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1.
Am J Respir Crit Care Med ; 207(5): 587-593, 2023 03 01.
Article in English | MEDLINE | ID: mdl-36094461

ABSTRACT

Rationale: Relatives of patients with familial interstitial pneumonia (FIP) are at increased risk for pulmonary fibrosis and develop preclinical pulmonary fibrosis (PrePF). Objectives: We defined the incidence and progression of new-onset PrePF and its relationship to survival among first-degree relatives of families with FIP. Methods: This is a cohort study of family members with FIP who were initially screened with a health questionnaire and chest high-resolution computed tomography (HRCT) scan, and approximately 4 years later, the evaluation was repeated. A total of 493 asymptomatic first-degree relatives of patients with FIP were evaluated at baseline, and 296 (60%) of the original subjects participated in the subsequent evaluation. Measurements and Main Results: The median interval between HRCTs was 3.9 years (interquartile range, 3.5-4.4 yr). A total of 252 subjects who agreed to repeat evaluation were originally determined not to have PrePF at baseline; 16 developed PrePF. A conservative estimate of the annual incidence of PrePF is 1,023 per 100,000 person-years (95% confidence interval, 511-1,831 per 100,000 person-years). Of 44 subjects with PrePF at baseline, 38.4% subjects had worsening dyspnea compared with 15.4% of those without PrePF (P = 0.002). Usual interstitial pneumonia by HRCT (P < 0.0002) and baseline quantitative fibrosis score (P < 0.001) are also associated with worsening dyspnea. PrePF at the initial screen is associated with decreased survival (P < 0.001). Conclusions: The incidence of PrePF in this at-risk population is at least 100-fold higher than that reported for sporadic idiopathic pulmonary fibrosis (IPF). Although PrePF and IPF represent distinct entities, our study demonstrates that PrePF, like IPF, is progressive and associated with decreased survival.


Subject(s)
Idiopathic Pulmonary Fibrosis , Lung Diseases, Interstitial , Humans , Cohort Studies , Incidence , Dyspnea , Lung , Retrospective Studies
2.
Am J Physiol Lung Cell Mol Physiol ; 323(3): L329-L337, 2022 09 01.
Article in English | MEDLINE | ID: mdl-35881171

ABSTRACT

Previously we have shown that a gain-of-function MUC5B promoter variant (rs35705950) is the strongest risk factor for the development of idiopathic pulmonary fibrosis. We have also found that Muc5b overexpression reduces mucociliary clearance in mice, potentially leading to recurrent injury to the bronchoalveolar epithelia. Hypersensitivity pneumonitis (HP) is induced by inhalation of numerous causative antigens that may be affected by mucociliary clearance. We conducted this study to determine the role of Muc5b in a mouse model of HP induced by Saccharopolyspora rectivirgula (SR) antigen. We used Muc5b-deficient and wild-type (WT) mice to determine whether Muc5b plays a role in inflammation and fibrosis at 3 and 6 wk in an SR model of HP. We measured cell concentrations and MUC5B expression in whole lung lavage (WLL) and quantified fibrosis using hydroxyproline assay and second harmonic generation. Muc5b expression in WLL fluid was significantly increased in SR-exposed WT mice compared with saline controls. WT mice challenged with SR developed more inflammation and lung fibrosis at 6 wk compared with 3 wk postexposure. Moreover, we found that 6 wk following challenge with SR, Muc5b-deficient mice had less lung inflammation and less lung fibrosis than Muc5b WT mice. Furthermore, Muc5b-deficient mice had significantly lower concentrations of TGF-ß1 in the WLL compared with Muc5b WT mice at 6 wk of exposure. Muc5b appears to play a role in fibrosis in the animal model of HP and this may have implications for HP in humans.


Subject(s)
Alveolitis, Extrinsic Allergic , Idiopathic Pulmonary Fibrosis , Saccharopolyspora , Animals , Bronchoalveolar Lavage Fluid , Disease Models, Animal , Humans , Idiopathic Pulmonary Fibrosis/genetics , Inflammation , Mice , Mice, Inbred C57BL , Mucin-5B/genetics
3.
Am J Physiol Lung Cell Mol Physiol ; 321(2): L440-L450, 2021 08 01.
Article in English | MEDLINE | ID: mdl-34160296

ABSTRACT

Idiopathic pulmonary fibrosis (IPF) is an incurable genetic disease that affects 5 million people worldwide. The gain-of-function MUC5B promoter variant rs35705950 is the dominant genetic risk factor for IPF, yet has a low penetrance. This raises the possibility that other genes and transcripts affect the penetrance of MUC5B. Previously, we have shown that the concentration of Muc5b in bronchoalveolar epithelia is directly associated with the extent and persistence of bleomycin-induced lung fibrosis in mice. In this study, we investigated whether bleomycin-induced lung injury is Muc5b dependent in genetically divergent strains of mice. Specifically, mice from the eight Diversity Outbred (DO) founders were phenotyped for Muc5b expression and lung fibrosis 3 wk after intratracheal bleomycin administration. Although we identified strains with low Muc5b expression and minimal lung fibrosis (CAST/EiJ and PWK/PhJ) and strains with high Muc5b expression and extensive lung fibrosis (NZO/H1LtJ and WSB/EiJ), there also were strains that did not demonstrate a clear relationship between Muc5b expression and lung fibrosis (129S1/SvlmJ, NOD/ShiLtJ, and C57BL/6J, A/J). Hierarchical clustering suggests that other factors may work in concert with or potentially independent of Muc5b to promote bleomycin-induced lung injury and fibrosis. This study suggests that these strains and their recombinant inbred crosses may prove helpful in identifying the genes and transcripts that interact with Muc5b and cause lung fibrosis.


Subject(s)
Bleomycin/adverse effects , Gene Expression Regulation/drug effects , Idiopathic Pulmonary Fibrosis , Mucin-5B , Respiratory Mucosa , Animals , Bleomycin/pharmacology , Idiopathic Pulmonary Fibrosis/chemically induced , Idiopathic Pulmonary Fibrosis/genetics , Idiopathic Pulmonary Fibrosis/metabolism , Lung Injury/chemically induced , Lung Injury/genetics , Lung Injury/metabolism , Lung Injury/pathology , Male , Mice , Mucin-5B/biosynthesis , Mucin-5B/genetics , Respiratory Mucosa/metabolism , Respiratory Mucosa/pathology
4.
J Thorac Dis ; 12(9): 4991-5019, 2020 Sep.
Article in English | MEDLINE | ID: mdl-33145073

ABSTRACT

Bronchoalveolar lavage (BAL) is a commonly used procedure in the evaluation of lung disease as it allows for sampling of the lower respiratory tract. In many circumstances, BAL differential cell counts have been reported to be typical of specific lung disorders. In addition, more specific diagnostic tests including molecular assays such as polymerase chain reaction (PCR) or enzyme-linked immunosorbent assay, special cytopathologic stains, or particular microscopic findings have been described as part of BAL fluid analysis. This review focuses on common cellular and molecular findings of BAL in a wide range of lung diseases. Since the performance of the first lung irrigation in 1927, BAL has become a common and important diagnostic tool. While some pulmonary disorders have a highly characteristic signature of BAL findings, BAL results alone often lack specificity and require interpretation along with other clinical and radiographic details. Development of new diagnostic assays is certain to reinforce the utility of BAL in the future. Our review of the BAL literature is intended to serve as a resource to assist clinicians in the care of patients with lung disorders.

5.
Am J Respir Crit Care Med ; 202(10): 1430-1444, 2020 11 15.
Article in English | MEDLINE | ID: mdl-32602730

ABSTRACT

Rationale: Chronic hypersensitivity pneumonitis (CHP) is caused by an immune response to antigen inhalation and is characterized by variable histopathological and clinical features. A subset of subjects with CHP have usual interstitial pneumonia and appear to be clinically similar to subjects with idiopathic pulmonary fibrosis (IPF).Objectives: To determine the common and unique molecular features of CHP and IPF.Methods: Transcriptome analysis of lung samples from CHP (n = 82), IPF (n = 103), and unaffected controls (n = 103) was conducted. Differential gene expression was determined adjusting for sex, race, age, and smoking history and using false discovery rate to control for multiple comparisons.Measurements and Main Results: When compared with controls, we identified 413 upregulated and 317 downregulated genes in CHP and 861 upregulated and 322 downregulated genes in IPF. Concordantly upregulated or downregulated genes in CHP and IPF were related to collagen catabolic processes and epithelial development, whereas genes specific to CHP (differentially expressed in CHP when compared with control and not differentially expressed in IPF) were related to chemokine-mediated signaling and immune responsiveness. Using weighted gene coexpression network analysis, we found that among subjects with CHP, genes involved in adaptive immunity or epithelial cell development were associated with improved or reduced lung function, respectively, and that MUC5B expression was associated with epithelial cell development. MUC5B expression was also associated with lung fibrosis and honeycombing.Conclusions: Gene expression analysis of CHP and IPF identified signatures common to CHP and IPF, as well as genes uniquely expressed in CHP. Select modules of gene expression are characterized by distinct clinical and pathological features of CHP.


Subject(s)
Alveolitis, Extrinsic Allergic/genetics , Alveolitis, Extrinsic Allergic/immunology , Gene Expression Profiling , Idiopathic Pulmonary Fibrosis/genetics , Idiopathic Pulmonary Fibrosis/immunology , Lung Diseases, Interstitial/genetics , Lung Diseases, Interstitial/immunology , Adult , Aged , Aged, 80 and over , Alveolitis, Extrinsic Allergic/physiopathology , Female , Gene Expression , Humans , Idiopathic Pulmonary Fibrosis/physiopathology , Lung Diseases, Interstitial/physiopathology , Male , Middle Aged
7.
Thorax ; 74(12): 1131-1139, 2019 12.
Article in English | MEDLINE | ID: mdl-31558622

ABSTRACT

BACKGROUND: Relatives of patients with familial interstitial pneumonia (FIP) are at increased risk for pulmonary fibrosis. We assessed the prevalence and risk factors for preclinical pulmonary fibrosis (PrePF) in first-degree relatives of patients with FIP and determined the utility of deep learning in detecting PrePF on CT. METHODS: First-degree relatives of patients with FIP over 40 years of age who believed themselves to be unaffected by pulmonary fibrosis underwent CT scans of the chest. Images were visually reviewed, and a deep learning algorithm was used to quantify lung fibrosis. Genotyping for common idiopathic pulmonary fibrosis risk variants in MUC5B and TERT was performed. FINDINGS: In 494 relatives of patients with FIP from 263 families of patients with FIP, the prevalence of PrePF on visual CT evaluation was 15.6% (95% CI 12.6 to 19.0). Compared with visual CT evaluation, deep learning quantitative CT analysis had 84% sensitivity (95% CI 0.72 to 0.89) and 86% sensitivity (95% CI 0.83 to 0.89) for discriminating subjects with visual PrePF diagnosis. Subjects with PrePF were older (65.9, SD 10.1 years) than subjects without fibrosis (55.8 SD 8.7 years), more likely to be male (49% vs 37%), more likely to have smoked (44% vs 27%) and more likely to have the MUC5B promoter variant rs35705950 (minor allele frequency 0.29 vs 0.21). MUC5B variant carriers had higher quantitative CT fibrosis scores (mean difference of 0.36%), a difference that remains significant when controlling for age and sex. INTERPRETATION: PrePF is common in relatives of patients with FIP. Its prevalence increases with age and the presence of a common MUC5B promoter variant. Quantitative CT analysis can detect these imaging abnormalities.


Subject(s)
Genetic Variation , Idiopathic Pulmonary Fibrosis/genetics , Mucin-5B/genetics , Aged , Algorithms , Colorado/epidemiology , Deep Learning , Female , Genetic Predisposition to Disease , Humans , Idiopathic Interstitial Pneumonias/diagnostic imaging , Idiopathic Interstitial Pneumonias/epidemiology , Idiopathic Interstitial Pneumonias/genetics , Idiopathic Pulmonary Fibrosis/diagnostic imaging , Idiopathic Pulmonary Fibrosis/epidemiology , Male , Middle Aged , Prevalence , Promoter Regions, Genetic/genetics , ROC Curve , Risk Factors , Telomerase/genetics , Tomography, X-Ray Computed
8.
Am J Respir Crit Care Med ; 200(2): 199-208, 2019 07 15.
Article in English | MEDLINE | ID: mdl-31034279

ABSTRACT

Rationale: Several common and rare genetic variants have been associated with idiopathic pulmonary fibrosis, a progressive fibrotic condition that is localized to the lung. Objectives: To develop an integrated understanding of the rare and common variants located in multiple loci that have been reported to contribute to the risk of disease. Methods: We performed deep targeted resequencing (3.69 Mb of DNA) in cases (n = 3,624) and control subjects (n = 4,442) across genes and regions previously associated with disease. We tested for associations between disease and 1) individual common variants via logistic regression and 2) groups of rare variants via sequence kernel association tests. Measurements and Main Results: Statistically significant common variant association signals occurred in all 10 of the regions chosen based on genome-wide association studies. The strongest risk variant is the MUC5B promoter variant rs35705950, with an odds ratio of 5.45 (95% confidence interval, 4.91-6.06) for one copy of the risk allele and 18.68 (95% confidence interval, 13.34-26.17) for two copies of the risk allele (P = 9.60 × 10-295). In addition to identifying for the first time that rare variation in FAM13A is associated with disease, we confirmed the role of rare variation in the TERT and RTEL1 gene regions in the risk of IPF, and found that the FAM13A and TERT regions have independent common and rare variant signals. Conclusions: A limited number of common and rare variants contribute to the risk of idiopathic pulmonary fibrosis in each of the resequencing regions, and these genetic variants focus on biological mechanisms of host defense and cell senescence.


Subject(s)
Cellular Senescence/genetics , Host-Pathogen Interactions/genetics , Idiopathic Pulmonary Fibrosis/genetics , ATP-Binding Cassette Transporters/genetics , Case-Control Studies , DNA Helicases/genetics , Exoribonucleases/genetics , Female , GTPase-Activating Proteins/genetics , Genetic Predisposition to Disease , Genetic Variation , Genome-Wide Association Study , High-Throughput Nucleotide Sequencing , Humans , Logistic Models , Male , Mucin-5B/genetics , Promoter Regions, Genetic/genetics , Pulmonary Surfactant-Associated Protein A/genetics , Pulmonary Surfactant-Associated Protein C/genetics , RNA/genetics , Sequence Analysis, DNA , Telomerase/genetics , Telomere-Binding Proteins/genetics
9.
Nat Commun ; 9(1): 5363, 2018 12 18.
Article in English | MEDLINE | ID: mdl-30560893

ABSTRACT

The gain-of-function MUC5B promoter variant rs35705950 is the dominant risk factor for developing idiopathic pulmonary fibrosis (IPF). Here we show in humans that MUC5B, a mucin thought to be restricted to conducting airways, is co-expressed with surfactant protein C (SFTPC) in type 2 alveolar epithelia and in epithelial cells lining honeycomb cysts, indicating that cell types involved in lung fibrosis in distal airspace express MUC5B. In mice, we demonstrate that Muc5b concentration in bronchoalveolar epithelia is related to impaired mucociliary clearance (MCC) and to the extent and persistence of bleomycin-induced lung fibrosis. We also establish the ability of the mucolytic agent P-2119 to restore MCC and to suppress bleomycin-induced lung fibrosis in the setting of Muc5b overexpression. Our findings suggest that mucociliary dysfunction might play a causative role in bleomycin-induced pulmonary fibrosis in mice overexpressing Muc5b, and that MUC5B in distal airspaces is a potential therapeutic target in humans with IPF.


Subject(s)
Genetic Predisposition to Disease , Idiopathic Pulmonary Fibrosis/genetics , Mucin-5B/genetics , Mucin-5B/metabolism , Mucociliary Clearance/genetics , Respiratory Mucosa/pathology , Animals , Bleomycin/toxicity , Disease Models, Animal , Epithelial Cells/metabolism , Epithelial Cells/pathology , Expectorants/pharmacology , Expectorants/therapeutic use , Female , Gain of Function Mutation , Humans , Idiopathic Pulmonary Fibrosis/chemically induced , Idiopathic Pulmonary Fibrosis/drug therapy , Idiopathic Pulmonary Fibrosis/pathology , Lung/cytology , Lung/metabolism , Lung/pathology , Male , Mice , Mice, Inbred C57BL , Mice, Transgenic , Mucociliary Clearance/drug effects , Promoter Regions, Genetic/genetics , Pulmonary Surfactant-Associated Protein C/metabolism , Respiratory Mucosa/cytology , Respiratory Mucosa/metabolism
10.
Eur Respir J ; 52(3)2018 09.
Article in English | MEDLINE | ID: mdl-30139770

ABSTRACT

We evaluated performance characteristics and estimated the minimal clinically important difference (MCID) of data-driven texture analysis (DTA), a high-resolution computed tomography (HRCT)-derived measurement of lung fibrosis, in subjects with idiopathic pulmonary fibrosis (IPF).The study population included 141 subjects with IPF from two interventional clinical trials who had both baseline and nominal 54- or 60-week follow-up HRCT. DTA scores were computed and compared with forced vital capacity (FVC), diffusing capacity of the lung for carbon monoxide, distance covered during a 6-min walk test and St George's Respiratory Questionnaire scores to assess the method's reliability, validity and responsiveness. Anchor- and distribution-based methods were used to estimate its MCID.DTA had acceptable reliability in subjects appearing stable according to anchor variables at follow-up. Correlations between the DTA score and other clinical measurements at baseline were moderate to weak and in the hypothesised directions. Acceptable responsiveness was demonstrated by moderate to weak correlations (in the directions hypothesised) between changes in the DTA score and changes in other parameters. Using FVC as an anchor, MCID was estimated to be 3.4%.Quantification of lung fibrosis extent on HRCT using DTA is reliable, valid and responsive, and an increase of ∼3.4% represents a clinically important change.


Subject(s)
Idiopathic Pulmonary Fibrosis/diagnostic imaging , Idiopathic Pulmonary Fibrosis/physiopathology , Lung/physiopathology , Tomography, X-Ray Computed , Aged , Data Interpretation, Statistical , Female , Humans , Lung/diagnostic imaging , Male , Middle Aged , Minimal Clinically Important Difference , Reproducibility of Results , Retrospective Studies , Severity of Illness Index , Surveys and Questionnaires , Vital Capacity
11.
Am J Physiol Lung Cell Mol Physiol ; 315(1): L1-L10, 2018 07 01.
Article in English | MEDLINE | ID: mdl-29565179

ABSTRACT

The common gain-of-function MUC5B promoter variant ( rs35705950 ) is the strongest risk factor for the development of idiopathic pulmonary fibrosis (IPF). While the role of complement in IPF is controversial, both MUC5B and the complement system play a role in lung host defense. The aim of this study was to evaluate the relationship between complement component 3 (C3) and MUC5B in patients with IPF and in bleomycin-induced lung injury in mice. To do this, we evaluated C3 gene expression in whole lung tissue from 300 subjects with IPF and 175 healthy controls. Expression of C3 was higher in IPF than healthy controls {1.40-fold increase [95% confidence interval (CI) 1.31-1.50]; P < 0.0001} and even greater among IPF subjects with the highest-risk IPF MUC5B promoter genotype [TT vs. GG = 1.59-fold (95% CI 1.15-2.20); P < 0.05; TT vs. GT = 1.66-fold (95% CI 1.20-2.30); P < 0.05]. Among subjects with IPF, C3 expression was significantly higher in the lung tissue without microscopic honeycombing than in the lung tissue with microscopic honeycombing [1.40-fold increase (95% CI 1.23- 1.59); P < 0.01]. In mice, while bleomycin exposure increased Muc5b protein expression, C3-deficient mice were protected from bleomycin-induced lung injury. In aggregate, our findings indicate that the MUC5B promoter variant is associated with higher C3 expression and suggest that the complement system may contribute to the pathogenesis of IPF.


Subject(s)
Bleomycin/adverse effects , Complement C3/biosynthesis , Genetic Variation , Genotype , Idiopathic Pulmonary Fibrosis/metabolism , Lung/metabolism , Mucin-5B/biosynthesis , A549 Cells , Animals , Bleomycin/pharmacology , Complement C3/genetics , Humans , Idiopathic Pulmonary Fibrosis/chemically induced , Idiopathic Pulmonary Fibrosis/genetics , Idiopathic Pulmonary Fibrosis/pathology , Lung/pathology , Mice , Mice, Knockout , Middle Aged , Mucin-5B/genetics , Promoter Regions, Genetic
12.
Lancet Respir Med ; 6(2): 154-160, 2018 02.
Article in English | MEDLINE | ID: mdl-29413083

ABSTRACT

Idiopathic pulmonary fibrosis (IPF) is a progressive, irreversible, and typically fatal lung disease characterised by subpleural fibrosis, subepithelial fibroblast foci, and microscopic honeycombing. Although understanding of the pathogenic mechanisms continues to evolve, evidence indicates that distal airway and alveolar epithelial cells are central drivers of the disease. In this Viewpoint, we review the history of naming and classifications used to define the disease now referred to as IPF, in the context of understanding the clinical presentation, causes, and pathogenesis of the disease. We aim to generate discussion on whether, given the substantial progress made in understanding the clinical, genetic, cellular, and molecular mechanisms involved in the development of IPF, a change of name should be considered. To initiate this discussion, we offer new suggestions to update the name of this disease and new approaches to classify all forms of pulmonary fibrosis.


Subject(s)
Idiopathic Pulmonary Fibrosis/classification , Idiopathic Pulmonary Fibrosis/pathology , Fibroblasts/pathology , Humans , Idiopathic Pulmonary Fibrosis/diagnosis , Lung/pathology , Risk Factors
13.
Radiology ; 285(1): 270-278, 2017 10.
Article in English | MEDLINE | ID: mdl-28493789

ABSTRACT

Purpose To evaluate associations between pulmonary function and both quantitative analysis and visual assessment of thin-section computed tomography (CT) images at baseline and at 15-month follow-up in subjects with idiopathic pulmonary fibrosis (IPF). Materials and Methods This retrospective analysis of preexisting anonymized data, collected prospectively between 2007 and 2013 in a HIPAA-compliant study, was exempt from additional institutional review board approval. The extent of lung fibrosis at baseline inspiratory chest CT in 280 subjects enrolled in the IPF Network was evaluated. Visual analysis was performed by using a semiquantitative scoring system. Computer-based quantitative analysis included CT histogram-based measurements and a data-driven textural analysis (DTA). Follow-up CT images in 72 of these subjects were also analyzed. Univariate comparisons were performed by using Spearman rank correlation. Multivariate and longitudinal analyses were performed by using a linear mixed model approach, in which models were compared by using asymptotic χ2 tests. Results At baseline, all CT-derived measures showed moderate significant correlation (P < .001) with pulmonary function. At follow-up CT, changes in DTA scores showed significant correlation with changes in both forced vital capacity percentage predicted (ρ = -0.41, P < .001) and diffusing capacity for carbon monoxide percentage predicted (ρ = -0.40, P < .001). Asymptotic χ2 tests showed that inclusion of DTA score significantly improved fit of both baseline and longitudinal linear mixed models in the prediction of pulmonary function (P < .001 for both). Conclusion When compared with semiquantitative visual assessment and CT histogram-based measurements, DTA score provides additional information that can be used to predict diminished function. Automatic quantification of lung fibrosis at CT yields an index of severity that correlates with visual assessment and functional change in subjects with IPF. © RSNA, 2017.


Subject(s)
Idiopathic Pulmonary Fibrosis/diagnostic imaging , Idiopathic Pulmonary Fibrosis/physiopathology , Lung/diagnostic imaging , Lung/physiopathology , Tomography, X-Ray Computed/methods , Adult , Aged , Aged, 80 and over , Female , Humans , Idiopathic Pulmonary Fibrosis/epidemiology , Male , Middle Aged , Radiographic Image Interpretation, Computer-Assisted , Respiratory Function Tests , Retrospective Studies
15.
Physiol Rev ; 96(4): 1567-91, 2016 10.
Article in English | MEDLINE | ID: mdl-27630174

ABSTRACT

Idiopathic pulmonary fibrosis (IPF) is an incurable complex genetic disorder that is associated with sequence changes in 7 genes (MUC5B, TERT, TERC, RTEL1, PARN, SFTPC, and SFTPA2) and with variants in at least 11 novel loci. We have previously found that 1) a common gain-of-function promoter variant in MUC5B rs35705950 is the strongest risk factor (genetic and otherwise), accounting for 30-35% of the risk of developing IPF, a disease that was previously considered idiopathic; 2) the MUC5B promoter variant can potentially be used to identify individuals with preclinical pulmonary fibrosis and is predictive of radiologic progression of preclinical pulmonary fibrosis; and 3) MUC5B may be involved in the pathogenesis of pulmonary fibrosis with MUC5B message and protein expressed in bronchiolo-alveolar epithelia of IPF and the characteristic IPF honeycomb cysts. Based on these considerations, we hypothesize that excessive production of MUC5B either enhances injury due to reduced mucociliary clearance or impedes repair consequent to disruption of normal regenerative mechanisms in the distal lung. In aggregate, these novel considerations should have broad impact, resulting in specific etiologic targets, early detection of disease, and novel biologic pathways for use in the design of future intervention, prevention, and mechanistic studies of IPF.


Subject(s)
Bronchioles/physiopathology , Idiopathic Pulmonary Fibrosis/genetics , Mucin-5B/genetics , Mucociliary Clearance/genetics , Pulmonary Alveoli/physiopathology , Animals , Genetic Predisposition to Disease , Humans , Idiopathic Pulmonary Fibrosis/physiopathology , Respiratory Mucosa/physiopathology
16.
BMC Genet ; 17(1): 74, 2016 06 07.
Article in English | MEDLINE | ID: mdl-27266705

ABSTRACT

BACKGROUND: Fibrotic idiopathic interstitial pneumonias (fIIP) are a group of fatal lung diseases with largely unknown etiology and without definitive treatment other than lung transplant to prolong life. There is strong evidence for the importance of both rare and common genetic risk alleles in familial and sporadic disease. We have previously used genome-wide single nucleotide polymorphism data to identify 10 risk loci for fIIP. Here we extend that work to imputed genome-wide genotypes and conduct new RNA sequencing studies of lung tissue to identify and characterize new fIIP risk loci. RESULTS: We performed genome-wide genotype imputation association analyses in 1616 non-Hispanic white (NHW) cases and 4683 NHW controls followed by validation and replication (878 cases, 2017 controls) genotyping and targeted gene expression in lung tissue. Following meta-analysis of the discovery and replication populations, we identified a novel fIIP locus in the HLA region of chromosome 6 (rs7887 P meta = 3.7 × 10(-09)). Imputation of classic HLA alleles identified two in high linkage disequilibrium that are associated with fIIP (DRB1*15:01 P = 1.3 × 10(-7) and DQB1*06:02 P = 6.1 × 10(-8)). Targeted RNA-sequencing of the HLA locus identified 21 genes differentially expressed between fibrotic and control lung tissue (Q < 0.001), many of which are involved in immune and inflammatory response regulation. In addition, the putative risk alleles, DRB1*15:01 and DQB1*06:02, are associated with expression of the DQB1 gene among fIIP cases (Q < 1 × 10(-16)). CONCLUSIONS: We have identified a genome-wide significant association between the HLA region and fIIP. Two HLA alleles are associated with fIIP and affect expression of HLA genes in lung tissue, indicating that the potential genetic risk due to HLA alleles may involve gene regulation in addition to altered protein structure. These studies reveal the importance of the HLA region for risk of fIIP and a basis for the potential etiologic role of auto-immunity in fIIP.


Subject(s)
Genome-Wide Association Study/methods , HLA-DQ beta-Chains/genetics , HLA-DRB1 Chains/genetics , Idiopathic Pulmonary Fibrosis/genetics , Pulmonary Fibrosis/genetics , Sequence Analysis, RNA/methods , Adult , Aged , Chromosomes, Human, Pair 6/genetics , Female , Gene Expression Profiling , Gene Expression Regulation , Genetic Loci , Genetic Predisposition to Disease , Humans , Linkage Disequilibrium , Male , Middle Aged
17.
Chest ; 149(5): 1215-22, 2016 05.
Article in English | MEDLINE | ID: mdl-26836909

ABSTRACT

BACKGROUND: To determine the effect of the MUC5B promoter polymorphism (rs35705950) on the CT imaging appearance of pulmonary fibrosis. METHODS: High-resolution CT scans of 1,764 subjects were scored as part of a, genomewide association study with institutional review board approval; 1,491 of these had pulmonary fibrosis on CT scans and were included in the study. Two thoracic radiologists independently scored CT scans systematically. Discrepancies were resolved by a third thoracic radiologist. All patients were genotyped specifically for the rs35705950 single-nucleotide polymorphism (SNP). Two-tailed Fisher exact or χ(2) tests and Student t tests or Mann-Whitney U tests were used to compare proportions and means, respectively. RESULTS: The major and minor alleles at the rs35705950 SNP are guanine (G) and thymine (T), respectively: 514 were homozygous for the major allele (G group), and 977 were heterozygous or homozygous for the minor allele (T group). The G group had a higher proportion than the T group with ground-glass opacity (62.1% vs 54.2%; P = .04). There was no significant difference between the G and T groups regarding presence of honeycombing. The T group showed a significantly higher subpleural axial distribution of fibrosis than did the G group (62.3% vs 42.2%; P < .0001). The T group showed a lower proportion of diagnoses inconsistent with usual interstitial pneumonitis (UIP; 20.3% compared with 30.5% for the G group) and a greater proportion of confident (probable UIP and UIP) UIP diagnoses (43.8% compared with 32.6% for the G group). CONCLUSIONS: The MUC5B promoter polymorphism identifies a pattern of fibrosis that is different from other causes of fibrosis and may respond differently to potential therapies.


Subject(s)
Idiopathic Pulmonary Fibrosis/diagnostic imaging , Lung/diagnostic imaging , Mucin-5B/genetics , Aged , Alleles , Cohort Studies , Female , Genotype , Heterozygote , Humans , Idiopathic Pulmonary Fibrosis/genetics , Male , Middle Aged , Phenotype , Polymorphism, Genetic , Polymorphism, Single Nucleotide , Promoter Regions, Genetic/genetics , Pulmonary Fibrosis/diagnostic imaging , Pulmonary Fibrosis/genetics , Tomography, X-Ray Computed
19.
Eur Respir J ; 47(4): 1189-97, 2016 Apr.
Article in English | MEDLINE | ID: mdl-26917616

ABSTRACT

The aim of this study was to compare the clinical, radiological and histological findings in a large population of subjects enrolled during a multicentre study of idiopathic pulmonary fibrosis, with a focus on discordance between imaging and histologic diagnoses of usual interstitial pneumonia (UIP).Two independent radiologists retrospectively reviewed 241 subjects who underwent high-resolution computed tomography (HRCT) and surgical lung biopsies. HRCT findings were classified as UIP, possible UIP and inconsistent with UIP. Histological findings were classified as definite, probable, possible and not UIP.Of the 241 cases, 102 (42.3%) had HRCT findings of UIP, 64 (26.6%) had possible UIP and 75 (31.1%) were inconsistent with UIP. Among those with UIP on HRCT, 99 (97.1%) had histologically definite or probable UIP (concordant group), and 71 (94.7%) of those with "inconsistent" HRCT features had histologically definite or probable UIP (discordant group). Discordant subjects were slightly younger and less likely to be smokers than concordant subjects, but no survival differences were identified.In this population of patients enrolled with a diagnosis of idiopathic pulmonary fibrosis, 94.7% of those with HRCT findings "inconsistent with UIP" demonstrated histological UIP. This suggests that the term "inconsistent with UIP" is misleading.


Subject(s)
Lung Diseases, Interstitial/diagnostic imaging , Lung Diseases, Interstitial/pathology , Aged , Biopsy , Female , Humans , Idiopathic Pulmonary Fibrosis/diagnosis , Lung/pathology , Male , Middle Aged , Observer Variation , Prognosis , Retrospective Studies , Surveys and Questionnaires , Tomography, X-Ray Computed , Treatment Outcome , United States
20.
Am J Respir Crit Care Med ; 193(10): 1151-60, 2016 05 15.
Article in English | MEDLINE | ID: mdl-26669357

ABSTRACT

RATIONALE: Sequence variation, methylation differences, and transcriptional changes in desmoplakin (DSP) have been observed in patients with idiopathic pulmonary fibrosis (IPF). OBJECTIVES: To identify novel variants in DSP associated with IPF and to characterize the relationship of these IPF sequence variants with DSP gene expression in human lung. METHODS: A chromosome 6 locus (7,370,061-7,606,946) was sequenced in 230 subjects with IPF and 228 control subjects. Validation genotyping of disease-associated variants was conducted in 936 subjects with IPF and 936 control subjects. DSP gene expression was measured in lung tissue from 334 subjects with IPF and 201 control subjects. MEASUREMENTS AND MAIN RESULTS: We identified 23 sequence variants in the chromosome 6 locus associated with IPF. Genotyping of selected variants in our validation cohort revealed that noncoding intron 1 variant rs2744371 (odds ratio = 0.77, 95% confidence interval [CI] = 0.66-0.91, P = 0.002) is protective for IPF, and a previously described IPF-associated intron 5 variant (rs2076295) is associated with increased risk of IPF (odds ratio = 1.36, 95% CI = 1.19-1.56, P < 0.001) after controlling for sex and age. DSP expression is 2.3-fold increased (95% CI = 1.91-2.71) in IPF lung tissue (P < 0.0001). Only the minor allele at rs2076295 is associated with decreased DSP expression (P = 0.001). Staining of fibrotic and normal human lung tissue localized DSP to airway epithelia. CONCLUSIONS: Sequence variants in DSP are associated with IPF, and rs2076295 genotype is associated with differential expression of DSP in the lung. DSP expression is increased in IPF lung and concentrated in the airway epithelia, suggesting a potential role for DSP in the pathogenesis of IPF.


Subject(s)
Desmoplakins/genetics , Genetic Variation/genetics , Idiopathic Pulmonary Fibrosis/genetics , Aged , Female , Gene Expression/genetics , Humans , Male , Middle Aged , Odds Ratio
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