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Goldmann T, Schmitt B, Müller J, Kröger M, Scheufele S, Marwitz S, Nitschkowski D, Schneider MA, Meister M, Muley T, Thomas M, Kugler C, Rabe KF, Siebert R, Reck M, Ammerpohl O. DNA methylation profiles of bronchoscopic biopsies for the diagnosis of lung cancer. Clin Epigenetics 2021; 13:38. [PMID: 33596996 PMCID: PMC7890863 DOI: 10.1186/s13148-021-01024-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 02/07/2021] [Indexed: 11/10/2022] Open
Abstract
Background Lung cancer is the leading cause of cancer-related death in most western countries in both, males and females, accounting for roughly 20–25% of all cancer deaths. For choosing the most appropriate therapy regimen a definite diagnosis is a prerequisite. However, histological characterization of bronchoscopic biopsies particularly with low tumor cell content is often challenging. Therefore, this study aims at (a) determining the value of DNA methylation analysis applied to specimens obtained by bronchoscopic biopsy for the diagnosis of lung cancer and (b) at comparing aberrantly CpG loci identified in bronchoscopic biopsy with those identified by analyzing surgical specimens. Results We report the HumanMethylation450-based DNA methylation analysis of paired samples of bronchoscopic biopsy specimens either from the tumor side or from the contralateral tumor-free bronchus in 37 patients with definite lung cancer diagnosis and 18 patients with suspicious diagnosis. A differential DNA methylation analysis between both biopsy sites of patients with definite diagnosis identified 1303 loci. Even those samples were separated by the set of 1303 loci in which histopathological analysis could not unambiguously define the dignity. Further differential DNA methylation analyses distinguished between SCLC and NSCLC. We validated our results in an independent cohort of 40 primary lung cancers obtained by open surgical resection and their corresponding controls from the same patient as well as in publically available DNA methylation data from a TCGA cohort which could also be classified with high accuracy. Conclusions Considering that the prognosis correlates with tumor stage at time of diagnosis, early detection of lung cancer is vital and DNA methylation analysis might add valuable information to reliably characterize lung cancer even in histologically ambiguous sample material. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01024-6.
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Affiliation(s)
- Torsten Goldmann
- Pathology of the University Medical Center Schleswig-Holstein (UKSH), Campus Lübeck and the Research Center Borstel, Lübeck, Borstel, Germany.,Airway Research Center North, Member of the German Center for Lung Research (DZL), Grosshansdorf, Germany
| | | | - Julia Müller
- Pathology of the University Medical Center Schleswig-Holstein (UKSH), Campus Lübeck and the Research Center Borstel, Lübeck, Borstel, Germany
| | - Maren Kröger
- Institute of Human Genetics, University Medical Center Schleswig-Holstein (UKSH), Campus Kiel, Germany
| | - Swetlana Scheufele
- Institute of Human Genetics, University Medical Center Schleswig-Holstein (UKSH), Campus Kiel, Germany.,Airway Research Center North, Member of the German Center for Lung Research (DZL), Grosshansdorf, Germany
| | - Sebastian Marwitz
- Pathology of the University Medical Center Schleswig-Holstein (UKSH), Campus Lübeck and the Research Center Borstel, Lübeck, Borstel, Germany.,Airway Research Center North, Member of the German Center for Lung Research (DZL), Grosshansdorf, Germany
| | - Dörte Nitschkowski
- Pathology of the University Medical Center Schleswig-Holstein (UKSH), Campus Lübeck and the Research Center Borstel, Lübeck, Borstel, Germany.,Airway Research Center North, Member of the German Center for Lung Research (DZL), Grosshansdorf, Germany
| | - Marc A Schneider
- Translational Research Unit, Thoraxklinik at University Hospital Heidelberg, 69126, Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany
| | - Michael Meister
- Translational Research Unit, Thoraxklinik at University Hospital Heidelberg, 69126, Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany
| | - Thomas Muley
- Translational Research Unit, Thoraxklinik at University Hospital Heidelberg, 69126, Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany
| | - Michael Thomas
- Internistische Onkologie der Thoraxtumoren, Thoraxklinik im Universitätsklinikum Heidelberg, Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | | | - Klaus F Rabe
- LungenClinic Grosshansdorf, Grosshansdorf, Germany.,Airway Research Center North, Member of the German Center for Lung Research (DZL), Grosshansdorf, Germany
| | - Reiner Siebert
- Institute of Human Genetics, University Medical Center Ulm, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Martin Reck
- LungenClinic Grosshansdorf, Grosshansdorf, Germany.,Airway Research Center North, Member of the German Center for Lung Research (DZL), Grosshansdorf, Germany
| | - Ole Ammerpohl
- Institute of Human Genetics, University Medical Center Ulm, Albert-Einstein-Allee 11, 89081, Ulm, Germany. .,Airway Research Center North, Member of the German Center for Lung Research (DZL), Grosshansdorf, Germany.
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Affinito O, Scala G, Palumbo D, Florio E, Monticelli A, Miele G, Avvedimento VE, Usiello A, Chiariotti L, Cocozza S. Modeling DNA methylation by analyzing the individual configurations of single molecules. Epigenetics 2016; 11:881-888. [PMID: 27748645 DOI: 10.1080/15592294.2016.1246108] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
DNA methylation is often analyzed by reporting the average methylation degree of each cytosine. In this study, we used a single molecule methylation analysis in order to look at the methylation conformation of individual molecules. Using D-aspartate oxidase as a model gene, we performed an in-depth methylation analysis through the developmental stages of 3 different mouse tissues (brain, lung, and gut), where this gene undergoes opposite methylation destiny. This approach allowed us to track both methylation and demethylation processes at high resolution. The complexity of these dynamics was markedly simplified by introducing the concept of methylation classes (MCs), defined as the number of methylated cytosines per molecule, irrespective of their position. The MC concept smooths the stochasticity of the system, allowing a more deterministic description. In this framework, we also propose a mathematical model based on the Markov chain. This model aims to identify the transition probability of a molecule from one MC to another during methylation and demethylation processes. The results of our model suggest that: 1) both processes are ruled by a dominant class of phenomena, namely, the gain or loss of one methyl group at a time; and 2) the probability of a single CpG site becoming methylated or demethylated depends on the methylation status of the whole molecule at that time.
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Affiliation(s)
- Ornella Affinito
- a Istituto di Endocrinologia ed Oncologia Sperimentale (IEOS) "Gaetano Salvatore ," Consiglio Nazionale delle Ricerche (CNR) , Naples , Italy.,b Dipartimento di Medicina Molecolare e Biotecnologie Mediche , Università degli Studi di Napoli "Federico II ," Naples , Italy
| | - Giovanni Scala
- c Istituto Nazionale di Fisica Nucleare , Sezione di Napoli , Naples , Italy
| | - Domenico Palumbo
- b Dipartimento di Medicina Molecolare e Biotecnologie Mediche , Università degli Studi di Napoli "Federico II ," Naples , Italy
| | - Ermanno Florio
- a Istituto di Endocrinologia ed Oncologia Sperimentale (IEOS) "Gaetano Salvatore ," Consiglio Nazionale delle Ricerche (CNR) , Naples , Italy.,b Dipartimento di Medicina Molecolare e Biotecnologie Mediche , Università degli Studi di Napoli "Federico II ," Naples , Italy
| | - Antonella Monticelli
- a Istituto di Endocrinologia ed Oncologia Sperimentale (IEOS) "Gaetano Salvatore ," Consiglio Nazionale delle Ricerche (CNR) , Naples , Italy
| | - Gennaro Miele
- c Istituto Nazionale di Fisica Nucleare , Sezione di Napoli , Naples , Italy.,d Dipartimento di Fisica , Università degli Studi di Napoli "Federico II ," Naples , Italy
| | - Vittorio Enrico Avvedimento
- a Istituto di Endocrinologia ed Oncologia Sperimentale (IEOS) "Gaetano Salvatore ," Consiglio Nazionale delle Ricerche (CNR) , Naples , Italy.,b Dipartimento di Medicina Molecolare e Biotecnologie Mediche , Università degli Studi di Napoli "Federico II ," Naples , Italy
| | - Alessandro Usiello
- e CEINGE Biotecnologie Avanzate , Naples , Italy.,f Department of Environmental, Biological and Pharmaceutical Science and Technologies , Second University of Naples , Caserta , Italy
| | - Lorenzo Chiariotti
- a Istituto di Endocrinologia ed Oncologia Sperimentale (IEOS) "Gaetano Salvatore ," Consiglio Nazionale delle Ricerche (CNR) , Naples , Italy.,b Dipartimento di Medicina Molecolare e Biotecnologie Mediche , Università degli Studi di Napoli "Federico II ," Naples , Italy.,g Dipartimento di Farmacia , Università degli Studi di Napoli "Federico II ," Naples , Italy
| | - Sergio Cocozza
- b Dipartimento di Medicina Molecolare e Biotecnologie Mediche , Università degli Studi di Napoli "Federico II ," Naples , Italy
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