Methylation Patterns and Chromatin Accessibility in Neuroendocrine Lung Cancer
Abstract
:1. Introduction
2. Results
2.1. Differentially Methylated Regions in Neuroendocrine Lung Cancer Correlated with Gene Expression
2.2. NE-DMR Genes Expression in Normal Tissues Defines Six Transcriptional Programs
2.3. Characterization of the Six GTEx Modules in Lung Cancer Gene Expression Data
2.4. Assay for Transposase-Accessible Chromatin Sequencing (ATAC-Seq) Identifies Regions of Open Chromatin Associated with NE Histology
2.5. ATAC-Seq Supports Epigenetic Regulation of NE-DMR Genes
2.6. Assessing the Regulatory Potential of Tumor Derived NE-DMRs in ATAC-Seq Data
3. Discussion
4. Materials and Methods
4.1. Patient Cohorts
4.2. DNA Methylation Analyses
4.3. Gene Expression Analyses
4.4. ATAC- and RNA-Seq of NSCLC and NE Cell Lines
4.5. Data Sharing
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Arbajian, E.; Aine, M.; Karlsson, A.; Vallon-Christersson, J.; Brunnström, H.; Davidsson, J.; Mohlin, S.; Planck, M.; Staaf, J. Methylation Patterns and Chromatin Accessibility in Neuroendocrine Lung Cancer. Cancers 2020, 12, 2003. https://doi.org/10.3390/cancers12082003
Arbajian E, Aine M, Karlsson A, Vallon-Christersson J, Brunnström H, Davidsson J, Mohlin S, Planck M, Staaf J. Methylation Patterns and Chromatin Accessibility in Neuroendocrine Lung Cancer. Cancers. 2020; 12(8):2003. https://doi.org/10.3390/cancers12082003
Chicago/Turabian StyleArbajian, Elsa, Mattias Aine, Anna Karlsson, Johan Vallon-Christersson, Hans Brunnström, Josef Davidsson, Sofie Mohlin, Maria Planck, and Johan Staaf. 2020. "Methylation Patterns and Chromatin Accessibility in Neuroendocrine Lung Cancer" Cancers 12, no. 8: 2003. https://doi.org/10.3390/cancers12082003