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Updated: Jun 26, 2025
Isolation of Endothelial Cells from the Lumen of Mouse Carotid Arteries for Single-Cell Multi-Omics Experiments
Published on: October 4, 2021
Screening and validation of atherosclerosis PAN-apoptotic immune-related genes based on single-cell sequencing
Yamin Song1,2, Bo Lou3, Huiting Wang4
1Department of Neurology, Liaocheng People's Hospital, Shandong University, Jinan, China.
Background:
Carotid atherosclerosis (CAS) is a complication of atherosclerosis (AS). PAN-optosome is an inflammatory programmed cell death pathway event regulated by the PAN-optosome complex. CAS's PAN-optosome-related genes (PORGs) have yet to be studied. Hence, screening the PAN-optosome-related diagnostic genes for treating CAS was vital.
Methods:
We introduced transcriptome data to screen out differentially expressed genes (DEGs) in CAS. Subsequently, WGCNA analysis was utilized to mine module genes about PANoptosis score. We performed differential expression analysis (CAS samples vs. standard samples) to obtain CAS-related differentially expressed genes at the single-cell level. Venn diagram was executed to identify PAN-optosome-related differential genes (POR-DEGs) associated with CAS. Further, LASSO regression and RF algorithm were implemented to were executed to build a diagnostic model. We additionally performed immune infiltration and gene set enrichment analysis (GSEA) based on diagnostic genes. We verified the accuracy of the model genes by single-cell nuclear sequencing and RT-qPCR validation of clinical samples, as well as in vitro cellular experiments.
Results:
We identified 785 DEGs associated with CAS. Then, 4296 module genes about PANoptosis score were obtained. We obtained the 7365 and 1631 CAS-related DEGs at the single-cell level, respectively. 67 POR-DEGs were retained Venn diagram. Subsequently, 4 PAN-optosome-related diagnostic genes (CNTN4, FILIP1, PHGDH, and TFPI2) were identified via machine learning. Cellular function tests on four genes showed that these genes have essential roles in maintaining arterial cell viability and resisting cellular senescence.
Conclusion:
We obtained four PANoptosis-related diagnostic genes (CNTN4, FILIP1, PHGDH, and TFPI2) associated with CAS, laying a theoretical foundation for treating CAS.
Insights
Researchers identified four key PANoptosis-related diagnostic genes (CNTN4, FILIP1, PHGDH, TFPI2) for carotid atherosclerosis (CAS). These findings provide a foundation for developing new treatments for this common complication of atherosclerosis.
Area of Science:
- Molecular Biology
- Genetics
- Cardiovascular Research
Background:
- Carotid atherosclerosis (CAS) is a significant complication of systemic atherosclerosis.
- PANoptosis is an inflammatory programmed cell death pathway crucial in disease pathogenesis.
- The specific role of PANoptosis-related genes in CAS remained largely uninvestigated.
Purpose of the Study:
- To identify and characterize PANoptosis-related diagnostic genes (PORGs) associated with carotid atherosclerosis.
- To develop a diagnostic model for CAS based on identified PORGs.
- To explore the functional significance of these genes in arterial health.
Main Methods:
- Transcriptome data analysis to identify differentially expressed genes (DEGs) in CAS.
- Weighted gene co-expression network analysis (WGCNA) to link gene modules to PANoptosis scores.
- Machine learning algorithms (LASSO regression, Random Forest) for diagnostic gene selection and model building.
- Single-cell sequencing, RT-qPCR, and in vitro experiments for validation.
Main Results:
- Identification of 67 PANoptosis-related differentially expressed genes (POR-DEGs) in CAS.
- Development of a diagnostic model using four key genes: CNTN4, FILIP1, PHGDH, and TFPI2.
- Functional validation confirmed these genes' roles in maintaining arterial cell viability and resisting senescence.
Conclusions:
- Four novel PANoptosis-related genes (CNTN4, FILIP1, PHGDH, TFPI2) are identified as potential diagnostic markers for CAS.
- These findings establish a theoretical basis for targeted therapeutic strategies against carotid atherosclerosis.
- The study highlights the importance of the PANoptosis pathway in CAS pathogenesis.
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