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Functional interactors of three genome-wide association study genes are differentially expressed in severe chronic obstructive pulmonary disease lung tissue.

ABSTRACT: In comparison to genome-wide association studies (GWAS), there has been poor replication of gene expression studies in chronic obstructive pulmonary disease (COPD). We performed microarray gene expression profiling on a large sample of resected lung tissues from subjects with severe COPD. Comparing 111 COPD cases and 40 control smokers, 204 genes were differentially expressed; none were at significant GWAS loci. The top differentially expressed gene was HMGB1, which interacts with AGER, a known COPD GWAS gene. Differentially expressed genes showed enrichment for putative interactors of the first three identified COPD GWAS genes IREB2, HHIP, and FAM13A, based on gene sets derived from protein and RNA binding studies, RNA-interference, a murine smoking model, and expression quantitative trait locus analyses. The gene module most highly associated for COPD in Weighted Gene Co-Expression Network Analysis (WGCNA) was enriched for B cell pathways, and shared seventeen genes with a mouse smoking model and twenty genes with previous emphysema studies. As in other common diseases, genes at COPD GWAS loci were not differentially expressed; however, using a combination of network methods, experimental studies and careful phenotype definition, we found differential expression of putative interactors of these genes, and we replicated previous human and mouse microarray results.

SUBMITTER: Morrow JD

PROVIDER: S-EPMC5347019 | biostudies-literature | 2017 Mar

REPOSITORIES: biostudies-literature

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Functional interactors of three genome-wide association study genes are differentially expressed in severe chronic obstructive pulmonary disease lung tissue.

Morrow Jarrett D JD Zhou Xiaobo X Lao Taotao T Jiang Zhiqiang Z DeMeo Dawn L DL Cho Michael H MH Qiu Weiliang W Cloonan Suzanne S Pinto-Plata Victor V Celli Bartholome B Marchetti Nathaniel N Criner Gerard J GJ Bueno Raphael R Washko George R GR Glass Kimberly K Quackenbush John J Choi Augustine M K AM Silverman Edwin K EK Hersh Craig P CP

Scientific reports 20170313

In comparison to genome-wide association studies (GWAS), there has been poor replication of gene expression studies in chronic obstructive pulmonary disease (COPD). We performed microarray gene expression profiling on a large sample of resected lung tissues from subjects with severe COPD. Comparing 111 COPD cases and 40 control smokers, 204 genes were differentially expressed; none were at significant GWAS loci. The top differentially expressed gene was HMGB1, which interacts with AGER, a known ...[more]

PMID: 28287180

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Project description:Multiple gene expression studies have been performed in lung or airway tissues from subjects with chronic obstructive pulmonary disease (COPD). However, in comparison to genome-wide association studies (GWAS), there has been poor replication across these studies. We sought to perform gene expression profiling on a large sample of severe COPD cases and control smokers and use network methods to identify interacting genes and pathways. We collected surgically-resected lung tissue samples from subjects with severe COPD and controls with normal lung function; all subjects were former smokers. Gene expression profiling on homogenized lung tissue was performed using Illumina HumanHT-12 BeadChips. Protein and RNA binding studies, RNA-interference, a murine smoking model, and expression quantitative trait locus analyses were used to identify genes and proteins that may interact with three known COPD GWAS genes: IREB2, HHIP and FAM13A. Weighted Gene Co-Expression Network Analysis (WGCNA) was used to define co-expressed gene modules. Comparing 111 COPD cases and 40 control smokers, 214 genes were differentially expressed; none of these genes were at significant GWAS loci. However, the top differentially expressed gene was HMGB1, which interacts with AGER, a gene implicated through COPD GWAS. The genes differentially expressed in lung tissue showed strong enrichment for putative interactors of IREB2 and HHIP, with less support for FAM13A, based on the gene sets from the in vitro, in vivo, and in silico studies. In the WGCNA, the module most highly associated for COPD was enriched for B-cell pathways, which shared seventeen genes with the results of the Hhip+/- mouse smoking model. As in other common diseases, genes at COPD GWAS loci were not differentially expressed with COPD status; however, using a combination of network methods, experimental studies of interaction and careful phenotype definition, we found differential expression of putative interactors of these genes, and we replicated previous human and mouse microarray results involving B cell pathways.

Project description:Rationale: Continued reliance on preclinical animal models and traditional human cell culture experiments conducted on supraphysiologically stiff surfaces in two dimensions often limits the translation of cellular and molecular mechanistic findings into effective therapies for patients suffering from chronic obstructive pulmonary disease (COPD). COPD ranks as the fourth highest cause of mortality in the United States, and thus it is imperative to improve ex vivo models of this devastating disease. One emerging novel model of study involves using precision-cut lung slices as three-dimensional lung tissue culture (3D-LTC) platforms. Although this model retains the complex pulmonary architecture required for more precise ex vivo modeling, it is limited by short-term viability (?5–7 d). Objectives: We hypothesized that this decrease in viability is related to slices losing the extracellular matrix adhesion foundation critical for normal cellular functioning and that encapsulation of slices in custom hydrogel microenvironments would improve maintenance of a stable phenotype for longer-term investigational studies. Methods: The 3D-LTC slices tested here were created according to standard protocols from healthy mouse lungs and from the lungs of a patient with COPD. We synthesized poly(ethylene glycol)–based polymers to create custom hydrogels for encapsulation of 3D-LTCs with mechanical properties that match each type of lung tissue. The Young’s modulus (E) or stiffness of hydrogels was measured with a parallel-plate rheometer. Lung slices were analyzed for viability with a colorimetric assay that measures cellular metabolism (WST-1; Millipore Sigma) and by staining for cell membrane integrity (Invitrogen LIVE/DEAD viability kit; Thermo Fisher Scientific). All fluorescently labeled samples were imaged by spinning disk confocal microscopy, and cell viability at all time points was analyzed with ImageJ software. Results: The average percent viability of cells within hybrid 3D-LTCs was consistently higher than control 3D-LTCs on Day 1 (35% increase; P?<?0.001) and Day 7 (55% increase; P?<?0.001) according to LIVE/DEAD staining results. The WST-1 assay further showed no significant difference in viability between the two systems up to Day 18 in culture. Conclusions: We have demonstrated that it is possible to create customized hydrogel platforms that replicate the stiffness of healthy mouse and human COPD lung tissues. Precision cut lung slices embedded in these materials maintain higher levels of viability compared with controls in culture. Further optimization of this technology platform is ongoing and will facilitate the development of more organotypic ex vivo models of chronic pulmonary disease.

Project description:Neutrophils play a central role in innate immunity, inflammation, and resolution. Unresolving neutrophilia features as a disrupted inflammatory process in the airways of patients with chronic obstructive pulmonary disease (COPD) and severe asthma. The extent to which this may be linked to disease pathobiology remains obscure and could be further confounded by indication of glucocorticoids or concomitant respiratory infections. The formation of neutrophil extracellular traps (NETs) represents a specialized host defense mechanism that entrap and eliminate invading microbes. NETs are web-like scaffolds of extracellular DNA in complex with histones and neutrophil granular proteins, such as myeloperoxidase and neutrophil elastase. Distinct from apoptosis, NET formation is an active form of cell death that could be triggered by various microbial, inflammatory, and endogenous or exogenous stimuli. NETs are reportedly enriched in neutrophil-dominant refractory lung diseases, such as COPD and severe asthma. Evidence for a pathogenic role for respiratory viruses (e.g., Rhinovirus), bacteria (e.g., Staphylococcus aureus) and fungi (e.g., Aspergillus fumigatus) in NET induction is emerging. Dysregulation of this process may exert localized NET burden and contribute to NETopathic lung inflammation. Disentangling the role of NETs in human health and disease offer unique opportunities for therapeutic modulation. The chemokine CXCR2 receptor regulates neutrophil activation and migration, and small molecule CXCR2 antagonists (e.g., AZD5069, danirixin) have been developed to selectively block neutrophilic inflammatory pathways. NET-stabilizing agents using CXCR2 antagonists are being investigated in proof-of-concept studies in patients with COPD to provide mechanistic insights. Clinical validation of this type could lead to novel therapeutics for multiple CXCR2-related NETopathologies. In this Review, we discuss the emerging role of NETs in the clinicopathobiology of COPD and severe asthma and provide an outlook on how novel NET-stabilizing therapies via CXCR2 blockade could be leveraged to disrupt NETopathic inflammation in disease-specific phenotypes.

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Functional interactors of three genome-wide association study genes are differentially expressed in severe chronic obstructive pulmonary disease lung tissue.

Publications

Functional interactors of three genome-wide association study genes are differentially expressed in severe chronic obstructive pulmonary disease lung tissue.

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