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.

Genome-wide DNA methylation profiling integrated with gene expression profiling identifies PAX9 as a novel prognostic marker in chronic lymphocytic leukemia

“…In the recent years, it has emerged as one of the biomarkers of cell proliferation in lung cancer [54]. A significant association of PAX9 expression with stage, IPI score, relative risk of treatment initiation, TTFT and OS in the present study strengthens its role as an important marker of prognosis in CLL as well.…”

Systematic review of lung function and COPD with peripheral blood DNA methylation in population based studies

“…Pulmonary Clinics at these hospitals and associated hospitals served as additional source of participants [32]Post-bronchodilator FEV1/FVC  < 0.7 and FEV1 < 70% predictedBell et al [22]2012UKTwins UKHealthy unselected volunteers who are a twin (MZ, DZ and singleton) representing the general populationParticipants recruited from media campaigns, initially only middle-aged women were included in the registry but from 1995 onwards, men and women >18 years of age were also recruited [28]Analysed lung function only (no COPD diagnosis) –FEV1 and FVCLepeule et al [25]2012USANormative AgeingHealthy male participants at enrolment, containing smokers and ex-smokers (Veterans Administration 1963 closed-cohort)Enrolled after an initial health screening determined that they were free of known chronic medical conditionsAnalysed lung function –FEV1, FVC, MMEF (did not specify pre-/post-bronchodilator)Lange et al [26]2012Boston (USA)Normative AgeingHealthy male participants at enrolment, containing smokers and ex-smokers (Veterans Administration 1963 closed-cohort)Enrolled after an initial health screening determined that they were free of known chronic medical conditionsGOLD stage II or higher (pre-bronchodilator FEV1/FVC < 0.7 and FEV1 < 80% predicted)Marioni et al [21]2015Scotland (UK)Lothian BirthChildhood inception cohort of ‘healthy b ’ participants with varying lung function, containing smokers, ex-smokers and never smokersIndividuals born in 1936 in the Lothian area were identified using the Community Health Index (registered at a general practitioner) or through media advertisements. The majority of the cohort were participants in the Scottish Mental Survey 1947 [27]Analysed lung function only (no COPD diagnosis)-FEV1Wielscher et al [24]2015AustriaN/ACOPD patients, GOLD 0 COPD patients and healthy controlsSelection of patient from Medical University of Vienna, 2008-2012Post-bronchodilator FEV1/FVC <0.7 Abbreviations : ICGN International COPD Genetics Network a Multi-centre: Cambridge, Copenhagen, Denver, Harvard, Holland, Italy, Liverpool, Nebraska, Spain, Vancouver EOCOPD: Early-onset COPD (Boston), AAT: Alpha-1-Antitrypsin, UK: United Kingdom, MZ: Monozygotic twin, DZ: Dizygotic twin, USA: United States of America, GOLD: Global Initiative for Chronic Obstructive Lung Disease b Healthy: participants free from chronic disease at enrolment, GOLD stage 0: FEV1/FVC ratio > 0.7 but with respiratory symptoms …”

DNA methylation biomarkers discovered in silico detect cancer in liquid biopsies from non-small cell lung cancer patients

“…These include markers or marker sets to detect e.g. lung [30][31][32][33][34][35], breast [12,13], colorectal [36,37] or pancreatic [38] cancers. A few DNA methylation cancer biomarkers are already in clinical use, e.g.…”