Circular RNA Expression and Interaction Patterns Are Perturbed in Amyotrophic Lateral Sclerosis
Abstract
:1. Introduction
2. Results
2.1. Differentially Expressed circRNAs
2.2. Binding Capacity of miRNAs to Differentially Expressed circRNAs
2.3. Comparison of Differentially Expressed circRNAs and mRNAs
3. Discussion
3.1. ALS-Specific Circular Transcriptome
3.2. circRNA‒miRNA‒mRNA Interactions
4. Materials and Methods
4.1. Dataset Structure and Quality Control
4.2. circRNA Detection and Differential Expression Analysis
4.3. Linear RNA Detection and Differential Expression Analysis
4.4. circRNA‒miRNA‒mRNA Interaction Analysis
4.5. Data Visualization
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Tissue | Condition | Number of Samples | Number of circRNAs Detected | Number of Detected circRNAs Common to ALS and Control Samples | Number of circRNAs Unique to the Condition |
---|---|---|---|---|---|
Spinal Cord Cervical | ALS | 18 | 24,259 | 12,557 | 11,702 |
Control | 7 | 15,210 | 2653 | ||
Spinal Cord Lumbar | ALS | 16 | 24,020 | 14,044 | 9976 |
Control | 6 | 18,262 | 4218 | ||
Spinal Cord Thoracic | ALS | 16 | 20,581 | 12,100 | 8481 |
Control | 6 | 16,209 | 4109 |
Spinal Cord Cervical | Spinal Cord Lumbar | Spinal Cord Thoracic | ||
---|---|---|---|---|
Number of DE genes (adjusted p value < 0.05) | Upregulated | 1944 | 524 | 242 |
Downregulated | 1052 | 460 | 90 | |
Total | 2996 | 984 | 332 | |
Total genes tested | 60,662 | 60,662 | 60,662 |
GO Accession and Name | Number of Genes in Overlap | p Value |
---|---|---|
GO:1901699: Cellular response to nitrogen compound | 7 | 2.97 × 10−6 |
GO:0198738: Cell‒cell signaling by wnt | 6 | 6.94 × 10−6 |
GO:0050806: Positive regulation of synaptic transmission | 4 | 9.41 × 10−6 |
GO:1901701: Cellular response to oxygen-containing compound | 8 | 9.67 × 10−6 |
GO:0071375: Cellular response to peptide hormone stimulus | 5 | 1.16 × 10−5 |
GO:0001837: Epithelial to mesenchymal transition | 4 | 1.20 × 10−5 |
GO:0051100: Negative regulation of binding | 4 | 1.39 × 10−5 |
GO:1905114: cell surface receptor signaling pathway involved in cell‒cell signaling | 6 | 1.88 × 10−5 |
GO:0032870: Cellular response to hormone stimulus | 6 | 1.98 × 10−5 |
GO:1901653: Cellular response to peptide | 5 | 2.83 × 10−5 |
Tissue | No. of Samples in ALS Cohort | No. of Samples in Control Cohort |
---|---|---|
Spinal Cord Cervical | 18 | 7 |
Spinal Cord Thoracic | 16 | 6 |
Spinal Cord Lumbar | 16 | 6 |
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Aquilina-Reid, C.; Brennan, S.; Curry-Hyde, A.; Teunisse, G.M.; The NYGC ALS Consortium; Janitz, M. Circular RNA Expression and Interaction Patterns Are Perturbed in Amyotrophic Lateral Sclerosis. Int. J. Mol. Sci. 2022, 23, 14665. https://doi.org/10.3390/ijms232314665
Aquilina-Reid C, Brennan S, Curry-Hyde A, Teunisse GM, The NYGC ALS Consortium, Janitz M. Circular RNA Expression and Interaction Patterns Are Perturbed in Amyotrophic Lateral Sclerosis. International Journal of Molecular Sciences. 2022; 23(23):14665. https://doi.org/10.3390/ijms232314665
Chicago/Turabian StyleAquilina-Reid, Chiara, Samuel Brennan, Ashton Curry-Hyde, Guus M. Teunisse, The NYGC ALS Consortium, and Michael Janitz. 2022. "Circular RNA Expression and Interaction Patterns Are Perturbed in Amyotrophic Lateral Sclerosis" International Journal of Molecular Sciences 23, no. 23: 14665. https://doi.org/10.3390/ijms232314665