Elucidating the Functional Roles of Long Non-Coding RNAs in Alzheimer’s Disease
Abstract
:1. Introduction
2. Results
2.1. Identification and Characterization of Novel lncRNAs
2.2. LncRNAs’ Roles in AD Formation and Development
2.2.1. Contributions to Key AD Phenotypes via Cell Polarity Changes
2.2.2. Contribution to Stress Generation
2.2.3. Contribution to Stress Response via Metabolic Reprogramming
2.3. LncRNA’s Discerning Power in Distinguishing AD Samples from Controls
3. Concluding Remarks
4. Materials and Methods
4.1. Data
4.2. Methods
4.2.1. RNA-seq Processing and lncRNA Identification
4.2.2. The Prediction Process for lncRNA Genes
4.2.3. Differential Analysis of All Assembled Transcripts
4.2.4. Ordering Disease Samples by the Level of Deviation from Control Tissues
4.2.5. ssGSEA Gene-Set Scores for Individual Samples
4.2.6. Co-Expression Analyses
4.2.7. Predicting Target Genes or Pathways of cis and trans Regulation by lncRNA
4.2.8. Construction of lncRNA-mRNA Co-Expression Network and Identification of Functional Modules
4.2.9. The Discerning Power of lncRNAs in Distinguishing Control from AD Samples
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Sub-List | Immune Activity | Metabolic Reprogramming | Cell Polarity | Stress Response |
---|---|---|---|---|
bin1 | 160 | 339 | 876 | 827 |
bin2 | 1069 | 729 | 1569 | 1291 |
bin3 | 863 | 1362 | 1522 | 1421 |
bin4 | 1916 | 5156 | 5230 | 5204 |
Phenotype | Normal_vs_allAD | Normal_vs_eAD | Normal_vs_aAD | eAD_vs_aAD |
---|---|---|---|---|
Aciding extrusion transporter | 0.7124 | 0.6018 | 0.8998 | 0.9499 |
Aciding loading transporter | 0.6448 | 0.6539 | 0.825 | 0.9602 |
Active oxygen | 0.7297 | 0.7365 | 0.8673 | 0.8543 |
Astrocytes | 0.6653 | 0.7124 | 0.8029 | 0.9718 |
Hydrogen peroxide | 0.6981 | 0.851 | 0.8412 | 0.9339 |
Microglia | 0.6669 | 0.581 | 0.8614 | 0.9429 |
Superoxide anion generation | 0.7015 | 0.823 | 0.944 | 0.9416 |
Bicarbonate transporter | 0.6819 | 0.6675 | 0.8595 | 0.9685 |
Extracellular acidosis | 0.6373 | 0.6425 | 0.8783 | 0.878 |
Na+/K+-ATPase | 0.7866 | 0.8256 | 0.8881 | 0.9615 |
Cholesterol | 0.6694 | 0.6871 | 0.8939 | 0.9557 |
Extracellular copper | 0.701 | 0.8783 | 0.8718 | 0.9018 |
Mitochondrial iron–sulfur | 0.6378 | 0.5979 | 0.8022 | 0.8228 |
H-producing enzyme | 0.6971 | 0.6662 | 0.8399 | 0.8652 |
Microtubule depolymerization | 0.7562 | 0.8256 | 0.8198 | 0.9268 |
Synapse assembly | 0.6909 | 0.7235 | 0.8979 | 0.8967 |
Amyloid formation | 0.6914 | 0.6012 | 0.8855 | 0.9634 |
Tau fiber formation | 0.6858 | 0.6291 | 0.8549 | 0.957 |
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Huang, Z.; Chen, Q.; Mu, X.; An, Z.; Xu, Y. Elucidating the Functional Roles of Long Non-Coding RNAs in Alzheimer’s Disease. Int. J. Mol. Sci. 2024, 25, 9211. https://doi.org/10.3390/ijms25179211
Huang Z, Chen Q, Mu X, An Z, Xu Y. Elucidating the Functional Roles of Long Non-Coding RNAs in Alzheimer’s Disease. International Journal of Molecular Sciences. 2024; 25(17):9211. https://doi.org/10.3390/ijms25179211
Chicago/Turabian StyleHuang, Zhenyu, Qiufen Chen, Xuechen Mu, Zheng An, and Ying Xu. 2024. "Elucidating the Functional Roles of Long Non-Coding RNAs in Alzheimer’s Disease" International Journal of Molecular Sciences 25, no. 17: 9211. https://doi.org/10.3390/ijms25179211