Gene Expression Changes Associated with Nintedanib Treatment in Idiopathic Pulmonary Fibrosis Fibroblasts: A Next-Generation Sequencing and Bioinformatics Study
Abstract
:1. Introduction
2. Experimental Section
2.1. Study Design
2.2. Cultures of IPF Lung Fibroblasts
2.3. Nintedanib Treatment
2.4. Cell Morphological Observation
2.5. Cell Proliferation Assay
2.6. Cell Apoptosis Assay
2.7. Next-Generation Sequencing (NGS) for miRNA and mRNA Expression Profiling
2.8. miRmap Database Analysis
2.9. TargetScan Database Analysis
2.10. miRDB Database Analysis
2.11. STRING Database Analysis
2.12. DAVID Database Analysis
2.13. RT-qPCR
3. Results
3.1. Effects of Nintedanib on Cell Morphology, Proliferation, and Apoptosis in IPF Fibroblasts
3.2. Overview of Differential Gene Expressions in Nintedanib-Treated IPF Fibroblasts
3.3. Protein–Protein Interaction, Biological Pathway, and Molecular Function Analysis
3.4. Dysregulated Genes with Potential miRNA–mRNA Interactions in Nintedanib-Treated IPF Fibroblasts
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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miRNA | Fold Change | Gene Symbol | Fold Change | miRmap Score | TargetScan Total Context++ Score | miRDB |
---|---|---|---|---|---|---|
hsa-miR-486-3p | 2.31 | DDX11 | −4.05 | 99.389 | −0.50 | 59 |
hsa-miR-486-3p | 2.31 | E2F1 | −5.78 | 99.597 | −0.85 | 65 |
hsa-miR-486-3p | 2.31 | NPTX1 | −2.89 | 99.908 | −0.62 | 95 |
hsa-miR-486-3p | 2.31 | PLXNA4 | −6.94 | 99.700 | −0.18 | 70 |
hsa-miR-92a-1-5p | −2.71 | SLC25A23 | 2.68 | 99.527 | −1.27 | 65 |
hsa-miR-1275 | −4.74 | PRELP | 3.87 | 99.724 | 65 | |
hsa-miR-1275 | −4.74 | HRK | 5.36 | 99.881 | 87 | |
hsa-miR-100-3p | −2.52 | GJA3 | 3.04 | 99.326 | −0.39 | |
hsa-miR-1275 | −4.74 | ZBED3 | 3.46 | 99.669 | −0.94 | |
hsa-miR-1275 | −4.74 | ANTXR1 | 2.69 | 99.535 | −0.66 | |
hsa-miR-486-3p | 2.31 | SUV39H1 | −4.35 | 99.421 | −0.47 | |
hsa-miR-1275 | −4.74 | MBP | 8.97 | 99.886 | ||
hsa-miR-326 | 4.64 | PLXNA4 | −6.94 | 99.932 |
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Sheu, C.-C.; Chang, W.-A.; Tsai, M.-J.; Liao, S.-H.; Chong, I.-W.; Kuo, P.-L. Gene Expression Changes Associated with Nintedanib Treatment in Idiopathic Pulmonary Fibrosis Fibroblasts: A Next-Generation Sequencing and Bioinformatics Study. J. Clin. Med. 2019, 8, 308. https://doi.org/10.3390/jcm8030308
Sheu C-C, Chang W-A, Tsai M-J, Liao S-H, Chong I-W, Kuo P-L. Gene Expression Changes Associated with Nintedanib Treatment in Idiopathic Pulmonary Fibrosis Fibroblasts: A Next-Generation Sequencing and Bioinformatics Study. Journal of Clinical Medicine. 2019; 8(3):308. https://doi.org/10.3390/jcm8030308
Chicago/Turabian StyleSheu, Chau-Chyun, Wei-An Chang, Ming-Ju Tsai, Ssu-Hui Liao, Inn-Wen Chong, and Po-Lin Kuo. 2019. "Gene Expression Changes Associated with Nintedanib Treatment in Idiopathic Pulmonary Fibrosis Fibroblasts: A Next-Generation Sequencing and Bioinformatics Study" Journal of Clinical Medicine 8, no. 3: 308. https://doi.org/10.3390/jcm8030308
APA StyleSheu, C.-C., Chang, W.-A., Tsai, M.-J., Liao, S.-H., Chong, I.-W., & Kuo, P.-L. (2019). Gene Expression Changes Associated with Nintedanib Treatment in Idiopathic Pulmonary Fibrosis Fibroblasts: A Next-Generation Sequencing and Bioinformatics Study. Journal of Clinical Medicine, 8(3), 308. https://doi.org/10.3390/jcm8030308