Altered DNA methylation is associated with aberrant gene expression in parenchymal but not airway fibroblasts isolated from individuals with COPD

[1]  I. Rahman,et al.  DNA methylation profiling in peripheral lung tissues of smokers and patients with COPD , 2017, Clinical Epigenetics.

[2]  Paul Flicek,et al.  Increased DNA methylation variability in type 1 diabetes across three immune effector cell types , 2016, Nature Communications.

[3]  John Quackenbush,et al.  DNA methylation profiling in human lung tissue identifies genes associated with COPD , 2016, Epigenetics.

[4]  A. Halayko,et al.  Human bronchial and parenchymal fibroblasts display differences in basal inflammatory phenotype and response to IL‐17A , 2016, Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology.

[5]  Matthias W. Beckmann,et al.  DNA methylation outliers in normal breast tissue identify field defects that are enriched in cancer , 2016, Nature Communications.

[6]  Antonio Ciampi,et al.  funtooNorm: an R package for normalization of DNA methylation data when there are multiple cell or tissue types , 2015, Bioinform..

[7]  Peter L Molloy,et al.  De novo identification of differentially methylated regions in the human genome , 2015, Epigenetics & Chromatin.

[8]  Matthew E. Ritchie,et al.  limma powers differential expression analyses for RNA-sequencing and microarray studies , 2015, Nucleic acids research.

[9]  Joshua D. Campbell,et al.  Integrative Analysis of DNA Methylation and Gene Expression Data Identifies EPAS1 as a Key Regulator of COPD , 2015, PLoS genetics.

[10]  Rafael A. Irizarry,et al.  Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays , 2014, Bioinform..

[11]  Avrum Spira,et al.  DNA methylation is globally disrupted and associated with expression changes in chronic obstructive pulmonary disease small airways. , 2014, American journal of respiratory cell and molecular biology.

[12]  K. Hansen,et al.  Functional normalization of 450k methylation array data improves replication in large cancer studies , 2014, Genome Biology.

[13]  D. Postma,et al.  Differential effects of fluticasone on extracellular matrix production by airway and parenchymal fibroblasts in severe COPD. , 2013, American journal of physiology. Lung cellular and molecular physiology.

[14]  Pau Farré,et al.  Additional annotation enhances potential for biologically-relevant analysis of the Illumina Infinium HumanMethylation450 BeadChip array , 2013, Epigenetics & Chromatin.

[15]  Avrum Spira,et al.  A gene expression signature of emphysema-related lung destruction and its reversal by the tripeptide GHK , 2012, Genome Medicine.

[16]  A. Baccarelli,et al.  Variable DNA methylation is associated with chronic obstructive pulmonary disease and lung function. , 2012, American journal of respiratory and critical care medicine.

[17]  C. Bai,et al.  Pro-inflammatory phenotype of COPD fibroblasts not compatible with repair in COPD lung , 2011, Journal of cellular and molecular medicine.

[18]  K. Morgan,et al.  The role of IREB2 and transforming growth factor beta-1 genetic variants in COPD: a replication case-control study , 2011, BMC Medical Genetics.

[19]  G. Gamble,et al.  Individual and Cumulative Effects of GWAS Susceptibility Loci in Lung Cancer: Associations after Sub-Phenotyping for COPD , 2011, PloS one.

[20]  G. Gamble,et al.  Chromosome 4q31 locus in COPD is also associated with lung cancer , 2010, European Respiratory Journal.

[21]  D. Knight,et al.  Human lung parenchyma but not proximal bronchi produces fibroblasts with enhanced TGF-beta signaling and alpha-SMA expression. , 2010, American journal of respiratory cell and molecular biology.

[22]  Xiao Zhang,et al.  Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis , 2010, BMC Bioinformatics.

[23]  Akshay Sood,et al.  Wood smoke exposure and gene promoter methylation are associated with increased risk for COPD in smokers. , 2010, American journal of respiratory and critical care medicine.

[24]  M. Dahlbäck,et al.  Altered fibroblast proteoglycan production in COPD , 2010, Respiratory research.

[25]  C. Hersh Faculty Opinions recommendation of Genome-wide association study identifies five loci associated with lung function. , 2010 .

[26]  Marc Decramer,et al.  The 15q24/25 susceptibility variant for lung cancer and chronic obstructive pulmonary disease is associated with emphysema. , 2010, American journal of respiratory and critical care medicine.

[27]  A. Hofman,et al.  Hedgehog-interacting protein is a COPD susceptibility gene: the Rotterdam Study , 2009, European Respiratory Journal.

[28]  Leena Peltonen,et al.  Genome-wide association study of smoking initiation and current smoking. , 2009, American journal of human genetics.

[29]  G. Gamble,et al.  Lung cancer gene associated with COPD: triple whammy or possible confounding effect? , 2008, European Respiratory Journal.

[30]  H. Magnussen,et al.  Lung fibroblast repair functions in patients with chronic obstructive pulmonary disease are altered by multiple mechanisms. , 2008, American journal of respiratory and critical care medicine.

[31]  S. Phan,et al.  Biology of fibroblasts and myofibroblasts. , 2008, Proceedings of the American Thoracic Society.

[32]  D. Postma,et al.  Different Modulation of Decorin Production by Lung Fibroblasts from Patients with Mild and Severe Emphysema , 2005, COPD.

[33]  A. Hofman,et al.  Meta-analyses of genome-wide association studies identify multiple loci associated with pulmonary function , 2010, Nature Genetics.

[34]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .