All Title Author
Keywords Abstract

PLOS Genetics  2015 

Exome Sequencing of Phenotypic Extremes Identifies CAV2 and TMC6 as Interacting Modifiers of Chronic Pseudomonas aeruginosa Infection in Cystic Fibrosis

DOI: 10.1371/journal.pgen.1005273

Full-Text   Cite this paper   Add to My Lib

Abstract:

Discovery of rare or low frequency variants in exome or genome data that are associated with complex traits often will require use of very large sample sizes to achieve adequate statistical power. For a fixed sample size, sequencing of individuals sampled from the tails of a phenotype distribution (i.e., extreme phenotypes design) maximizes power and this approach was recently validated empirically with the discovery of variants in DCTN4 that influence the natural history of P. aeruginosa airway infection in persons with cystic fibrosis (CF; MIM219700). The increasing availability of large exome/genome sequence datasets that serve as proxies for population-based controls affords the opportunity to test an alternative, potentially more powerful and generalizable strategy, in which the frequency of rare variants in a single extreme phenotypic group is compared to a control group (i.e., extreme phenotype vs. control population design). As proof-of-principle, we applied this approach to search for variants associated with risk for age-of-onset of chronic P. aeruginosa airway infection among individuals with CF and identified variants in CAV2 and TMC6 that were significantly associated with group status. These results were validated using a large, prospective, longitudinal CF cohort and confirmed a significant association of a variant in CAV2 with increased age-of-onset of P. aeruginosa airway infection (hazard ratio = 0.48, 95% CI=[0.32, 0.88]) and variants in TMC6 with diminished age-of-onset of P. aeruginosa airway infection (HR = 5.4, 95% CI=[2.2, 13.5]) A strong interaction between CAV2 and TMC6 variants was observed (HR=12.1, 95% CI=[3.8, 39]) for children with the deleterious TMC6 variant and without the CAV2 protective variant. Neither gene showed a significant association using an extreme phenotypes design, and conditions for which the power of an extreme phenotype vs. control population design was greater than that for the extreme phenotypes design were explored.

References

[1]  Accurso FJ, Rowe SM, Clancy JP, Boyle MP, Dunitz JM, et al. (2010) Effect of VX-770 in persons with cystic fibrosis and the G551D-CFTR mutation. N Engl J Med 363: 1991–2003. doi: 10.1056/NEJMoa0909825. pmid:21083385
[2]  Chmiel JF, Konstan MW (2007) Inflammation and anti-inflammatory therapies for cystic fibrosis. Clin Chest Med 28: 331–346. pmid:17467552 doi: 10.1016/j.ccm.2007.02.002
[3]  Gibson RL, Burns JL, Ramsey BW (2003) Pathophysiology and management of pulmonary infections in cystic fibrosis. Am J Respir Crit Care Med 168: 918–951. pmid:14555458 doi: 10.1164/rccm.200304-505so
[4]  Lee TW, Brownlee KG, Conway SP, Denton M, Littlewood JM (2003) Evaluation of a new definition for chronic Pseudomonas aeruginosa infection in cystic fibrosis patients. J Cyst Fibros 2: 29–34. pmid:15463843 doi: 10.1016/s1569-1993(02)00141-8
[5]  Emerson J, Rosenfeld M, McNamara S, Ramsey B, Gibson RL (2002) Pseudomonas aeruginosa and other predictors of mortality and morbidity in young children with cystic fibrosis. Pediatr Pulmonol 34: 91–100. pmid:12112774 doi: 10.1002/ppul.10127
[6]  Proesmans M, Balinska-Miskiewicz W, Dupont L, Bossuyt X, Verhaegen J, et al. (2006) Evaluating the "Leeds criteria" for Pseudomonas aeruginosa infection in a cystic fibrosis centre. Eur Respir J 27: 937–943. pmid:16707392
[7]  Li Z, Kosorok MR, Farrell PM, Laxova A, West SE, et al. (2005) Longitudinal development of mucoid Pseudomonas aeruginosa infection and lung disease progression in children with cystic fibrosis. JAMA 293: 581–588. pmid:15687313 doi: 10.1001/jama.293.5.581
[8]  Demko CA, Byard PJ, Davis PB (1995) Gender differences in cystic fibrosis: Pseudomonas aeruginosa infection. J Clin Epidemiol 48: 1041–1049. pmid:7775991 doi: 10.1016/0895-4356(94)00230-n
[9]  Henry RL, Mellis CM, Petrovic L (1992) Mucoid Pseudomonas aeruginosa is a marker of poor survival in cystic fibrosis. Pediatr Pulmonol 12: 158–161. pmid:1641272 doi: 10.1002/ppul.1950120306
[10]  Doring G, Taccetti G, Campana S, Festini F, Mascherini M (2006) Eradication of Pseudomonas aeruginosa in cystic fibrosis patients. Eur Respir J 27: 653. pmid:16507869 doi: 10.1183/09031936.06.00132105
[11]  Zemanick ET, Accurso FJ (2014) Cystic fibrosis transmembrane conductance regulator and pseudomonas. Am J Respir Crit Care Med 189: 763–765. doi: 10.1164/rccm.201402-0209ED. pmid:24684355
[12]  Green DM, Collaco JM, McDougal KE, Naughton KM, Blackman SM, et al. (2012) Heritability of respiratory infection with Pseudomonas aeruginosa in cystic fibrosis. J Pediatr 161: 290–295 e291. doi: 10.1016/j.jpeds.2012.01.042. pmid:22364820
[13]  Dorfman R, Sandford A, Taylor C, Huang B, Frangolias D, et al. (2008) Complex two-gene modulation of lung disease severity in children with cystic fibrosis. J Clin Invest 118: 1040–1049. doi: 10.1172/JCI33754. pmid:18292811
[14]  Dorfman R, Taylor C, Lin F, Sun L, Sandford A, et al. (2011) Modulatory effect of the SLC9A3 gene on susceptibility to infections and pulmonary function in children with cystic fibrosis. Pediatr Pulmonol 46: 385–392. doi: 10.1002/ppul.21372. pmid:20967843
[15]  Haerynck F, Van Steen K, Cattaert T, Loeys B, Van Daele S, et al. (2012) Polymorphisms in the lectin pathway genes as a possible cause of early chronic Pseudomonas aeruginosa colonization in cystic fibrosis patients. Hum Immunol 73: 1175–1183. doi: 10.1016/j.humimm.2012.08.010. pmid:22940091
[16]  Emond MJ, Louie T, Emerson J, Zhao W, Mathias RA, et al. (2012) Exome sequencing of extreme phenotypes identifies DCTN4 as a modifier of chronic Pseudomonas aeruginosa infection in cystic fibrosis. Nat Genet 44: 886–889. doi: 10.1038/ng.2344. pmid:22772370
[17]  Drumm ML, Konstan MW, Schluchter MD, Handler A, Pace R, et al. (2005) Genetic modifiers of lung disease in cystic fibrosis. N Engl J Med 353: 1443–1453. pmid:16207846 doi: 10.1056/nejmoa051469
[18]  Wright FA, Strug LJ, Doshi VK, Commander CW, Blackman SM, et al. (2011) Genome-wide association and linkage identify modifier loci of lung disease severity in cystic fibrosis at 11p13 and 20q13.2. Nat Genet 43: 539–546. doi: 10.1038/ng.838. pmid:21602797
[19]  Treggiari MM, Rosenfeld M, Mayer-Hamblett N, Retsch-Bogart G, Gibson RL, et al. (2009) Early anti-pseudomonal acquisition in young patients with cystic fibrosis: rationale and design of the EPIC clinical trial and observational study'. Contemp Clin Trials 30: 256–268. doi: 10.1016/j.cct.2009.01.003. pmid:19470318
[20]  Lee S, Emond MJ, Bamshad MJ, Barnes KC, Rieder MJ, et al. (2012) Optimal unified approach for rare-variant association testing with application to small-sample case-control whole-exome sequencing studies. Am J Hum Genet 91: 224–237. doi: 10.1016/j.ajhg.2012.06.007. pmid:22863193
[21]  McKone EF, Goss CH, Aitken ML (2006) CFTR genotype as a predictor of prognosis in cystic fibrosis. Chest 130: 1441–1447. pmid:17099022 doi: 10.1378/chest.130.5.1441
[22]  Lawless JF (2003) Statistical Models and Methods for Lifetime Data. Hoboken, New Jersey and Canada: John Wiley & Sons.
[23]  Zaas DW, Swan ZD, Brown BJ, Li G, Randell SH, et al. (2009) Counteracting signaling activities in lipid rafts associated with the invasion of lung epithelial cells by Pseudomonas aeruginosa. J Biol Chem 284: 9955–9964. doi: 10.1074/jbc.M808629200. pmid:19211560
[24]  Zaas DW, Swan Z, Brown BJ, Wright JR, Abraham SN (2009) The expanding roles of caveolin proteins in microbial pathogenesis. Commun Integr Biol 2: 535–537. pmid:20195460 doi: 10.4161/cib.2.6.9259
[25]  Wright JM, Joseloff E, Nikolsky Y, Serebriyskaya T, Wetmore D (2010) Interactions between an inflammatory response to infection and protein trafficking pathways favor correction of defective protein trafficking in Cystic Fibrosis. Bioinformation 5: 228–233. pmid:21364822 doi: 10.6026/97320630005228
[26]  Bajmoczi M, Gadjeva M, Alper SL, Pier GB, Golan DE (2009) Cystic fibrosis transmembrane conductance regulator and caveolin-1 regulate epithelial cell internalization of Pseudomonas aeruginosa. Am J Physiol Cell Physiol 297: C263–277. doi: 10.1152/ajpcell.00527.2008. pmid:19386787
[27]  Zaas DW, Duncan MJ, Li G, Wright JR, Abraham SN (2005) Pseudomonas invasion of type I pneumocytes is dependent on the expression and phosphorylation of caveolin-2. J Biol Chem 280: 4864–4872. pmid:15545264 doi: 10.1074/jbc.m411702200
[28]  Wright JM, Nikolsky Y, Serebryiskaya T, Wetmore DR (2009) MetaMiner (CF): a disease-oriented bioinformatics analysis environment. Methods Mol Biol 563: 353–367. doi: 10.1007/978-1-60761-175-2_18. pmid:19597794
[29]  Kircher M, Witten DM, Jain P, O'Roak BJ, Cooper GM, et al. (2014) A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet 46: 310–315. doi: 10.1038/ng.2892. pmid:24487276
[30]  Singh PK, Schaefer AL, Parsek MR, Moninger TO, Welsh MJ, et al. (2000) Quorum-sensing signals indicate that cystic fibrosis lungs are infected with bacterial biofilms. Nature 407: 762–764. pmid:11048725 doi: 10.1038/35037627
[31]  Burns JL, Gibson RL, McNamara S, Yim D, Emerson J, et al. (2001) Longitudinal assessment of Pseudomonas aeruginosa in young children with cystic fibrosis. J Infect Dis 183: 444–452. pmid:11133376 doi: 10.1086/318075
[32]  Carlsson M, Eriksson L, Pressler T, Kornfalt R, Mared L, et al. (2007) Autoantibody response to BPI predict disease severity and outcome in cystic fibrosis. J Cyst Fibros 6: 228–233. pmid:17166780 doi: 10.1016/j.jcf.2006.10.005
[33]  Trzcinska-Daneluti AM, Ly D, Huynh L, Jiang C, Fladd C, et al. (2009) High-content functional screen to identify proteins that correct F508del-CFTR function. Mol Cell Proteomics 8: 780–790. doi: 10.1074/mcp.M800268-MCP200. pmid:19088066
[34]  Lazarczyk M, Dalard C, Hayder M, Dupre L, Pignolet B, et al. (2012) EVER proteins, key elements of the natural anti-human papillomavirus barrier, are regulated upon T-cell activation. PLoS One 7: e39995. doi: 10.1371/journal.pone.0039995. pmid:22761942
[35]  Lazarczyk M, Favre M (2008) Role of Zn2+ ions in host-virus interactions. J Virol 82: 11486–11494. doi: 10.1128/JVI.01314-08. pmid:18787005
[36]  Bezzerri V, d'Adamo P, Rimessi A, Lanzara C, Crovella S, et al. (2011) Phospholipase C-beta3 is a key modulator of IL-8 expression in cystic fibrosis bronchial epithelial cells. Journal of immunology 186: 4946–4958. doi: 10.4049/jimmunol.1003535. pmid:21411730
[37]  Harder J, Meyer-Hoffert U, Teran LM, Schwichtenberg L, Bartels J, et al. (2000) Mucoid Pseudomonas aeruginosa, TNF-alpha, and IL-1beta, but not IL-6, induce human beta-defensin-2 in respiratory epithelia. American journal of respiratory cell and molecular biology 22: 714–721. pmid:10837369 doi: 10.1165/ajrcmb.22.6.4023
[38]  Smith JL, Campos SK, Ozbun MA (2007) Human papillomavirus type 31 uses a caveolin 1- and dynamin 2-mediated entry pathway for infection of human keratinocytes. J Virol 81: 9922–9931. pmid:17626097 doi: 10.1128/jvi.00988-07
[39]  Day PM, Lowy DR, Schiller JT (2003) Papillomaviruses infect cells via a clathrin-dependent pathway. Virology 307: 1–11. pmid:12667809 doi: 10.1016/s0042-6822(02)00143-5
[40]  Derkach A, Chiang T, Gong J, Addis L, Dobbins S, et al. (2014) Association analysis using next-generation sequence data from publicly available control groups: the robust variance score statistic. Bioinformatics 30: 2179–2188. doi: 10.1093/bioinformatics/btu196. pmid:24733292
[41]  Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078–2079. doi: 10.1093/bioinformatics/btp352. pmid:19505943
[42]  Rosenfeld M, Emerson J, McNamara S, Thompson V, Ramsey BW, et al. (2012) Risk factors for age at initial Pseudomonas acquisition in the cystic fibrosis epic observational cohort. J Cyst Fibros 11: 446–453. doi: 10.1016/j.jcf.2012.04.003. pmid:22554417
[43]  Fleming TR, Harrington , David P (2005) Conting Processes and Survival Analysis. Hoboken, New Jersey: John Wiley and Sons.

Full-Text

comments powered by Disqus