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Zhou H, Hong X, Jiang S, Dong H, Xu X, Xu X. Analyses of associations between three positionally cloned asthma candidate genes and asthma or asthma-related phenotypes in a Chinese population. BMC MEDICAL GENETICS 2009; 10:123. [PMID: 19951440 PMCID: PMC2799396 DOI: 10.1186/1471-2350-10-123] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2009] [Accepted: 12/01/2009] [Indexed: 12/02/2022]
Abstract
Background Six asthma candidate genes, ADAM33, NPSR1, PHF11, DPP10, HLA-G, and CYFIP2, located at different chromosome regions have been positionally cloned following the reported linkage studies. For ADAM33, NPSR1, and CYFIP2, the associations with asthma or asthma-related phenotypes have been studied in East Asian populations such as Chinese and Japanese. However, for PHF11, DPP10, and HLA-G, none of the association studies have been conducted in Asian populations. Therefore, the aim of the present study is to test the associations between these three positionally cloned genes and asthma or asthma-related phenotypes in a Chinese population. Methods Two, five, and two single nucleotide polymorphisms (SNPs) in the identified top regions of PHF11, DPP10, and HLA-G, respectively, were genotyped in 1183 independent samples. The study samples were selected based on asthma affectation status and extreme values in at least one of the following three asthma-related phenotypes: total serum immunoglobulin E levels, bronchial responsiveness test, and skin prick test. Both single SNP and haplotype analyses were performed. Results We found that DPP10 was significantly associated with bronchial hyperresponsiveness (BHR) and BHR asthma after the adjustment for multiple testing; while the associations of PHF11 with positive skin reactions to antigens and the associations of HLA-G with BHR asthma were only nominally significant. Conclusion Our study is the first one to provide additional evidence that supports the roles of DPP10 in influencing asthma or BHR in a Chinese population.
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Affiliation(s)
- Huanyu Zhou
- Program for Population Genetics, Harvard School of Public Health, Boston, Massachusetts, USA.
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Taylor JM, Street TL, Hao L, Copley R, Taylor MS, Hayden PJ, Stolper G, Mott R, Hein J, Moffatt MF, Cookson WOCM. Dynamic and physical clustering of gene expression during epidermal barrier formation in differentiating keratinocytes. PLoS One 2009; 4:e7651. [PMID: 19888454 PMCID: PMC2766255 DOI: 10.1371/journal.pone.0007651] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2009] [Accepted: 10/09/2009] [Indexed: 11/18/2022] Open
Abstract
The mammalian epidermis is a continually renewing structure that provides the interface between the organism and an innately hostile environment. The keratinocyte is its principal cell. Keratinocyte proteins form a physical epithelial barrier, protect against microbial damage, and prepare immune responses to danger. Epithelial immunity is disordered in many common diseases and disordered epithelial differentiation underlies many cancers. In order to identify the genes that mediate epithelial development we used a tissue model of the skin derived from primary human keratinocytes. We measured global gene expression in triplicate at five times over the ten days that the keratinocytes took to fully differentiate. We identified 1282 gene transcripts that significantly changed during differentiation (false discovery rate <0.01%). We robustly grouped these transcripts by K-means clustering into modules with distinct temporal expression patterns, shared regulatory motifs, and biological functions. We found a striking cluster of late expressed genes that form the structural and innate immune defences of the epithelial barrier. Gene Ontology analyses showed that undifferentiated keratinocytes were characterised by genes for motility and the adaptive immune response. We systematically identified calcium-binding genes, which may operate with the epidermal calcium gradient to control keratinocyte division during skin repair. The results provide multiple novel insights into keratinocyte biology, in particular providing a comprehensive list of known and previously unrecognised major components of the epidermal barrier. The findings provide a reference for subsequent understanding of how the barrier functions in health and disease.
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Affiliation(s)
| | - Teresa L. Street
- Oxford Centre for Gene Function, Department of Statistics, University of Oxford, Oxford, England
| | - Lizhong Hao
- National Heart and Lung Institute, Imperial College, London, England
| | - Richard Copley
- Wellcome Trust Centre for Human Genetics, Oxford, England
| | | | - Patrick J. Hayden
- MatTek Corporation, Ashland, Massachusetts, United States of America
| | - Gina Stolper
- MatTek Corporation, Ashland, Massachusetts, United States of America
| | - Richard Mott
- Wellcome Trust Centre for Human Genetics, Oxford, England
| | - Jotun Hein
- Oxford Centre for Gene Function, Department of Statistics, University of Oxford, Oxford, England
| | - Miriam F. Moffatt
- National Heart and Lung Institute, Imperial College, London, England
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Mapp CE, Ferrazzoni S, Rizzo R, Miotto D, Stignani M, Boschetto P, Maestrelli P, Baricordi OR. Soluble human leucocyte antigen-G and interleukin-10 levels in isocyanate-induced asthma. Clin Exp Allergy 2009; 39:812-9. [PMID: 19302248 DOI: 10.1111/j.1365-2222.2009.03215.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
BACKGROUND We previously reported that in moderate-to-severe asthma there is a deficit of IL-10 secretion that could prevent the production of soluble HLA-G (sHLA-G), a non-classical human leucocyte antigen class I molecule with tissue-protective properties in inflammatory responses. OBJECTIVE Our objective was to investigate the production of sHLA-G and the secretion of IL-10 by peripheral blood mononuclear cells (PBMCs) in asthma induced by isocyanates and to compare the results with those obtained in non-occupational allergic asthma. METHOD sHLA-G and IL-10 were measured by ELISA in the culture supernatants of unstimulated or lipopolysaccharide (LPS)-stimulated PBMCs obtained from 20 subjects with isocyanate asthma, 16 asymptomatic subjects exposed to isocyanates, 18 subjects with non-occupational allergic asthma, and 26 healthy control subjects. RESULTS Occupational exposure to isocyanates was associated with high baseline levels of secretion of IL-10 by PBMCs, whether or not the exposed subjects had asthmatic symptoms. However, spontaneous production of sHLA-G by PBMC was significantly higher in subjects with isocyanate asthma compared with asymptomatic-exposed controls. In contrast, PBMCs from subjects with non-occupational allergic asthma produced sHLA-G only after LPS stimulation. CONCLUSIONS sHLA-G production and IL-10 secretion are influenced by workplace exposure to isocyanates and by development of asthma. The different behaviour of both sHLA-G and IL-10 in asthma induced by isocyanates compared with non-occupational allergic asthma suggests a heterogeneous biological role for HLA-G molecules and for IL-10, a key cytokine of immune and inflammatory responses.
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Affiliation(s)
- C E Mapp
- Department of Clinical and Experimental Medicine, Section of Hygiene and Occupational Medicine, University of Ferrara, Ferrara, Italy
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104
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Human leukocyte antigen-G polymorphism in relation to expression, function, and disease. Hum Immunol 2009; 70:1026-34. [PMID: 19651180 DOI: 10.1016/j.humimm.2009.07.015] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Revised: 07/24/2009] [Accepted: 07/28/2009] [Indexed: 02/07/2023]
Abstract
Human leukocyte antigen-G (HLA-G) is a nonclassical class Ib molecule belonging to the major histocompatibility complex. HLA-G appears to play a role in the suppression of immune responses and contribute to long-term immune escape or tolerance. The focus of this review is polymorphism in the HLA-G gene and protein and its possible importance in expression, function, and disease associations.
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105
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Nicolae DL, Ober C. (Too) great expectations: the challenges in replicating asthma disease genes. Am J Respir Crit Care Med 2009; 179:1078-9. [PMID: 19498061 DOI: 10.1164/rccm.200903-0456ed] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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106
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Teerlink CC, Camp NJ, Bansal A, Crapo R, Hughes D, Kort E, Rowe K, Cannon-Albright LA. Significant evidence for linkage to chromosome 5q13 in a genome-wide scan for asthma in an extended pedigree resource. Eur J Hum Genet 2009; 17:636-43. [PMID: 19092775 PMCID: PMC2672963 DOI: 10.1038/ejhg.2008.236] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2008] [Revised: 11/06/2008] [Accepted: 11/13/2008] [Indexed: 12/18/2022] Open
Abstract
Asthma is a multifactorial disease with undetermined genetic factors. We performed a genome-wide scan to identify predisposition loci for asthma. The asthma phenotype consisted of physician-confirmed presence or absence of asthma symptoms. We analyzed 81 extended Utah pedigrees ranging from three to six generations, including 742 affected individuals, ranging from 2 to 40 per pedigree. We performed parametric multipoint linkage analyses with dominant and recessive models. Our analysis revealed genome-wide significant evidence of linkage to region 5q13 (log of the odds ratio (LOD)=3.8, recessive model), and suggestive evidence for linkage to region 6p21 (LOD=2.1, dominant model). Both the 5q13 and 6p21 regions indicated in these analyses have been previously identified as regions of interest in other genome-wide scans for asthma-related phenotypes. The evidence of linkage at the 5q13 region represents the first significant evidence for linkage on a genome-wide basis for this locus. Linked pedigrees localize the region to approximately between 92.3-105.5 Mb.
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Affiliation(s)
- Craig C Teerlink
- Department of Biomedical Informatics, Division of Genetic Epidemiology, University of Utah School of Medicine, Salt Lake City, UT 84112-5750, USA.
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McEvoy BP, Montgomery GW, McRae AF, Ripatti S, Perola M, Spector TD, Cherkas L, Ahmadi KR, Boomsma D, Willemsen G, Hottenga JJ, Pedersen NL, Magnusson PKE, Kyvik KO, Christensen K, Kaprio J, Heikkilä K, Palotie A, Widen E, Muilu J, Syvänen AC, Liljedahl U, Hardiman O, Cronin S, Peltonen L, Martin NG, Visscher PM. Geographical structure and differential natural selection among North European populations. Genome Res 2009; 19:804-14. [PMID: 19265028 DOI: 10.1101/gr.083394.108] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Population structure can provide novel insight into the human past, and recognizing and correcting for such stratification is a practical concern in gene mapping by many association methodologies. We investigate these patterns, primarily through principal component (PC) analysis of whole genome SNP polymorphism, in 2099 individuals from populations of Northern European origin (Ireland, United Kingdom, Netherlands, Denmark, Sweden, Finland, Australia, and HapMap European-American). The major trends (PC1 and PC2) demonstrate an ability to detect geographic substructure, even over a small area like the British Isles, and this information can then be applied to finely dissect the ancestry of the European-Australian and European-American samples. They simultaneously point to the importance of considering population stratification in what might be considered a small homogeneous region. There is evidence from F(ST)-based analysis of genic and nongenic SNPs that differential positive selection has operated across these populations despite their short divergence time and relatively similar geographic and environmental range. The pressure appears to have been focused on genes involved in immunity, perhaps reflecting response to infectious disease epidemic. Such an event may explain a striking selective sweep centered on the rs2508049-G allele, close to the HLA-G gene on chromosome 6. Evidence of the sweep extends over a 8-Mb/3.5-cM region. Overall, the results illustrate the power of dense genotype and sample data to explore regional population variation, the events that have crafted it, and their implications in both explaining disease prevalence and mapping these genes by association.
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Affiliation(s)
- Brian P McEvoy
- Queensland Institute of Medical Research, Brisbane, Queensland, Australia.
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108
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Maestrelli P, Boschetto P, Fabbri LM, Mapp CE. Mechanisms of occupational asthma. J Allergy Clin Immunol 2009; 123:531-42; quiz 543-4. [DOI: 10.1016/j.jaci.2009.01.057] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2008] [Revised: 01/23/2009] [Accepted: 01/26/2009] [Indexed: 11/29/2022]
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109
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Eike MC, Humphreys K, Becker T, Olsson M, Lie BA. Three microsatellites from the T1DGC MHC data set show highly significant association with type 1 diabetes, independent of the HLA-DRB1, -DQA1 and -DQB1 genes. Diabetes Obes Metab 2009; 11 Suppl 1:17-24. [PMID: 19143811 PMCID: PMC2760257 DOI: 10.1111/j.1463-1326.2008.00999.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIM The aim of this study was to test the microsatellites in the Type 1 Diabetes Genetics Consortium major histocompatibility complex (MHC) data set for association with type 1 diabetes (T1D) independent of the HLA-DRB1, -DQA1 and -DQB1 genes. METHODS The data set was edited to contain only one affected child per family, and broad ethnic subgroups were defined. Genotypes for HLA-DRB1, -DQA1 and -DQB1 were replaced by a haplotype code spanning all three loci, with phase inferred based on common haplotypes. The final data set contained 8190 samples in 2301 families, 59 microsatellites and the DRB1-DQA1-DQB1 haplotype code. Statistical analyses consisted of conditional logistic regression and haplotype estimations and linkage disequilibrium calculations. RESULTS The data set was screened using a main effects test approach adjusted for DRB1-DQA1-DQB1, and significant results tested for validity. After these procedures, four markers remained significant at the Bonferroni-corrected threshold: D6S2773 (p = 0.00014), DG6S185 (p = 0.00015), DG6S398 (p = 0.00043) and D6S2998 (p = 0.00015). These results were supported by allelic tests conditioned on DRB1-DQA1-DQB1 haplotypes, except for DG6S185, which may contain artefacts. CONCLUSIONS We have identified three microsatellites that mark additional risk factors for T1D at highly significant levels in the MHC. Further analyses are needed to establish the relationship with other possible genetic determinants in this region.
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Affiliation(s)
- M C Eike
- Institute of Immunology, Rikshospitalet University Hospital, Oslo, Norway.
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Abstract
PURPOSE OF REVIEW Asthma is a disease of unknown aetiology characterized by intermittent inflammation of the small airways of the lung. Asthma is familial due to an interaction between strong genetic and environmental factors. This article aims to review the current understanding of the genetic factors underlying asthma, looking historically as well as highlighting the latest developments in the field. RECENT FINDINGS Findings from recent candidate gene studies and microsatellite genome screens have continued to highlight the importance of the epithelial barrier and its defence mechanisms in asthma. Completion of the human genome sequence and the advent of genome-wide association studies have resulted in the identification of two novel asthma susceptibility genes, ORMDL3 and CHI3L1, in the past year. SUMMARY With the advances in genetics and genomics substantial steps have been taken in the last decade in understanding the genetic factors underlying asthma. Studies have highlighted the importance of the role of the epithelium with many of the genes so far identified being expressed in this key barrier. With the application of genome-wide expression, microRNA studies, metagenomics, proteomics and metabolomics the next decade will undoubtedly result in a further substantial increment in our understanding of the mechanisms underlying asthma.
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111
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Eike MC, Becker T, Humphreys K, Olsson M, Lie BA. Conditional analyses on the T1DGC MHC dataset: novel associations with type 1 diabetes around HLA-G and confirmation of HLA-B. Genes Immun 2008; 10:56-67. [PMID: 18830248 DOI: 10.1038/gene.2008.74] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The major histocompatibility complex (MHC) is known to harbour genetic risk factors for type 1 diabetes (T1D) additional to the class II determinants HLA-DRB1, -DQA1 and -DQB1, but strong linkage disequilibrium (LD) has made efforts to establish their location difficult. This study utilizes a dataset generated by the T1D genetics consortium (T1DGC), with genotypes for 2965 markers across the MHC in 2321 T1D families of multiple (mostly Caucasian) ethnicities. Using a comprehensive approach consisting of complementary conditional methods and LD analyses, we identified three regions with T1D association, independent both of the known class II determinants and of each other. A subset of polymorphisms that could explain most of the association in each region included single nucleotide polymorphisms (SNPs) in the vicinity of HLA-G, particular HLA-B and HLA-DPB1 alleles, and SNPs close to the COL11A2 and RING1 genes. Apart from HLA-B and HLA-DPB1, all of these represent novel associations, and subpopulation analyses did not indicate large population-specific differences among Caucasians for our findings. On account of the unusual genetic complexity of the MHC, further fine mapping is demanded, with the possible exception of HLA-B. However, our results mean that these efforts can be focused on narrow, defined regions of the MHC.
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Affiliation(s)
- M C Eike
- Institute of Immunology, Rikshospitalet University Hospital, Oslo, Norway.
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112
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Brasch-Andersen C, Møller MU, Haagerup A, Vestbo J, Kruse TA. Evidence for an asthma risk locus on chromosome Xp: a replication linkage study. Allergy 2008; 63:1235-8. [PMID: 18699940 DOI: 10.1111/j.1398-9995.2008.01699.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND Asthma is a complex genetic disorder characterized by chronic inflammation in the airways. Identification of genetic risk factors for asthma has been complicated due to genetic heterogeneity and influence from environmental risk factors. Despite the fact that multiple genetic linkage studies have been carried out the results are still conflicting and call for replication experiments. A Danish genome-wide scan has prior reported evidence for candidate regions for asthma susceptibility genes on chromosomes 1p, 5q, 6p, 12q and Xp. Linkage to chromosome 12q was later confirmed in the same replication sample as used in the present study. The aim of the study was to replicate linkage to candidate regions for asthma in an independent Danish sample. METHODS We performed a replication study investigating linkage to candidate regions for asthma on chromosomes 1p36.31-p36.21, 5q15-q23.2, 6p24.3-p22.3, and Xp22.31-p11.4 using additional markers in an independent set of 136 Danish asthmatic sib pair families. RESULTS Nonparametric multipoint linkage analyses yielded suggestive evidence for linkage to asthma to chromosome Xp21.2 (MLS 2.92) but failed to replicate linkage to chromosomes 1p36.31-p36.21, 5q15-q23.2 and 6p24.3-p22.3. CONCLUSIONS The replication results provide evidence for chromosome Xp21 to harbour a susceptibility gene for asthma in the Danish population. To our knowledge, the study is the first to replicate evidence for linkage to chromosome X. A susceptibility gene for asthma on chromosome X could potentially explain observed gender differences in asthma prevalence.
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Affiliation(s)
- C Brasch-Andersen
- Department of Biochemistry, Pharmacology and Genetics, Odense University Hospital, and Clinical Pharmacology, Institute of Public Health, University of Southern Denmark, Odense, Denmark
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Castelli EC, Mendes-Junior CT, Viana de Camargo JL, Donadi EA. HLA-Gpolymorphism and transitional cell carcinoma of the bladder in a Brazilian population. ACTA ACUST UNITED AC 2008; 72:149-57. [DOI: 10.1111/j.1399-0039.2008.01091.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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114
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Papadopoulos NG, Borres M, Gern J, Nieto A. New visions in respiratory allergy (asthma and allergic rhinitis): an iPAC summary and future trends. Pediatr Allergy Immunol 2008; 19 Suppl 19:51-9. [PMID: 18665963 DOI: 10.1111/j.1399-3038.2008.00767.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
In many aspects, respiratory allergies, i.e., allergic asthma and rhinitis, represent the hallmarks of allergy. Epidemiologic data highlight their large prevalence of most parts of the world, socioeconomic analysis reveal their large impact on global health and the large number of scientific publications in this field regularly brings to light many new aspects of these diseases. However, the current understanding of respiratory allergies, in particular in children remains scarce. How can we efficiently prevent respiratory allergies in allergy-prone infants? How can we prevent the progression of the disease? What therapeutic strategies could efficiently address efficient immunomodulation? the international Pediatric Allergy and Asthma Consortium, addressed these issues by a thorough review of the literature providing a state-of-the-art current knowledge in respiratory allergy, and identified a series of needs to be addressed in future studies.
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Suryanarayana V, Rao L, Kanakavalli M, Padmalatha V, Raseswari T, Deenadayal M, Singh L. Association Between Novel HLA-G Genotypes and Risk of Recurrent Miscarriages: A Case-Control Study in a South Indian Population. Reprod Sci 2008; 15:817-24. [DOI: 10.1177/1933719107314061] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
| | - Lakshmi Rao
- Centre for Cellular and Molecular Biology, Hyderabad, Andhra Pradesh, India
| | - Murthy Kanakavalli
- Centre for Cellular and Molecular Biology, Hyderabad, Andhra Pradesh, India
| | - Venkata Padmalatha
- Centre for Cellular and Molecular Biology, Hyderabad, Andhra Pradesh, India
| | | | - Mamata Deenadayal
- Infertility Institute and Research Centre, Secunderabad, Andhra Pradesh, India
| | - Lalji Singh
- Centre for Cellular and Molecular Biology, Hyderabad, Andhra Pradesh, India,
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Holloway JW, Yang IA, Holgate ST. Interpatient variability in rates of asthma progression: can genetics provide an answer? J Allergy Clin Immunol 2008; 121:573-9. [PMID: 18328888 DOI: 10.1016/j.jaci.2008.01.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2007] [Revised: 01/09/2008] [Accepted: 01/10/2008] [Indexed: 12/01/2022]
Abstract
Asthma is a heterogeneous disorder with a variable natural history. In children 3 patterns of the natural history of asthma have been described: early onset but transient, persistent, and later onset, with only the former leading to persistent asthma later in childhood. In adults a range of different asthma phenotypes differing in their environmental, inflammatory, and prognostic characteristics have also been described. These extend beyond allergic (extrinsic) and nonallergic (intrinsic) asthma to include persistent airflow obstruction and accelerated decrease in lung function over time. Asthma progression can be defined as the change in an individual's phenotype along a continuum ranging from nonasthmatic to asthmatic and subsequent development of severe chronic disease. It is clear that for prevention of asthma progression in patients, there is a need for both better understanding of the pathophysiology of asthma and identification of predictors of progression. Interpatient genetic variability has been shown to affect multiple facets of asthma progression, including increased susceptibility to atopy and subsequent asthma, progression to severe disease, and modification of the response to treatment. Thus genetic testing might provide a means for predicting the likely progression of an individual along the continuum, allowing targeting of preventative treatment. However, the prospect of the use of genetic information in clinical practice raises important social and ethical issues that will need to be addressed before genetic testing can be used to inform the preventative treatment of patients to prevent the development of progression of asthma in individuals.
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Affiliation(s)
- John W Holloway
- Division of Infection, Inflammation and Repair, School of Medicine, University of Southampton, Southampton, United Kingdom.
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117
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Meta-analysis of genome-wide linkage studies of asthma and related traits. Respir Res 2008; 9:38. [PMID: 18442398 PMCID: PMC2391165 DOI: 10.1186/1465-9921-9-38] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2007] [Accepted: 04/28/2008] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Asthma and allergy are complex multifactorial disorders, with both genetic and environmental components determining disease expression. The use of molecular genetics holds great promise for the identification of novel drug targets for the treatment of asthma and allergy. Genome-wide linkage studies have identified a number of potential disease susceptibility loci but replication remains inconsistent. The aim of the current study was to complete a meta-analysis of data from genome-wide linkage studies of asthma and related phenotypes and provide inferences about the consistency of results and to identify novel regions for future gene discovery. METHODS The rank based genome-scan meta-analysis (GSMA) method was used to combine linkage data for asthma and related traits; bronchial hyper-responsiveness (BHR), allergen positive skin prick test (SPT) and total serum Immunoglobulin E (IgE) from nine Caucasian asthma populations. RESULTS Significant evidence for susceptibility loci was identified for quantitative traits including; BHR (989 pedigrees, n = 4,294) 2p12-q22.1, 6p22.3-p21.1 and 11q24.1-qter, allergen SPT (1,093 pedigrees, n = 4,746) 3p22.1-q22.1, 17p12-q24.3 and total IgE (729 pedigrees, n = 3,224) 5q11.2-q14.3 and 6pter-p22.3. Analysis of the asthma phenotype (1,267 pedigrees, n = 5,832) did not identify any region showing genome-wide significance. CONCLUSION This study represents the first linkage meta-analysis to determine the relative contribution of chromosomal regions to the risk of developing asthma and atopy. Several significant results were obtained for quantitative traits but not for asthma confirming the increased phenotype and genetic heterogeneity in asthma. These analyses support the contribution of regions that contain previously identified asthma susceptibility genes and provide the first evidence for susceptibility loci on 5q11.2-q14.3 and 11q24.1-qter.
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118
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Szalai C, Ungvári I, Pelyhe L, Tölgyesi G, Falus A. Asthma from a pharmacogenomic point of view. Br J Pharmacol 2008; 153:1602-14. [PMID: 18311188 PMCID: PMC2438267 DOI: 10.1038/bjp.2008.55] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2007] [Revised: 01/28/2008] [Accepted: 02/01/2008] [Indexed: 12/25/2022] Open
Abstract
Pharmacogenomics, a fascinating, emerging area of biomedical research is strongly influenced by growing availability of genomic databases, high-throughput genomic technologies, bioinformatic tools and artificial computational modelling approaches. One main area of pharmacogenomics is the discovery of new drugs and drug targets with molecular genetic, genomic or even bioinformatic methods; the other is the study of how genomic differences influence the variability in patients' responses to drugs. From a genetic point of view, asthma is multifactorial, which means that the susceptibility to the disease is determined by interactions between multiple genes, and involves important non-genetic factors such as the environment for their expression. In this review, we summarize collective evidence from linkage and association studies that have consistently reported suggestive linkage or association of asthma or its associated phenotypes to polymorphic markers and single nucleotide polymorphisms in selected chromosomes. Genes that have been found implicated in the disease are potential new drug targets and several pharmacological investigations are underway to utilize these new discoveries. Next, we will focus on the inter-individual variability in anti-asthmatic drug responses and review the recent results in this topic.
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Affiliation(s)
- C Szalai
- Laboratory of Molecular Biology, Heim Pál Pediatric Hospital Budapest, Hungary
- Inflammation Biology and Immunogenomics Research Group, Hungarian Academy of Sciences, Semmelweis University Budapest, Hungary
| | - I Ungvári
- Department of Genetics, Cell and Immunobiology, Semmelweis University Budapest, Hungary
| | - L Pelyhe
- Faculty of Biology, Eötvös Lóránd University Budapest, Hungary
| | - G Tölgyesi
- Department of Genetics, Cell and Immunobiology, Semmelweis University Budapest, Hungary
| | - A Falus
- Inflammation Biology and Immunogenomics Research Group, Hungarian Academy of Sciences, Semmelweis University Budapest, Hungary
- Department of Genetics, Cell and Immunobiology, Semmelweis University Budapest, Hungary
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Rizzo R, Hviid TVF, Govoni M, Padovan M, Rubini M, Melchiorri L, Stignani M, Carturan S, Grappa MT, Fotinidi M, Ferretti S, Voss A, Laustrup H, Junker P, Trotta F, Baricordi OR. HLA-G genotype and HLA-G expression in systemic lupus erythematosus: HLA-G as a putative susceptibility gene in systemic lupus erythematosus. ACTA ACUST UNITED AC 2008; 71:520-9. [PMID: 18380776 DOI: 10.1111/j.1399-0039.2008.01037.x] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disease mainly mediated by the deposit of immune complexes and defects in T lymphocytes and antigen-presenting cells along with a high production of T-helper 2 cytokines. A tolerance-inducible function of nonclassical class Ib human leukocyte antigen (HLA)-G molecule in innate and adaptive cellular responses has been reported, suggesting a role in inflammatory diseases. A 14 bp sequence insertion/deletion polymorphism (rs16375) in the 3'-untranslated region of the HLA-G gene has been associated to the stability of HLA-G messenger RNA. The insertion of the 14 bp sequence seems to be associated with lower levels of soluble HLA-G (sHLA-G). The aim of this study was to evaluate the possible association of the presence of the 14 bp sequence (+14 bp) with SLE. We have HLA-G genotyped 200 SLE patients and 451 healthy control subjects (HS; Italian) and analyzed the plasma levels of sHLA-G and interleukin-10 (IL-10) in a subset of SLE patients and healthy subjects (Italian and Danish). A significant increase of the +14 bp HLA-G allele was detected in the Italian SLE patients compared with HS [P = 0.003, OR 1.44 (95% CI 1.13-1.82)]. A significant increased frequency of HLA-G +14/+14 bp and a decreased frequency of HLA-G -14/-14 bp were observed in SLE patients. There median concentration of sHLA-G was significantly lower in the plasma of SLE patients compared with that in the plasma of healthy controls (P < 0.0001). Furthermore, the results confirmed higher concentrations of IL-10-positive plasma in SLE patients. These results support a potential role for HLA-G in the susceptibility of SLE.
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Affiliation(s)
- R Rizzo
- Department of Experimental and Diagnostic Medicine, University of Ferrara, Ferrara, Italy.
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Abstract
Asthma and asthma-related traits are complex diseases with strong genetic and environmental components. Rapid progress in asthma genetics has led to the identification of several candidate genes that are associated with asthma-related traits. Typically the phenotypic impact of each of these genes, including the ones most often replicated in association studies, is mild, but larger effects may occur when multiple variants synergize within a permissive environmental context. Despite the achievements made in asthma genetics formidable challenges remain. The development of novel, powerful tools for gene discovery, and a closer integration of genetics and biology, should help to overcome these challenges.
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121
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Yan WH, Lin A, Li M, Xu HH, Zhang ZP, Wang XX. Analysis of the 14 bp insertion and deletion polymorphism in human leukocyte antigen-G gene in two Chinese ethnic populations. ACTA ACUST UNITED AC 2008; 71:227-33. [DOI: 10.1111/j.1399-0039.2008.01006.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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122
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Hui J, Oka A, James A, Palmer LJ, Musk AW, Beilby J, Inoko H. A genome-wide association scan for asthma in a general Australian population. Hum Genet 2008; 123:297-306. [PMID: 18253752 DOI: 10.1007/s00439-008-0477-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2007] [Accepted: 01/25/2008] [Indexed: 01/31/2023]
Abstract
To date, almost every chromosome has been implicated in genetic susceptibility to asthma to some degree. When compared with single nucleotide polymorphism, microsatellite markers exhibit high levels of heterozygosity and therefore provide higher statistical power in association. The objective of this study was to perform a genome-wide association study using 23,465 in-house microsatellite markers to detect asthma susceptibility regions in the Busselton population. In this study, three separate pooled DNA screenings yielded 18 markers with significantly different estimated frequencies in the three separate "case and control" pools: each pool consisting of 60 males and 60 females. These markers were evaluated by individual typing in 360 cases and 360 controls. Two markers showed significant differences between cases and controls (P = 0.001 and P = 0.003). Regions surrounding the two markers were subjected to high-density association mapping with a total of 14 additional markers. We were able to confirm and fine map the association in these two regions by typing 14 additional microsatellite markers (1805A09 (D18S0325i), P = 0.002; 1806D05 (D18S0181i), P = 0.001). Each region contains a predicted gene that showed strong associations with asthma. Further studies are underway to characterize the novel candidate asthma susceptibility genes identified in this genome-wide study.
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Affiliation(s)
- J Hui
- Western Australian Institute for Medical Research and UWA Centre for Medical Research, B Block, QEII Medical Centre, The University of Western Australia, Nedlands, WA, 6009, Australia.
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123
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Windelinckx A, Vlietinck R, Aerssens J, Beunen G, Thomis MAI. Selection of genes and single nucleotide polymorphisms for fine mapping starting from a broad linkage region. Twin Res Hum Genet 2008; 10:871-85. [PMID: 18179400 DOI: 10.1375/twin.10.6.871] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Fine mapping of linkage peaks is one of the great challenges facing researchers who try to identify genes and genetic variants responsible for the variation in a certain trait or complex disease. Once the trait is linked to a certain chromosomal region, most studies use a candidate gene approach followed by a selection of polymorphisms within these genes, either based on their possibility to be functional, or based on the linkage disequilibrium between adjacent markers. For both candidate gene selection and SNP selection, several approaches have been described, and different software tools are available. However, mastering all these information sources and choosing between the different approaches can be difficult and time-consuming. Therefore, this article lists several of these in silico procedures, and the authors describe an empirical two-step fine mapping approach, in which candidate genes are prioritized using a bioinformatics approach (ENDEAVOUR), and the top genes are chosen for further SNP selection with a linkage disequilibrium based method (Tagger). The authors present the different actions that were applied within this approach on two previously identified linkage regions for muscle strength. This resulted in the selection of 331 polymorphisms located in 112 different candidate genes out of an initial set of 23,300 SNPs.
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Affiliation(s)
- An Windelinckx
- Research Center for Exercise and Health, Department of Biomedical Kinesiology, Faculty of Kinesiology and Rehabilitation Sciences, Katholieke Universiteit Leuven, Leuven, Belgium
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124
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Miller RL, Ho SM. Environmental epigenetics and asthma: current concepts and call for studies. Am J Respir Crit Care Med 2008; 177:567-73. [PMID: 18187692 DOI: 10.1164/rccm.200710-1511pp] [Citation(s) in RCA: 224] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Recent studies suggest that epigenetic regulation (heritable changes in gene expression that occur in the absence of alterations in DNA sequences) may in part mediate the complex gene-by-environment interactions that can lead to asthma. The variable natural history of asthma (i.e., incidence and remission of symptoms) may be a result of epigenetic changes, such as DNA methylation, covalent histone modifications, microRNA changes, and chromatin alterations, after early or later environmental exposures. Findings from multiple epidemiologic and experimental studies indicate that asthma risk may be modified by epigenetic regulation. One study suggested that the transmission of asthma risk may occur across multiple generations. Experimental studies provide substantial in vitro data indicating that DNA methylation of genes critical to T-helper cell differentiation may induce polarization toward or away from an allergic phenotype. Despite this initial progress, fundamental questions remain that need to be addressed by well-designed research studies. Data generated from controlled experiments using in vivo models and/or clinical specimens collected after environmental exposure monitoring are limited. Importantly, cohort-driven epigenetic research has the potential to address key questions, such as those concerning the influence of timing of exposure, dose of exposure, diet, and ethnicity on susceptibility to asthma development. There is immense promise that the study of environmental epigenetics will help us understand a theoretically preventable environmental disease.
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Affiliation(s)
- Rachel L Miller
- PH8E, 630 W. 168th Street, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA.
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125
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Scirica CV, Celedón JC. Genetics of asthma: potential implications for reducing asthma disparities. Chest 2008; 132:770S-781S. [PMID: 17998341 DOI: 10.1378/chest.07-1905] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Although genetic factors may partly explain the differences in asthma prevalence, morbidity, and mortality among ethnic groups in the United States, few studies of the genetics of asthma have included members of ethnic minority groups. Only one genome-wide linkage analysis of asthma and/or asthma-related phenotypes (conducted by the Collaborative Study on the Genetics of Asthma) has included any members of ethnic minority populations. The interpretation of the findings of genetic association studies of asthma in ethnic minority groups is complicated by reduced statistical power due to small sample sizes; the failure to correct for multiple comparisons; a lack of homogeneity of the populations studied with regard to area of residence, ancestral background, and/or country of origin; a lack of measurement of relevant environmental exposures; and (for case-control studies of genetic association) a lack of detection and control of potential population stratification. Genetic studies may improve our understanding of asthma and lead to new methods to prevent, diagnose, and treat this disease. Limited study of asthma genetics in ethnic minority populations is unacceptable, as it may prevent these groups from benefiting from future developments in asthma management and thus widen existing disparities in asthma care. Future genetic association studies of asthma among ethnic minorities in the United States should include large samples of populations that have been adequately defined with regard to area of residence, self-designated ancestry, and country of origin. These studies should also include an adequate assessment of potentially relevant environmental exposures and (for case-control association studies) population stratification.
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126
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Abstract
In asthma, as in many other common multifactorial diseases, the identification of the susceptibility genes has been challenging because consistent results at the genome-wide significance level have been scarce. So far, genome-wide scans have been reported in 17 study populations. By means of genome-wide linkage and hierarchical association analysis, six positional candidate genes (ADAM33, PHF11, DPP10, GPR154, HLA-G, and CYFIP2) for asthma-related traits have been cloned. The interactions of the proteins encoded by these genes and the biological relevance of these signaling pathways in the development of asthma are still poorly understood. Also, the disease mechanisms resulting from the genetic variance in the genes identified remain largely unknown. Although this information is gradually accumulating, we can examine the statistical robustness of each genetic finding in combination with the limited data available on the functional properties of the corresponding proteins to estimate the strengths and weaknesses in the chains of evidence.
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127
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Hersh CP, Raby BA, Soto-Quirós ME, Murphy AJ, Avila L, Lasky-Su J, Sylvia JS, Klanderman BJ, Lange C, Weiss ST, Celedón JC. Comprehensive testing of positionally cloned asthma genes in two populations. Am J Respir Crit Care Med 2007; 176:849-57. [PMID: 17702965 PMCID: PMC2048676 DOI: 10.1164/rccm.200704-592oc] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2007] [Accepted: 08/07/2007] [Indexed: 11/16/2022] Open
Abstract
RATIONALE Replication of gene-disease associations has become a requirement in complex trait genetics. OBJECTIVES In studies of childhood asthma from two different ethnic groups, we attempted to replicate associations with five potential asthma susceptibility genes previously identified by positional cloning. METHODS We analyzed two family-based samples ascertained through an asthmatic proband: 497 European-American children from the Childhood Asthma Management Program and 439 Hispanic children from the Central Valley of Costa Rica. We genotyped 98 linkage disequilibrium-tagging single-nucleotide polymorphisms (SNPs) in five genes: ADAM33, DPP10, GPR154 (HUGO name: NPSR1), HLA-G, and the PHF11 locus (includes genes SETDB2 and RCBTB1). SNPs were tested for association with asthma and two intermediate phenotypes: airway hyperresponsiveness and total serum immunoglobulin E levels. MEASUREMENTS AND MAIN RESULTS Despite differing ancestries, linkage disequilibrium patterns were similar in both cohorts. Of the five evaluated genes, SNP-level replication was found only for GPR154 (NPSR1). In this gene, three SNPs were associated with asthma in both cohorts, although the opposite alleles were associated in either study. Weak evidence for locus-level replication with asthma was found in the PHF11 locus, although there was no overlap in the associated SNP across the two cohorts. No consistent associations were observed for the three other genes. CONCLUSIONS These results provide some further support for the role of genetic variation in GPR154 (NPSR1) and PHF11 in asthma susceptibility and also highlight the challenges of replicating genetic associations in complex traits such as asthma, even for genes identified by linkage analysis.
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Affiliation(s)
- Craig P Hersh
- Channing Laboratory and Center for Genomic Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA.
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128
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Tan Z, Randall G, Fan J, Camoretti-Mercado B, Brockman-Schneider R, Pan L, Solway J, Gern JE, Lemanske RF, Nicolae D, Ober C. Allele-specific targeting of microRNAs to HLA-G and risk of asthma. Am J Hum Genet 2007; 81:829-34. [PMID: 17847008 PMCID: PMC2227932 DOI: 10.1086/521200] [Citation(s) in RCA: 301] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2007] [Accepted: 06/13/2007] [Indexed: 12/19/2022] Open
Abstract
HLA-G is a nonclassic, class I HLA molecule that has important immunomodulatory properties. Previously, we identified HLA-G as an asthma-susceptibility gene and discovered that the risk of asthma in a child was determined by both the child's HLA-G genotype and the mother's affection status. Here we report a SNP in the 3' untranslated region of HLA-G that influences the targeting of three microRNAs (miRNAs) to this gene, and we suggest that allele-specific targeting of these miRNAs accounts, at least in part, for our earlier observations on HLA-G and the risk of asthma.
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Affiliation(s)
- Zheng Tan
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.
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129
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Lin A, Yan WH, Xu HH, Tang LJ, Chen XF, Zhu M, Zhou MY. 14 bp deletion polymorphism in the HLA-G gene is a risk factor for idiopathic dilated cardiomyopathy in a Chinese Han population. ACTA ACUST UNITED AC 2007; 70:427-31. [PMID: 17854427 DOI: 10.1111/j.1399-0039.2007.00926.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Human leukocyte antigen (HLA) has been reported to be associated with the pathogenesis of autoimmune-associated idiopathic dilated cardiomyopathy (IDC). However, the HLA-G in this context is limited. In the current study, a total of 117 IDC patients and age and sex matched 401 unrelated healthy controls in a Chinese Han population were HLA-G genotyped for the 14 bp insertion and deletion polymorphism. IDC patients showed markedly increased frequencies of -14 bp/-14 bp genotype [Pc = 0.00049, odds ratio (OR) = 2.17] and -14 bp alleles (Pc = 4.1 x 10(-5), OR = 1.97) when compared with healthy controls. Whereas the frequencies of +14 bp/+14 bp genotype (Pc = 0.0036, OR = 0.35) and +14 bp alleles (Pc = 4.1 x 10(-5), OR = 0.51) were significantly lower in IDC. These data, for the first time, indicated that 14 bp insertion/deletion polymorphism in HLA-G gene could be a genetic risk factor for the susceptibility to IDC.
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Affiliation(s)
- A Lin
- Medical Research Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical College, Linhai, Zhejiang, China
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130
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131
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Tan Z, Randall G, Fan J, Camoretti-Mercado B, Brockman-Schneider R, Pan L, Solway J, Gern JE, Lemanske RF, Nicolae D, Ober C. Allele-specific targeting of microRNAs to HLA-G and risk of asthma. Am J Hum Genet 2007. [PMID: 17847008 DOI: 10.1086/521200.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
HLA-G is a nonclassic, class I HLA molecule that has important immunomodulatory properties. Previously, we identified HLA-G as an asthma-susceptibility gene and discovered that the risk of asthma in a child was determined by both the child's HLA-G genotype and the mother's affection status. Here we report a SNP in the 3' untranslated region of HLA-G that influences the targeting of three microRNAs (miRNAs) to this gene, and we suggest that allele-specific targeting of these miRNAs accounts, at least in part, for our earlier observations on HLA-G and the risk of asthma.
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Affiliation(s)
- Zheng Tan
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.
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132
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Abstract
Asthma is a chronic inflammatory airways disease, with a rising prevalence, particularly in childhood, and is considered an important public health problem. Its familial transmission is recognised, while the description and identification of the genes implicated in this disease are a challenge. In this revision paper the authors give a comprehensive explanation of the associated genes as well as the laboratorial methods that allow their identification.
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Affiliation(s)
- Paula Alexandra Videira
- Faculty of Medical Sciences, Department of Immunology, Universidade Nova de Lisboa, Campo dos Mártires da Pátria no. 130, 1169-056 Lisbon
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133
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Castelli EC, Mendes-Junior CT, Donadi EA. HLA-G alleles and HLA-G 14 bp polymorphisms in a Brazilian population. ACTA ACUST UNITED AC 2007; 70:62-8. [PMID: 17559583 DOI: 10.1111/j.1399-0039.2007.00855.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Brazilians represent one of the most heterogeneous populations in the world as the result of five centuries of interethnic crosses. We investigated the polymorphism of the HLA-G locus in a Brazilian urban sample. HLA-G alleles were determined by SBT analysis of exons 2-4 and 8 in 103 unrelated individuals. The genotyping analysis identified 11 different HLA-G alleles, including the recently described G*010110 allele, and four new variants in this population. These data indicate that this Brazilian population presents high HLA-G allelic polymorphism, suggesting increased levels of intrapopulational genetic diversity that may be because of the admixed nature of the sample. This is the first study regarding HLA-G genotyping that was performed at such refined resolution level in this heterogeneous population.
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Affiliation(s)
- E C Castelli
- Division of Clinical Immunology, Department of Medicine, School of Medicine of Ribeirão Preto, University of São Paulo, Avenida Bandeirantes 3900, 14049-900 Ribeirão Preto, São Paulo, Brazil.
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134
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Abstract
Epidemiological and twin studies have demonstrated that asthma is under genetic and environmental influences. Numerous candidate gene association studies as well as genome-wide linkage scans have followed, aiming to elucidate the genetic architecture underlying this complex disease. Several promising asthma susceptibility genes were identified, and a comprehensive catalogue of these genes seems a realistic goal within 5 to 10 years. However, a key challenge is to understand the combination of genes and environmental factors that gives rise to the disease in a specific individual. Currently, most of the reports of asthma susceptibility genes are either preliminary or controversial, with little knowledge about the genetic mechanisms leading to abnormal function of the gene that promotes the development of asthma. Replications of published associations are relatively few. Many factors, including the inherent complexity of asthma as well as methodological issues, can explain these inconsistencies. Promising genetic tools are emerging with the completion of the International HapMap Project that will increase the scope of gene-discovery investigations. It is hoped that these tools, combined with validation studies in additional populations, will enable the creation of a comprehensive catalogue of susceptibility genes for asthma. Notwithstanding the difficulties in making sense of the vast amount of new genetic data, we already see the emergence of new biological pathways of atopy, airway remodeling, and asthma that may lead to novel therapeutic approaches.
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Affiliation(s)
- Yohan Bossé
- McGill University, Génome Québec Innovation Center, Montréal, Québec, Canada
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135
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Holloway JW, Koppelman GH. Identifying novel genes contributing to asthma pathogenesis. Curr Opin Allergy Clin Immunol 2007; 7:69-74. [PMID: 17218814 DOI: 10.1097/aci.0b013e328013d51b] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW To illustrate recent examples of novel asthma genes such as those encoding G-protein-coupled receptor for asthma susceptibility, filaggrin and tenascin-C, and to describe the process that is needed to translate these findings to the clinic. RECENT FINDINGS Many hundreds of studies have been published investigating the association of genetic polymorphisms in candidate genes with asthma. These genes were selected on the basis of the gene's product known involvement in the disease process. Moreover, it is the identification of novel genes through hypothesis-independent approaches such as genome-wide linkage studies that is likely to radically alter our understanding of asthma pathophysiology. The identification of a gene is, however, only the first step in a long process that may eventually lead from gene to treatment. This process includes replication, functional studies and, finally, intervention studies. SUMMARY While significant progress has been made in the identification of asthma susceptibility genes, it is clear that issues such as replication and functional characterization mean that considerably more research is required. This may enable us to realize benefits to patient treatment that studies of the genetic basis of asthma have the potential to deliver.
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Affiliation(s)
- John W Holloway
- Divisions of Infection, Inflammation and Repair, University of Southampton, Southampton, UK.
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136
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Barnes KC, Grant AV, Hansel NN, Gao P, Dunston GM. African Americans with asthma: genetic insights. Ann Am Thorac Soc 2007; 4:58-68. [PMID: 17202293 PMCID: PMC2647616 DOI: 10.1513/pats.200607-146jg] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
It has been well established that genetic factors strongly affect susceptibility to asthma and its associated traits. It is less clear to what extent genetic variation contributes to the ethnic disparities observed for asthma morbidity and mortality. Individuals of African descent with asthma have more severe asthma, higher IgE levels, a higher degree of steroid dependency, and more severe clinical symptoms than individuals of European descent with asthma but relatively few studies have focused on this particularly vulnerable ethnic group. Similar underrepresentation exists for other minorities, including Hispanics. In this review, a summary of linkage and association studies in populations of African descent is presented, and the role of linkage disequilibrium in the dissection of a complex trait such as asthma is discussed. Consideration for the impact of population stratification in recently admixed populations (i.e., European, African) is essential in genetic association studies focusing on African ancestry groups. With the most recent update on the International HapMap Project, efficient selection of haplotype tagging single nucleotide polymorphisms (htSNPs) for African Americans has accelerated and efficiency of htSNPs chosen from one population to represent other continental groups (e.g., African) has been demonstrated. Cutting-edge approaches, such as genomewide association studies, admixture mapping, and phylogenetic analyses, offer new opportunities for dissecting the genetic basis for asthma in populations of African descent.
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Affiliation(s)
- Kathleen C Barnes
- Division of Allergy and Clinical Immunology, Department of Medicine, The Johns Hopkins University, Baltimore, Maryland, USA.
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137
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Thompson MD, Takasaki J, Capra V, Rovati GE, Siminovitch KA, Burnham WM, Hudson TJ, Bossé Y, Cole DEC. G-protein-coupled receptors and asthma endophenotypes: the cysteinyl leukotriene system in perspective. Mol Diagn Ther 2007; 10:353-66. [PMID: 17154652 DOI: 10.1007/bf03256212] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Genetic variation in specific G-protein coupled receptors (GPCRs) is associated with a spectrum of respiratory disease predispositions and drug response phenotypes. Although certain GPCR gene variants can be disease-causing through the expression of inactive, overactive, or constitutively active receptor proteins, many more GPCR gene variants confer risk for potentially deleterious endophenotypes. Endophenotypes are traits, such as bronchiole hyperactivity, atopy, and aspirin intolerant asthma, which have a strong genetic component and are risk factors for a variety of more complex outcomes that may include disease states. GPCR genes implicated in asthma endophenotypes include variants of the cysteinyl leukotriene receptors (CYSLTR1 and CYSLTR2), and prostaglandin D2 receptors (PTGDR and CRTH2), thromboxane A2 receptor (TBXA2R), beta2-adrenergic receptor (ADRB2), chemokine receptor 5 (CCR5), and the G protein-coupled receptor associated with asthma (GPRA). This review of the contribution of variability in these genes places the contribution of the cysteinyl leukotriene system to respiratory endophenotypes in perspective. The genetic variant(s) of receptors that are associated with endophenotypes are discussed in the context of the extent to which they contribute to a disease phenotype or altered drug efficacy.
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Affiliation(s)
- Miles D Thompson
- Department of Laboratory Medicine and Pathobiology, University of Toronto, and Department of Medical Genetics and Microbiology, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
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138
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Singh AM, Moore PE, Gern JE, Lemanske RF, Hartert TV. Bronchiolitis to asthma: a review and call for studies of gene-virus interactions in asthma causation. Am J Respir Crit Care Med 2006; 175:108-19. [PMID: 17053206 DOI: 10.1164/rccm.200603-435pp] [Citation(s) in RCA: 163] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Viral infections are important causes of asthma exacerbations in children, and lower respiratory tract infections (LRTIs), caused by viruses such as respiratory syncytial virus (RSV) and rhinovirus (RV), are a leading cause of bronchiolitis in infants. Infants hospitalized with bronchiolitis are at significantly increased risk for both recurrent wheezing and childhood asthma. To date, studies addressing the incidence of asthma after bronchiolitis severe enough to warrant hospitalization have focused almost exclusively on RSV, but a number of recent studies suggest that other respiratory pathogens, including RV, may contribute as well. It is not known whether viral bronchiolitis directly contributes to asthma causation or simply identifies infants at risk for subsequent wheezing, as from an atopic predisposition or preexisting abnormal lung function. Alternatively, the properties of the infecting virus may be important. Thus, many possible determinants exist that may contribute to the severity of bronchiolitis and the subsequent development of asthma. One such determinant is the potential involvement of genetic susceptibility loci to asthma after viral bronchiolitis, a critical area that is just beginning to be evaluated. By clarifying the roles of both host- (genetic) and virus- (environment) specific factors that contribute to the frequency and severity of viral LRTI, it may be possible to determine if severe LRTIs cause asthma, or if asthma susceptibility predisposes patients to severe LRTI in response to viral infection. Characterizing these relationships offers the potential of identifying at-risk hosts in whom preventing or delaying infection could alter the phenotypic expression of asthma.
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Affiliation(s)
- Anne Marie Singh
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53792, USA.
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139
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Abstract
Asthma is a chronic inflammatory disease of the airways that is highly prevalent in the Western world. It is a genetically complex disease caused by multiple genetic and environmental factors, which may interact. Genetic research has recently incorporated environmental factors to investigate gene by environment interaction, and the first examples of gene by environment interaction in asthma have been reported. Linkage analyses indicate that one or more genes on chromosome 5q interact with environmental tobacco smoke in infancy in asthma development. Several candidate genes have been consistently shown to interact with the environment. These include the innate immunity genes CD14 and Toll-like receptor 4, and microbial exposures, as well as the detoxifying gene family glutathione-S-transferase and environmental tobacco smoke exposure and air pollutants. Gene by environment interaction is important in asthma pathogenesis, and future studies should take the interaction of both factors into account.
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Affiliation(s)
- Gerard H Koppelman
- Department of Pediatric Pulmonology, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, PO Box 30.001, 9700 RB Groningen, the Netherlands.
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140
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Vendelin J, Bruce S, Holopainen P, Pulkkinen V, Rytilä P, Pirskanen A, Rehn M, Laitinen T, Laitinen LA, Haahtela T, Saarialho-Kere U, Laitinen A, Kere J. Downstream target genes of the neuropeptide S-NPSR1 pathway. Hum Mol Genet 2006; 15:2923-35. [PMID: 16926187 DOI: 10.1093/hmg/ddl234] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The neuropeptide S (NPS)-NPS receptor 1 (NPSR1) pathway has recently been implicated in the pathogenesis of asthma. The purpose of this study was to identify downstream gene targets regulated by NPSR1 upon NPS stimulation. A total of 104 genes were found significantly up-regulated and 42 down-regulated by microarray analysis 6 h after NPS administration. By Gene Ontology enrichment analysis, the categories 'cell proliferation', 'morphogenesis' and 'immune response' were among the most altered. A TMM microarray database comparison suggested a common co-regulated pathway, which includes JUN/FOS oncogene homologs, early growth response genes, nuclear receptor subfamily 4 members and dual specificity phosphatases. The expression of four up-regulated genes, matrix metallopeptidase 10 (MMP10), INHBA (activin A), interleukin 8 (IL8) and EPH receptor A2 (EPHA2), exhibited a significant NPS dose-response relationship as confirmed by quantitative reverse-transcriptase-PCR and for MMP10 by immunoassay. Immunohistochemical analyses revealed that MMP10 and TIMP metallopeptidase inhibitor 3 (TIMP3) were both strongly expressed in bronchial epithelium, and macrophages and eosinophils expressed MMP10 in asthmatic sputum samples. Because remodeling of airway epithelium is a feature of chronic asthma, the up-regulation of MMP10 and TIMP3 by NPS-NPSR1 signaling may be of relevance in the pathogenesis of asthma.
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Affiliation(s)
- Johanna Vendelin
- Department of Medical Genetics, Biomedicum Helsinki, University of Helsinki, Finland, and Department of Biosciences and Nutrition, Clinical Research Centre, Karolinska Institutet, Karolinska University Hospital, Huddinge, Sweden
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141
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Tahan F, Patiroglu T. Plasma soluble human leukocyte antigen G levels in asthmatic children. Int Arch Allergy Immunol 2006; 141:213-6. [PMID: 16926540 DOI: 10.1159/000095290] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2006] [Accepted: 04/20/2006] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Human leukocyte antigen G (HLA-G) is a nonclassical major histocompatibility complex class I gene. HLA-G stimulates Th2 cytokine secretion by peripheral blood mononuclear cells. The role of soluble HLA-G (sHLA-G) in bronchial asthma is incompletely understood and the plasma level of sHLA-G in asthmatic children has not been investigated. OBJECTIVE It was the aim of this study to investigate the plasma level of sHLA-G in asthmatic children. METHODS Asthmatic (n = 53) and healthy children (n = 16) were included in the study. Levels of sHLA-G were determined in plasma using ELISA. Spirometry, total immunoglobulin E and eosinophil counts were obtained and skin testing done with a battery of 25 antigens with appropriate positive and negative controls. RESULTS No significant difference was observed in the plasma level of sHLA-G between the asthmatic and healthy children (p > 0.05). When we compared atopic asthmatics with healthy controls, we found significantly higher levels of sHLA-G in atopic asthmatics (p < 0.05). There was a significant difference in the peripheral blood eosinophil counts and total immunoglobulin E levels among the groups (p < 0.001). CONCLUSION Our study shows that plasma sHLA-G levels do not differ between asthmatic children and healthy controls. However, higher plasma levels of sHLA-G in atopic asthmatics may suggest a role for sHLA-G in atopy. Further investigations are required to better define the mechanism of the production and the role of sHLA-G molecules observed in patients with asthma.
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Affiliation(s)
- Fulya Tahan
- Department of Pediatric Allergy, Erciyes University School of Medicine, Kayseri, Turkey
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142
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Aoki T, Hirota T, Tamari M, Ichikawa K, Takeda K, Arinami T, Shibasaki M, Noguchi E. An association between asthma and TNF-308G/A polymorphism: meta-analysis. J Hum Genet 2006; 51:677-685. [PMID: 16865291 DOI: 10.1007/s10038-006-0007-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2006] [Accepted: 04/30/2006] [Indexed: 11/29/2022]
Abstract
Tumor necrosis factor (TNF) is a potent inflammatory cytokine that contributes to airway inflammation in asthma. Previous studies have reported that a G-to-A transition at position -308 (-308G/A, also referred to as TNF-alpha-308*1 and 308*2 respectively), is associated with asthma, but other studies have shown conflicting results. To investigate a possible association between the TNF-308G/A polymorphism and asthma, we performed transmission disequilibrium tests and a case-control study (family samples: 495 members in 165 Japanese trio families with one asthmatic child and both parents; case-control samples: 461 Japanese asthmatic children and 465 healthy controls). To increase the sample size and power, we performed a meta-analysis of all available relevant studies, including 2,477 asthmatics and 3,217 controls. We did not find a significant association between the TNF-308G/A polymorphism and childhood atopic asthma in two independent Japanese populations (P>0.05); however, meta-analysis revealed that the TNF-308G/A polymorphism was statistically significantly associated with asthma. The combined odds ratio with a fixed effects model and with a random effects for TNF-308A was 1.46 (95% confidence interval [CI], 1.27-1.68, P=0.0000001) and 1.46 (95% CI, 1.20-1.77, P=0.00014) respectively. Our data further support the importance of the TNF region in the development of asthma.
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Affiliation(s)
- Takeshi Aoki
- Department of Pediatrics, Tsukuba Medical Center Hospital, Tsukuba, Japan
| | - Tomomitsu Hirota
- Laboratory of Genetics of Allergic Diseases, RIKEN SNP Research Center, Yokohama, Japan
| | - Mayumi Tamari
- Laboratory of Genetics of Allergic Diseases, RIKEN SNP Research Center, Yokohama, Japan
| | - Kunio Ichikawa
- Department of Pediatrics, Tsukuba Medical Center Hospital, Tsukuba, Japan
| | | | - Tadao Arinami
- Department of Medical Genetics, Graduate School of Comprehensive Human Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, 305-8577, Japan
| | - Masanao Shibasaki
- Department of Pediatrics, Tsukuba College of Technology, Tsukuba, Japan
| | - Emiko Noguchi
- Department of Medical Genetics, Graduate School of Comprehensive Human Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, 305-8577, Japan.
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143
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Krawczak M, Nikolaus S, von Eberstein H, Croucher PJP, El Mokhtari NE, Schreiber S. PopGen: population-based recruitment of patients and controls for the analysis of complex genotype-phenotype relationships. Public Health Genomics 2006; 9:55-61. [PMID: 16490960 DOI: 10.1159/000090694] [Citation(s) in RCA: 206] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVE Patient samples used for mapping complex human disease genes are unlikely to be representative of the phenotype spectrum of the respective population as a whole. On the other hand, most ongoing prospective studies are probably too small for evaluating polygenic disease markers. DESIGN Precise estimates of population-specific genotypic risks can be obtained efficiently through the complete ascertainment of patients in a geographically confined area. The PopGen project uses the most northern part of Germany as a target region for such a pursuit. RESULTS PopGen currently pursues recruitment, sampling and processing activities in close collaboration with a multitude of clinical partners, covering cardiovascular, neuropsychiatric and environmental diseases. CONCLUSION PopGen has successfully established itself as a large-scale genetic epidemiological project of international recognition.
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Affiliation(s)
- Michael Krawczak
- Institute of Medical Informatics and Statistics, Christian Albrechts University, Kiel, Germany.
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144
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Schedel M, Depner M, Schoen C, Weiland SK, Vogelberg C, Niggemann B, Lau S, Illig T, Klopp N, Wahn U, von Mutius E, Nickel R, Kabesch M. The role of polymorphisms in ADAM33, a disintegrin and metalloprotease 33, in childhood asthma and lung function in two German populations. Respir Res 2006; 7:91. [PMID: 16784537 PMCID: PMC1550399 DOI: 10.1186/1465-9921-7-91] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2006] [Accepted: 06/19/2006] [Indexed: 11/28/2022] Open
Abstract
Background ADAM33, the first asthma candidate gene identified by positional cloning, may be associated with childhood asthma, lung function decline and bronchial hyperresponsiveness. However, replication results have been inconclusive in smaller previous study populations probably due to inconsistencies in asthma phenotypes or yet unknown environmental influences. Thus, we tried to further elucidate the role of ADAM33 polymorphisms (SNPs) in a genetic analysis of German case control and longitudinal populations. Methods Using MALDI-TOF, ten ADAM33 SNPs were genotyped in 1,872 children from the International Study of Asthma and Allergy in Childhood (ISAAC II) in a case control setting and further 824 children from the longitudinal cohort Multicentre Study of Allergy (MAS). In both populations the effects of single SNPs and haplotypes were studied and a gene environment analysis with passive smoke exposure was performed using SAS/Genetics. Results No single SNP showed a significant association with doctor's diagnosis of asthma. A trend for somewhat more profound effects of ADAM33 SNPs was observed in individuals with asthma and BHR. Haplotype analyses suggested a minor effect of the ADAM33 haplotype H4 on asthma (p = 0.033) but not on BHR. Associations with non atopic asthma and baseline lung function were identified but no interaction with passive smoke exposure could be detected. Conclusion The originally reported association between ADAM33 polymorphisms and asthma and BHR could not be confirmed. However, our data may suggest a complex role of ADAM33 polymorphisms in asthma ethiology, especially in non atopic asthma.
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Affiliation(s)
- Michaela Schedel
- University Children's Hospital, Ludwig Maximilian's University Munich, Germany
| | - Martin Depner
- University Children's Hospital, Ludwig Maximilian's University Munich, Germany
| | - Carola Schoen
- University Children's Hospital, Ludwig Maximilian's University Munich, Germany
| | | | | | - Bodo Niggemann
- Department of Pediatric Pneumology and Immunology, Charité Humbolt University Berlin, Germany
| | - Susanne Lau
- Department of Pediatric Pneumology and Immunology, Charité Humbolt University Berlin, Germany
| | - Thomas Illig
- Institute of Epidemiology, GSF -Research Centre for Environment and Health, Neuherberg, Germany
| | - Norman Klopp
- Institute of Epidemiology, GSF -Research Centre for Environment and Health, Neuherberg, Germany
| | - Ulrich Wahn
- Department of Pediatric Pneumology and Immunology, Charité Humbolt University Berlin, Germany
| | - Erika von Mutius
- University Children's Hospital, Ludwig Maximilian's University Munich, Germany
| | - Renate Nickel
- Department of Pediatric Pneumology and Immunology, Charité Humbolt University Berlin, Germany
| | - Michael Kabesch
- University Children's Hospital, Ludwig Maximilian's University Munich, Germany
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145
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Brasch-Andersen C, Tan Q, Børglum AD, Haagerup A, Larsen TR, Vestbo J, Kruse TA. Significant linkage to chromosome 12q24.32-q24.33 and identification of SFRS8 as a possible asthma susceptibility gene. Thorax 2006; 61:874-9. [PMID: 16738036 PMCID: PMC2104763 DOI: 10.1136/thx.2005.055475] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BACKGROUND Asthma is a complex genetic disorder. Many studies have suggested that chromosome 12q harbours a susceptibility gene for asthma and atopy. Linkage on chromosome 12q24.21-q24.33 was investigated in 167 Danish families with asthma. METHODS A two step procedure was used: (1) a genome-wide scan in one set of families followed by (2) fine scale mapping in an independent set of families in candidate regions with a maximum likelihood score (MLS) of > or =1.5 in the genome-wide scan. Polymorphisms in a candidate gene in the region on 12q24.33 were tested for association with asthma in a family based transmission disequilibrium test. RESULTS An MLS of 3.27 was obtained at 12q24.33. The significance of this result was tested by simulation, resulting in a significant empirical genome-wide p value of 0.018. To our Knowledge, this is the first significant evidence for linkage on chromosome 12q, and suggests a candidate region distal to most previously reported regions. Three single nucleotide polymorphisms in splicing factor, arginine/serine-rich 8 (SFRS8) had an association with asthma (p < or = 0.0020-0.050) in a sample of 136 asthmatic sib pairs. SFRS8 regulates the splicing of CD45, a protein which, through alternative splice variants, has an essential role in activating T cells. T cells are involved in the pathogenesis of atopic diseases such as asthma, so SFRS8 is a very interesting candidate gene in the region. CONCLUSIONS Linkage and simulation studies show that the very distal part of chromosome 12q contains a gene that increases the susceptibility to asthma. SFRS8 could act as a weak predisposing gene for asthma in our sample.
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Affiliation(s)
- C Brasch-Andersen
- Department of Biochemistry, Pharmacology and Genetics, Odense University Hospital, DK-5000 Odense C, Denmark.
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146
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Pyo CW, Williams LM, Moore Y, Hyodo H, Li SS, Zhao LP, Sageshima N, Ishitani A, Geraghty DE. HLA-E, HLA-F, and HLA-G polymorphism: genomic sequence defines haplotype structure and variation spanning the nonclassical class I genes. Immunogenetics 2006; 58:241-51. [PMID: 16570139 DOI: 10.1007/s00251-005-0076-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2005] [Accepted: 12/01/2005] [Indexed: 10/24/2022]
Abstract
Despite several studies that defined the polymorphism of the nonclassical human leukocyte antigen-E (HLA-E), HLA-F, and HLA-G genes, most polymorphisms thus far examined in correlative studies were derived from the coding sequences of these genes. In addition, some discrepancies and ambiguities in the available data have persisted in current databases. To expand the data available and to resolve some of the discrepant data, we have defined protocols that allow for the amplification of 6 to 7 kb of contiguous genomic sequence for each gene, including all of the coding and intron sequences, approximately 2 kb of 5' flanking promoter sequence, and 1 kb of 3' flanking sequence. Using long-range polymerase chain reaction (PCR) protocols, generating either one or two PCR products depending on the locus, amplified genomic DNA was directly sequenced to completion using a set of about 30 primers over each locus to yield contiguous sequence data from both strands. Using this approach, we sequenced 33 genomic DNAs, from Asian, African American, and Caucasian samples. The results of this analysis confirmed several previously reported coding sequence variants, identified several new allelic variants, and also defined extensive variation in intron and flanking sequences. It was possible to construct haplotype maps and to identify tagging single nucleotide polymorphisms that can be used to detect the composite variation spanning all three genes.
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Affiliation(s)
- Chul-Woo Pyo
- The Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave., N. Seattle, WA 98109-1024, USA
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147
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Abstract
Asthma and atopy are complex phenotypes that are influenced by both genetic and environmental factors. A review of nearly 500 papers on disease association studies identified 25 genes that have been associated with an asthma or atopy phenotype in six or more populations. An additional 54 genes have been associated in 2-5 populations. Here, we discuss the methods that have been used to identify susceptibility genes for common diseases and overview the status of asthma genetic research. Finally, current challenges and future directions are discussed.
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Affiliation(s)
- C Ober
- Department of Human Genetics, The University of Chicago, Chicago, IL 60615, USA.
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148
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Abstract
Several key conditions that are necessary to identify disease susceptibility genes in common diseases such as asthma are now available, including (1) increasingly comprehensive genomic information on gene location, genomic structure, and sequence variants, from the Human Genome Project (and from other species); (2) better understanding of the biologic functions of relevant genes and inflammatory and immunity pathways important in asthma; (3) newer high throughput and accurate technologies for DNA sequencing and SNP genotyping; (4) improved statistical methods for analyzing genetic data from families and populations; and (5) availability of methods to characterize function of sequence variants and study biologic responses. Collectively, these conditions will allow the prioritization of candidate genes based on available knowledge of map position and biologic relevance; obtain genomic structure of these genes; and study sequence variants in these genes in populations to facilitate the identification of genes that are important in the development and expression (severity) of asthma and associated phenotypes. Although, it is still a labor-intensive and expensive project to identify susceptibility genes in common diseases such as asthma, the new techniques that are now being used will greatly facilitate gene mapping. The techniques discussed in this article include genome-by-genome analysis in family data, such as those listed in Box 2. This analysis has already been shown to be a powerful too in mapping genes for another common disease (prostate cancer) with interesting preliminary results for asthma. Second, the use of man-mouse homology mapping that has proven very useful in cardiovascular studies is beginning to be applied to asthma and related phenotypes. finally with new available technology, genome-wide screens using very dense SNP maps are now a reality and a significant new development in family linkage and case-control association studies. In summary, these new approaches should be considered in designing studies to detect genes that are important in asthma and allergy.
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Affiliation(s)
- Deborah A Meyers
- Center for Human Genomics, Wake Forest University School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157, USA.
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149
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Abstract
We identified HLA-G as an asthma susceptibility gene in multiple populations and demonstrated that variation in this gene influences subsequent risk for asthma. Prenatal exposure to factors that are correlated with maternal BHR (or perhaps BHR itself) interacts with fetal genotype to determine risk, however. Among fetuses of unaffected mothers, the +1489TT genotype is a marker for increased risk, whereas among fetuses of affected mothers the +1489CC genotype is a marker for increased risk. Studies are underway to understand the mechanism for this interaction and the role of this gene in the pathogenesis of asthma.
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Affiliation(s)
- Carole Ober
- Department of Human Genetics and Obstetrics and Gynecology, University of Chicago, 920 East 58th Street, Chicago, IL 60637, USA.
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150
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Smith AK, Meyers DA. Family studies and positional cloning of genes for asthma and related phenotypes. Immunol Allergy Clin North Am 2006; 25:641-54. [PMID: 16257630 DOI: 10.1016/j.iac.2005.09.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Although it is not yet known how many genes may contribute to the susceptibility or the severity of asthma and related phenotypes, genome-wide screens and positional cloning techniques have been successful in identifying contributing genes in multiple populations. The results of these studies provide additional insight into the molecular mechanisms responsible for the development of a variety of phenotypes. Replication with additional populations--particularly in large-scale studies--has been used to distinguish between false positive results or population-specific effects or to further quantify the conferred risk. Even when individual markers do not replicate in multiple population, association of the same region or gene has been useful in directing future studies. As further understanding of linkage disequilibrium patterns within the genome has allowed greater efficiency for genetic studies, advances in high-throughput genotyping technology, genetic analysis methodologies, and a more in-depth understanding of clinical phenotypes has made genome-wide studies more accessible and cost-effective. In the future, identification of function variants with clinical relevance may be used to influence the diagnosis and treatment of asthma.
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Affiliation(s)
- Alicia K Smith
- Centers for Disease Control and Prevention, Atlanta, GA, USA
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