Integration of Genomic and Genetic Approaches Implicates IREB2 as a COPD Susceptibility Gene Dawn L. DeMeo, Thomas Mariani, Soumyaroop Bhattacharya,

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Integration of Genomic and Genetic Approaches Implicates IREB2 as a COPD Susceptibility Gene Dawn L. DeMeo, Thomas Mariani, Soumyaroop Bhattacharya, Sorachai Srisuma, Christoph Lange, Augusto Litonjua, Raphael Bueno, Sreekumar G. Pillai, David A. Lomas, David Sparrow, Steven D. Shapiro, Gerard J. Criner, Hong P. Kim, Zhihua Chen, Augustine M.K. Choi, John Reilly, Edwin K. Silverman The American Journal of Human Genetics Volume 85, Issue 4, Pages 493-502 (October 2009) DOI: 10.1016/j.ajhg.2009.09.004 Copyright © 2009 The American Society of Human Genetics Terms and Conditions

Figure 1 Workflow of Tiered Replication Approach: SNP Selection and Replication of SNP Associations We performed LD tagging of 62 autosomal regions identified by microarray analysis on human lung tissue. LD tagging of the regions (plus or minus 5 kb from the start and stop locations) resulted in 889 SNPs tested for association in the NETT-NAS cohorts. We carried forward 71 SNPs associated at p ≤ 0.050 for attempted replication, using a family-based approach, in the BEOCOPD cohort. Finally, we performed a gene-based replication for IREB2 variants in the ICGN cohort, testing all seven SNPs that were associated in the NETT-NAS cohort. The American Journal of Human Genetics 2009 85, 493-502DOI: (10.1016/j.ajhg.2009.09.004) Copyright © 2009 The American Society of Human Genetics Terms and Conditions

Figure 2 Increased IREB2 Protein and mRNA Expression in Human COPD Lung Tissues Human lung-tissue homogenates from control (n = 18) and COPD (n = 22) subjects were analyzed for IREB2 protein expression by immunoblot analysis. Total IREB2 protein expression was normalized to β-actin, and the quantified results are depicted by graph. Data represent mean ± SD (n = 18 normal and n = 22 COPD patients), p < 0.01, comparing COPD lung tissue with normal lung. mRNA expression was extracted from the same lung tissues and quantified with RT-PCR (n = 11 normal and n = 20 COPD patients), p < 0.05, comparing COPD lung tissue with normal lung. The American Journal of Human Genetics 2009 85, 493-502DOI: (10.1016/j.ajhg.2009.09.004) Copyright © 2009 The American Society of Human Genetics Terms and Conditions

Figure 3 IREB2 Localization in Normal and Emphysematous Human Lung Tissue (A–D) IREB2 protein expression by DBA staining (brown) and counterstaining by nuclei staining (blue). IREB2 expression in control tissue localized to (A) bronchial epithelial cells and (B) vascular endothelial cells; IREB2 expression in emphysematous tissue localized to (C) bronchial epithelial cells and (D) macrophages (red arrows). (E) Negative control without primary antibody in control tissue. Magnification is 200×. The American Journal of Human Genetics 2009 85, 493-502DOI: (10.1016/j.ajhg.2009.09.004) Copyright © 2009 The American Society of Human Genetics Terms and Conditions

Figure 4 IREB2 Localizes to Human Epithelial Cell Cilial Surface Localization of IREB2 protein expression along the cilial border in human lung epithelial cells from normal lung tissue (A) 200× magnification. (B) Enlarged image of (A) at 400× magnification. The American Journal of Human Genetics 2009 85, 493-502DOI: (10.1016/j.ajhg.2009.09.004) Copyright © 2009 The American Society of Human Genetics Terms and Conditions

Figure 5 Linkage Disequilibrium Map for All IREB2 SNPs Genotyped in NETT-NAS Plus Two CHRNA3 Region SNPs Previously Associated with Lung Cancer and COPD LD map of the 12 SNPs genotyped in IREB2 in NETT-NAS demonstrate high LD across the gene. Additionally, there is high LD in the NETT-NAS cohort between the IREB2 SNPs and two SNPs in the CHRNA3 region (rs8034191, rs1051730; association data published by Pillai et al.12) Red corresponds to r2 ≥ 0.8. Values for D′ are included in the text of boxes. The American Journal of Human Genetics 2009 85, 493-502DOI: (10.1016/j.ajhg.2009.09.004) Copyright © 2009 The American Society of Human Genetics Terms and Conditions