Profiling the Gut Microbiome Unraveled Signature Bacterial Groups in Autoimmune Diabetes, which Remain Unperturbed by the Low Ionic Strength of the Drinking Water in NOD mice.

BACKGROUND: Non-obese diabetic (NOD) mice develop type 1 diabetes (T1D) spontaneously and serve as a good model for investigating the underlying pathological mechanisms and devising novel treatment procedures. Although acid water consumption has been reported to exaggerate or reduce diabetes incidence in female NOD mice by two groups, the causative bacteria responsible for these contrasting changes remain unclear. On the contrary, we and others failed to observe the effect of acid water consumption on diabetes incidence. This study aimed to determine whether the consumption of low-pH drinking water could alter the frequencies of prominent bacterial groups independent of diabetes manifestation. METHODS: Six-week-old female NOD mice maintained on acidified drinking water at the Jackson Laboratories were transferred to neutral pH water or continuously provided with low pH drinking water at our facility. Diabetes was monitored weekly using a glucometer. Using the 454-pyrosequencing methodology, we profiled the gut microbiome of mice transferred to neutral water and developed diabetes. Further, we performed quantitative real-time polymerase chain reactions (qRT-PCR) using primers specific for prominent 16S rRNA genes on the fecal DNA of mice provided with low pH or neutral water and displayed diabetes similarly. RESULTS: Consistent with our earlier report, the incidence of T1D was robust (80-100%) regardless of whether female NOD mice consumed acid (~pH 2.9) or neutral water. The 454-pyrosequencing of fecal DNA indicated no substantial influence of transferring mice to neutral pH drinking water on the gut microbiome. To validate these findings, we conducted qRT-PCR on the fecal DNA of mice longitudinally from six weeks of age to adulthood that consumed acidic or neutral pH water and developed diabetes similarly. Among the 15 selected bacterial groups examined, the frequency of Lactobacillus sp. remained consistently lower (p < 0.05) throughout the life of NOD mice compared to that found in young (6-week-old) mice, regardless of the pH of the drinking water. The relative frequencies of the Firmicutes Ruminococcaceae and the Bactereoidetes members Anaerophaga sp. and Paludibacter sp. increased significantly (p < 0.05) during the transition to the overtly diabetic stage irrespective of the ionic strength of the drinking water. Interestingly, the Firmicutes members Clostridium coccoides, C. leptum, and Lachnospiraceae and the Bacteroidetes members Bacteroides sp. and Prevottella sp. remained unchanged throughout the analysis irrespective of the pH of the drinking water. Paradoxically, the representations of Akkermansia muciniphila and the segmented filamentous bacteria implicated in diabetes protection did not differ regardless of the age or the ionic strength of the drinking water. CONCLUSIONS: The data presented herein validate the lack of influence of acidic drinking water on T1D development in female NOD mice. Diabetes was associated with the lower representation of Lactobacillus sp. throughout life, which was not influenced by the differing pH of the drinking water. Significantly, segmented filamentous bacteria and A. muciniphila, previously implicated in protection against T1D, were not perturbed by the varying pH of the water consumed. These data indicate that although acidified water consumption was reported previously to diminish specific gastrointestinal pathogens, it failed to perturb gut commensals that influence diabetes development.

Impact of histone modifier-induced protection against autoimmune encephalomyelitis on multiple sclerosis treatment.

Multiple sclerosis is a progressive demyelinating central nervous system disorder with unknown etiology. The condition has heterogeneous presentations, including relapsing-remitting multiple sclerosis and secondary and primary progressive multiple sclerosis. The genetic and epigenetic mechanisms underlying these various forms of multiple sclerosis remain elusive. Many disease-modifying therapies approved for multiple sclerosis are broad-spectrum immunomodulatory drugs that reduce relapses but do not halt the disease progression or neuroaxonal damage. Some are also associated with many severe side effects, including fatalities. Improvements in disease-modifying treatments especially for primary progressive multiple sclerosis remain an unmet need. Several experimental animal models are available to decipher the mechanisms involved in multiple sclerosis. These models help us decipher the advantages and limitations of novel disease-modifying therapies for multiple sclerosis.

Epigenetic drug ameliorated type 1 diabetes via decreased generation of Th1 and Th17 subsets and restoration of self-tolerance in CD4+ T cells.

Female NOD mice develop autoimmune diabetes spontaneously without extrinsic manipulation. Previously, we have shown that weekly administration of the prediabetic female NOD mice with the histone modifier Trichostatin A (TSA) prevented diabetes onset. Herein we show that T lymphocytes from diabetic mice transferred diabetes into immunodeficient NOD.scid recipients while those isolated from drug-treated mice displayed reduced disease-causing ability. Drug treatment also repressed T cell receptor-mediated IFN-γ transcription. Splenic CD4+ T-cells purified from prediabetic mice could be polarized into IFN-γ -producing Th1 and IL-17A-expressing Th17 subsets ex vivo. Adoptive transfer of these cells into immunocompromised NOD.scid mice caused diabetes comparably. Polarized Th1 cells were devoid of IL-17A-producing cells and did not transdifferentiate into Th17 cells in the spleen of immunodeficient recipients. However, polarized Th17 cell preparation had a few contaminant Th1 cells. Adoptive transfer of polarized Th17 cells into NOD.scid recipients led to IFN-γ transcription in recipient splenocytes. Notably, TSA treatment of prediabetic mice abolished the ability of CD4+ T-cells to differentiate into diabetogenic Th1 and Th17 cells ex vivo. This was accompanied by the absence of Ifng and Il17a transcription in the spleen of NOD.scid recipients receiving cells, respectively cultured under Th1 and Th17 polarizing conditions. Significantly, the histone modifier restored the ability of CD4+ but not CD8+ T-cells to undergo CD3-mediated apoptosis ex vivo in a caspase-dependent manner. These results indicate that the histone modifier bestowed protection against type 1 diabetes via negative regulation of signature lymphokines and restitution of self-tolerance in CD4+ T cells.

Histone Modifier Differentially Regulates Gene Expression and Unravels Survival Role of MicroRNA-494 in Jurkat Leukemia.

BACKGROUND: Although the protein-coding genes are subject to histone hyperacetylation- mediated regulation, it is unclear whether microRNAs are similarly regulated in the T cell leukemia Jurkat. OBJECTIVE: To determine whether treatment with the histone modifier Trichostatin A could concurrently alter the expression profiles of microRNAs and protein-coding genes. METHODS: Changes in histone hyperacetylation and viability in response to drug treatment were analyzed, respectively, using western blotting and flow cytometry. Paired global expression profiling of microRNAs and coding genes was performed and highly regulated genes have been validated by qRT-PCR. The interrelationships between the drug-induced miR-494 upregulation, the expression of putative target genes, and T cell receptor-mediated apoptosis were evaluated using qRT-PCR, flow cytometry, and western blotting following lipid-mediated transfection with specific anti-microRNA inhibitors. RESULTS: Treatment of Jurkat cells with Trichostatin A resulted in histone hyperacetylation and apoptosis. Global expression profiling indicated prominent upregulation of miR-494 in contrast to differential regulation of many protein-coding and non-coding genes validated by qRT-PCR. Although transfection with synthetic anti-miR-494 inhibitors failed to block drug-induced apoptosis or miR-494 upregulation, it induced the transcriptional repression of the PVRIG gene. Surprisingly, miR-494 inhibition in conjunction with low doses of Trichostatin A enhanced the weak T cell receptor- mediated apoptosis, indicating a subtle pro-survival role of miR-494. Interestingly, this prosurvival effect was overwhelmed by mitogen-mediated T cell activation and higher drug doses, which mediated caspase-dependent apoptosis. CONCLUSION: Our results unravel a pro-survival function of miR-494 and its putative interaction with the PVRIG gene and the apoptotic machinery in Jurkat cells.

Epigenetic modulation of selected immune response genes and altered functions of T lymphocytes and macrophages collectively contribute to autoimmune diabetes protection.

We have previously demonstrated that weekly treatment of female prediabetic NOD mice with a low dose of the histone deacetylase inhibitor Trichostatin A (TSA) bestowed long-lasting, irreversible protection against autoimmune diabetes. Herein we show that drug treatment diminished the infiltration of the pancreas with CD4+, CD8+ T cells, and Ly-6C+ monocytes. Significantly, TSA administration selectively repressed the expression of a set of genes exaggerated during diabetes and constitutively expressed primarily in the spleen and rarely in the pancreas. These genes encode lymphokines, macrophage-associated determinants, and transcription factors. Although the copy numbers of many histone deacetylases increased during diabetes in the spleen and pancreas, only those upregulated in the spleen were rendered sensitive to repression by TSA treatment. Mitogen-activated T lymphocytes derived from drug-treated donors displayed diminished diabetogenic potential following transfer into immunodeficient NOD.scid mice. In the immunocompromised recipients, diabetes caused by the transfer of activated T lymphocytes from untreated diabetic mice was hampered by the co-transfer of highly purified splenic CD11b+Ly-6C+ macrophages from drug-treated mice. However, the transfer of CD11b+Ly-6C+ macrophages from drug-treated mice failed to block ongoing diabetes in wild-type NOD mice. These data demonstrate that the modified gene expression and functional alteration of T lymphocytes and macrophages collectively contribute to diabetes protection afforded by the histone modifier in female NOD mice.

Treatment of autoimmune encephalomyelitis with a histone deacetylase inhibitor.

We have previously shown that treatment of female NOD mice with a potent nonselective histone deacetylase inhibitor attenuated experimental autoimmune encephalomyelitis, a model for progressive multiple sclerosis. Herein we show that immunization with the MOG35-55 peptide induced prolonged upregulation of genes encoding interleukin 17A (IL-17A), aryl hydrocarbon receptor, and histone deacetylase 11 in the spinal cord whereas the subunits of IL-27, IL-27p28 and IL-27ebi3 were significantly increased in secondary lymphoid organs after a lag period. Interestingly, the nitric oxide synthase gene was prominently expressed in both of these anatomic compartments following immunization. Treatment with the histone modifier repressed the transcription of all of these genes induced by immunization. Moreover, the drug suppressed the steady-state levels of the migration inhibitory factor and CD274 genes in both the spinal cord and peripheral lymphoid tissues. At the same time, the CD39 gene was downregulated only in secondary lymphoid organs. Paradoxically, the epigenetic drug enhanced the expression of Declin-1 in the spinal cord, suggesting a protective role in neuronal disease. Immunization profoundly enhanced transcription of the chemokine CCL2 in the secondary lymphoid tissues without a corresponding increase in the translation of CCL2 protein. Histone hyperacetylation neither altered the transcription of CCL2 nor its cognate receptor CCR2 in the central nervous system and peripheral lymphoid tissues. Surprisingly, the drug did not exert modulatory influence on most other immune response-related genes previously implicated in encephalomyelitis. Nevertheless, our data uncover several potential molecular targets for the intervention of experimental autoimmune encephalomyelitis that have implications for the treatment of progressive multiple sclerosis.

DNA hypermethylation does not negatively impact the transcription of the TNF-α gene in an acute T-cell leukemia.

Aims: To better understand the roles of DNA methylation and histone acetylation in the transcription of the TNF-α gene (TNFA) in leukemic T cells. Materials & methods: Methylation levels of cytosine-guanosine dinucleotides (CPGs) were assessed by mass spectrometry. The influence of epigenetic modifiers on DNA methylation and TNFA transcription was also determined. Results: CPG at the 5' promoter region, first exon and first intron of TNFA were hypermethylated in leukemic T cells and not impacted by epigenetic drugs. Activation of the class III histone deacetylases but not inhibitors of DNA methylation or histone deacetylases repressed TNFA transcription. Conclusion: These results lend insights into the impact of epigenetic mechanisms on the TNFA transcription in leukemic T cells.

Long-Term Provision of Acidified Drinking Water Fails to Influence Autoimmune Diabetes and Encephalomyelitis.

Induction of autoimmune diseases is predisposed by background genetics and influenced by environmental factors including diet and infections. Since consumption of acidified drinking water leads to eradication of gastrointestinal pathogens in animals, we tested whether it may also influence the development of autoimmune diseases. The frequency of spontaneously occurring type 1 diabetes in female NOD mice that were maintained on acidified drinking water by the vendor did not alter after switching to neutral water in our facility. In addition, experimentally induced autoimmune encephalomyelitis was also unaffected by the pH of the drinking water. Interestingly, administration of complete Freund's adjuvant alone or emulsified with a neuronal peptide to induce neurodegenerative disease during the prediabetic stage completely prevented the onset of diabetes regardless of the pH of the drinking water. However, exposure to microbial products later in life had only a partial blocking effect on diabetes induction, which was also not influenced by the ionic content of the drinking water. Taken together, these data indicate that the onset of autoimmune diseases is not influenced by the gastrointestinal pathogen-depleting treatment, acidified drinking water. Thus, administration of acidic drinking water does not appear to be an option for treating autoimmune diseases.

Amelioration of progressive autoimmune encephalomyelitis by epigenetic regulation involves selective repression of mature neutrophils during the preclinical phase.

We have recently demonstrated that treatment of NOD mice with the epigenetic drug Trichostatin A (TSA) ameliorated myelin peptide induced progressive experimental autoimmune encephalomyelitis (P-EAE). Protection was accompanied by induction of antigen-specific T-cell tolerance in the periphery and reduced influx of T cells into the spinal cord. In this investigation, we examined whether the epigenetic drug could impact the innate immune system as well. Whereas the mature (MHC class II+) CD11b+Ly-6G+ neutrophils expanded substantially in the peripheral lymphoid compartment during the preclinical phase, the MHC class II+, CD11b+Ly-6C+ mature monocytes increased modestly throughout the disease course. Amelioration of the clinical disease by TSA treatment was accompanied by diminished abundance of CD11b+Ly-6Gdim activated neutrophils in secondary lymphoid organs and their influx into the spinal cord without affecting monocytes. Interestingly, the co-inhibitory ligand CD274+ (PD-L1+) but not CD275+ (ICOS-L+), CD39+ or CD11c+ dendritic cells were decreased in the peripheral lymphoid compartment of drug treated mice. Thus, in addition to myelin-specific T cell tolerance induction observed previously, selective repression of mature neutrophils and PD-L1+ cells is critically involved in the epigenetic regulation of P-EAE.

The epigenetic drug Trichostatin A ameliorates experimental autoimmune encephalomyelitis via T cell tolerance induction and impaired influx of T cells into the spinal cord.

Multiple sclerosis is a T cell mediated chronic demyelinating disease of the central nervous system. Although currently available therapies reduce relapses, they do not facilitate tolerization of myelin antigen-specific T lymphocytes to ensure prolonged protection against multiple sclerosis. Here, we show that treatment of NOD mice with the histone deacetylase inhibitor, Trichostatin A affords robust protection against myelin peptide induced experimental autoimmune encephalomyelitis, a mouse model of multiple sclerosis. Protection was accompanied by histone hyperacetylation, and reduced inflammation and axonal damage in the spinal cord. Drug treatment diminished the generation of CD4+ memory T cells and induced tolerance in CD4+ T cells recognizing the immunizing myelin peptide. During the early immunization period, CD4+ T cells producing GM-CSF+IFN-γ, GM-CSF+IL-17A, as well as those expressing both IL-17A+IFN-γ (double-producers) were detected in the secondary lymphoid organs followed by the appearance of cells producing IFN-γ and GM-CSF. On the other hand, IFN-γ producing Th1 cells appear first in the spinal cord followed by cells producing IL-17A and GM-CSF. Treatment with Trichostatin A substantially reduced the frequencies of all T cells secreting various lymphokines both in the periphery and in the spinal cord. These data indicate that epigenetic modifications induced by histone hyperacetylation facilitates T cell tolerance induction in the periphery leading to reduced migration of T cells to the spinal cord and mitigation of neuronal damage and improved clinical outcome. These results suggest that epigenetic modulation of the genome may similarly offer benefits to multiple sclerosis patients via abrogating the function of encephalitogenic T lymphocytes without exerting severe side effects associated with currently used disease-modifying therapies.

Targeting the metabolic pathway of human colon cancer overcomes resistance to TRAIL-induced apoptosis.

Colon cancer is a leading cause of cancer-related mortality for which targeted therapy is needed; however, trials using apoptosis-inducing ligand monotherapy to overcome resistance to apoptosis have not shown clinical responses. Since colon cancer cells selectively uptake and rapidly metabolize glucose, a property utilized for clinical staging, we investigated mechanisms to alter glucose metabolism in order to selectively target the cancer cells and to overcome evasion of apoptosis. We demonstrate TRAIL (tumor necrosis factor-related apoptosis-inducing ligand) resistance in the majority of human colon cancers tested and utilize the glucose analog 2-deoxy-d-glucose to sensitize TRAIL-resistant gastrointestinal adenocarcinoma cells, and not normal gastrointestinal epithelial cells, to TRAIL-induced apoptosis through enhanced death receptor 5 expression, downstream modulation of MAPK signaling and subsequent miRNA expression modulation by increasing the expression of miR-494 via MEK activation. Further, established human colon cancer xenografts treated with this strategy experience anti-tumor responses. These findings in colon adenocarcinoma support further investigation of manipulation of cellular energetics to selectively overcome resistance to apoptosis and to impart tumor regressions in established colon cancer tumors.

Novel methods of type 1 diabetes treatment.

Type 1 diabetes is an autoimmune disease characterized by the cell-mediated destruction of insulin-producing ß-cells, leading to impaired glucose homeostasis, insulin insufficiency, and other complications. Although classic genetic studies have linked numerous genes to the susceptibility of developing diabetes, the mechanisms by which they influence the disease course remain poorly understood. Epigenetics, inheritable changes in gene expression that occur without accompanying genetic mutation, can both serve as a link between the environment and genetic causes of disease and help explain some of the observed vagaries of diabetes. Elucidation of the epigenetic landscape as it relates to putative treatment modalities is highly warranted. Drugs with histone deacetylase activity are in clinical trials for cancer and certain inflammatory diseases with high safety profiles and they hold similar promise for amelioration of type 1 diabetes with diminished secondary complications. Full-fledged studies on the epigenetics of type 1 diabetes are highly likely to provide novel tools for the manipulation of the disease in the years to come. In this review, epigenetic regulation mediated by small molecular inhibitors of histone deacetylases and their potential for preventing diabetes are discussed. Insights into the nature of the genetic mechanisms unraveled by these studies are also highlighted.

T-bet in the spot light: roles in distinct T-cell fate determination.

The transcription factor T-bet was originally described to be important for the differentiation of the CD4(+) Th1 subset. More recent investigations implicate T-bet in the lineage commitment of a variety of innate immune cells also. The T-bet appears to have a dual role in the immune system. Under certain conditions T-bet provides a beneficial role, whereas the exaggerated expression of T-bet in certain innate lymphoid cells can be detrimental to the host. Therefore, this transcription factor needs to be carefully regulated. The feedback control and the epigenetic mechanisms involved in the expression of T-bet remain to be fully elucidated.

Role of migratory inhibition factor in age-related susceptibility to radiation lung injury via NF-E2-related factor-2 and antioxidant regulation.

Microvascular injury and increased vascular leakage are prominent features of radiation-induced lung injury (RILI), and often follow cancer-associated thoracic irradiation. Our previous studies demonstrated that polymorphisms in the gene (MIF) encoding macrophage migratory inhibition factor (MIF), a multifunctional pleiotropic cytokine, confer susceptibility to acute inflammatory lung injury and increased vascular permeability, particularly in senescent mice. In this study, we exposed wild-type and genetically engineered mif(-/-) mice to 20 Gy single-fraction thoracic radiation to investigate the age-related role of MIF in murine RILI (mice were aged 8 wk, 8 mo, or 16 mo). Relative to 8-week-old mice, decreased MIF was observed in bronchoalveolar lavage fluid and lung tissue of 8- to 16-month-old wild-type mice. In addition, radiated 8- to 16-month-old mif(-/-) mice exhibited significantly decreased bronchoalveolar lavage fluid total antioxidant concentrations with progressive age-related decreases in the nuclear expression of NF-E2-related factor-2 (Nrf2), a transcription factor involved in antioxidant gene up-regulation in response to reactive oxygen species. This was accompanied by decreases in both protein concentrations (NQO1, GCLC, and heme oxygenase-1) and mRNA concentrations (Gpx1, Prdx1, and Txn1) of Nrf2-influenced antioxidant gene targets. In addition, MIF-silenced (short, interfering RNA) human lung endothelial cells failed to express Nrf2 after oxidative (H2O2) challenge, an effect reversed by recombinant MIF administration. However, treatment with an antioxidant (glutathione reduced ester), but not an Nrf2 substrate (N-acetyl cysteine), protected aged mif(-/-) mice from RILI. These findings implicate an important role for MIF in radiation-induced changes in lung-cell antioxidant concentrations via Nrf2, and suggest that MIF may contribute to age-related susceptibility to thoracic radiation.

Transcriptome analysis of epigenetically modulated genome indicates signature genes in manifestation of type 1 diabetes and its prevention in NOD mice.

Classic genetic studies implicated several genes including immune response genes in the risk of developing type 1 diabetes in humans. However, recent evidence including discordant diabetes incidence among monozygotic twins suggested a role for epigenetics in disease manifestation. NOD mice spontaneously develop type 1 diabetes like humans and serve as an excellent model system to study the mechanisms of type 1 diabetes as well as the efficacy of maneuvers to manipulate the disease. Using this preclinical model, we have recently demonstrated that pharmacological inhibition of histone deacetylases can lead to histone hyperacetylation, selective up-regulation of interferon-γ and its transactivator Tbx21/Tbet, and amelioration of autoimmune diabetes. In the current study, we show that chromatin remodeling can render splenocytes incapable of transferring diabetes into immunodeficient NOD.scid mice. To elucidate the underlying mechanisms of drug-mediated protection against type 1 diabetes, we performed global gene expression profiling of splenocytes using high throughput microarray technology. This unbiased transcriptome analysis unraveled the exaggerated expression of a novel set of closely related inflammatory genes in splenocytes of acutely diabetic mice and their repression in mice cured of diabetes by chromatin remodeling. Analysis of gene expression by qRT-PCR using RNA derived from spleens and pancreata of cured mice validated the suppression of most of these genes, indicating an inverse correlation between the high levels of these inflammatory genes and protection against diabetes in NOD mice. In addition, higher-level expression of genes involved in insulin sensitivity, erythropoiesis, hemangioblast generation, and cellular redox control was evident in spleens of cured mice, indicating their possible contribution to protection against type 1 diabetes. Taken together, these results are consistent with the involvement of epistatic mechanisms in the manifestation of autoimmune diabetes and further indicate the utility of chromatin remodeling in curing this complex autoimmune disorder.

Epigenetics of autoimmune diabetes.

Classical genetic studies established a link between Type 1 diabetes, a common childhood autoimmune disease and genes that encode MHC antigens and several immune-related determinants. The mechanisms by which these genes contribute to the initiation and perpetuation of Type 1 diabetes remain enigmatic. Emerging data indicate a role for epigenetic mechanisms involving hyperacetylation of histones in the differential gene expression and amelioration of autoimmune diabetes in a mouse model. In this article the implications of these and other epigenetic mechanisms including ncRNA-mediated gene regulation in the abrogation of autoimmune diabetes are discussed. Concerted efforts to decipher the epigenetics of Type 1 diabetes may provide novel perspectives on autoimmune diabetogenesis.

Chromatin remodeling resets the immune system to protect against autoimmune diabetes in mice.

Epigenetic alteration of the genome has been shown to provide palliative effects in mouse models of certain human autoimmune diseases. We have investigated whether chromatin remodeling could provide protection against autoimmune diabetes in NOD mice. Treatment of female mice during the transition from prediabetic to diabetic stage (18-24 weeks of age) with the well-characterized histone deacetylase inhibitor, trichostatin A effectively reduced the incidence of diabetes. However, similar treatment of overtly diabetic mice during the same time period failed to reverse the disease. Protection against diabetes was accompanied by histone hyperacetylation in pancreas and spleen, enhanced frequency of CD4(+) CD62L(+) cells in the spleen, reduction in cellular infiltration of islets, restoration of normoglycemia and glucose-induced insulin release by beta cells. Activation of splenic T lymphocytes derived from protected mice in vitro with pharmacological agents that bypass the antigen receptor or immobilized anti-CD3 antibody resulted in enhanced expression of Ifng mRNA and protein without altering the expression of Il4, Il17, Il18, Inos and Tnfa genes nor the secretion of IL-2, IL-4, IL-17 and TNF-α proteins. Consistently, expression of the transcription factor involved in Ifng transcription, Tbet/Tbx21 but not Gata3 and Rorgt, respectively, required for the transcription of Il4 and Il17, was upregulated in activated splenocytes of protected mice. These results indicate that chromatin remodeling can lead to amelioration of diabetes by using multiple mechanisms including differential gene transcription. Thus, epigenetic modulation could be a novel therapeutic approach to block the transition from benign to frank diabetes.