title: DNA methylation at modifier genes of lung disease severity is altered in cystic fibrosis.
abstract: Lung disease progression is variable among cystic fibrosis (CF) patients and depends on DNA mutations in theCFTRgene, polymorphic variations in disease modifier genes, and environmental exposure. The contribution of genetic factors has been extensively investigated, whereas the mechanism whereby environmental factors modulate the lung disease is unknown. In this project, we hypothesized that (i) reiterative stress alters the epigenome in CF-affected tissues and (ii) DNA methylation variations at disease modifier genes modulate the lung function in CF patients.
  
  
  
  We profiled DNA methylation atCFTR, the disease-causing gene, and at 13 lung modifier genes in nasal epithelial cells and whole blood samples from 48 CF patients and 24 healthy controls. CF patients homozygous for the p.Phe508del mutation and ≥18-year-old were stratified according to the lung disease severity. DNA methylation was measured by bisulfite and next-generation sequencing. The DNA methylation profile allowed us to correctly classify 75% of the subjects, thus providing a CF-specific molecular signature. Moreover, in CF patients, DNA methylation at specific genes was highly correlated in the same tissue sample. We suggest that gene methylation in CF cells may be co-regulated by disease-specifictrans-factors. Three genes were differentially methylated in CF patients compared with controls and/or in groups of pulmonary severity:HMOX1andGSTM3in nasal epithelial samples;HMOX1andEDNRAin blood samples. The association between pulmonary severity and DNA methylation atEDNRAwas confirmed in blood samples from an independent set of CF patients. Also, lower DNA methylation levels atGSTM3were associated with theGSTM3*Ballele, a polymorphic 3-bp deletion that has a protective effect in cystic fibrosis.
  
  
  
  DNA methylation levels are altered in nasal epithelial and blood cell samples from CF patients. Analysis ofCFTRand 13 lung disease modifier genes shows DNA methylation changes of small magnitude: some of them are a consequence of the disease; other changes may result in small expression variations that collectively modulate the lung disease severity.
authors.affiliation: Laboratoire de Génétique de Maladies Rares, EA7402 Montpellier University, Montpellier, France.
authors.forename: Milena
authors.initials: M
authors.lastname: Magalhães
authors.affiliation: Equipe de Statistique Appliquée-ESPCI ParisTech, PSL Research University-UMRS1158, Paris, France.
authors.forename: Isabelle
authors.initials: I
authors.lastname: Rivals
authors.affiliation: Laboratoire de Génétique de Maladies Rares, EA7402 Montpellier University, Montpellier, France.|Laboratoire de Génétique Moléculaire-CHU Montpellier, Montpellier, France.
authors.forename: Mireille
authors.initials: M
authors.lastname: Claustres
authors.affiliation: Laboratoire de Génétique de Maladies Rares, EA7402 Montpellier University, Montpellier, France.|Laboratoire de Génétique Moléculaire-CHU Montpellier, Montpellier, France.
authors.forename: Jessica
authors.initials: J
authors.lastname: Varilh
authors.affiliation: Laboratoire de Génétique de Maladies Rares, EA7402 Montpellier University, Montpellier, France.
authors.forename: Mélodie
authors.initials: M
authors.lastname: Thomasset
authors.affiliation: Laboratoire de Génétique de Maladies Rares, EA7402 Montpellier University, Montpellier, France.|Laboratoire de Génétique Moléculaire-CHU Montpellier, Montpellier, France.
authors.forename: Anne
authors.initials: A
authors.lastname: Bergougnoux
authors.affiliation: CRCM, Renée Sabran Hospital-CHU Lyon, Hyères, France.
authors.forename: Laurent
authors.initials: L
authors.lastname: Mely
authors.affiliation: CRCM, Pasteur Hospital-CHU Nice, Nice, France.
authors.forename: Sylvie
authors.initials: S
authors.lastname: Leroy
authors.affiliation: Sorbonne Universités, UPMC Univ Paris 06, Paris, France.|INSERM U938-CRSA, Paris, France.|APHP, Trousseau Hospital, Paris, France.
authors.forename: Harriet
authors.initials: H
authors.lastname: Corvol
authors.affiliation: Sorbonne Universités, UPMC Univ Paris 06, Paris, France.|INSERM U938-CRSA, Paris, France.
authors.forename: Loïc
authors.initials: L
authors.lastname: Guillot
authors.affiliation: CRCM, Larrey Hospital-CHU Toulouse, Toulouse, France.
authors.forename: Marlène
authors.initials: M
authors.lastname: Murris
authors.affiliation: Laboratoire de Génétique de Maladies Rares, EA7402 Montpellier University, Montpellier, France.|Laboratoire de Génétique Moléculaire-CHU Montpellier, Montpellier, France.
authors.forename: Emmanuelle
authors.initials: E
authors.lastname: Beyne
authors.affiliation: CRCM, Arnaud de Villeneuve Hospital-CHU Montpellier, Montpellier, France.
authors.forename: Davide
authors.initials: D
authors.lastname: Caimmi
authors.affiliation: CRCM, Arnaud de Villeneuve Hospital-CHU Montpellier, Montpellier, France.
authors.forename: Isabelle
authors.initials: I
authors.lastname: Vachier
authors.affiliation: CRCM, Arnaud de Villeneuve Hospital-CHU Montpellier, Montpellier, France.
authors.forename: Raphaël
authors.initials: R
authors.lastname: Chiron
authors.affiliation: Laboratoire de Génétique de Maladies Rares, EA7402 Montpellier University, Montpellier, France.
authors.forename: Albertina
authors.identifier: 0000-0002-9997-1645
authors.initials: A
authors.lastname: De Sario
mesh_terms: D000328:Adult; D003550:Cystic Fibrosis / Q000097:blood / Q000235:genetics*; D019005:Cystic Fibrosis Transmembrane Conductance Regulator / Q000235:genetics*; D019175:DNA Methylation; D057890:Epigenomics; D005260:Female; D060045:Genes, Modifier; D005982:Glutathione Transferase / Q000235:genetics; D051547:Heme Oxygenase-1 / Q000235:genetics; D006801:Humans; D008171:Lung Diseases / Q000097:blood / Q000150:complications / Q000235:genetics*; D008297:Male; D009666:Nose / Q000737:chemistry; D044022:Receptor, Endothelin A / Q000235:genetics; D017422:Sequence Analysis, DNA; D017384:Sequence Deletion; D012720:Severity of Illness Index; D055815:Young Adult
chemical_list: C505032:CFTR protein, human; D044022:Receptor, Endothelin A; D019005:Cystic Fibrosis Transmembrane Conductance Regulator; C496541:HMOX1 protein, human; D051547:Heme Oxygenase-1; C483009:GSTM3 protein, human; D005982:Glutathione Transferase
keywords: Co-methylation; Cystic fibrosis; DNA methylation; Modifier gene; Nasal epithelial cells; Next-generation sequencing; Polymorphism; Pulmonary function; Pyrosequencing