New DNA Methylation Signals for Malignant Pleural Mesothelioma Risk Assessment

Abstract

Malignant pleural mesothelioma (MPM) is a rare and aggressive neoplasm. Patients are usually diagnosed when current treatments have limited benefits, highlighting the need for noninvasive tests aimed at an MPM risk assessment tool that might improve life expectancy. Three hundred asbestos-exposed subjects (163 MPM cases and 137 cancer-free controls), from the same geographical region in Italy, were recruited. The evaluation of asbestos exposure was conducted considering the frequency, the duration and the intensity of occupational, environmental and domestic exposure. A genome-wide methylation array was performed to identify novel blood DNA methylation (DNAm) markers of MPM. Multiple regression analyses adjusting for potential confounding factors and interaction between asbestos exposure and DNAm on the MPM odds ratio were applied. Epigenome-wide analysis (EWAS) revealed 12 single-CpGs associated with the disease. Two of these showed high statistical power (99%) and effect size (>0.05) after false discovery rate (FDR) multiple comparison corrections: (i) cg03546163 in FKBP5, significantly hypomethylated in cases (Mean Difference in beta values (MD) = −0.09, 95% CI = −0.12|−0.06, p = 1.2 × 10−7), and (ii) cg06633438 in MLLT1, statistically hypermethylated in cases (MD = 0.07, 95% CI = 0.04|0.10, p = 1.0 × 10−6). Based on the interaction analysis, asbestos exposure and epigenetic profile together may improve MPM risk assessment. Above-median asbestos exposure and hypomethylation of cg03546163 in FKBP5 (OR = 20.84, 95% CI = 8.71|53.96, p = 5.5 × 10−11) and hypermethylation of cg06633438 in MLLT1 (OR = 11.71, 95% CI = 4.97|29.64, p = 5.9 × 10−8) genes compared to below-median asbestos exposure and hyper/hypomethylation of single-CpG DNAm, respectively. Receiver Operation Characteristics (ROC) for Case-Control Discrimination showed a significant increase in MPM discrimination when DNAm information was added in the model (baseline model, BM: asbestos exposure, age, gender and white blood cells); area under the curve, AUC = 0.75; BM + cg03546163 at FKBP5. AUC = 0.89, 2.1 × 10−7; BM + cg06633438 at MLLT1. AUC = 0.89, 6.3 × 10−8. Validation and replication procedures, considering independent sample size and a different DNAm analysis technique, confirmed the observed associations. Our results suggest the potential application of DNAm profiles in blood to develop noninvasive tests for MPM risk assessment in asbestos-exposed subjects.

Blood cell DNA methylation biomarkers in preclinical malignant pleural mesothelioma: The EPIC prospective cohort

“…We previously observed DNAm biomarkers in MPM patients 11,13 : among them only cg01521397 in TAF4 gene is differentially hypomethylated in preclinical samples (as well as in MPM patients), but with any significant changes closer to MPM diagnosis. The meaning of this results is interesting in the context of biomarkers reverse causality interpretation, discriminating biomarkers related to the presence of MPM from those associated to prediagnostic biological changes.…”

“…We aimed to assess whether previously reported DNAm biomarkers in MPM patients at diagnosis 11,13 are also informative in DNA blood samples taken up to 5 years before MPM diagnosis. To do this, we performed a multiple regression model on MESO_5YRS dataset of DNAm biomarkers previously identified as differentially methylated in a case/control study (Table S9).…”

“…11 More recently, we identified one single-CpG signal in FKBP5 gene associated with asbestos-exposure as a biomarker of MPM and MPM survival. 12,13 In the current study we investigated, for the first time, the relationship between DNA methylation profiles in prediagnostic blood samples and MPM, in a case-control study nested in the prospective European Prospective Investigation into Cancer and nutrition (EPIC) cohort. 14 Our aim was to identify predictive biomarkers of MPM development in asbestos-exposed individuals by DNAm analysis in blood samples.…”

“…We previously identified DNAm biomarkers in blood taken at MPM diagnosis able to discriminate between MPM and non‐MPM asbestos‐exposed individuals, assuming that DNAm profile of blood cells may contribute to identify early changes associated with MPM development 11 . More recently, we identified one single‐CpG signal in FKBP5 gene associated with asbestos‐exposure as a biomarker of MPM and MPM survival 12,13 …”

Malignant Mesothelioma

“…In this Special Issue, 168 authors representing 71 affiliations from 13 countries over three continents have made 19 contributions, and it is a great privilege and pleasure for the editors to introduce this collective work which summarizes important insights in this field of research. As MM is mostly related to genetic and epigenetic alterations caused by prolonged exposure to asbestos fibers, in the search for a noninvasive prognosis test, Cugliari et al showed the potential predictive value of DNA methylation changes in white blood cells as a MM survival biomarker [ 1 ], and investigated differences between MM cases and asbestos-exposed cancer-free controls [ 2 ]. Another important question concerns the discrimination between MM and benign proliferation of mesothelial cells (also frequently treated by surgery), for which Shresta et al propose a genomic differential characterization [ 3 ].…”