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Neuroinflammatory Gene Expression Pattern Is Similar between Allergic Rhinitis and Atopic Dermatitis but Distinct from Atopic Asthma. BIOMED RESEARCH INTERNATIONAL 2020; 2020:7196981. [PMID: 32596360 PMCID: PMC7305544 DOI: 10.1155/2020/7196981] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/22/2020] [Accepted: 05/05/2020] [Indexed: 11/18/2022]
Abstract
Methods In the study, we included 86 children diagnosed with atopic asthma (n = 25), allergic rhinitis (n = 20), and atopic dermatitis (n = 20) and healthy control subjects (n = 21) of Caucasian origin from the Polish population. The blood leukocyte expression of 31 genes involved in neuroinflammatory response (neurotrophins, their receptors, neuropeptides, and histamine signaling pathway) was analysed using TaqMan low-density arrays. The relative expression of selected proteins from plasma was done using TaqMan Protein Assays. Statistical analysis was done using Statistica. Results Blood expression of 31 genes related to neuroimmune interactions showed significant increase in both allergic diseases, allergic rhinitis and atopic dermatitis, in comparison to the control group. We found 12 genes significantly increased in allergic rhinitis and 9 genes in which the expression was elevated in atopic dermatitis. Moreover, 9 genes with changed expression in atopic dermatitis overlapped with those in allergic rhinitis. Atopic asthma showed 5 genes with altered expression. The peripheral expression of neuroinflammatory genes in the human study was verified in target tissues (nasal epithelium and skin) in a rat model of allergic inflammation. Conclusions A common pattern of neuroinflammatory gene expression between allergic rhinitis and atopic dermatitis may reflect similar changes in sensory nerve function during chronic allergic inflammation.
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Abstract
BACKGROUND Inflammation is a core element of many different, systemic and chronic diseases that usually involve an important autoimmune component. The clinical phase of inflammatory diseases is often the culmination of a long series of pathologic events that started years before. The systemic characteristics and related mechanisms could be investigated through the multi-omic comparative analysis of many inflammatory diseases. Therefore, it is important to use molecular data to study the genesis of the diseases. Here we propose a new methodology to study the relationships between inflammatory diseases and signalling molecules whose dysregulation at molecular levels could lead to systemic pathological events observed in inflammatory diseases. RESULTS We first perform an exploratory analysis of gene expression data of a number of diseases that involve a strong inflammatory component. The comparison of gene expression between disease and healthy samples reveals the importance of members of gene families coding for signalling factors. Next, we focus on interested signalling gene families and a subset of inflammation related diseases with multi-omic features including both gene expression and DNA methylation. We introduce a phylogenetic-based multi-omic method to study the relationships between multi-omic features of inflammation related diseases by integrating gene expression, DNA methylation through sequence based phylogeny of the signalling gene families. The models of adaptations between gene expression and DNA methylation can be inferred from pre-estimated evolutionary relationship of a gene family. Members of the gene family whose expression or methylation levels significantly deviate from the model are considered as the potential disease associated genes. CONCLUSIONS Applying the methodology to four gene families (the chemokine receptor family, the TNF receptor family, the TGF- β gene family, the IL-17 gene family) in nine inflammation related diseases, we identify disease associated genes which exhibit significant dysregulation in gene expression or DNA methylation in the inflammation related diseases, which provides clues for functional associations between the diseases.
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Affiliation(s)
- Hui Xiao
- Computer Laboratory, University of Cambridge, Cambridge, UK
| | - Krzysztof Bartoszek
- Department of Computer and Information Science, Linköping University, Linköping, Sweden
| | - Pietro Lio’
- Computer Laboratory, University of Cambridge, Cambridge, UK
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Bruhn S, Fang Y, Barrenäs F, Gustafsson M, Zhang H, Konstantinell A, Krönke A, Sönnichsen B, Bresnick A, Dulyaninova N, Wang H, Zhao Y, Klingelhöfer J, Ambartsumian N, Beck MK, Nestor C, Bona E, Xiang Z, Benson M. A generally applicable translational strategy identifies S100A4 as a candidate gene in allergy. Sci Transl Med 2014; 6:218ra4. [PMID: 24401939 DOI: 10.1126/scitranslmed.3007410] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The identification of diagnostic markers and therapeutic candidate genes in common diseases is complicated by the involvement of thousands of genes. We hypothesized that genes co-regulated with a key gene in allergy, IL13, would form a module that could help to identify candidate genes. We identified a T helper 2 (TH2) cell module by small interfering RNA-mediated knockdown of 25 putative IL13-regulating transcription factors followed by expression profiling. The module contained candidate genes whose diagnostic potential was supported by clinical studies. Functional studies of human TH2 cells as well as mouse models of allergy showed that deletion of one of the genes, S100A4, resulted in decreased signs of allergy including TH2 cell activation, humoral immunity, and infiltration of effector cells. Specifically, dendritic cells required S100A4 for activating T cells. Treatment with an anti-S100A4 antibody resulted in decreased signs of allergy in the mouse model as well as in allergen-challenged T cells from allergic patients. This strategy, which may be generally applicable to complex diseases, identified and validated an important diagnostic and therapeutic candidate gene in allergy.
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Affiliation(s)
- Sören Bruhn
- The Center for Individualized Medication, Department of Clinical and Experimental Medicine, Linköping University, 581 85 Linköping, Sweden
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Chavali S, Bruhn S, Tiemann K, Sætrom P, Barrenäs F, Saito T, Kanduri K, Wang H, Benson M. MicroRNAs act complementarily to regulate disease-related mRNA modules in human diseases. RNA (NEW YORK, N.Y.) 2013; 19:1552-1562. [PMID: 24062574 PMCID: PMC3851722 DOI: 10.1261/rna.038414.113] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 08/20/2013] [Indexed: 06/02/2023]
Abstract
MicroRNAs (miRNAs) play a key role in regulating mRNA expression, and individual miRNAs have been proposed as diagnostic and therapeutic candidates. The identification of such candidates is complicated by the involvement of multiple miRNAs and mRNAs as well as unknown disease topology of the miRNAs. Here, we investigated if disease-associated miRNAs regulate modules of disease-associated mRNAs, if those miRNAs act complementarily or synergistically, and if single or combinations of miRNAs can be targeted to alter module functions. We first analyzed publicly available miRNA and mRNA expression data for five different diseases. Integrated target prediction and network-based analysis showed that the miRNAs regulated modules of disease-relevant genes. Most of the miRNAs acted complementarily to regulate multiple mRNAs. To functionally test these findings, we repeated the analysis using our own miRNA and mRNA expression data from CD4+ T cells from patients with seasonal allergic rhinitis. This is a good model of complex diseases because of its well-defined phenotype and pathogenesis. Combined computational and functional studies confirmed that miRNAs mainly acted complementarily and that a combination of two complementary miRNAs, miR-223 and miR-139-3p, could be targeted to alter disease-relevant module functions, namely, the release of type 2 helper T-cell (Th2) cytokines. Taken together, our findings indicate that miRNAs act complementarily to regulate modules of disease-related mRNAs and can be targeted to alter disease-relevant functions.
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Affiliation(s)
- Sreenivas Chavali
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, United Kingdom
| | - Sören Bruhn
- The Centre for Individualized Medication, Linköping University Hospital, Linköping University, Linköping, SE-58185, Sweden
| | - Katrin Tiemann
- The Centre for Individualized Medication, Linköping University Hospital, Linköping University, Linköping, SE-58185, Sweden
| | - Pål Sætrom
- Department of Computer and Information Science, Norwegian University of Science and Technology, Trondheim, NO-7491, Norway
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, NO-7491, Norway
| | - Fredrik Barrenäs
- The Centre for Individualized Medication, Linköping University Hospital, Linköping University, Linköping, SE-58185, Sweden
| | - Takaya Saito
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, NO-7491, Norway
| | - Kartiek Kanduri
- The Unit for Clinical Systems Biology, University of Gothenburg, Gothenburg, SE 40530, Sweden
| | - Hui Wang
- The Centre for Individualized Medication, Linköping University Hospital, Linköping University, Linköping, SE-58185, Sweden
- The Unit for Clinical Systems Biology, University of Gothenburg, Gothenburg, SE 40530, Sweden
| | - Mikael Benson
- The Centre for Individualized Medication, Linköping University Hospital, Linköping University, Linköping, SE-58185, Sweden
- Pediatric Allergy Unit, Queen Silvia Children's Hospital, Gothenburg, SE 41685, Sweden
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Couto Alves A, Bruhn S, Ramasamy A, Wang H, Holloway JW, Hartikainen AL, Jarvelin MR, Benson M, Balding DJ, Coin LJM. Dysregulation of complement system and CD4+ T cell activation pathways implicated in allergic response. PLoS One 2013; 8:e74821. [PMID: 24116013 PMCID: PMC3792967 DOI: 10.1371/journal.pone.0074821] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 08/06/2013] [Indexed: 11/18/2022] Open
Abstract
Allergy is a complex disease that is likely to involve dysregulated CD4+ T cell activation. Here we propose a novel methodology to gain insight into how coordinated behaviour emerges between disease-dysregulated pathways in response to pathophysiological stimuli. Using peripheral blood mononuclear cells of allergic rhinitis patients and controls cultured with and without pollen allergens, we integrate CD4+ T cell gene expression from microarray data and genetic markers of allergic sensitisation from GWAS data at the pathway level using enrichment analysis; implicating the complement system in both cellular and systemic response to pollen allergens. We delineate a novel disease network linking T cell activation to the complement system that is significantly enriched for genes exhibiting correlated gene expression and protein-protein interactions, suggesting a tight biological coordination that is dysregulated in the disease state in response to pollen allergen but not to diluent. This novel disease network has high predictive power for the gene and protein expression of the Th2 cytokine profile (IL-4, IL-5, IL-10, IL-13) and of the Th2 master regulator (GATA3), suggesting its involvement in the early stages of CD4+ T cell differentiation. Dissection of the complement system gene expression identifies 7 genes specifically associated with atopic response to pollen, including C1QR1, CFD, CFP, ITGB2, ITGAX and confirms the role of C3AR1 and C5AR1. Two of these genes (ITGB2 and C3AR1) are also implicated in the network linking complement system to T cell activation, which comprises 6 differentially expressed genes. C3AR1 is also significantly associated with allergic sensitisation in GWAS data.
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MESH Headings
- Allergens/pharmacology
- CD4-Positive T-Lymphocytes/drug effects
- CD4-Positive T-Lymphocytes/immunology
- CD4-Positive T-Lymphocytes/metabolism
- Cell Differentiation/drug effects
- Cell Differentiation/genetics
- Cytokines/genetics
- Cytokines/metabolism
- GATA3 Transcription Factor/genetics
- GATA3 Transcription Factor/metabolism
- Gene Expression Profiling
- Humans
- Leukocytes, Mononuclear/drug effects
- Leukocytes, Mononuclear/immunology
- Leukocytes, Mononuclear/metabolism
- Lymphocyte Activation/drug effects
- Lymphocyte Activation/genetics
- Lymphocyte Activation/immunology
- Pollen
- Receptors, Complement/genetics
- Receptors, Complement/metabolism
- Rhinitis, Allergic, Seasonal/genetics
- Rhinitis, Allergic, Seasonal/immunology
- Rhinitis, Allergic, Seasonal/metabolism
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Affiliation(s)
- Alexessander Couto Alves
- Department of Epidemiology and Biostatistics, Imperial College London, MRC-HPA Centre for Environment and Health, Imperial College London, London, United Kingdom
| | - Sören Bruhn
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Adaikalavan Ramasamy
- Department of Epidemiology and Biostatistics, Imperial College London, MRC-HPA Centre for Environment and Health, Imperial College London, London, United Kingdom
- Department of Medical and Molecular Genetics, King's College London, London, United Kingdom
| | - Hui Wang
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
- Dept of Paediatrics, Gothenburg University, Gothenburg, Sweden
| | - John W. Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Anna-Liisa Hartikainen
- Department of Clinical Sciences, Obstetrics and Gynecology, Institute of Clinical Medicine, University of Oulu, Oulu, Finland
| | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Biostatistics, Imperial College London, MRC-HPA Centre for Environment and Health, Imperial College London, London, United Kingdom
- Institute of Health Sciences, University of Oulu, and Unit of General Practice, University Hospital of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- National Institute of Health and Welfare, Oulu, Finland
| | - Mikael Benson
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - David J. Balding
- Department of Epidemiology and Biostatistics, Imperial College London, MRC-HPA Centre for Environment and Health, Imperial College London, London, United Kingdom
- Genetics Institute, University College London, United Kingdom
| | - Lachlan J. M. Coin
- Department of Genomics of Common Diseases, School of Public Health, Imperial College London, London, United Kingdom
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
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Comprehensive Profiling of Peripheral Immune Cells and Subsets in Patients with Intermittent Allergic Rhinitis Compared to Healthy Controls and After Treatment with Glucocorticoids. Inflammation 2013; 36:821-9. [DOI: 10.1007/s10753-013-9608-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Barrenäs F, Chavali S, Alves AC, Coin L, Jarvelin MR, Jörnsten R, Langston MA, Ramasamy A, Rogers G, Wang H, Benson M. Highly interconnected genes in disease-specific networks are enriched for disease-associated polymorphisms. Genome Biol 2012; 13:R46. [PMID: 22703998 PMCID: PMC3446318 DOI: 10.1186/gb-2012-13-6-r46] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Revised: 05/25/2012] [Accepted: 06/15/2012] [Indexed: 02/07/2023] Open
Abstract
Background Complex diseases are associated with altered interactions between thousands of genes. We developed a novel method to identify and prioritize disease genes, which was generally applicable to complex diseases. Results We identified modules of highly interconnected genes in disease-specific networks derived from integrating gene-expression and protein interaction data. We examined if those modules were enriched for disease-associated SNPs, and could be used to find novel genes for functional studies. First, we analyzed publicly available gene expression microarray and genome-wide association study (GWAS) data from 13, highly diverse, complex diseases. In each disease, highly interconnected genes formed modules, which were significantly enriched for genes harboring disease-associated SNPs. To test if such modules could be used to find novel genes for functional studies, we repeated the analyses using our own gene expression microarray and GWAS data from seasonal allergic rhinitis. We identified a novel gene, FGF2, whose relevance was supported by functional studies using combined small interfering RNA-mediated knock-down and gene expression microarrays. The modules in the 13 complex diseases analyzed here tended to overlap and were enriched for pathways related to oncological, metabolic and inflammatory diseases. This suggested that this union of the modules would be associated with a general increase in susceptibility for complex diseases. Indeed, we found that this union was enriched with GWAS genes for 145 other complex diseases. Conclusions Modules of highly interconnected complex disease genes were enriched for disease-associated SNPs, and could be used to find novel genes for functional studies.
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Affiliation(s)
- Fredrik Barrenäs
- The Centre for Individualized Medication, Linköping University Hospital, Linköping University, Linköping, Sweden
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Sjogren AKM, Barrenas F, Muraro A, Gustafsson M, Saetrom P, Wang H, Benson M. Monozygotic twins discordant for intermittent allergic rhinitis differ in mRNA and protein levels. Allergy 2012; 67:831-3. [PMID: 22515200 DOI: 10.1111/j.1398-9995.2012.02828.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/15/2012] [Indexed: 11/28/2022]
Abstract
Monozygotic (MZ) twins discordant for complex diseases may help to find disease mechanisms that are not due to genetic variants. Intermittent allergic rhinitis (IAR) is an optimal disease model because it occurs at defined time points each year, owing to known external antigens. We hypothesized that MZ twins discordant for IAR could help to find gene expression differences that are not dependent on genetic variants. We collected blood outside of the season from MZ twins discordant for IAR, challenged their peripheral blood mononuclear cells (PBMC) with pollen allergen in vitro, collected supernatants and isolated CD4+ T cells. We identified disease-relevant mRNAs and proteins that differed between the discordant MZ twins. By contrast, no differences in microRNA expression were found. Our results indicate that MZ twins discordant for IAR is an optimal model to identify disease mechanisms that are not due to genetic variants.
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Affiliation(s)
- A.-K. M. Sjogren
- The Unit for Clinical Systems Biology; Queen Silvia Children's Hospital; University of Gothenburg; Gothenburg; Sweden
| | - F. Barrenas
- Department of Clinical and Experimental Medicine; Faculty of Health Sciences; Linköping University; Linköping, Sweden
| | - A. Muraro
- Department of Pediatrics; Referral Centre for Food Allergy; Veneto Region; Padua General University Hospital; Padua; Italy
| | - M. Gustafsson
- Department of Clinical and Experimental Medicine; Faculty of Health Sciences; Linköping University; Linköping, Sweden
| | | | - H. Wang
- Department of Clinical and Experimental Medicine; Faculty of Health Sciences; Linköping University; Linköping, Sweden
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9
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Matsumoto Y, Noguchi E, Imoto Y, Nanatsue K, Takeshita K, Shibasaki M, Arinami T, Fujieda S. Upregulation of IL17RB during natural allergen exposure in patients with seasonal allergic rhinitis. Allergol Int 2011; 60:87-92. [PMID: 21252617 DOI: 10.2332/allergolint.10-oa-0230] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Accepted: 09/13/2010] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Seasonal allergic rhinitis (SAR) to Japanese cedar (Cryptomeria japonica; JC) is an IgE-mediated type I allergy affecting the nasal mucosa. However, the molecular mechanisms that underlie SAR are only partially understood. The aim of the study was to identify novel genes related to SAR during natural exposure to pollens, by using microarray analysis. METHODS Subjects were 32 SAR patients and 25 controls. Total RNA was extracted from CD4(+) T cells isolated from peripheral blood mononuclear cells and subjected to microarray analysis with Illumina Human Ref8 BeadChip arrays. The Mann-Whitney test was performed to identify genes whose expression was altered during allergen exposure. Quantitative real-time reverse transcription-polymerase chain reaction (RT-PCR) was performed on samples collected from SAR patients and controls to verify the microarray results. RESULTS Microarray analysis showed that the expression of 3 genes was significantly altered during allergen exposure. Among these 3 genes, the expression of interleukin 17 receptor beta (IL17RB) was confirmed to be upregulated in SAR patients compared to that of the IL17RB gene in healthy, non-allergic controls. The average fold change of IL17RB expression in the real-time RT-PCR experiment was 3.9 (P = 0.003). CONCLUSIONS The present study identified upregulation of IL17RB during natural allergen exposure in patients with SAR, which may further elucidate the molecular mechanisms underlying SAR.
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Affiliation(s)
- Yuri Matsumoto
- Department of Medical Genetics, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Ibaraki, Japan
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10
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Wang H, Chavali S, Mobini R, Muraro A, Barbon F, Boldrin D, Aberg N, Benson M. A pathway-based approach to find novel markers of local glucocorticoid treatment in intermittent allergic rhinitis. Allergy 2011; 66:132-40. [PMID: 20659080 DOI: 10.1111/j.1398-9995.2010.02444.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND Glucocorticoids (GCs) may affect the expression of hundreds of genes in different cells and tissues from patients with intermittent allergic rhinitis (IAR). It is a formidable challenge to understand these complex changes by studying individual genes. In this study, we aimed to identify (i) pathways affected by local GC treatment and (ii) examine if those pathways could be used to find novel markers of local GC treatment in nasal fluids from patients with IAR. METHODS Gene expression microarray- and iTRAQ-based proteomic analyses of nasal fluids, nasal fluid cells and nasal mucosa from patients with IAR were performed to find pathways enriched for differentially expressed genes and proteins. Proteins representing those pathways were analyzed with ELISA in an independent material of nasal fluids from 23 patients with IAR before and after treatment with a local GC. RESULTS Transcriptomal and proteomic high-throughput analyses of nasal fluids, nasal fluid cells and nasal mucosal showed that local GC treatment affected a wide variety of pathways in IAR such as the glucocorticoid receptor pathway and the acute phase response pathway. Extracellular proteins encoded by genes in those pathways were analyzed in an independent material of nasal fluids from patients. Proteins that changed significantly in expression included known biomarkers such as eosinophil cationic protein but also proteins that had not been previously described in IAR, namely CCL2, M-CSF, CXCL6 and apoH. CONCLUSION Pathway-based analyses of genomic and proteomic high-throughput data can be used as a complementary approach to identify novel potential markers of GC treatment in IAR.
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Affiliation(s)
- H Wang
- The Unit for Clinical Systems Biology, University of Gothenburg, Gothenburg, Sweden.
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11
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Combining network modeling and gene expression microarray analysis to explore the dynamics of Th1 and Th2 cell regulation. PLoS Comput Biol 2010; 6:e1001032. [PMID: 21187905 PMCID: PMC3002992 DOI: 10.1371/journal.pcbi.1001032] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2010] [Accepted: 11/11/2010] [Indexed: 01/14/2023] Open
Abstract
Two T helper (Th) cell subsets, namely Th1 and Th2 cells, play an important role in inflammatory diseases. The two subsets are thought to counter-regulate each other, and alterations in their balance result in different diseases. This paradigm has been challenged by recent clinical and experimental data. Because of the large number of genes involved in regulating Th1 and Th2 cells, assessment of this paradigm by modeling or experiments is difficult. Novel algorithms based on formal methods now permit the analysis of large gene regulatory networks. By combining these algorithms with in silico knockouts and gene expression microarray data from human T cells, we examined if the results were compatible with a counter-regulatory role of Th1 and Th2 cells. We constructed a directed network model of genes regulating Th1 and Th2 cells through text mining and manual curation. We identified four attractors in the network, three of which included genes that corresponded to Th0, Th1 and Th2 cells. The fourth attractor contained a mixture of Th1 and Th2 genes. We found that neither in silico knockouts of the Th1 and Th2 attractor genes nor gene expression microarray data from patients with immunological disorders and healthy subjects supported a counter-regulatory role of Th1 and Th2 cells. By combining network modeling with transcriptomic data analysis and in silico knockouts, we have devised a practical way to help unravel complex regulatory network topology and to increase our understanding of how network actions may differ in health and disease.
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Lucas JM. Microarrays: Molecular allergology and nanotechnology for personalised medicine (II). Allergol Immunopathol (Madr) 2010; 38:217-23. [PMID: 20537785 DOI: 10.1016/j.aller.2010.04.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2010] [Accepted: 04/20/2010] [Indexed: 02/07/2023]
Abstract
Progress in nanotechnology and DNA recombination techniques have produced tools for the diagnosis and investigation of allergy at molecular level. The most advanced examples of such progress are the microarray techniques, which have been expanded not only in research in the field of proteomics but also in application to the clinical setting. Microarrays of allergic components offer results relating to hundreds of allergenic components in a single test, and using a small amount of serum which can be obtained from capillary blood. The availability of new molecules will allow the development of panels including new allergenic components and sources, which will require evaluation for clinical use. Their application opens the door to component-based diagnosis, to the holistic perception of sensitisation as represented by molecular allergy, and to patient-centred medical practice by allowing great diagnostic accuracy and the definition of individualised immunotherapy for each patient. The present article reviews the application of allergenic component microarrays to allergology for diagnosis, management in the form of specific immunotherapy, and epidemiological studies. A review is also made of the use of protein and gene microarray techniques in basic research and in allergological diseases. Lastly, an evaluation is made of the challenges we face in introducing such techniques to clinical practice, and of the future perspectives of this new technology.
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Affiliation(s)
- J M Lucas
- Section of Pediatric Allergy, Virgen de la Arrixaca University Hospital, Murcia, Spain.
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13
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Peripheral blood gene expression in alopecia areata reveals molecular pathways distinguishing heritability, disease and severity. Genes Immun 2010; 11:531-41. [PMID: 20535136 DOI: 10.1038/gene.2010.32] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Alopecia areata (AA) is an autoimmune hair loss disorder in which systemic disturbances have been described, but are poorly understood. To evaluate disease mechanisms, we examined gene expression in the blood of defined clinical subgroups (patchy AA persistent type, AAP, n=5; alopecia universalis, AU, n=4) and healthy controls (unaffected relatives, UaR, n=5; unaffected non-relatives, UaNR, n=4) using microarrays. Unsupervised hierarchical clustering separates all four patient and control groups, producing three distinct expression patterns reflective of 'inheritance', 'disease' and 'severity' signatures. Functional classification of differentially expressed genes (DEGs) comparing disease (AAP, AU) vs normal (UaR) groups reveals upregulation in immune response, cytokine signaling, signal transduction, cell cycle, proteolysis and cell adhesion-related genes. Pathway analysis further reveals the activation of several genes related to natural killer-cell cytotoxicity, apoptosis, mitogen activated protein kinase, Wnt signaling and B- and T-cell receptor signaling in AA patients. Finally, 35 genes differentially expressed in AA blood overlap with DEGs previously identified in AA skin lesions. Our results implicate innate and adaptive immune processes while also revealing novel pathways, such as Wnt signaling and apoptosis, relevant to AA pathogenesis. Our data suggest that peripheral blood expression profiles of AA patients likely carry new biomarkers associated with disease susceptibility and expression.
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Wang H, Mobini R, Fang Y, Barrenäs F, Zhang H, Xiang Z, Benson M. Allergen challenge of peripheral blood mononuclear cells from patients with seasonal allergic rhinitis increases IL-17RB, which regulates basophil apoptosis and degranulation. Clin Exp Allergy 2010; 40:1194-202. [PMID: 20545698 DOI: 10.1111/j.1365-2222.2010.03542.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND Previously, expression profiling has been used to analyse allergen-challenged T-helper type 2 cells, nasal biopsies and nasal fluid cells from patients with seasonal allergic rhinitis (SAR). Allergen-challenged peripheral blood mononuclear cells (PBMCs) provide a human in vitro model of how antigen-presenting cells, CD4+ T cells and effector cells such as basophils interact in allergic inflammation. OBJECTIVE To identify novel genes and pathways in allergen-challenged PBMCs from patients with SAR using gene expression profiling and functional studies. METHODS PBMCs from 11 patients with SAR and 23 healthy controls were analysed with gene expression profiling. mRNA expression of IL17RB in basophils was evaluated using quantitative real-time PCR. Membrane protein expression and apoptosis of basophils were examined by flow cytometry. Degranulation of basophils was assessed by measuring beta-hexosaminidase release. Cytokine release was measured using ELISA. RESULTS Gene expression microarray analysis of allergen-challenged PBMCs showed that 209 out of 44000 genes were differentially expressed in patients compared with controls. IL17RB was the gene whose expression increased most in patients (P<0.0001). FACS analysis of PBMCs showed, for the first time, that basophils express IL-17RB. Following allergen challenge, IL-17RB protein increased significantly on basophils from patients compared with controls (P<0.05). IL-3 significantly increased both mRNA and protein expressions of IL17RB. Activation of IL-17RB by its ligand, IL-25, inhibited apoptosis of basophils. Moreover, IgE-mediated degranulation was enhanced by IL-25. CONCLUSION Increased expression of IL-17RB on allergen-challenged basophil is regulated by IL-3, inhibits apoptosis and promotes IgE-mediated degranulation of basophils.
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Affiliation(s)
- H Wang
- The Unit for Clinical Systems Biology, Department of Microbiology and Immunology, Mucosal Immunobiology and Vaccine Research Center, Sahlgrenska Academy, University of Gothenburg, and The Pediatric Allergy Unit, The Queen Silvia Children's Hospital, Gothenburg, Sweden.
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Benson M, Mobini R, Barrenäs F, Halldén C, Naluai AT, Säll T, Cardell LO. A haplotype in the inducible T-cell tyrosine kinase is a risk factor for seasonal allergic rhinitis. Allergy 2009; 64:1286-91. [PMID: 19222422 DOI: 10.1111/j.1398-9995.2009.01991.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
BACKGROUND Identification of disease-associated single nucleotide polymorphisms (SNPs) in seasonal allergic rhinitis (SAR) may be facilitated by focusing on genes in a disease-associated pathway. OBJECTIVE To search for SNPs in genes that belong to the T-cell receptor (TCR) pathway and that change in expression in allergen-challenged CD4+ cells from patients with SAR. METHODS CD4+ cells from patients with SAR were analysed with gene expression microarrays. Allele, genotype and haplotype frequencies were compared in 251 patients and 386 healthy controls. RESULTS Gene expression microarray analysis of allergen-challenged CD4+ cells from patients with SAR showed that 25 of 38 TCR pathway genes were differentially expressed. A total of 62 SNPs were analysed in eight of the 25 genes; ICOS, IL4, IL5, IL13, CSF2, CTLA4, the inducible T-cell tyrosine kinase (ITK) and CD3D. Significant chi-squared values were identified for several markers in the ITK kinase gene region. A total of five SNPs were nominally significant at the 5% level. Haplotype analysis of the five significant SNPs showed increased frequency of a haplotype that covered most of the coding part of ITK. The functional relevance of ITK was supported by analysis of an independent material, which showed increased expression of ITK in allergen-challenged CD4+ cells from patients, but not from controls. CONCLUSION Analysis of SNPs in TCR pathway genes revealed that a haplotype that covers a major part of the coding sequence of ITK is a risk factor for SAR.
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MESH Headings
- Adolescent
- Adult
- Alleles
- Allergens/pharmacology
- CD4-Positive T-Lymphocytes/drug effects
- CD4-Positive T-Lymphocytes/enzymology
- CD4-Positive T-Lymphocytes/immunology
- CD4-Positive T-Lymphocytes/metabolism
- Exons/genetics
- Exons/immunology
- Female
- Gene Expression Profiling
- Gene Frequency/genetics
- Gene Frequency/immunology
- Genetic Predisposition to Disease
- Haplotypes/genetics
- Haplotypes/immunology
- Humans
- Introns/genetics
- Introns/immunology
- Male
- Middle Aged
- Oligonucleotide Array Sequence Analysis
- Pollen/immunology
- Polymorphism, Single Nucleotide/genetics
- Polymorphism, Single Nucleotide/immunology
- Protein-Tyrosine Kinases/drug effects
- Protein-Tyrosine Kinases/genetics
- Protein-Tyrosine Kinases/immunology
- Receptors, Antigen, T-Cell/drug effects
- Receptors, Antigen, T-Cell/immunology
- Rhinitis, Allergic, Seasonal/genetics
- Rhinitis, Allergic, Seasonal/immunology
- Signal Transduction/genetics
- Signal Transduction/immunology
- Th2 Cells/drug effects
- Th2 Cells/enzymology
- Th2 Cells/immunology
- Th2 Cells/metabolism
- Young Adult
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Affiliation(s)
- M Benson
- Department of Pediatrics, Queen Silvia Children's Hospital, Gothenburg, Sweden
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16
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de Jonge JD, Pennings JLA, Baken KA, Konings J, Ezendam J, Van Loveren H. Gene expression changes in the mesenteric lymph nodes of rats after oral peanut extract exposure. J Immunotoxicol 2009; 5:385-94. [PMID: 19404872 DOI: 10.1080/15476910802586126] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
New techniques are needed to broaden the understanding of the food allergic response. The capacity of peanut extract to influence gene expression profiles was investigated in a Brown Norway rat model for food allergy. Brown Norway rats were sensitized to peanut extract (0, 1 and 10 mg/rat/d) by daily oral gavage and were dissected after 3, 7 or 14 days of exposure. RNA extracted from mesenteric lymph nodes of individual rats were hybridized against a common reference pool on Agilent whole rat genome (4*44k) arrays. The raw data were normalized and statistically analyzed using the statistical program R. A False Discovery Rate of 10% and a Fold Ratio of - 1.5 < or = Fold Ratio or Fold Ratio > or = 1.5 between the experimental groups and their respective control groups were applied. Differentially expressed genes were clustered into a heatmap. Functional annotation and GeneOntology term enrichment were examined. Furthermore, the involvement of the differentially expressed genes in specific cellular pathways was investigated with MetaCore. Gene expression changes, which were both dose- and time-dependent, were detected after sensitization to peanut. A total of 64 genes were differentially expressed, of which 60 were up-regulated and four were down-regulated. These changes were related to the regulation of immunological processes, most notably increased cell division. The findings indicate that responses to peanut include proliferation of immunologically relevant tissues, which can be identified by analysis of gene expression profiles. This may lay a basis for further research into possibilities for discrimination of allergenic from non-allergenic proteins.
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Affiliation(s)
- Jonathan D de Jonge
- University Maastricht, Nutrition and Toxicology Research Institute Maastricht, Department of Health Risk Analysis and Toxicology, Maastricht, Netherlands.
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17
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Spazierer D, Skvara H, Dawid M, Fallahi N, Gruber K, Rose K, Lloyd P, Heuerding S, Stingl G, Jung T. T helper 2 biased de novo immune response to Keyhole Limpet Hemocyanin in humans. Clin Exp Allergy 2009; 39:999-1008. [PMID: 19236409 DOI: 10.1111/j.1365-2222.2008.03177.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
BACKGROUND Allergen-specific T helper 2 (Th2) cells play an important role in the pathogenesis of atopic disorders. To date, no model system exists in humans that would allow the monitoring of a developing de novo Th2 immune response in vivo. OBJECTIVE The aim of the experiment was to establish an immunization protocol inducing a de novo Th2 response in humans using Keyhole Limpet Hemocyanin (KLH) as neo-antigen. METHODS The double-blind placebo-controlled, parallel-group study was conducted in two groups of subjects (16 healthy volunteers and 16 patients with allergic rhinitis). Subjects received three i.m. injections of 100 microg KLH adsorbed to aluminium hydroxide or matching placebo (alum alone) in intervals of 2 weeks. On day 43, KLH alone (10 microg) was given intra-dermally (i.d.) to all subjects to assess immediate and late-phase skin responses. RESULTS The immunization protocol was well tolerated, highly specific and efficient. Antigen-specific production of Th2-cytokines (mainly IL-5 and IL-13) by PBMCs suggested a Th2 pattern, as did the presence of KLH-specific IgG4 in sera. Intra-dermal KLH challenge induced an immediate-type of response predominantly in atopic subjects followed by a late-phase skin reaction. The latter was accompanied by the presence of IgE(+) cells, eosinophils and a strong up-regulation of IL-4 and IL-13 along with the absence of Th1 transcripts in biopsies taken from the site of antigen challenge. IL-17 and IL-22 transcripts were detected only in healthy subjects skin following KLH challenge, while IL-1beta and IL-33 expression did not differ between the healthy and the atopics. CONCLUSIONS The immunization protocol resulted in the elicitation of a local and peripheral Th2 immune response in both healthy and atopic individuals. This may permit the investigation and monitoring of novel immunomodulatory strategies aiming to interfere with Th2 responses in man. The relevance of lack of Th17 cells in atopic skin in this model remains to be determined.
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Affiliation(s)
- D Spazierer
- Department of Dermatology, Division of Immunology, Allergy and Infectious Diseases, Medical University of Vienna, Vienna Competence Center, 1090 Vienna, Austria
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18
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Mobini R, Andersson BA, Erjefält J, Hahn-Zoric M, Langston MA, Perkins AD, Cardell LO, Benson M. A module-based analytical strategy to identify novel disease-associated genes shows an inhibitory role for interleukin 7 Receptor in allergic inflammation. BMC SYSTEMS BIOLOGY 2009; 3:19. [PMID: 19216740 PMCID: PMC2653464 DOI: 10.1186/1752-0509-3-19] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2008] [Accepted: 02/12/2009] [Indexed: 12/04/2022]
Abstract
Background The identification of novel genes by high-throughput studies of complex diseases is complicated by the large number of potential genes. However, since disease-associated genes tend to interact, one solution is to arrange them in modules based on co-expression data and known gene interactions. The hypothesis of this study was that such a module could be a) found and validated in allergic disease and b) used to find and validate one ore more novel disease-associated genes. Results To test these hypotheses integrated analysis of a large number of gene expression microarray experiments from different forms of allergy was performed. This led to the identification of an experimentally validated reference gene that was used to construct a module of co-expressed and interacting genes. This module was validated in an independent material, by replicating the expression changes in allergen-challenged CD4+ cells. Moreover, the changes were reversed following treatment with corticosteroids. The module contained several novel disease-associated genes, of which the one with the highest number of interactions with known disease genes, IL7R, was selected for further validation. The expression levels of IL7R in allergen challenged CD4+ cells decreased following challenge but increased after treatment. This suggested an inhibitory role, which was confirmed by functional studies. Conclusion We propose that a module-based analytical strategy is generally applicable to find novel genes in complex diseases.
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Affiliation(s)
- Reza Mobini
- Unit for Clinical Systems Biology, Department of Pediatrics, University of Gothenburg, Gothenburg, Sweden.
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19
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Srinivas S, Dai J, Eskdale J, Gallagher GE, Megjugorac NJ, Gallagher G. Interferon-lambda1 (interleukin-29) preferentially down-regulates interleukin-13 over other T helper type 2 cytokine responses in vitro. Immunology 2008; 125:492-502. [PMID: 18547367 PMCID: PMC2612545 DOI: 10.1111/j.1365-2567.2008.02862.x] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2008] [Revised: 03/26/2008] [Accepted: 04/08/2008] [Indexed: 01/27/2023] Open
Abstract
Interferon (IFN)-lambda1 [interleukin (IL)-29] is a member of the interferon lambda family (also known as type III interferons), whose members are distantly related to both the type I interferons and members of the IL-10 family. While IFN-lambda1 has significant antiviral activity, it is also becoming apparent that it has important immunoregulatory properties, especially with regard to the T helper type 2 (Th2) response. Previously, we have shown that IFN-lambda1 is capable of down-regulating IL-13 production in an IFN-gamma-independent manner and that this is mediated in part via monocyte-derived dendritic cells. Here, we have extended our knowledge of IFN-lambda1 regulation of the human in vitro Th2 response by examining the regulation of three major Th2 cytokines, IL-4, IL-5 and IL-13, by IFN-lambda1. Our results reveal that IFN-lambda1 preferentially inhibits IL-13 production, compared with IL-4 or IL-5. Levels of IL-13 mRNA, the amount of secreted IL-13 protein and numbers of IL-13-positive CD3(+) CD4(+) cells were all significantly diminished by IFN-lambda1. IFN-lambda1 significantly decreased some aspects of IL-4 and IL-5 production, but its effects were not as consistent as those seen on IL-13. IFN-lambda1 was also effective at decreasing IL-13 secretion under conditions designed to support the generation of Th2 cells. Irrespective of whether Concanavalin-A or T-cell-stimulatory microbeads were used, IFN-lambda1 markedly diminished IL-13 secretion in cultures where IL-4 had been added. Thus, IFN-lambda1 appears to be an inhibitor of human Th2 responses whose action is primarily directed towards IL-13 but which may also affect Th2 responses generally and does not invoke a complementary elevation of IFN-gamma secretion.
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Affiliation(s)
- Shekar Srinivas
- The Institute for Genetic Immunology, Hamilton, NJ 08690, USA
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20
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Patel AC. Basic science for the practicing physician: gene expression microarrays. Ann Allergy Asthma Immunol 2008; 101:325-32. [PMID: 18814457 DOI: 10.1016/s1081-1206(10)60499-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
OBJECTIVE To provide a general overview of gene expression microarray technology and its relevance to physicians practicing allergy/immunology. DATA SOURCES The PubMed interface to MEDLINE was searched for primary and review articles on gene expression microarrays. Specific articles on clinical applications of microarrays were retrieved, along with articles on use of microarrays in models of allergy, asthma, and immunologic diseases. STUDY SELECTION The author's knowledge of the field was used to include sources of information other than those obtained through the MEDLINE search. RESULTS A synopsis of gene expression microarray technology, with emphasis on the relevance to allergy, asthma, and immunology, is presented. CONCLUSIONS Gene expression microarray technology allows investigators to measure gene expression across the genome. This has allowed researchers to improve our understanding of immunologic mechanisms in disease models. Initially used solely as a research tool, microarray-based clinical tests are now available, and many more are in development. Use of microarrays in allergy, asthma, and immunology will support the development of novel diagnostic tests for the physician and facilitate exploration of the basic mechanisms underlying allergic and immunologic diseases.
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Affiliation(s)
- Anand C Patel
- Division of Allergy/Pulmonary Medicine, Department of Pediatrics, Washington University School of Medicine, St Louis, Missouri, 63110, USA.
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21
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Rouchka EC, Krushkal J, Goldowitz D. Proceedings of the Seventh Annual UT-ORNL-KBRIN Bioinformatics Summit 2008. BMC Bioinformatics 2008. [PMCID: PMC3313171 DOI: 10.1186/1471-2105-9-s7-i1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Barrenäs F, Andersson B, Cardell LO, Langston M, Mobini R, Perkins A, Soini J, Ståhl A, Benson M. Gender differences in inflammatory proteins and pathways in seasonal allergic rhinitis. Cytokine 2008; 42:325-9. [DOI: 10.1016/j.cyto.2008.03.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2007] [Revised: 02/21/2008] [Accepted: 03/05/2008] [Indexed: 11/15/2022]
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23
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Tan K, Tegner J, Ravasi T. Integrated approaches to uncovering transcription regulatory networks in mammalian cells. Genomics 2008; 91:219-31. [PMID: 18191937 DOI: 10.1016/j.ygeno.2007.11.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2007] [Revised: 11/14/2007] [Accepted: 11/16/2007] [Indexed: 11/16/2022]
Abstract
Integrative systems biology has emerged as an exciting research approach in molecular biology and functional genomics that involves the integration of genomics, proteomics, and metabolomics datasets. These endeavors establish a systematic paradigm by which to interrogate, model, and iteratively refine our knowledge of the regulatory events within a cell. Here we review the latest technologies available to collect high-throughput measurements of a cellular state as well as the most successful methods for the integration and interrogation of these measurements. In particular we will focus on methods available to infer transcription regulatory networks in mammals.
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Affiliation(s)
- Kai Tan
- Department of Bioengineering, Jacobs School of Engineering, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
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