Genetic analysis of an allergic rhinitis cohort reveals an intercellular epistasis between FAM134B and CD39

BMC Medical Genetics

Olaf Rotzschke³  Michael Poidinger³  De Yun Wang⁴  Anis Larbi³  Fook Tim Chew²  Tuck Siong Lai³  Kerstin Petsch³  Li Zhuang³  Mireille Starke³  Tuang Yeow Poh³  Anand Kumar Andiappan³  Kia Joo Puan³  Rossella Melchiotti¹ 

[1] Doctoral School in Translational and Molecular Medicine (DIMET), University of Milano-Bicocca, Milan 20126, Italy;Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore;SIgN (Singapore Immunology Network), A*STAR (Agency for Science, Technology and Research), Singapore 138648, Singapore;Department of Otolaryngology, National University of Singapore, Singapore 119228, Singapore

关键词: Allergic rhinitis;    eQTLs;    Monocyte;    Treg;    Epistasis;   

Others  :  848392
DOI  :  10.1186/1471-2350-15-73

 received in 2014-03-05, accepted in 2014-06-23,  发布年份 2014

【 摘 要 】

Background

Extracellular ATP is a pro-inflammatory molecule released by damaged cells. Regulatory T cells (Treg) can suppress inflammation by hydrolysing this molecule via ectonucleoside triphosphate diphosphohydrolase 1 (ENTPD1), also termed as CD39. Multiple studies have reported differences in CD39⁺ Treg percentages in diseases such as multiple sclerosis, Hepatitis B and HIV-1. In addition, CD39 polymorphisms have been implicated in immune-phenotypes such as susceptibility to inflammatory bowel disease and AIDS progression. However none of the studies published so far has linked disease-associated variants with differences in CD39 Treg surface expression. This study aims at identifying variants affecting CD39 expression on Treg and at evaluating their association with allergic rhinitis, a disease characterized by a strong Treg involvement.

Methods

Cohorts consisting of individuals of different ethnicities were employed to identify any association of CD39 variants to surface expression. Significant variant(s) were tested for disease association in a published GWAS cohort by one-locus and two-locus genetic analyses based on logistic models. Further functional characterization was performed using existing microarray data and quantitative RT-PCR on sorted cells.

Results

Our study shows that rs7071836, a promoter SNP in the CD39 gene region, affects the cell surface expression on Treg cells but not on other CD39+ leukocyte subsets. Epistasis analysis revealed that, in conjunction with a SNP upstream of the FAM134B gene (rs257174), it increased the risk of allergic rhinitis (P = 1.98 × 10^-6). As a promoter SNP, rs257174 controlled the expression of the gene in monocytes but, notably, not in Treg cells. Whole blood transcriptome data of three large cohorts indicated an inverse relation in the expression of the two proteins. While this observation was in line with the epistasis data, it also implied that a functional link must exist. Exposure of monocytes to extracellular ATP resulted in an up-regulation of FAM134B gene expression, suggesting that extracellular ATP released from damaged cells represents the connection for the biological interaction of CD39 on Treg cells with FAM134B on monocytes.

Conclusions

The interplay between promoter SNPs of CD39 and FAM134B results in an intercellular epistasis which influences the risk of a complex inflammatory disease.

【 授权许可】

   
2014 Melchiotti et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

Figure 3.

Figure 4.

Figure 5.

Figure 6.

【 参考文献 】

• [1]Bousquet J, Khaltaev N, Cruz AA, Denburg J, Fokkens WJ, Togias A, Zuberbier T, Baena-Cagnani CE, Canonica GW, Van Weel C, Agache I, Aït-Khaled N, Bachert C, Blaiss MS, Bonini S, Boulet L-P, Bousquet P-J, Camargos P, Carlsen K-H, Chen Y, Custovic A, Dahl R, Demoly P, Douagui H, Durham SR, Van Wijk RG, Kalayci O, Kaliner MA, Kim Y-Y, Kowalski ML, et al.: Allergic Rhinitis and its Impact on Asthma (ARIA) 2008 update (in collaboration with the World Health Organization, GA(2)LEN and AllerGen). Allergy 2008, 63(Suppl 86):8-160.
• [2]Li L, Xia Y, Nguyen A, Lai YH, Feng L, Mosmann TR, Lo D: Effects of Th2 cytokines on chemokine expression in the lung: IL-13 potently induces eotaxin expression by airway epithelial cells. J Immunol 1999, 162:2477-2487.
• [3]Durham SR, Ying S, Varney VA, Jacobson MR, Sudderick RM, Mackay IS, Kay AB, Hamid QA: Cytokine messenger RNA expression for IL-3, IL-4, IL-5, and granulocyte/macrophage-colony-stimulating factor in the nasal mucosa after local allergen provocation: relationship to tissue eosinophilia. J Immunol 1992, 148:2390-2394.
• [4]Bischoff SC, Sellge G, Lorentz A, Sebald W, Raab R, Manns MP: IL-4 enhances proliferation and mediator release in mature human mast cells. Proc Natl Acad Sci 1999, 96:8080-8085.
• [5]Shi C, Pamer EG: Monocyte recruitment during infection and inflammation. Nat Rev Immunol 2011, 11:762-774.
• [6]Egawa M, Mukai K, Yoshikawa S, Iki M, Mukaida N, Kawano Y, Minegishi Y, Karasuyama H: Inflammatory monocytes recruited to allergic skin acquire an anti-inflammatory M2 phenotype via basophil-derived interleukin-4. Immunity 2013, 38:570-580.
• [7]Palomares O, Yaman G, Azkur AK, Akkoc T, Akdis M, Akdis CA: Role of Treg in immune regulation of allergic diseases. Eur J Immunol 2010, 40:1232-1240.
• [8]Ling EM, Smith T, Nguyen XD, Pridgeon C, Dallman M, Arbery J, Carr VA, Robinson DS: Relation of CD4+ CD25+ regulatory T-cell suppression of allergen-driven T-cell activation to atopic status and expression of allergic disease. Lancet 2004, 363:608-615.
• [9]Robinson DS, Larché M, Durham SR: Tregs and allergic disease. J Clin Invest 2004, 114:1389-1397.
• [10]Bellinghausen I, Klostermann B, Knop J, Saloga J: Human CD4 + CD25+ T cells derived from the majority of atopic donors are able to suppress TH1 and TH2 cytokine production. J Allergy Clin Immunol 2003, 111:862-868.
• [11]Borsellino G, Kleinewietfeld M, Di Mitri D, Sternjak A, Diamantini A, Giometto R, Höpner S, Centonze D, Bernardi G, Dell’Acqua ML, Rossini PM, Battistini L, Rötzschke O, Falk K: Expression of ectonucleotidase CD39 by Foxp3+ Treg cells: hydrolysis of extracellular ATP and immune suppression. Blood 2007, 110:1225-1232.
• [12]Deaglio S, Dwyer KM, Gao W, Friedman D, Usheva A, Erat A, Chen J-F, Enjyoji K, Linden J, Oukka M, Kuchroo VK, Strom TB, Robson SC: Adenosine generation catalyzed by CD39 and CD73 expressed on regulatory T cells mediates immune suppression. J Exp Med 2007, 204:1257-1265.
• [13]Kouzaki H, Iijima K, Kobayashi T, O’Grady SM, Kita H: The danger signal, extracellular ATP, is a sensor for an airborne allergen and triggers IL-33 release and innate Th2-type responses. J Immunol 2011, 186:4375-4387.
• [14]Idzko M, Hammad H, van Nimwegen M, Kool M, Willart MAM, Muskens F, Hoogsteden HC, Luttmann W, Ferrari D, Di Virgilio F, Virchow JC, Lambrecht BN: Extracellular ATP triggers and maintains asthmatic airway inflammation by activating dendritic cells. Nat Med 2007, 13:913-919.
• [15]Friedman DJ, Künzli BM, A-Rahim YI, Sevigny J, Berberat PO, Enjyoji K, Csizmadia E, Friess H, Robson SC: CD39 deletion exacerbates experimental murine colitis and human polymorphisms increase susceptibility to inflammatory bowel disease. Proc Natl Acad Sci 2009, 106:16788-16793.
• [16]Fletcher JM, Lonergan R, Costelloe L, Kinsella K, Moran B, O’Farrelly C, Tubridy N, Mills KHG: CD39 + Foxp3+ regulatory T cells suppress pathogenic Th17 cells and are impaired in multiple sclerosis. J Immunol 2009, 183:7602-7610.
• [17]Nikolova M, Carriere M, Jenabian M-A, Limou S, Younas M, Kök A, Huë S, Seddiki N, Hulin A, Delaneau O, Schuitemaker H, Herbeck JT, Mullins JI, Muhtarova M, Bensussan A, Zagury J-F, Lelievre J-D, Lévy Y: CD39/Adenosine Pathway Is Involved in AIDS Progression. PLoS Pathog 2011, 7:e1002110.
• [18]Tang Y, Jiang L, Zheng Y, Ni B, Wu Y: Expression of CD39 on FoxP3+ T regulatory cells correlates with progression of HBV infection. BMC Immunol 2012, 13:17.
• [19]Andiappan AK, Wang DY, Anantharaman R, Parate PN, Suri BK, Low HQ, Li Y, Zhao W, Castagnoli P, Liu J, Chew FT: Genome-wide association study for atopy and allergic rhinitis in a Singapore Chinese population. PLoS One 2011, 6:e19719.
• [20]Westra H-J, Peters MJ, Esko T, Yaghootkar H, Schurmann C, Kettunen J, Christiansen MW, Fairfax BP, Schramm K, Powell JE, Zhernakova A, Zhernakova DV, Veldink JH, Van den Berg LH, Karjalainen J, Withoff S, Uitterlinden AG, Hofman A, Rivadeneira F, ‘t Hoen PAC, Reinmaa E, Fischer K, Nelis M, Milani L, Melzer D, Ferrucci L, Singleton AB, Hernandez DG, Nalls MA, Homuth G, et al.: Systematic identification of trans eQTLs as putative drivers of known disease associations. Nat Genet 2013, 45:1238-1243.
• [21]Inouye M, Silander K, Hamalainen E, Salomaa V, Harald K, Jousilahti P, Männistö S, Eriksson JG, Saarela J, Ripatti S, Perola M, van Ommen G-JB, Taskinen M-R, Palotie A, Dermitzakis ET, Peltonen L: An immune response network associated with blood lipid levels. PLoS Genet 2010, 6:e1001113.
• [22]Mayerle J, den Hoed CM, Schurmann C, Stolk L, Homuth G, Peters MJ, Capelle LG, Zimmermann K, Rivadeneira F, Gruska S, Völzke H, de Vries AC, Völker U, Teumer A, van Meurs JBJ, Steinmetz I, Nauck M, Ernst F, Weiss F-U, Hofman A, Zenker M, Kroemer HK, Prokisch H, Uitterlinden AG, Lerch MM, Kuipers EJ, Kuipers E: Identification of genetic loci associated with Helicobacter pylori serologic status. JAMA 2013, 309:1912-1920.
• [23]De Rosa SC: Multicolor immunophenotyping: human mature immune system. Methods Cell Biol 2004, 75:577-594.
• [24]R Development Core Team: R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing; 2012.
• [25]Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP: Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 2003, 4:249-264.
• [26]Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, De Bakker PIW, Daly MJ, Sham PC: PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses. Am J Hum Genet 2007, 81:559-575.
• [27]Melchiotti R, Rötzschke O, Poidinger M: ArchiLD: Hierarchical Visualization of Linkage Disequilibrium in Human Populations. PLoS One 2014, 9:e86761.
• [28]The 1000 Genomes Project Consortium: A map of human genome variation from population-scale sequencing. Nature 2010, 467:1061-1073.
• [29]Gauderman WJ: Sample size requirements for association studies of gene-gene interaction. Am J Epidemiol 2002, 155:478-484.
• [30]The International HapMap Consortium: The International HapMap Project. Nature 2003, 426:789-796.
• [31]The International HapMap Consortium: A haplotype map of the human genome. Nature 2005, 437:1299-1320.
• [32]The International HapMap Consortium: A second generation human haplotype map of over 3.1 million SNPs. Nature 2007, 449:851-861.
• [33]The International HapMap Consortium: Integrating common and rare genetic variation in diverse human populations. Nature 2010, 467:52-58.
• [34]Orrù V, Steri M, Sole G, Sidore C, Virdis F, Dei M, Lai S, Zoledziewska M, Busonero F, Mulas A, Floris M, Mentzen WI, Urru SAM, Olla S, Marongiu M, Piras MG, Lobina M, Maschio A, Pitzalis M, Urru MF, Marcelli M, Cusano R, Deidda F, Serra V, Oppo M, Pilu R, Reinier F, Berutti R, Pireddu L, Zara I, et al.: Genetic Variants Regulating Immune Cell Levels in Health and Disease. Cell 2013, 155:242-256.
• [35]Andiappan AK, Puan KJ, Lee B, Nardin A, Poidinger M, Connolly J, Chew FT, Wang DY, Rotzschke O: Allergic airway diseases in a tropical urban environment are driven by dominant mono-specific sensitization against house dust mites. Allergy 2014, 69:501-509.
• [36]Fairfax BP, Makino S, Radhakrishnan J, Plant K, Leslie S, Dilthey A, Ellis P, Langford C, Vannberg FO, Knight JC: Genetics of gene expression in primary immune cells identifies cell type-specific master regulators and roles of HLA alleles. Nat Genet 2012, 44:502-510.
• [37]Zeller T, Wild P, Szymczak S, Rotival M, Schillert A, Castagne R, Maouche S, Germain M, Lackner K, Rossmann H, Eleftheriadis M, Sinning CR, Schnabel RB, Lubos E, Mennerich D, Rust W, Perret C, Proust C, Nicaud V, Loscalzo J, Hübner N, Tregouet D, Münzel T, Ziegler A, Tiret L, Blankenberg S, Cambien F: Genetics and beyond-the transcriptome of human monocytes and disease susceptibility. PLoS One 2010, 5:e10693.
• [38]Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B, Garg K, John S, Sandstrom R, Bates D, Boatman L, Canfield TK, Diegel M, Dunn D, Ebersol AK, Frum T, Giste E, Johnson AK, Johnson EM, Kutyavin T, Lajoie B, Lee B-K, Lee K, London D, Lotakis D, Neph S, et al.: The accessible chromatin landscape of the human genome. Nature 2012, 489:75-82.
• [39]Wang DY, Gordon BR: Management of persistent allergic rhinitis in the tropics: Singapore experiences. Clin Exp Allergy 2008, 8:37-44.
• [40]Kurth I, Pamminger T, Hennings JC, Soehendra D, Huebner AK, Rotthier A, Baets J, Senderek J, Topaloglu H, Farrell SA, Nürnberg G, Nürnberg P, De Jonghe P, Gal A, Kaether C, Timmerman V, Hübner CA: Mutations in FAM134B, encoding a newly identified Golgi protein, cause severe sensory and autonomic neuropathy. Nat Genet 2009, 41:1179-1181.
• [41]Verpoorten N, De Jonghe P, Timmerman V: Disease mechanisms in hereditary sensory and autonomic neuropathies. Neurobiol Dis 2006, 21:247-255.
• [42]Kong M, Kim Y, Lee C: A strong synergistic epistasis between FAM134B and TNFRSF19 on the susceptibility to vascular dementia. Psychiatr Genet 2011, 21:37-41.
• [43]Tang WK, Chui CH, Fatima S, Kok SHL, Pak KC, Ou TM, Hui KS, Wong MM, Wong J, Law S, Tsao SW, Lam KY, Beh PSL, Srivastava G, Chan ASC, Ho KP, Tang JCO: Oncogenic properties of a novel gene JK-1 located in chromosome 5p and its overexpression in human esophageal squamous cell carcinoma. Int J Mol Med 2007, 19:915-923.
• [44]Ritchie MD: Using biological knowledge to uncover the mystery in the search for epistasis in genome-wide association studies. Ann Hum Genet 2011, 75:172-182.
• [45]Pattin KA, Moore JH: Exploiting the proteome to improve the genome-wide genetic analysis of epistasis in common human diseases. Hum Genet 2008, 124:19-29.
• [46]Emily M, Mailund T, Hein J, Schauser L, Schierup MH: Using biological networks to search for interacting loci in genome-wide association studies. Eur J Hum Genet 2009, 17:1231-1240.