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Screening of m6A-associated ferroptosis-related genes in atherosclerosis based on WGCNA
Meiling Jiang1, Weidong Zhao1, Liyong Wu1
1Cardiology Department, The Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China.
Background:
N6-methyladenosine (m6A) has been shown to mediate ferroptosis but its role in atherosclerosis (AS) is unclear.
Methods:
Differentially expressed m6A-associated ferroptosis-related genes (DE-m6A-Ferr-RGs) were obtained using differential expression analysis and Pearson correlation analysis. Weighted gene co-expression network analysis (WGCNA) was also performed. The intersection of the module genes and the DE-m6A-Ferr-RGs were recorded as candidate m6A-Ferr-related signature genes. Finally, the m6A-Ferr-related signature genes were screened using least absolute shrinkage and selection operator (LASSO) analysis. Expression validation, receiver operating characteristic ( mapping, and immune correlation analysis were also performed based on the m6A-Ferr-related signature genes. The expression of m6A-Ferr-related signature genes was further validated using a real-time polymerase chain reaction (RT-qPCR).
Results:
In total, 6,167 differentially expressed genes were intersected with 24 m6A- and 259 ferroptosis-related genes, respectively, resulting in 113 DE-m6A-Ferr-RGs obtained using Pearson's correlation analysis. The module genes obtained from the WGCNA and the 113 DE-m6A-Ferr-RGs were intersected to obtain 48 candidate m6A-Ferr-related signature genes. LASSO analysis was performed and six m6A-Ferr-related signature genes were screened. In addition, the area under the curve values of all six m6A-Ferr-related signature genes were greater than 0.7, indicating that they had potential diagnostic value. Furthermore, the RT-qPCR results revealed that the expression of SLC3A2, NOX4, and CDO1 was consistent with the transcriptome level. Moreover, there was a significant difference in two types of immune cells between the AS and control groups. Naive B cells, CD8+ T cells, regulatory T cells, and activated natural killer cells were positively correlated with CDO1 and NOX4 but negatively correlated with ATG7, CYBB, and SLC3A2.
Conclusion:
In total, three m6A-Ferr-related signature genes (NOX4, CDO1, and SLC3A2) were obtained through a series of bioinformatics analyses and an RT-qPCR.
Insights
N6-methyladenosine (m6A) and ferroptosis are linked to atherosclerosis (AS). This study identifies three key genes (NOX4, CDO1, SLC3A2) as potential diagnostic markers for AS, offering new insights into disease mechanisms.
Area of Science:
- Biochemistry
- Molecular Biology
- Genetics
Background:
- N6-methyladenosine (m6A) is implicated in ferroptosis, but its specific role in atherosclerosis (AS) remains largely uncharacterized.
- Investigating the interplay between m6A modification and ferroptosis pathways is crucial for understanding AS pathogenesis.
Purpose of the Study:
- To identify key m6A-associated ferroptosis-related genes (m6A-Ferr-RGs) that serve as potential diagnostic biomarkers for atherosclerosis.
- To elucidate the diagnostic value and immune cell correlations of these identified genes in AS.
Main Methods:
- Differential gene expression analysis and Pearson correlation were used to identify DE-m6A-Ferr-RGs.
- Weighted gene co-expression network analysis (WGCNA) and least absolute shrinkage and selection operator (LASSO) analysis were employed to screen for signature genes.
- Gene expression was validated using RT-qPCR, and diagnostic potential was assessed via receiver operating characteristic (ROC) curve analysis.
Main Results:
- A total of 113 DE-m6A-Ferr-RGs were identified, leading to 48 candidate signature genes after WGCNA.
- LASSO analysis selected six m6A-Ferr-related signature genes, all demonstrating diagnostic potential (Area Under Curve > 0.7).
- RT-qPCR confirmed the expression of SLC3A2, NOX4, and CDO1. Immune correlation analysis revealed associations between specific immune cells and genes like CDO1, NOX4, ATG7, CYBB, and SLC3A2.
Conclusions:
- Three m6A-Ferr-related signature genes, namely NOX4, CDO1, and SLC3A2, were successfully identified through comprehensive bioinformatics and experimental validation.
- These genes hold significant potential as diagnostic biomarkers for atherosclerosis.
- The study highlights the intricate relationship between m6A-mediated ferroptosis and immune cell infiltration in the context of AS.
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