Soo-Zin Kim-Wanner1, Yassen Assenov2, Mridul B Nair2, Dieter Weichenhan2, Axel Benner3, Natalia Becker3, Katharina Landwehr4, Ruprecht Kuner5, Holger Sültmann6, Manel Esteller7, Ina Koch8, Michael Lindner8, Michael Meister9, Michael Thomas9, Matthias Bieg10, Ursula Klingmüller11, Matthias Schlesner12, Arne Warth13, Benedikt Brors14, Erhard Seifried4, Halvard Bönig4, Christoph Plass15, Angela Risch16, Thomas Muley9. 1. Division of Epigenomics, German Cancer Research Center (Deutsches Krebsforschungszentrum [DKFZ]), Heidelberg, Germany; German Red Cross Blood Donor Service, Institute of Transfusion Medicine and Immune Hematology of the Goethe University Medical School, Frankfurt, Germany. 2. Division of Epigenomics, German Cancer Research Center (Deutsches Krebsforschungszentrum [DKFZ]), Heidelberg, Germany. 3. Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany. 4. German Red Cross Blood Donor Service, Institute of Transfusion Medicine and Immune Hematology of the Goethe University Medical School, Frankfurt, Germany. 5. Division of Cancer Genome Research, German Cancer Research Center (DKFZ), German Cancer Consortium (Deutsches Konsortium für Translationale Krebsforschung) and National Center for Tumor Diseases, Heidelberg, Germany; Translational Oncology at the University Medical Center of Johannes Gutenberg University, Mainz, Germany. 6. Division of Cancer Genome Research, German Cancer Research Center (DKFZ), German Cancer Consortium (Deutsches Konsortium für Translationale Krebsforschung) and National Center for Tumor Diseases, Heidelberg, Germany; Translational Lung Research Centre Heidelberg, Member of the German Centre for Lung Research (Deutsches Zentrum für Lungenforschung), Heidelberg, Germany. 7. Josep Carreras Leukaemia Research Institute, Badalona, Barcelona, Catalonia, Spain; Institució Catalana de Recerca i Estudis Avançats, Barcelona, Catalonia, Spain; Centro de Investigacion Biomedica en Red Cancer, Madrid, Spain; Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona, Barcelona, Catalonia, Spain. 8. Center of Thoracic Surgery, Asklepios Fachkliniken München-Gauting, Ludwig Maximilians University, Gauting; Comprehensive Pneumology Centre Munich, German Centre for Lung Research (Deutsches Zentrum für Lungenforschung), Munich, Germany. 9. Translational Lung Research Centre Heidelberg, Member of the German Centre for Lung Research (Deutsches Zentrum für Lungenforschung), Heidelberg, Germany; Translational Research Unit, Thoraxklinik at University Hospital Heidelberg, Heidelberg, Germany. 10. Division of Theoretical Bioinformatics, and Heidelberg Center for Personalized Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany. 11. Translational Lung Research Centre Heidelberg, Member of the German Centre for Lung Research (Deutsches Zentrum für Lungenforschung), Heidelberg, Germany; Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), Heidelberg, Germany. 12. Translational Lung Research Centre Heidelberg, Member of the German Centre for Lung Research (Deutsches Zentrum für Lungenforschung), Heidelberg, Germany; Division of Theoretical Bioinformatics, and Heidelberg Center for Personalized Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany; Bioinformatics and Omics Data Analytics, German Cancer Research Center (DKFZ), Heidelberg, Germany. 13. Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany. 14. Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany. 15. Division of Epigenomics, German Cancer Research Center (Deutsches Krebsforschungszentrum [DKFZ]), Heidelberg, Germany; Translational Lung Research Centre Heidelberg, Member of the German Centre for Lung Research (Deutsches Zentrum für Lungenforschung), Heidelberg, Germany. 16. Division of Epigenomics, German Cancer Research Center (Deutsches Krebsforschungszentrum [DKFZ]), Heidelberg, Germany; Translational Lung Research Centre Heidelberg, Member of the German Centre for Lung Research (Deutsches Zentrum für Lungenforschung), Heidelberg, Germany; University of Salzburg, Department of Biosciences, Allergy-Cancer-BioNano Research Centre, Salzburg, Austria; Cancer Cluster Salzburg, Universität Salzburg, Salzburg, Austria. Electronic address: angela.risch@sbg.ac.at.
Abstract
INTRODUCTION: Surgical procedure is the treatment of choice in early stage I lung adenocarcinoma. However, a considerable number of patients experience recurrence within the first 2 years after complete resection. Suitable prognostic biomarkers that identify patients at high risk of recurrence (who may probably benefit from adjuvant treatment) are still not available. This study aimed at identifying methylation markers for early recurrence that may become important tools for the development of new treatment modalities. METHODS: Genome-wide DNA methylation profiling was performed on 30 stage I lung adenocarcinomas, comparing 14 patients with early metastatic recurrence with 16 patients with a long-term relapse-free survival period using methylated-CpG-immunoprecipitation followed by high-throughput next-generation sequencing. The differentially methylated regions between the two subgroups were validated for their prognostic value in two independent cohorts using the MassCLEAVE assay, a high-resolution quantitative methylation analysis. RESULTS: Unsupervised clustering of patients in the discovery cohort on the basis of differentially methylated regions identified patients with shorter relapse-free survival (hazard ratio: 2.23; 95% confidence interval: 0.66-7.53; p = 0.03). In two validation cohorts, promoter hypermethylation of the long noncoding RNA PLUT was significantly associated with shorter relapse-free survival (hazard ratio: 0.54; 95% confidence interval: 0.31-0.93; p < 0.026) and could be reported as an independent prognostic factor in the multivariate Cox regression analysis. CONCLUSIONS: Promoter hypermethylation of the long noncoding RNA PLUT is predictive in patients with early stage I adenocarcinoma at high risk for early recurrence. Further studies are needed to validate its role in carcinogenesis and its use as a biomarker to facilitate patient selection and risk stratification.
INTRODUCTION: Surgical procedure is the treatment of choice in early stage I lung adenocarcinoma. However, a considerable number of patients experience recurrence within the first 2 years after complete resection. Suitable prognostic biomarkers that identify patients at high risk of recurrence (who may probably benefit from adjuvant treatment) are still not available. This study aimed at identifying methylation markers for early recurrence that may become important tools for the development of new treatment modalities. METHODS: Genome-wide DNA methylation profiling was performed on 30 stage I lung adenocarcinomas, comparing 14 patients with early metastatic recurrence with 16 patients with a long-term relapse-free survival period using methylated-CpG-immunoprecipitation followed by high-throughput next-generation sequencing. The differentially methylated regions between the two subgroups were validated for their prognostic value in two independent cohorts using the MassCLEAVE assay, a high-resolution quantitative methylation analysis. RESULTS: Unsupervised clustering of patients in the discovery cohort on the basis of differentially methylated regions identified patients with shorter relapse-free survival (hazard ratio: 2.23; 95% confidence interval: 0.66-7.53; p = 0.03). In two validation cohorts, promoter hypermethylation of the long noncoding RNA PLUT was significantly associated with shorter relapse-free survival (hazard ratio: 0.54; 95% confidence interval: 0.31-0.93; p < 0.026) and could be reported as an independent prognostic factor in the multivariate Cox regression analysis. CONCLUSIONS: Promoter hypermethylation of the long noncoding RNA PLUT is predictive in patients with early stage I adenocarcinoma at high risk for early recurrence. Further studies are needed to validate its role in carcinogenesis and its use as a biomarker to facilitate patient selection and risk stratification.