title: Diagnostic Performance of Plasma DNA Methylation Profiles in Lung Cancer, Pulmonary Fibrosis and COPD.
abstract: Disease-specific alterations of the cell-free DNA methylation status are frequently found in serum samples and are currently considered to be suitable biomarkers. Candidate markers were identified by bisulfite conversion-based genome-wide methylation screening of lung tissue from lung cancer, fibrotic ILD, and COPD. cfDNA from 400 μl serum (n = 204) served to test the diagnostic performance of these markers. Following methylation-sensitive restriction enzyme digestion and enrichment of methylated DNA via targeted amplification (multiplexed MSRE enrichment), a total of 96 markers were addressed by highly parallel qPCR. Lung cancer was efficiently separated from non-cancer and controls with a sensitivity of 87.8%, (95%CI: 0.67-0.97) and specificity 90.2%, (95%CI: 0.65-0.98). Cancer was distinguished from ILD with a specificity of 88%, (95%CI: 0.57-1), and COPD from cancer with a specificity of 88% (95%CI: 0.64-0.97). Separation of ILD from COPD and controls was possible with a sensitivity of 63.1% (95%CI: 0.4-0.78) and a specificity of 70% (95%CI: 0.54-0.81). The results were confirmed using an independent sample set (n = 46) by use of the four top markers discovered in the study (HOXD10, PAX9, PTPRN2, and STAG3) yielding an AUC of 0.85 (95%CI: 0.72-0.95). This technique was capable of distinguishing interrelated complex pulmonary diseases suggesting that multiplexed MSRE enrichment might be useful for simple and reliable diagnosis of diverse multifactorial disease states.
authors.affiliation: AIT - Austrian Institute of Technology, Health & Environment Department, Molecular Diagnostics Unit, Muthgasse 11/2, 1190 Vienna, Austria.
authors.forename: Matthias
authors.initials: M
authors.lastname: Wielscher
authors.affiliation: AIT - Austrian Institute of Technology, Health & Environment Department, Molecular Diagnostics Unit, Muthgasse 11/2, 1190 Vienna, Austria.
authors.forename: Klemens
authors.initials: K
authors.lastname: Vierlinger
authors.affiliation: AIT - Austrian Institute of Technology, Health & Environment Department, Molecular Diagnostics Unit, Muthgasse 11/2, 1190 Vienna, Austria.
authors.forename: Ulrike
authors.initials: U
authors.lastname: Kegler
authors.affiliation: Medical University of Vienna, Clinical Department for Pulmonology, Spitalgasse 23, 1090 Vienna, Austria.
authors.forename: Rolf
authors.initials: R
authors.lastname: Ziesche
authors.affiliation: Medical University of Vienna, Institute of Cancer Research, Borschkegasse 8A, 1090 Vienna, Austria.
authors.forename: Andrea
authors.initials: A
authors.lastname: Gsur
authors.affiliation: AIT - Austrian Institute of Technology, Health & Environment Department, Molecular Diagnostics Unit, Muthgasse 11/2, 1190 Vienna, Austria.
authors.forename: Andreas
authors.initials: A
authors.lastname: Weinhäusel
mesh_terms: D000368:Aged; D019175:DNA Methylation; D004273:DNA, Neoplasm / Q000097:blood* / Q000235:genetics; D005260:Female; D006801:Humans; D008175:Lung Neoplasms / Q000097:blood* / Q000235:genetics; D008297:Male; D008875:Middle Aged; D029424:Pulmonary Disease, Chronic Obstructive / Q000097:blood* / Q000235:genetics; D011658:Pulmonary Fibrosis / Q000097:blood* / Q000235:genetics
chemical_list: D004273:DNA, Neoplasm
keywords: AUC, area under curve; Biomarker; COPD, chronic obstructive pulmonary disease; Ct-value, cycle threshold; HOXD10; HP, hypersensitivity pneumonitis; ILD, interstitial lung disease, IPF, idiopathic pulmonary fibrosis; Liquid biopsy; MSP, methyl specific priming; MSRE, methyl sensitive restriction enzyme; NSIP, non-specific interstitial pneumonitis; PAX9; ROC, receiver operating characteristics; UIP, usual interstitial pneumonia; cfDNA, cell-free DNA; methyl-sensitive restriction enzyme; multiplex PCR