A Multi-Omics Study of Epigenetic Changes in Type II Alveolar Cells of A/J Mice Exposed to Environmental Tobacco Smoke
Abstract
:1. Introduction
2. Results
2.1. Animal Studies
2.2. Histopathological Examination of Lung Tissues
2.3. Global Changes in DNA Methylation and Hydroxymethylation in Type II Alveolar Cells of Mice Exposed to ECS
2.4. Differential Methylation Analysis Reveals Extensive DMRs and DhMRs in Type II Alveolar Epithelial CELLS of Female A/J Mice Exposed to ECS
2.5. Gene Expression Changes in Type II Alveolar Epithelial cells of A/J Mice Exposed to ECS
2.6. Protein Abundance Changes in Type II Alveolar Epithelial Cells of A/J Mice Exposed to ECS
2.7. Integration of Epigenomic and Transcriptomic Data Identifies DEGs Regulated by DNA Methylation and Hydroxymethylation
2.8. Identification of Smoking-Induced Early Epigenetic Changes Found in Lung Adenocarcinoma (LUAD)
2.9. Identification of Smoking-Induced Protein Abundance Changes Relevant to Lung Adenocarcinoma (LUAD)
3. Discussion
4. Materials and Methods
4.1. Animal Treatments
4.2. Histopathology Examination
4.3. Isolation of Alveolar Type II Epithelial Cells
4.4. Extraction of DNA, RNA, and Protein from Alveolar Type II Epithelial Cells
4.5. RNA-Seq Analysis of Alveolar Type II Epithelial Cell RNA
4.5.1. RNA-Seq Read Processing
4.5.2. Gene Expression Quantification and Filtering
4.5.3. Differential Gene Expression Testing
4.5.4. Network Analysis
4.6. RNA-Seq Validation via qRT-PCR
4.7. RRBS and Oxo-RRBS
4.7.1. Reduced Representation Bisulfite Sequencing Read Handling
4.7.2. Methylation and Hydroxymethylation Analysis
4.8. DNA Digestion and HPLC Enrichment of mC and hmC
4.9. HPLC-ESI+-MS/MS Quantitation of Global Levels of mC and hmC
4.10. Protein Extraction and Quantitation
4.11. Protein Digestion and Processing
4.12. C18 Stage-Tip TMT Labeling of Peptides
4.13. High pH Fractionation of Peptides
4.14. HPLC-MS/MS Analysis of Proteins
4.15. Proteomics Data Analysis
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Han, Q.; Fernandez, J.; Rajczewski, A.T.; Kono, T.J.Y.; Weirath, N.A.; Rahim, A.; Lee, A.S.; Seabloom, D.; Tretyakova, N.Y. A Multi-Omics Study of Epigenetic Changes in Type II Alveolar Cells of A/J Mice Exposed to Environmental Tobacco Smoke. Int. J. Mol. Sci. 2024, 25, 9365. https://doi.org/10.3390/ijms25179365
Han Q, Fernandez J, Rajczewski AT, Kono TJY, Weirath NA, Rahim A, Lee AS, Seabloom D, Tretyakova NY. A Multi-Omics Study of Epigenetic Changes in Type II Alveolar Cells of A/J Mice Exposed to Environmental Tobacco Smoke. International Journal of Molecular Sciences. 2024; 25(17):9365. https://doi.org/10.3390/ijms25179365
Chicago/Turabian StyleHan, Qiyuan, Jenna Fernandez, Andrew T. Rajczewski, Thomas J. Y. Kono, Nicholas A. Weirath, Abdur Rahim, Alexander S. Lee, Donna Seabloom, and Natalia Y. Tretyakova. 2024. "A Multi-Omics Study of Epigenetic Changes in Type II Alveolar Cells of A/J Mice Exposed to Environmental Tobacco Smoke" International Journal of Molecular Sciences 25, no. 17: 9365. https://doi.org/10.3390/ijms25179365