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Integrated genome-wide association, coexpression network, and expression single nucleotide polymorphism analysis identifies novel pathway in allergic rhinitis.

Bunyavanich S, Schadt EE, Himes BE, Lasky-Su J, Qiu W, Lazarus R, Ziniti JP, Cohain A, Linderman M, Torgerson DG, Eng CS, Pino-Yanes M, Padhukasahasram B, Yang JJ, Mathias RA, Beaty TH, Li X, Graves P, Romieu I, Navarro Bdel R, Salam MT, Vora H, Nicolae DL, Ober C, Martinez FD, Bleecker ER, Meyers DA, Gauderman WJ, Gilliland F, Burchard EG, Barnes KC, Williams LK, London SJ, Zhang B, Raby BA, Weiss ST - BMC Med Genomics (2014)

Bottom Line: GWAS revealed ethnicity-specific findings, with 4 genome-wide significant loci among Latinos and 1 genome-wide significant locus in the GWAS meta-analysis across ethnic groups.Pathway analysis revealed that the module was enriched for mitochondrial pathways (8.6-fold enrichment, P-value 4.5 × 10-72).Our integrated approach can be applied to provide biologic context for GWAS of other diseases.

View Article: PubMed Central - HTML - PubMed

ABSTRACT

Background: Allergic rhinitis is a common disease whose genetic basis is incompletely explained. We report an integrated genomic analysis of allergic rhinitis.

Methods: We performed genome wide association studies (GWAS) of allergic rhinitis in 5633 ethnically diverse North American subjects. Next, we profiled gene expression in disease-relevant tissue (peripheral blood CD4+ lymphocytes) collected from subjects who had been genotyped. We then integrated the GWAS and gene expression data using expression single nucleotide (eSNP), coexpression network, and pathway approaches to identify the biologic relevance of our GWAS.

Results: GWAS revealed ethnicity-specific findings, with 4 genome-wide significant loci among Latinos and 1 genome-wide significant locus in the GWAS meta-analysis across ethnic groups. To identify biologic context for these results, we constructed a coexpression network to define modules of genes with similar patterns of CD4+ gene expression (coexpression modules) that could serve as constructs of broader gene expression. 6 of the 22 GWAS loci with P-value ≤ 1x10-6 tagged one particular coexpression module (4.0-fold enrichment, P-value 0.0029), and this module also had the greatest enrichment (3.4-fold enrichment, P-value 2.6 × 10-24) for allergic rhinitis-associated eSNPs (genetic variants associated with both gene expression and allergic rhinitis). The integrated GWAS, coexpression network, and eSNP results therefore supported this coexpression module as an allergic rhinitis module. Pathway analysis revealed that the module was enriched for mitochondrial pathways (8.6-fold enrichment, P-value 4.5 × 10-72).

Conclusions: Our results highlight mitochondrial pathways as a target for further investigation of allergic rhinitis mechanism and treatment. Our integrated approach can be applied to provide biologic context for GWAS of other diseases.

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CD4+ lymphocyte coexpression network with detail of the brown coexpression module. A. Each circle represents a gene. Weighted gene coexpression analysis identified groups of genes with similar patterns of gene expression and interconnectivity (coexpression modules). The 41 coexpression modules identified are labeled by color. Pathways associated with the largest coexpression modules are denoted in the legend. B. Interconnectivity of the brown coexpression module is shown in detail. Tagged by 6 allergic rhinitis GWAS loci, this coexpression module was highly enriched for allergic rhinitis-associated eSNPs (3.4-fold enrichment, FDR-adjusted P value = 2.6 × 10−24) and also highly enriched for pathways related to mitochondrial function (8.6-fold enrichment, FDR-adjusted P value = 4.5 × 10−72). Genes containing allergic rhinitis-associated eSNPs are marked in brown, with those containing eSNPs with lowest P-value for association between genotype and gene expression marked with greatest brown saturation. Genes in pathways related to mitochondrial function are marked by diamonds with blue outline. Higher correlation between gene expression is shown with thicker and darker edges.
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Figure 4: CD4+ lymphocyte coexpression network with detail of the brown coexpression module. A. Each circle represents a gene. Weighted gene coexpression analysis identified groups of genes with similar patterns of gene expression and interconnectivity (coexpression modules). The 41 coexpression modules identified are labeled by color. Pathways associated with the largest coexpression modules are denoted in the legend. B. Interconnectivity of the brown coexpression module is shown in detail. Tagged by 6 allergic rhinitis GWAS loci, this coexpression module was highly enriched for allergic rhinitis-associated eSNPs (3.4-fold enrichment, FDR-adjusted P value = 2.6 × 10−24) and also highly enriched for pathways related to mitochondrial function (8.6-fold enrichment, FDR-adjusted P value = 4.5 × 10−72). Genes containing allergic rhinitis-associated eSNPs are marked in brown, with those containing eSNPs with lowest P-value for association between genotype and gene expression marked with greatest brown saturation. Genes in pathways related to mitochondrial function are marked by diamonds with blue outline. Higher correlation between gene expression is shown with thicker and darker edges.

Mentions: We achieved CD4+ lymphocyte yields of ~4x106 cells at ≥95% purity per collection. Bioanalyzer (Agilent Technologies, Santa Clara, CA) analysis confirmed average total RNA yields of 2 μg per collection, with minimal evidence of RNA degradation and 28S:18S ratios approaching 2.0.Figure 4A shows the coexpression network we constructed using weighted gene coexpression network analysis of the CD4+ lymphocyte gene expression data. In total, there were 41 coexpressed gene modules identified by the coexpression network, and their interconnectivities are shown. For ease of visualization, modules are identified by color.Using pathway analysis, we found that the modules were enriched for a variety of gene ontology (GO) pathways reflecting the functions being carried out by each module. Pathways associated with the largest coexpression modules are shown in the legend of Figure 4A. For example, the brown module highlighted in Figure 4B was enriched for mitochondrial function. Zinc finger, inflammatory response, and immunoglobulin domain were other pathways highlighted by examining the coexpression modules for functional enrichment (Figure 4A).


Integrated genome-wide association, coexpression network, and expression single nucleotide polymorphism analysis identifies novel pathway in allergic rhinitis.

Bunyavanich S, Schadt EE, Himes BE, Lasky-Su J, Qiu W, Lazarus R, Ziniti JP, Cohain A, Linderman M, Torgerson DG, Eng CS, Pino-Yanes M, Padhukasahasram B, Yang JJ, Mathias RA, Beaty TH, Li X, Graves P, Romieu I, Navarro Bdel R, Salam MT, Vora H, Nicolae DL, Ober C, Martinez FD, Bleecker ER, Meyers DA, Gauderman WJ, Gilliland F, Burchard EG, Barnes KC, Williams LK, London SJ, Zhang B, Raby BA, Weiss ST - BMC Med Genomics (2014)

CD4+ lymphocyte coexpression network with detail of the brown coexpression module. A. Each circle represents a gene. Weighted gene coexpression analysis identified groups of genes with similar patterns of gene expression and interconnectivity (coexpression modules). The 41 coexpression modules identified are labeled by color. Pathways associated with the largest coexpression modules are denoted in the legend. B. Interconnectivity of the brown coexpression module is shown in detail. Tagged by 6 allergic rhinitis GWAS loci, this coexpression module was highly enriched for allergic rhinitis-associated eSNPs (3.4-fold enrichment, FDR-adjusted P value = 2.6 × 10−24) and also highly enriched for pathways related to mitochondrial function (8.6-fold enrichment, FDR-adjusted P value = 4.5 × 10−72). Genes containing allergic rhinitis-associated eSNPs are marked in brown, with those containing eSNPs with lowest P-value for association between genotype and gene expression marked with greatest brown saturation. Genes in pathways related to mitochondrial function are marked by diamonds with blue outline. Higher correlation between gene expression is shown with thicker and darker edges.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
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Figure 4: CD4+ lymphocyte coexpression network with detail of the brown coexpression module. A. Each circle represents a gene. Weighted gene coexpression analysis identified groups of genes with similar patterns of gene expression and interconnectivity (coexpression modules). The 41 coexpression modules identified are labeled by color. Pathways associated with the largest coexpression modules are denoted in the legend. B. Interconnectivity of the brown coexpression module is shown in detail. Tagged by 6 allergic rhinitis GWAS loci, this coexpression module was highly enriched for allergic rhinitis-associated eSNPs (3.4-fold enrichment, FDR-adjusted P value = 2.6 × 10−24) and also highly enriched for pathways related to mitochondrial function (8.6-fold enrichment, FDR-adjusted P value = 4.5 × 10−72). Genes containing allergic rhinitis-associated eSNPs are marked in brown, with those containing eSNPs with lowest P-value for association between genotype and gene expression marked with greatest brown saturation. Genes in pathways related to mitochondrial function are marked by diamonds with blue outline. Higher correlation between gene expression is shown with thicker and darker edges.
Mentions: We achieved CD4+ lymphocyte yields of ~4x106 cells at ≥95% purity per collection. Bioanalyzer (Agilent Technologies, Santa Clara, CA) analysis confirmed average total RNA yields of 2 μg per collection, with minimal evidence of RNA degradation and 28S:18S ratios approaching 2.0.Figure 4A shows the coexpression network we constructed using weighted gene coexpression network analysis of the CD4+ lymphocyte gene expression data. In total, there were 41 coexpressed gene modules identified by the coexpression network, and their interconnectivities are shown. For ease of visualization, modules are identified by color.Using pathway analysis, we found that the modules were enriched for a variety of gene ontology (GO) pathways reflecting the functions being carried out by each module. Pathways associated with the largest coexpression modules are shown in the legend of Figure 4A. For example, the brown module highlighted in Figure 4B was enriched for mitochondrial function. Zinc finger, inflammatory response, and immunoglobulin domain were other pathways highlighted by examining the coexpression modules for functional enrichment (Figure 4A).

Bottom Line: GWAS revealed ethnicity-specific findings, with 4 genome-wide significant loci among Latinos and 1 genome-wide significant locus in the GWAS meta-analysis across ethnic groups.Pathway analysis revealed that the module was enriched for mitochondrial pathways (8.6-fold enrichment, P-value 4.5 × 10-72).Our integrated approach can be applied to provide biologic context for GWAS of other diseases.

View Article: PubMed Central - HTML - PubMed

ABSTRACT

Background: Allergic rhinitis is a common disease whose genetic basis is incompletely explained. We report an integrated genomic analysis of allergic rhinitis.

Methods: We performed genome wide association studies (GWAS) of allergic rhinitis in 5633 ethnically diverse North American subjects. Next, we profiled gene expression in disease-relevant tissue (peripheral blood CD4+ lymphocytes) collected from subjects who had been genotyped. We then integrated the GWAS and gene expression data using expression single nucleotide (eSNP), coexpression network, and pathway approaches to identify the biologic relevance of our GWAS.

Results: GWAS revealed ethnicity-specific findings, with 4 genome-wide significant loci among Latinos and 1 genome-wide significant locus in the GWAS meta-analysis across ethnic groups. To identify biologic context for these results, we constructed a coexpression network to define modules of genes with similar patterns of CD4+ gene expression (coexpression modules) that could serve as constructs of broader gene expression. 6 of the 22 GWAS loci with P-value ≤ 1x10-6 tagged one particular coexpression module (4.0-fold enrichment, P-value 0.0029), and this module also had the greatest enrichment (3.4-fold enrichment, P-value 2.6 × 10-24) for allergic rhinitis-associated eSNPs (genetic variants associated with both gene expression and allergic rhinitis). The integrated GWAS, coexpression network, and eSNP results therefore supported this coexpression module as an allergic rhinitis module. Pathway analysis revealed that the module was enriched for mitochondrial pathways (8.6-fold enrichment, P-value 4.5 × 10-72).

Conclusions: Our results highlight mitochondrial pathways as a target for further investigation of allergic rhinitis mechanism and treatment. Our integrated approach can be applied to provide biologic context for GWAS of other diseases.

Show MeSH
Related in: MedlinePlus