• Alterations of renal phenotype and gene expression profiles due to protein overload in NOD-related mouse strains.

      Wilson, Karen H S; McIndoe, Richard A; Eckenrode, Sarah E; Morel, Laurence; Agarwal, Anupam; Croker, Byron P; She, Jin-Xiong; Center for Biotechnology and Genomic Medicine (2006-01-19)
      BACKGROUND: Despite multiple causes, Chronic Kidney Disease is commonly associated with proteinuria. A previous study on Non Obese Diabetic mice (NOD), which spontaneously develop type 1 diabetes, described histological and gene expression changes incurred by diabetes in the kidney. Because proteinuria is coincident to diabetes, the effects of proteinuria are difficult to distinguish from those of other factors such as hyperglycemia. Proteinuria can nevertheless be induced in mice by peritoneal injection of Bovine Serum Albumin (BSA). To gain more information on the specific effects of proteinuria, this study addresses renal changes in diabetes resistant NOD-related mouse strains (NON and NOD.B10) that were made to develop proteinuria by BSA overload. METHODS: Proteinuria was induced by protein overload on NON and NOD.B10 mouse strains and histology and microarray technology were used to follow the kidney response. The effects of proteinuria were assessed and subsequently compared to changes that were observed in a prior study on NOD diabetic nephropathy. RESULTS: Overload treatment significantly modified the renal phenotype and out of 5760 clones screened, 21 and 7 kidney transcripts were respectively altered in the NON and NOD.B10. Upregulated transcripts encoded signal transduction genes, as well as markers for inflammation (Calmodulin kinase beta). Down-regulated transcripts included FKBP52 which was also down-regulated in diabetic NOD kidney. Comparison of transcripts altered by proteinuria to those altered by diabetes identified mannosidase 2 alpha 1 as being more specifically induced by proteinuria. CONCLUSION: By simulating a component of diabetes, and looking at the global response on mice resistant to the disease, by virtue of a small genetic difference, we were able to identify key factors in disease progression. This suggests the power of this approach in unraveling multifactorial disease processes.
    • APPLICATIONS OF MACHINE LEARNING TO GENOMICS: STUDIES IN TYPE 1 DIABETES AND CANCER

      Tran, Paul; Center for Biotechnology and Genomic Medicine (Augusta University, 2020-04)
      Introduction: A major aim of modern medicine is to translate basic genomics findings using machine learning and other data analysis methods into clinical tests for improving patient care. Herein, I applied machine learning methods to publicly available genetic and genomic data to address three clinical problems in cancer and type 1 diabetes (T1D) research. Project 1: Cancer classification mostly depends on the anatomic pathology workforce; hence, diagnosis is slow, stepwise, and prone to errors and systemic bias. Using a transcriptome-based cancer classification method, I reconciled the 18% disagreement rate between histology and mutation-based classifier for brain cancer. Project 2: I applied the same transcriptome-based classification method to lung adenocarcinoma and identified 3 novel subgroups comprising ~30% of lung adenocarcinoma. Project 3: The estimated genetic heritability of T1D is up to 80%. Identifying those most genetically susceptible to T1D can lead to reduction of the number of islet autoimmunity cases and the number diabetic ketoacidosis episodes. I developed a genetic risk prediction model using neural networks which performs better than currently published methods. I applied model interpretation methods to the neural network and identified important genetic drivers for characterizing T1D molecular subgroups. Conclusion: These projects are small steps in translating genomic medicine projects to clinical applications but represent a future with more objective and automated tools to aid in clinical decision making.
    • The Autoimmune Regulator (Aire) Confers Immunosuppressive Properties to Dendritic Cells

      Eisenman, Daniel; Center for Biotechnology and Genomic Medicine (2007-05)
      The Autoimmune regulator (Aire) is a transcription factor that controls expression of self antigens by thymic epithelium and it plays a critical role in the deletion of autoreactive thymocytes and prevention of autoimmunity. Recent studies have reported Aire expression in dendritic cells (DC) located in spleen and lymph nodes, suggesting a role for Aire in extra-thymic tolerance induction. Molecular and functional studies conducted in this dissertation revealed that Aire induction in bone marrow derived DC results in expression of immunosuppressive cytokines and decreased expression of co-stimulatory molecules. Similar results were also obtained from lenti-virus-mediated Aire overexpression in the DC2.4 dendritic cell line. It was further shown that DC from Aire'7' mice exhibited greater antigen presenting function both in vitro and in vivo. These DC were more potent stimulators of T cell proliferation leading to increased IL-2 and IFNy production. These studies suggest that Aire7' DC may play a role in exacerbating the autoimmunity seen in Aire7' mice. DC over-expressing Aire were shown to suppress activation and proliferation of naive T cells and promote activation-induced cell death of activated T cells. Furthermore, we demonstrate that Aire also controls transcription of tissue-specific antigens in DC. These results, together, suggest that Aire plays an important role in the tolerogenic function of DC.
    • Chemokine (C-C Motif) Ligand 2 (CCL2) in Sera of Patients with Type 1 Diabetes and Diabetic Complications

      Guan, Ruili; Purohit, Sharad; Wang, Hongjie; Bode, Bruce; Reed, John Chip; Steed, R. Dennis; Anderson, Stephen W.; Steed, Leigh; Hopkins, Diane; Xia, Chun; et al. (2011-04-12)
      Background: Chemokine (C-C motif) ligand 2 (CCL2), commonly known as monocyte chemoattractant protein-1 (MCP-1), has been implicated in the pathogenesis of many diseases characterized by monocytic infiltration. However, limited data have been reported on MCP-1 in type 1 diabetes (T1D) and the findings are inconclusive and inconsistent.
    • Country-specific birth weight and length in type 1 diabetes high-risk HLA genotypes in combination with prenatal characteristics

      Sterner, Y; Torn, C; Lee, H-S; Larsson, H; Winkler, C; McLeod, W; Lynch, K; Simell, O; Ziegler, A; Schatz, Desmond; et al. (2011-04-28)
      Objective
    • Critical role of Bcl11b in suppressor function of T regulatory cells and prevention of inflammatory bowel disease

      VanValkenburgh, Jeffrey; Albu, Diana I.; Bapanpally, Chandra; Casanova, Sarah; Califano, Danielle; Jones, David M.; Ignatowicz, Leszek; Kawamoto, Shimpei; Fagarasan, Sidonia; Jenkins, Nancy A.; et al. (2011-09-26)
      Dysregulated CD4+ T cell responses and alterations in T regulatory cells (Treg cells) play a critical role in autoimmune diseases, including inflammatory bowel disease (IBD). The current study demonstrates that removal of Bcl11b at the double-positive stage of T cell development or only in Treg cells causes IBD because of proinflammatory cytokine-producing CD4+ T cells infiltrating the colon. Provision of WT Treg cells prevented IBD, demonstrating that alterations in Treg cells are responsible for the disease. Furthermore, Bcl11b-deficient Treg cells had reduced suppressor activity with altered gene expression profiles, including reduced expression of the genes encoding Foxp3 and IL-10, and up-regulation of genes encoding proinflammatory cytokines. Additionally, the absence of Bcl11b altered the induction of Foxp3 expression and reduced the generation of induced Treg cells (iTreg cells) after Tgf-b treatment of conventional CD4+ T cells. Bcl11b bound to Foxp3 and IL-10 promoters, as well as to critical conserved noncoding sequences within the Foxp3 and IL-10 loci, and mutating the Bcl11b binding site in the Foxp3 promoter reduced expression of a luciferase reporter gene. These experiments demonstrate that Bcl11b is indispensable for Treg suppressor function and for maintenance of optimal Foxp3 and IL-10 gene expression, as well as for the induction of Foxp3 expression in conventional CD4+ T cells in response to Tgf-b and generation of iTreg cells.
    • Differential gene expression in the salivary gland during development and onset of xerostomia in Sj??gren's syndrome-like disease of the C57BL/6.NOD-Aec1Aec2 mouse.

      Nguyen, Cuong Q; Sharma, Ashok; Lee, Byung Ha; She, Jin-Xiong; McIndoe, Richard A; Peck, Ammon B; Center for Biotechnology and Genomic Medicine (2009-05-28)
      INTRODUCTION: Recently, we reported the development of the C57BL/6.NOD-Aec1Aec2 mouse that carries two genetic intervals derived from the non-obese diabetic (NOD) mouse capable of conferring Sj??gren's syndrome (SjS)-like disease in SjS-non-susceptible C57BL/6 mice. In an attempt to define the molecular bases underlying the onset of stomatitis sicca (xerostomia) in this C57BL/6.NOD-Aec1Aec2 mouse model, we have carried out a study using genomic microarray technology. METHODS: By means of oligonucleotide microarrays, gene expression profiles of salivary glands at 4, 8, 12, 16, and 20 weeks of age were generated for C57BL/6.NOD-Aec1Aec2 male mice. Using Linear Models for Microarray Analysis and B-statistics software, 480 genes were identified as being differentially expressed (P < 0.01 and Q < 0.0001) during the development of SjS-like disease in the salivary glands. RESULTS: The 480 genes could be arranged into four clusters, with each cluster defining a unique pattern of temporal expression, while the individual genes within each cluster could be grouped according to related biological functions. By means of pair-wise analysis, temporal changes in transcript expressions provided profiles indicating that many additional genes are differentially expressed at specific time points during the development of disease. Multiple genes reportedly showing an association with autoimmunity and/or SjS, in either humans or mouse models, were found to exhibit differential expressions, both quantitatively and temporally. Selecting various families of genes associated with specific functions (for example, antibody production, complement, and chemokines), we noted that only a limited number of family members showed differential expressions and these correlated with specific phases of disease. CONCLUSIONS: Taking advantage of known functions of these genes, investigators can construct interactive gene pathways, leading to modeling of possible underlying events inducing salivary gland dysfunction. Thus, these different approaches to analyzing microarray data permit the identification of multiple sets of genes of interest whose expressions and expression profiles may correlate with molecular mechanisms, signaling pathways, and/or immunological processes involved in the development and onset of SjS.
    • Extracellular high-mobility group box 1 acts as an innate immune mediator to enhance autoimmune progression and diabetes onset in NOD mice.

      Han, Junyan; Zhong, Jinxin; Wei, Wenzhong; Wang, Ying; Huang, Yafei; Yang, Ping; Purohit, Sharad; Dong, Zheng; Wang, Mong-Heng; She, Jin-Xiong; et al. (2008-07-29)
      OBJECTIVE: The implication of innate immunity in type 1 diabetes development has long been proposed. High-mobility group box 1 (HMGB1), an evolutionarily conserved chromosomal protein, was recently recognized to be a potent innate inflammatory mediator when released extracellularly. We sought to test the hypothesis that HMGB1 acts as an innate immune mediator implicated in type 1 diabetes pathogenesis. RESEARCH DESIGN AND METHODS: Eight- and 12-week-old NOD mice were treated with an HMGB1 neutralizing antibody once a week until 25 weeks of age and monitored for insulitis progression and diabetes onset. The underlying mechanisms of HMGB1 regulation of autoimmune response were further explored. RESULTS: During autoimmunity, HMGB1 can be passively released from damaged pancreatic beta-cells and actively secreted by islet infiltrated immune cells. Extracellular HMGB1 is potent in inducing NOD dendritic cell maturation and stimulating macrophage activation. Blockade of HMGB1 significantly inhibited insulitis progression and diabetes development in both 8- and 12-week-old NOD mice. HMGB1 antibody treatment decreased the number and maturation of pancreatic lymph node (PLN) CD11c(++)CD11b(+) dendritic cells, a subset of dendritic cells probably associated with autoantigen presentation to na??ve T-cells, but increased the number for PLN CD4(+)Foxp3(+) regulatory T-cells. Blockade of HMGB1 also decreased splenic dendritic cell allo-stimulatory capability associated with increased tolergenic CD11c(+)CD8a(+) dendritic cells. Interestingly, the number of CD8(+)interferon-gamma(+) (Tc1) T-cells was increased in the PLNs and spleen after blockade of HMGB1, which could be associated with retarded migration of activated autoreactive T-cells into the pancreatic islets. CONCLUSIONS: Extracellular HMGB1 functions as a potent innate immune mediator contributing to insulitis progression and diabetes onset.
    • Genetic and Molecular Basis of QTL of Diabetes in Mouse: Genes and Polymorphisms.

      Gao, Peng; Jiao, Yan; Xiong, Qing; Wang, Cong-Yi; Gerling, Ivan; Gu, Weikuan; Center for Biotechnology and Genomic Medicine (2009-05-27)
      A systematic study has been conducted of all available reports in PubMed and OMIM (Online Mendelian Inheritance in Man) to examine the genetic and molecular basis of quantitative genetic loci (QTL) of diabetes with the main focus on genes and polymorphisms. The major question is, What can the QTL tell us? Specifically, we want to know whether those genome regions differ from other regions in terms of genes relevant to diabetes. Which genes are within those QTL regions, and, among them, which genes have already been linked to diabetes? whether more polymorphisms have been associated with diabetes in the QTL regions than in the non-QTL regions.Our search revealed a total of 9038 genes from 26 type 1 diabetes QTL, which cover 667,096,006 bp of the mouse genomic sequence. On one hand, a large number of candidate genes are in each of these QTL; on the other hand, we found that some obvious candidate genes of QTL have not yet been investigated. Thus, the comprehensive search of candidate genes for known QTL may provide unexpected benefit for identifying QTL genes for diabetes.
    • Genetically dependent ERBB3 expression modulates antigen presenting cell function and type 1 diabetes risk.

      Wang, Hongjie; Jin, Yulan; Reddy, M V Prasad Linga; Podolsky, Robert H.; Liu, Siyang; Yang, Ping; Bode, Bruce; Reed, John Chip; Steed, R. Dennis; Anderson, Stephen W.; et al. (2010-07-29)
      Type 1 diabetes (T1D) is an autoimmune disease resulting from the complex interaction between multiple susceptibility genes, environmental factors and the immune system. Over 40 T1D susceptibility regions have been suggested by recent genome-wide association studies; however, the specific genes and their role in the disease remain elusive. The objective of this study is to identify the susceptibility gene(s) in the 12q13 region and investigate the functional link to the disease pathogenesis. A total of 19 SNPs in the 12q13 region were analyzed by the TaqMan assay for 1,434 T1D patients and 1,865 controls. Thirteen of the SNPs are associated with T1D (best p = 4x10(-11)), thus providing confirmatory evidence for at least one susceptibility gene in this region. To identify candidate genes, expression of six genes in the region was analyzed by real-time RT-PCR for PBMCs from 192 T1D patients and 192 controls. SNP genotypes in the 12q13 region are the main factors that determine ERBB3 mRNA levels in PBMCs. The protective genotypes for T1D are associated with higher ERBB3 mRNA level (p<10(-10)). Furthermore, ERBB3 protein is expressed on the surface of CD11c(+) cells (dendritic cells and monocytes) in peripheral blood after stimulation with LPS, polyI:C or CpG. Subjects with protective genotypes have significantly higher percentages of ERBB3(+) monocytes and dendritic cells (p = 1.1x10(-9)); and the percentages of ERBB3(+) cells positively correlate with the ability of APC to stimulate T cell proliferation (R(2) = 0.90, p<0.0001). Our results indicate that ERBB3 plays a critical role in determining APC function and potentially T1D pathogenesis.
    • Genomic Predictions in Uterine Cancers

      Tran, Lynn Kim Hoang; Center for Biotechnology and Genomic Medicine (Augusta University, 2020-05)
      Introduction: Current uterine cancer classification provides suboptimal treatment stratification and often groups together patients with significant differences in survival outcome and/or response. We used transcriptomic information to devise genomic scores for improved prediction of uterine cancer patient outcomes and validated these scores in our institutional cohorts. Project 1: In an early iteration of our gene signature discovery pipeline, we developed USC73, a genomic score for uterine serous carcinoma patients, which grouped patients into a low score (lower 66.7 percentile), good prognosis group and a high score (upper 33.3 percentile), poor prognosis group (5-year overall survival: 83.3% and 13.3%, respectively). USC73 predicts survival independently of stage, and can be combined with stage for further resolution of patient survival. Poor survivors have faster-growing tumors and lower rates of complete response to primary therapy. Project 2: We applied our pipeline to uterine endometrioid carcinoma, the most common histotype of uterine cancer, and developed UEC_IGS, an immune gene score that separates early stage patients into a high lymphocytic infiltration, good prognosis group (IGS 1) and a low lymphocytic infiltration, poor prognosis group (IGS 2). UEC_IGS predicts overall survival independent of grade and treatment. IGS 1 patients have higher levels of CD8+ tumor infiltrating lymphocytes (TILs), more CD45RO+/CD3+ memory T cells, and lower levels of FOXP3+ Tregs compared to IGS 2. Conclusion: Using transcriptomic data, we can reliably stratify uterine cancer patients into good and poor survival groups. This information can be used to facilitate recruitment of only poor prognosis patients into clinical trials, mitigating some heterogeneity in patient response and allowing clinicians to better identify treatments for patients who will not survive on the current therapy. Additionally, biological functions (e.g. cellular proliferation or immune infiltration) are associated with each genomic score, and these can serve as potential pathways to target for improving the outcome of poor survival groups.
    • Hepatic gene expression profiling reveals key pathways involved in leptin-mediated weight loss in ob/ob mice.

      Sharma, Ashok; Bartell, Shoshana M; Baile, Clifton A; Chen, Bo; Podolsky, Robert H.; McIndoe, Richard A; She, Jin-Xiong; Center for Biotechnology and Genomic Medicine; Department of Medicine; Department of Pathology (2010-09-02)
      BACKGROUND: Leptin, a cytokine-like protein, plays an important role in the regulation of body weight through inhibition of food intake and stimulation of energy expenditure. Leptin circulates in blood and acts on the brain, which sends downstream signals to regulate body weight. Leptin therapy has been successful in treating leptin deficient obese patients. However, high levels of leptin have been observed in more common forms of obesity indicating a state of leptin resistance which limits the application of leptin in the treatment of obesity. If the central effect of leptin could be by-passed and genes which respond to leptin treatment could be regulated directly, new therapeutic targets for the treatment of obesity may be possible. The purpose of this study was to identify genes and subsequent pathways correlated with leptin-mediated weight loss. METHODOLOGY/PRINCIPAL FINDINGS: WE UTILIZED MICROARRAY TECHNOLOGY TO COMPARE HEPATIC GENE EXPRESSION CHANGES AFTER TWO TYPES OF LEPTIN ADMINISTRATION: one involving a direct stimulatory effect when administered peripherally (subcutaneous: SQ) and another that is indirect, involving a hypothalamic relay that suppresses food intake when leptin is administered centrally (intracerebroventricular: ICV). We identified 214 genes that correlate with leptin mediated weight loss. Several biological processes such as mitochondrial metabolic pathways, lipid metabolic and catabolic processes, lipid biosynthetic processes, carboxylic acid metabolic processes, iron ion binding and glutathione S-transferases were downregulated after leptin administration. In contrast, genes involved in the immune system inflammatory response and lysosomal activity were found to be upregulated. Among the cellular compartments mitochondrion (32 genes), endoplasmic reticulum (22 genes) and vacuole (8 genes) were significantly over represented. CONCLUSIONS/SIGNIFICANCE: In this study we have identified key molecular pathways and downstream genes which respond to leptin treatment and are involved in leptin-mediated weight loss. Many of these genes have previously been shown to be associated with obesity; however, we have also identified a number of other novel target genes. Further investigation will be required to assess the possible use of these genes and their associated protein products as therapeutic targets for the treatment of obesity.
    • The IL-10 and IFN-gamma pathways are essential to the potent immunosuppressive activity of cultured CD8+ NKT-like cells.

      Zhou, Li; Wang, Hongjie; Zhong, Xing; Jin, Yulan; Mi, Qing-Sheng; Sharma, Ashok; McIndoe, Richard A; Garge, Nikhil; Podolsky, Robert H.; She, Jin-Xiong; et al. (2008-09-05)
      BACKGROUND: CD8+ NKT-like cells are naturally occurring but rare T cells that express both T cell and natural killer cell markers. These cells may play key roles in establishing tolerance to self-antigens; however, their mechanism of action and molecular profiles are poorly characterized due to their low frequencies. We developed an efficient in vitro protocol to produce CD8+ T cells that express natural killer cell markers (CD8+ NKT-like cells) and extensively characterized their functional and molecular phenotypes using a variety of techniques. RESULTS: Large numbers of CD8+ NKT-like cells were obtained through culture of na??ve CD8+ T cells using anti-CD3/anti-CD28-coated beads and high dose IL-2. These cells possess potent activity in suppressing the proliferation of na??ve responder T cells. Gene expression profiling suggests that the cultured CD8+ NKT-like cells and the na??ve CD8+ T cells differ by more than 2-fold for about 3,000 genes, among which 314 are upregulated by more than 5-fold and 113 are upregulated by more than 10-fold in the CD8+ NKT-like cells. A large proportion of the highly upregulated genes are soluble factors or surface markers that have previously been implicated in immune suppression or are likely to possess immunosuppressive properties. Many of these genes are regulated by two key cytokines, IL-10 and IFN-gamma. The immunosuppressive activities of cells cultured from IL-10-/- and IFN-gamma-/- mice are reduced by about 70% and about 50%, respectively, compared to wild-type mice. CONCLUSION: Immunosuppressive CD8+ NKT-like cells can be efficiently produced and their immunosuppressive activity is related to many surface and soluble molecules regulated by IL-10 and IFN-gamma.
    • Influence of common variants in FTO and near INSIG2 and MC4R on growth curves for adiposity in Africanâ and Europeanâ American youth

      Liu, Gaifen; Zhu, Haidong; Dong, Yanbin; Podolsky, Robert H.; Treiber, Frank A.; Snieder, Harold; Center for Biotechnology and Genomic Medicine (2011-06-5)
      Electronic supplementary material: The online version of this article (doi:10.1007/s10654-011-9583-4) contains supplementary material, which is available to authorized users.
    • Intratumoral Convergence of the TCR Repertoires of Effector and Foxp3+ CD4+ T cells

      Kuczma, Michal; Kopij, Magdalena; Pawlikowska, Iwona; Wang, Cong-Yi; Rempala, Grzegorz A.; Kraj, Piotr; Center for Biotechnology and Genomic Medicine; Department of Biostatistics and Epidemiology; GHSU Cancer Center (2010-10-26)
      The presence of Foxp3+ regulatory CD4+ T cells in tumor lesions is considered one of the major causes of ineffective immune response in cancer. It is not clear whether intratumoral Treg cells represent Treg cells pre-existing in healthy mice, or arise from tumor-specific effector CD4+ T cells and thus representing adaptive Treg cells. The generation of Treg population in tumors could be further complicated by recent evidence showing that both in humans and mice the peripheral population of Treg cells is heterogenous and consists of subsets which may differentially respond to tumor-derived antigens. We have studied Treg cells in cancer in experimental mice that express naturally selected, polyclonal repertoire of CD4+ T cells and which preserve the heterogeneity of the Treg population. The majority of Treg cells present in healthy mice maintained a stable suppressor phenotype, expressed high level of Foxp3 and an exclusive set of TCRs not used by naive CD4+ T cells. A small Treg subset, utilized TCRs shared with effector T cells and expressed a lower level of Foxp3. We show that response to tumor-derived antigens induced efficient clonal recruitment and expansion of antigen-specific effector and Treg cells. However, the population of Treg cells in tumors was dominated by cells expressing TCRs shared with effector CD4+ T cells. In contrast, Treg cells expressing an exclusive set of TCRs, that dominate in healthy mice, accounted for only a small fraction of all Treg cells in tumor lesions. Our results suggest that the Treg repertoire in tumors is generated by conversion of effector CD4+ T cells or expansion of a minor subset of Treg cells. In conclusion, successful cancer immunotherapy may depend on the ability to block upregulation of Foxp3 in effector CD4+ T cells and/or selectively inhibiting the expansion of a minor Treg subset.
    • Lack of an association of miR-938 SNP in IDDM10 with human type 1 diabetes

      Mi, Xiaofan; He, Hongzhi; Deng, Yangxin; Levin, Abert M; She, Jin-Xiong; Mi, Qing-Sheng; Zhou, Li; Center for Biotechnology and Genomic Medicine (2011-10-20)
      MicroRNAs (miRNAs) are a newly discovered type of small non-protein coding RNA that function in the inhibition of effective mRNA translation, and may serve as susceptibility genes for various disease developments. The SNP rs12416605, located in human type 1 diabetes IDDM10 locus, changes the seeding sequence (UGU[G/A]CCC) of miRNA miR-938 and potentially alters miR-938 targets, including IL-16 and IL-17A. In an attempt to test whether miR-938 may be a susceptibility gene for IDDM10, we assessed the possible association of the miR-938 SNP with T1D in an American Caucasian cohort of 622 patients and 723 healthy controls by TaqMan assay. Our current data do not support the association between the SNP in miR-938 and type 1 diabetes.
    • Lack of correlation between the levels of soluble cytotoxic T-lymphocyte associated antigen-4 (CTLA-4) and the CT-60 genotypes.

      Purohit, Sharad; Podolsky, Robert H.; Collins, Christin; Zheng, Weipeng; Schatz, Desmond; Muir, Andy; Hopkins, Diane; Huang, Yi-Hua; She, Jin-Xiong; Center for Biotechnology and Genomic Medicine (2005-11-24)
      BACKGROUND: Cytotoxic T lymphocyte-associated antigen-4 (CTLA-4) plays a critical role in downregulation of antigen-activated immune response and polymorphisms at the CTLA-4 gene have been shown to be associated with several autoimmune diseases including type-1 diabetes (T1D). The etiological mutation was mapped to the CT60-A/G single nucleotide polymorphism (SNP) that is believed to control the processing and production of soluble CTLA-4 (sCTLA-4). METHODS: We therefore determined sCTLA-4 protein levels in the sera from 82 T1D patients and 19 autoantibody positive (AbP) subjects and 117 autoantibody negative (AbN) controls using ELISA. The CT-60 SNP was genotyped for these samples by using PCR and restriction enzyme digestion of a 268 bp DNA segment containing the SNP. Genotyping of CT-60 SNP was confirmed by dye terminating sequencing reaction. RESULTS: Higher levels of sCTLA-4 were observed in T1D (2.24 ng/ml) and AbP (mean = 2.17 ng/ml) subjects compared to AbN controls (mean = 1.69 ng/ml) with the differences between these subjects becoming significant with age (p = 0.02). However, we found no correlation between sCTLA-4 levels and the CTLA-4 CT-60 SNP genotypes. CONCLUSION: Consistent with the higher serum sCTLA-4 levels observed in other autoimmune diseases, our results suggest that sCTLA-4 may be a risk factor for T1D. However, our results do not support the conclusion that the CT-60 SNP controls the expression of sCTLA-4.
    • Large Scale Gene Expression Analysis Reveals Insight into Pathways Related to Type 1 Diabetes and Associated Complications

      Carey, Colleen M.; Center for Biotechnology and Genomic Medicine (2013-08)
      Type 1 Diabetes (T1D) is a chronic inflammatory disease resulting from complex interactions between susceptibility genes, the environment, and the immune system, ultimately leading to the destruction o f pancreatic islet cells and insulin deficiency. Previous studies have examined the series o f molecular, cellular, and protein changes occurring within subsets of individuals and how these are associated with particular disease states. Genome wide association studies have revealed a large number o f genetic susceptibility intervals including those implicated in disease pathogenesis, the identification o f various markers for risk assessment, the classification o f disease or complications, and finally markers for monitoring therapies for disease. However, none of these studies to date is without seriously limitations. First, although microarray based gene expression profiling is a powerful tool in discovery; results must be validated by alternate techniques. Second, due to the inherent heterogeneity of the human population large sample sizes in each group must be used in order to handle the expected large expression variations among individual subject. Third, for accurate normalization of Real-Time PCR expression data appropriate reference genes must be selected. We proposed a large scale gene expression validation study to address the limitations of previous studies. Validation studies were performed using high throughput Real-Time RT-PCR on peripheral blood mononuclear cells (PBMCs) o f 928 individuals with T1D and 922 individuals as antibody negative (AbN) controls, recruited through the Prospective Assessment in Newborns of Diabetes Autoimmunity (PANDA) study. This dissertation work validated the gene expression changes among 28 genes shown to have differential expression in T1D patients as compared to controls. These genes were selected based on their function, role in inflammatory or the immune response, and any previously documented reference to a role in T1D. Our aims were to 1) identify gene expression changes which may be occurring specifically in diabetic complications, and 2) identify gene expression changes which may result in an increased state o f oxidative stress in the diabetic state. For validation studies, we divided the 28 genes into two subsets based on related function to ask whether any gene expression signatures could be associated with diabetes, diabetic complications, or oxidative stress in the diabetic state. Our studies revealed genes that are involved in inflammation, immune regulation, and antigen processing and presentation are significantly altered in the PBMCs o f T1D patients. Eight genes (S100A8, S100A9, MNDA, SELL, TGFB1, PSMB3, CD74, and IL12A) were shown to have higher expression, with three genes (GNLY, PSMA4, and SMAD7) having lower expression, in T1D when compared to controls. The data also suggested that inflammatory mediators secreted mainly by myeloid cells are implicated in T1D and its complications (Odds ratios OR = 1.3-2.6, adjusted P value= 0.005- 1.08 x 10 8), and particularly in those patients with nephropathy (OR=4.8-7.9, adjusted P value < 0.005). Validation studies also revealed nine genes (LAT2, MAPK1, APOBEC3B, SOD2, NDUFB3, STK40, PRKD2, ITGB2, and COX7B) with higher expression in T1D. These genes are involved in general pathways of inflammation and immune response; however SOD2, NDUFB3, and COX7B (OR=l.l-1.27, adjusted P value= 0.007-0.47) are functionally involved in the mechanisms o f the mitochondria and may play a role in the increased state of oxidative stress seen in T1D. In these studies we have validated and confirmed the gene expression differences between T1D and control subjects initially suggested by microarray. Our experimental design has addressed each of the limitations posed by earlier studies in the largest scale study to date on gene expression profiles in human T1D. We have demonstrated that gene expression is significantly different between autoantibody negative (AbN) controls and T1D patients without any complications. Genes implicated in immune function (S100A8, S100A9, MNDA, IL12A), immune regulation and promotion (TGFB1, SELL), antigen processing and presentation (CD74, PSMB3), and mitochondrial function (SOD2, NDUFB3, COX7B) have higher expression in T1D and support the notion that chronic inflammation and cellular oxidative stress contribute to the development of T1D and associated complications. The understanding gained from our results implies a translational potential for the use o f gene expression profiles in the classification o f at risk individuals for both T1D and complication. Further, our understanding into the role that the immune system plays in cellular oxidative stress leading to the diabetic state may serve to provide prevention therapies however there remains much to be learned before this is attainable.
    • Loss of Jak2 selectively suppresses DC-mediated innate immune response and protects mice from lethal dose of LPS-induced septic shock.

      Zhong, Jixin; Yang, Ping; Muta, Kenjiro; Dong, Robert; Marrero, Mario; Gong, Feili; Wang, Cong-Yi; Center for Biotechnology and Genomic Medicine; Vascular Biology Center (2010-03-16)
      Given the importance of Jak2 in cell signaling, a critical role for Jak2 in immune cells especially dendritic cells (DCs) has long been proposed. The exact function for Jak2 in DCs, however, remained poorly understood as Jak2 deficiency leads to embryonic lethality. Here we established Jak2 deficiency in adult Cre(+/+)Jak2(fl/fl) mice by tamoxifen induction. Loss of Jak2 significantly impaired DC development as manifested by reduced BMDC yield, smaller spleen size and reduced percentage of DCs in total splenocytes. Jak2 was also crucial for the capacity of DCs to mediate innate immune response. Jak2(-/-) DCs were less potent in response to inflammatory stimuli and showed reduced capacity to secrete proinflammatory cytokines such as TNFalpha and IL-12. As a result, Jak2(-/-) mice were defective for the early clearance of Listeria after infection. However, their potency to mediate adaptive immune response was not affected. Unlike DCs, Jak2(-/-) macrophages showed similar capacity secretion of proinflammatory cytokines, suggesting that Jak2 selectively modulates innate immune response in a DC-dependent manner. Consistent with these results, Jak2(-/-) mice were remarkably resistant to lethal dose of LPS-induced septic shock, a deadly sepsis characterized by the excessive innate immune response, and adoptive transfer of normal DCs restored their susceptibility to LPS-induced septic shock. Mechanistic studies revealed that Jak2/SATA5 signaling is pivotal for DC development and maturation, while the capacity for DCs secretion of proinflammatory cytokines is regulated by both Jak2/STAT5 and Jak2/STAT6 signaling.
    • Molecular cloning and characterization of the mouse Acdp gene family.

      Wang, Cong-Yi; Yang, Ping; Shi, Jing-Da; Purohit, Sharad; Guo, Dehuang; An, Haiqian; Gu, Jian-Guo; Ling, Jennifer X; Dong, Zheng; She, Jin-Xiong; et al. (2004-05-11)
      BACKGROUND: We have recently cloned and characterized a novel gene family named ancient conserved domain protein (ACDP) in humans. To facilitate the functional study of this novel gene family, we have cloned and characterized Acdp, the mouse homologue of the human ACDP gene family. RESULTS: The four Acdp genes (Acdp1, Acdp2, Acdp3 and Acdp4) contain 3,631 bp, 3,244 bp, 2,684 bp and 2,743 bp of cDNA sequences, and encode deduced proteins of 951, 874, 713 and 771 amino acids, respectively. The mouse Acdp genes showed very strong homologies (>90%) in both nucleotide and amino acid sequences to their human counterparts. In addition, both nucleotide and amino acid sequences within the Ancient Conserved Domain (ACD) are highly conserved in many different taxonomic species. Particularly, Acdp proteins showed very strong AA homologies to the bacteria CorC protein (35% AA identity with 55% homology), which is involved in magnesium and cobalt efflux. The Acdp genes are widely expressed in all tissues tested except for Acdp1, which is only highly expressed in the brain with low levels of expression in kidney and testis. Immunostaining of Acdp1 in hippocampus neurons revealed a predominant localization on the plasma membrane. CONCLUSION: The Acdp genes are evolutionarily conserved in diverse species and ubiquitously expressed throughout development and adult tissues suggesting that Acdp may be an essential gene. Acdp showed strong homology to bacteria CorC protein and predominantly localized on the plasma membrane. These results suggest that Acdp is probably a family of proteins involved in ion transport in mammalian cells