Integrated Single-Cell Transcriptome Analysis Reveals Novel Insights into the Role of Opioid Signaling in the Pathophysiology of Inflammatory Bowel Disease
Abstract
:1. Introduction
2. Materials and Methods
2.1. Single-Cell Transcriptome Sequence Data
2.2. Quality Control and Removing Doublets
2.3. Cell Clustering, Annotating, and Proportion Calculation
2.4. Opioid Signaling Evaluating and Function Enrichment Analysis
2.5. Cell Communication Speculating
2.6. Cell Pseudotime Analysis
2.7. Cell Transcription Factor Analysis
2.8. Chip Transcriptome Sequence Analysis and Clinical Prediction Model Building
2.9. Statistical Analyses
3. Results
3.1. The Cellular Landscape of IBD Identified by scRNA-seq
3.2. The Expression of Opioid Signaling-Related Gene Is Significantly Increased in Monocytes from IBD Tissues
3.3. TNF-Related Signaling Pathway Is Significantly Upregulated in OpiHi Monocytes
3.4. The Inflammatory Microenvironment in IBD Tissues Drives the Generation of OpiHi Monocytes
3.5. OpiHi Monocytes Signature Gene Can Predict the Response of Anti-TNF Therapy
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
IBD | Inflammatory Bowel Disease |
CD | Crohn’s Disease |
UC | Ulcerative Colitis |
OpiHi monocytes | Monocytes with high expression level of opioid signaling-related genes |
OpiLo monocytes | Monocytes with low expression level of opioid signaling-related genes |
NC | Normal Controls |
scRNA-seq | Single-cell Transcriptomics |
DC | Dendritic Cell |
TNF | Tumor Necrosis Factor |
AUC | The Area Under the Curve |
GEO | Gene Expression Omnibus |
ssGSEA | Single Sample Gene Set Enrichment Analysis |
DEG | Differentially Expressed Gene |
KEGG | Kyoto Encyclopedia of Genes and Genomes |
ROC | Receiver Operating Characteristic |
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Zhang, M.; Xie, Z.; Zhang, S.; Zhou, G. Integrated Single-Cell Transcriptome Analysis Reveals Novel Insights into the Role of Opioid Signaling in the Pathophysiology of Inflammatory Bowel Disease. Biomedicines 2025, 13, 1398. https://doi.org/10.3390/biomedicines13061398
Zhang M, Xie Z, Zhang S, Zhou G. Integrated Single-Cell Transcriptome Analysis Reveals Novel Insights into the Role of Opioid Signaling in the Pathophysiology of Inflammatory Bowel Disease. Biomedicines. 2025; 13(6):1398. https://doi.org/10.3390/biomedicines13061398
Chicago/Turabian StyleZhang, Mudan, Zhuo Xie, Shenghong Zhang, and Gaoshi Zhou. 2025. "Integrated Single-Cell Transcriptome Analysis Reveals Novel Insights into the Role of Opioid Signaling in the Pathophysiology of Inflammatory Bowel Disease" Biomedicines 13, no. 6: 1398. https://doi.org/10.3390/biomedicines13061398
APA StyleZhang, M., Xie, Z., Zhang, S., & Zhou, G. (2025). Integrated Single-Cell Transcriptome Analysis Reveals Novel Insights into the Role of Opioid Signaling in the Pathophysiology of Inflammatory Bowel Disease. Biomedicines, 13(6), 1398. https://doi.org/10.3390/biomedicines13061398