH1]) to deliver its effector functions. To examine regulation of IFN-gamma gene expression in a model system which recapitulates TH1 differentiation, we prepared reporter transgenic mice which express the luciferase gene under the control of proximal and distal regulatory elements (prox.IFN gamma and dist.IFN gamma) from the IFN-gamma promoter. Memory T cells, but not naive T cells, secreted IFN-gamma and expressed both prox.IFN gamma and dist.IFN gamma transcriptional activities. Naive T cells required priming to become producers of IFN-gamma and to direct transcription by these elements. While both CD4+ and CD8+ T cells produced IFN-gamma, only CD4+ T cells expressed prox.IFN gamma transcriptional activity. Induction of transcriptional activity was inhibited by known antagonists of effector T-cell populations. Cyclosporin A inhibited transcriptional activity directed by both elements in effector T cells. Elevated cyclic AMP inhibited transcriptional activity directed by prox.IFN gamma in primed CD4+ T cells but enhanced transcriptional activity directed by dist.IFN gamma in primed CD8+ T cells. Taken together, these data show that prox.IFN gamma and dist.IFN gamma transcriptional activities mirror IFN-gamma gene expression in naive and memory CD4+ T cells but suggest that differences exist in regulation of IFN-gamma gene expression in CD4+ and CD8+ T-cell subsets.

Role and function of antigen nonspecific suppressor factors.

Although antigen-nonspecific suppressor factors described by various investigators appear to exhibit a certain amount of heterogeneity in both physical and biological properties, these proteins also exhibit significant similarities. Nonspecific suppressor factors are generally produced by Ly 2+ (murine) or OKT8+ (human) T lymphocytes. One protein, soluble immune response suppressor (SIRS), is produced by T lymphocytes after incubation with mitogens, interferons, or histamine, and must be activated by peroxides to inhibit cell division or immune function. SIRS appears to inhibit cell division by causing oxidation of a portion of cellular protein sylfhydryls and, in particular, causes a decrease in intracellular levels of deoxyribonucleotide triphosphates. This decrease is readily reversed by sulhydryl reducing agents, such as 2-mercaptoethanol. The activity of SIRS and other suppressor factors is inhibited by growth factors, such as interleukin 2, and the activity of interleukin 2 is inhibited by antigen-nonspecific suppressor factors. Further, SIRS or SIRS-like proteins are produced during various diseases associated with suppressed immune responsiveness including acquired immune deficiency syndrome, schistosomiasis, and nephrotic syndrome. These data suggest that antigen-nonspecific suppressor factors may have an important physiological role in regulating immune responses and cell division in general.

Cell contact between T cells and synovial fibroblasts causes induction of adhesion molecules and cytokines.

Human activated T cells adhere to synovial fibroblast-like cells in vitro. The present study was conducted to investigate the consequences of T cell-synovial fibroblast interactions with regard to induction of adhesion molecules and proinflammatory cytokines. A sensitive Western blot technique, polymerase chain reaction (PCR) amplification, and fluorescence-activated cell sorter (FACS) analysis were used to analyze the induction of VCAM-1 and ICAM-1 expression in T cell-synovial fibroblast cocultures. VCAM-1 and ICAM-1 expression could be induced in synovial fibroblast-like cells by 2 h. PCR amplification showed that both forms of VCAM-1 mRNA are found after the interaction of synovial fibroblasts with T cells. Up-regulation of VCAM-1 and ICAM-1 was confined to synovial fibroblasts; T cells did not express VCAM-1 or increased ICAM-1. In contrast to the T cell-synoviocyte interaction, the interaction between T cells and dermal fibroblasts resulted in the up-regulation of ICAM-1 but not VCAM-1, suggesting tissue-specific regulation of VCAM-1. The T cell-synovial fibroblast interaction also resulted in increased levels of tumor necrosis factor (TNF), interferon-gamma, and interleukin-6 in coculture supernatant. Of the neutralizing antibodies used against these cytokines, only anti-TNF could significantly inhibit VCAM-1 and ICAM-1 expression. When T cells were separated from synoviocytes by a chamber that allowed medium exchange but no cell contact, VCAM-1 and ICAM-1 failed to be up-regulated and cytokine accumulation in cocultures was drastically reduced. Our results demonstrate mutual cell activation of T cells and synoviocytes upon cell contact as shown by the release of T cell- and synoviocyte-specific cytokines and suggest a cell contact-mediated and T cell-initiated mechanism for the chronic accumulation and retention of mononuclear cells via VCAM-1/ICAM-1 by synovial fibroblasts in the rheumatoid synovium.

Transcriptional reprogramming during T helper cell differentiation.

Our laboratory employs reporter transgenic mice as model systems to study the transcriptional reprogramming that accompanies T helper cell differentiation. These studies demonstrate that changes in the activity of simple transcriptional elements associated with the IFN-gamma gene can recapitulate alterations in gene expression. In addition, our studies have revealed a key role for the transcription factor, CAMP response element binding protein (CREB), in the protection of differentiating T cells from apoptosis. Together, these findings further our understanding of the logic employed by T cells to alter gene expression profiles in response to differentiation signals.

ELISA for the detection of the lymphokine soluble immune response suppressor.

Murine soluble immune response suppressor (SIRS) is a product of Ly 2+ suppressor T cells which is activated to SIRSox by peroxide produced by macrophages. SIRSox inhibits cell division by normal and transformed cell lines and antibody secretion by B lymphocytes. Rat monoclonal anti-SIRS antibodies were developed to determine if ELISA methodology could replace bioassays for quantitation of SIRS in biological samples. Purified SIRS, applied to nitrocellulose, was detected with an avidin-biotin-horseradish peroxidase system. This ELISA was capable of detecting pg quantities of SIRS and detected SIRS after fractionation by high performance liquid chromatography. However, SIRS in crude supernatant fluids was undetectable by this method, presumably due to the small percentage of SIRS protein in relation to total protein in these samples. Thus, a competitive ELISA was adopted which, in initial experiments, detected SIRS in impure sources. This competitive ELISA may be useful in evaluating the presence or absence of SIRS in various biological samples.

Preparation of soluble immune response suppressor and macrophage-derived suppressor factor.

Concanavalin A-activated murine suppressor T cells act via the mediator, soluble immune response suppressor (SIRS) which non-specifically suppresses IgM and IgG antibody responses to a variety of antigens, cytotoxic T lymphocyte responses and proliferative responses to alloantigens and mitogens in vitro. SIRS is a protein with an apparent MW of 45,000-55,000; the target of SIRS is the macrophage (M phi). M phi following treatment with SIRS release a second factor, M phi-derived suppressor factor (M phi-SF), which is directly responsible for the observed suppression of responses. Moreover. M phi-SF appears to be modified SIRS by all criteria used to date; M phi-SF can be obtained by reacting SIRS with low concentrations of H2O2 in the absence of M phi. Thus, M phi appear to serve only as a source of H2O2 and the mechanism of M phi-SF action action appears to have an oxidative basis. M phi-SF activity is lost following treatment with sulfhydryl reagents such as 2-mercaptoethanol, dithiothreitol or cysteine, reducing agents such as NaBH4 and a variety of peroxidase substrates such as pyrogallol, phenylenediamine, and ascorbic acid. Additionally, M phi-SF-mediated inhibition can be reversed by high concentrations of 2 mercaptoethanol or dithiothreitol under appropriate conditions. Since M phi-SF appears to be modified SIRS, oxidized by peroxide, and not a distinct second mediator produced by M phi in response to SIRS, we propose eliminating the term M phi-SF and using SIRSox to denote the active form of SIRS produced either by the SIRS-H2O2 reaction or SIRS-treated M phi.

Selective matrix attachment regions in T helper cell subsets support loop conformation in the Ifng gene.

Cytokine genes undergo progressive changes in chromatin organization when naïve CD4+ T helper (Th) cells differentiate into committed Th1 and Th2 lineages. Here, we analyzed nuclear matrix attachment regions (MARs) in the Ifng gene by DNA array technique in unactivated and activated CD4+ Th cells. This approach was combined with analysis of spatial organization of the Ifng gene by chromosome conformation capture approach to assess the relationship between the gene conformation and matrix attachment organization in functionally different cell subsets. We report that the Ifng gene in unactivated cells displays a linear conformation, but in T-cell receptor-activated cells, it adopts a loop conformation. The selective MARs support the spatial gene organization and characteristically define the Ifng gene in functionally different cell subsets. The pattern of interaction of the Ifng gene with the nuclear matrix dynamically changes in a lineage-specific manner in parallel with the changes in Ifng gene conformation. The data suggest that such structural dynamics provide the means for transcriptional regulation of the Ifng gene in the course of activation and differentiation of CD4+Th cells.

Deregulated stress system in non-obese diabetic lymphocyte.

Lymphopenia-induced homeostatic expansion in non-obese diabetic (NOD) mice may lead to autoimmunity. We demonstrated that NOD lymphocytes are more susceptible to apoptosis than those of non-diabetic C57BL/6 or NOD.H2(h4) mice in vivo and in vitro, which may be an underlying mechanism causing lymphopenia in NOD mice. Gene expression profiling identified a set of genes that are differentially expressed between NOD and B6 mice. Identity of these genes suggested that NOD T cells have a deregulated stress response system, especially heat-shock protein family, making them overly sensitive to apoptosis. Thus, we hypothesize that this strain-specific gene expression profile may confer a liability upon NOD T cells making them more susceptible to apoptosis that may lead to lymphopenia in NOD mice and contribute to development of autoimmunity.

Highly conserved gene expression profiles in humans with allergic rhinitis altered by immunotherapy.

BACKGROUND: Atopic diseases, resulting from hypersensitivity to a wide variety of allergens, affect 10-20% of the population. Immunotherapy is an effective treatment for atopic diseases, but its mechanisms are not fully understood. OBJECTIVE: We studied gene expression profiles in the peripheral blood mononuclear cells (PBMC) and examined whether the individuals with allergic rhinitis (AR) have a unique gene expression profile and how the immunotherapy affect the gene expression profiles. METHODS: We used cDNA microarray and 'expression analysis systemic explorer' to examine the gene expression profiles in the PBMC of atopic subjects and other groups. RESULTS: We identified a highly conserved gene expression profile in atopic subjects that permitted their accurate segregation from control or autoimmune subjects. A major feature of this profile was the under-expression of a variety of genes that encode proteins required for apoptosis and over-expression of genes that encode proteins critical for stress responses and signal transduction. We also identified 563 genes that can segregate individuals with AR based upon receipt of immunotherapy. CONCLUSION: There is a highly conserved gene expression profile in the PBMC of individuals with AR. This profile can be used to identify individuals with AR and to evaluate responses to immunotherapy. Quantitative endpoints, such as gene expression, may assist clinicians faced with clinical decisions in the diagnosis of patients and the evaluation of response to therapy. The knowledge of the possible genetic basis for immunotherapy efficacy may also lead to novel therapeutic approaches for atopic diseases.

Modification of cellular protein sulfhydryl groups by activated soluble immune response suppressor.

Soluble immune response suppressor (SIRS), a product of murine Ly-2+ T lymphocytes, is activated to SIRSox by H2O2 produced by macrophages: SIRSox directly inhibits cell division by normal and neoplastic cells and antibody secretion by B lymphocytes. To examine the mechanism of SIRSox-mediated inhibition, a variety of cellular functions were measured after treatment of cells with SIRSox. These included respiration, glucose transport, microtubule content, glutathione content, production of H2O2 or superoxide anion, and the activities of a variety of different enzymes. Several cellular activities or measurements were inhibited or lowered after SIRSox-treatment, including cell division, microtubule content, glutathione reductase activity, and thioredoxin reductase activity; inhibition was partially reversed by the sulfhydryl reducing agent dithiothreitol. Protein sulfhydryl content of P815 mastocytoma cells and several other cell types was lowered by 35 to 45% after exposure to SIRSox. Protein sulfhydryl loss was also partially restored after incubation with dithiothreitol. Sulfhydryl loss was not due to cell lysis. In addition, treatment of crude cellular particulate fractions with SIRSox resulted in protein sulfhydryl loss and formation of protein sulfenyl derivatives. A comparison of the amount of SIRS and H2O2 present to the number of protein sulfhydryls lost or sulfenyl derivatives formed suggests that SIRSox acts catalytically, serves as a co-factor in protein sulfhydryl oxidation, or that it activates a second pathway that is directly responsible for sulfhydryl oxidation.

Two different pathways of interferon mediated suppression of antibody secretion.

Interferon suppresses a variety of in vitro immune responses by a mechanism which has not been well defined. Both direct suppression and activation of suppressor T cells have been suggested as possible mechanisms of interferon action. In an attempt to examine this question interferon-alpha (IFN alpha)-mediated suppression of a plaque forming cell response to a T cell independent antigen by spleen cells or by B cells was examined. Somewhat greater quantities of IFN alpha were required to suppress plaque forming cell responses by B cells than by spleen cells to the antigen fluoresceinated-Brucella abortus (FITC-BA). However, suppression of spleen cell responses could be blocked by addition of either 2-mercaptoethanol, levamisole or monoclonal antibodies against the lymphokine, soluble immune response suppressor (SIRS), whereas suppression of B cell responses by interferon-alpha was unaffected by these agents. Each of these agents interferes with SIRS mediated suppression of immune responses. Addition of T cells to B cell cultures stimulated with FITC-BA did not affect the total plaque forming cell response nor the extent of suppression by IFN alpha, but it did restore 2-mercaptoethanol sensitivity to IFN alpha-mediated suppression. As few as 1 X 10(5) T cells were effective and it was necessary to add T cells within 3 h of addition of IFN alpha to confer 2-mercaptoethanol sensitivity to IFN alpha mediated suppression. These data suggest that IFN alpha can suppress immune responses by two different pathways and that in the presence of T cells, activation of suppressor T cells is the dominant pathway. The presence of T cells must also prevent direct suppression of B cells by IFN alpha.