Comprehensive Analysis of PANoptosis-Related Gene Signature of Ulcerative Colitis
Abstract
:1. Introduction
2. Results
2.1. GSEA Revealed the Innate Immune-Related Biological Processes between Healthy Individuals and UC Patients
2.2. Colonic PANoptosis Signaling Is Significantly Activated in UC Patients
2.3. Screening and Functional Enrichment Analysis of Differential PANoptosis Genes
2.4. The PPI Network Analysis Indicated That the Hub Gene Mainly Comprises PANoptosis Sensors and Effectors
2.5. Patients with Active UC and Inflammatory Tissues of the Colon Exhibit High Expression of Hub Genes and TFs of PANoptosis
2.6. Hub Genes and TFs of PANoptosis Are Associated with UC Patients’ Response to Biologics
2.7. PANoptosis Is Associated with Increased Immune Cells and Proinflammatory Factors in the Colonic Mucosa of UC Patients
2.8. Prediction of Potential Drugs Targeting PANoptosis Signaling in UC Patients
2.9. Construction of Reliable ceRNA Regulatory Network for PANoptosis Signaling
2.10. Animal Models Validate the Core Genes of PANoptosis Signaling
3. Discussion
4. Methods
4.1. Datasets and Sample Selection
4.2. Identification of Differentially Expressed Genes (DEGs)
4.3. Robust Rank Aggregation (RRA) Analysis
4.4. Biological Function and Pathway Enrichment Analysis
4.5. PANoptosis Gene Sets
4.6. Gene Set Variation Analysis (GSVA) Analysis
4.7. PPI Network Analysis
4.8. Evaluation of Tissue Infiltrating Immune Cells
4.9. Correction Analysis
4.10. Small Molecule Agents Screening and Molecular Docking Analysis
4.11. CeRNA Network Construction
4.12. Animal Model of Colitis
4.13. Intestinal Permeability Assay to FITC-Dextran
4.14. H&E and IF Staining
4.15. RNA Extraction and RT-PCR
4.16. Statistical Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
IECs | Intestinal epithelial cells |
UC | Ulcerative colitis |
RRA | Robust Rank Aggregation |
GSEA | Gene set enrichment analysis |
GSVA | Geneset variation analysis |
TFs | Transcription factors |
CeRNA | Competitive endogenous RNA |
PCD | Programmed cell death |
FDR | False discovery rate |
GO | Gene Ontology |
KEGG | Kyoto Encyclopedia of Genes and Genomes |
CMap | Connectivity map database |
ZBP1 | Z-DNA-binding protein 1 |
AIM2 | Absent in melanoma 2 |
GSDMD | Gasdermin-D |
IRF1 | Interferon Regulatory Factor 1 |
CAC | Colorectal cancer |
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GEO ID | RNA Type | Platform | Tissues | Attribute |
---|---|---|---|---|
GSE193677 | mRNA | GPL16791 | Colonic mucosal | Training set |
GSE206285 | mRNA | GPL13158 | Colonic mucosal | Training set |
GSE87466 | mRNA | GPL13158 | Colonic mucosal | Validation set |
GSE66407 | mRNA | GPL19833 | Colonic mucosal | Validation set |
GSE128682 | mRNA | GPL21697 | Colonic mucosal | Validation set |
GSE73661 | mRNA | GPL6244 | Colonic mucosal | Validation set |
GSE92415 | mRNA | GPL13158 | Colonic mucosal | Validation set |
GSE48957 | miRNA | GPL14613 | Colonic mucosal | Validation set |
GSE77013 | lncRNA | GPL16956 | Colonic mucosal | Validation set |
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Wang, J.-M.; Yang, J.; Xia, W.-Y.; Wang, Y.-M.; Zhu, Y.-B.; Huang, Q.; Feng, T.; Xie, L.-S.; Li, S.-H.; Liu, S.-Q.; et al. Comprehensive Analysis of PANoptosis-Related Gene Signature of Ulcerative Colitis. Int. J. Mol. Sci. 2024, 25, 348. https://doi.org/10.3390/ijms25010348
Wang J-M, Yang J, Xia W-Y, Wang Y-M, Zhu Y-B, Huang Q, Feng T, Xie L-S, Li S-H, Liu S-Q, et al. Comprehensive Analysis of PANoptosis-Related Gene Signature of Ulcerative Colitis. International Journal of Molecular Sciences. 2024; 25(1):348. https://doi.org/10.3390/ijms25010348
Chicago/Turabian StyleWang, Jun-Meng, Jiao Yang, Wan-Yu Xia, Yue-Mei Wang, Yuan-Bing Zhu, Qin Huang, Tong Feng, Lu-Shuang Xie, Si-Hui Li, Shu-Qing Liu, and et al. 2024. "Comprehensive Analysis of PANoptosis-Related Gene Signature of Ulcerative Colitis" International Journal of Molecular Sciences 25, no. 1: 348. https://doi.org/10.3390/ijms25010348