Genome-wide DNA methylation analysis reveals a unique methylation pattern for pleural mesothelioma compared to healthy pleura and other lung diseases
Abstract Background Pleural mesothelioma (PM) is a rare and aggressive cancer type, typically diagnosed at advanced stages. Distinguishing PM from other lung diseases is often challenging. There is an urgent need for biomarkers that can enable early detection. Interest in the field of epigenetics ha...
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BMC
2024-12-01
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| Series: | Clinical Epigenetics |
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| Online Access: | https://doi.org/10.1186/s13148-024-01790-z |
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| author | Janah Vandenhoeck Joe Ibrahim Nele De Meulenaere Dieter Peeters Jo Raskin Jeroen M. H. Hendriks Paul Van Schil Jan van Meerbeeck Guy Van Camp Ken Op de Beeck |
| author_facet | Janah Vandenhoeck Joe Ibrahim Nele De Meulenaere Dieter Peeters Jo Raskin Jeroen M. H. Hendriks Paul Van Schil Jan van Meerbeeck Guy Van Camp Ken Op de Beeck |
| author_sort | Janah Vandenhoeck |
| collection | DOAJ |
| description | Abstract Background Pleural mesothelioma (PM) is a rare and aggressive cancer type, typically diagnosed at advanced stages. Distinguishing PM from other lung diseases is often challenging. There is an urgent need for biomarkers that can enable early detection. Interest in the field of epigenetics has increased, particularly in the context of tumour development and biomarker discovery. This study aims to identify specific changes in DNA methylation from healthy pleural tissue to PM and to compare these methylation patterns with those found in other lung diseases. Results EPIC methylation array data (850 K) were generated for 11 PM and 29 healthy pleura in-house collected samples. This is the first time such a large dataset of healthy pleura samples has been generated. Additional EPIC methylation array data (850 K) for pleural mesothelioma and other lung-related diseases were downloaded from public databases. We conducted pairwise differential methylation analyses across all tissue types, which facilitated the identification of significantly differentially methylated CpG sites. Extensive differential methylation between PM and healthy pleura was observed, identifying 81,968 differentially methylated CpG sites across all genomic regions. Among these, five CpG sites located within four genes (MIR21, RNF39, SPEN and C1orf101) exhibited the most significant and pronounced methylation differences between PM and healthy pleura. Moreover, our analysis delineated distinct methylation patterns specific to PM subtypes. Finally, the methylation profiles of PM were distinctly different from those of other lung cancers, enabling accurate differentiation. Conclusions DNA methylation analyses provide a robust method for distinguishing PM from healthy pleural tissues, and specific methylation patterns exist within PM subtypes. These methylation differences underscore their importance in understanding disease progression and may serve as viable biomarkers or therapeutic targets. Moreover, differential methylation patterns between PM and other lung cancers highlights its diagnostic potential. These findings necessitate further translational studies to explore their clinical applications. |
| format | Article |
| id | doaj-art-af16fa6948c043a6a1663eb565744f43 |
| institution | OA Journals |
| issn | 1868-7083 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | BMC |
| record_format | Article |
| series | Clinical Epigenetics |
| spelling | doaj-art-af16fa6948c043a6a1663eb565744f432025-08-20T02:30:59ZengBMCClinical Epigenetics1868-70832024-12-0116111710.1186/s13148-024-01790-zGenome-wide DNA methylation analysis reveals a unique methylation pattern for pleural mesothelioma compared to healthy pleura and other lung diseasesJanah Vandenhoeck0Joe Ibrahim1Nele De Meulenaere2Dieter Peeters3Jo Raskin4Jeroen M. H. Hendriks5Paul Van Schil6Jan van Meerbeeck7Guy Van Camp8Ken Op de Beeck9Centre of Medical Genetics, University of Antwerp and Antwerp University HospitalCentre of Medical Genetics, University of Antwerp and Antwerp University HospitalCentre of Medical Genetics, University of Antwerp and Antwerp University HospitalDepartment of Pathology, Antwerp University HospitalDepartment of Thoracic Oncology, Antwerp University HospitalDepartment of Thoracic and Vascular Surgery, Antwerp University HospitalDepartment of Thoracic and Vascular Surgery, Antwerp University HospitalDepartment of Thoracic Oncology, Antwerp University HospitalCentre of Medical Genetics, University of Antwerp and Antwerp University HospitalCentre of Medical Genetics, University of Antwerp and Antwerp University HospitalAbstract Background Pleural mesothelioma (PM) is a rare and aggressive cancer type, typically diagnosed at advanced stages. Distinguishing PM from other lung diseases is often challenging. There is an urgent need for biomarkers that can enable early detection. Interest in the field of epigenetics has increased, particularly in the context of tumour development and biomarker discovery. This study aims to identify specific changes in DNA methylation from healthy pleural tissue to PM and to compare these methylation patterns with those found in other lung diseases. Results EPIC methylation array data (850 K) were generated for 11 PM and 29 healthy pleura in-house collected samples. This is the first time such a large dataset of healthy pleura samples has been generated. Additional EPIC methylation array data (850 K) for pleural mesothelioma and other lung-related diseases were downloaded from public databases. We conducted pairwise differential methylation analyses across all tissue types, which facilitated the identification of significantly differentially methylated CpG sites. Extensive differential methylation between PM and healthy pleura was observed, identifying 81,968 differentially methylated CpG sites across all genomic regions. Among these, five CpG sites located within four genes (MIR21, RNF39, SPEN and C1orf101) exhibited the most significant and pronounced methylation differences between PM and healthy pleura. Moreover, our analysis delineated distinct methylation patterns specific to PM subtypes. Finally, the methylation profiles of PM were distinctly different from those of other lung cancers, enabling accurate differentiation. Conclusions DNA methylation analyses provide a robust method for distinguishing PM from healthy pleural tissues, and specific methylation patterns exist within PM subtypes. These methylation differences underscore their importance in understanding disease progression and may serve as viable biomarkers or therapeutic targets. Moreover, differential methylation patterns between PM and other lung cancers highlights its diagnostic potential. These findings necessitate further translational studies to explore their clinical applications.https://doi.org/10.1186/s13148-024-01790-zEpigeneticsDNA methylationPleural mesotheliomaLung cancerHealthy pleura |
| spellingShingle | Janah Vandenhoeck Joe Ibrahim Nele De Meulenaere Dieter Peeters Jo Raskin Jeroen M. H. Hendriks Paul Van Schil Jan van Meerbeeck Guy Van Camp Ken Op de Beeck Genome-wide DNA methylation analysis reveals a unique methylation pattern for pleural mesothelioma compared to healthy pleura and other lung diseases Clinical Epigenetics Epigenetics DNA methylation Pleural mesothelioma Lung cancer Healthy pleura |
| title | Genome-wide DNA methylation analysis reveals a unique methylation pattern for pleural mesothelioma compared to healthy pleura and other lung diseases |
| title_full | Genome-wide DNA methylation analysis reveals a unique methylation pattern for pleural mesothelioma compared to healthy pleura and other lung diseases |
| title_fullStr | Genome-wide DNA methylation analysis reveals a unique methylation pattern for pleural mesothelioma compared to healthy pleura and other lung diseases |
| title_full_unstemmed | Genome-wide DNA methylation analysis reveals a unique methylation pattern for pleural mesothelioma compared to healthy pleura and other lung diseases |
| title_short | Genome-wide DNA methylation analysis reveals a unique methylation pattern for pleural mesothelioma compared to healthy pleura and other lung diseases |
| title_sort | genome wide dna methylation analysis reveals a unique methylation pattern for pleural mesothelioma compared to healthy pleura and other lung diseases |
| topic | Epigenetics DNA methylation Pleural mesothelioma Lung cancer Healthy pleura |
| url | https://doi.org/10.1186/s13148-024-01790-z |
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