BMC pregnancy and childbirth · 2024
Identification of hub genes, diagnostic model, and immune infiltration in preeclampsia by integrated bioinformatics analysis and machine learning.
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Zheng Yihan, Fang Zhuanji, Wu Xizhu, Zhang Huale, Sun Pengming
Аннотация
PURPOSE: This study aimed to identify novel biomarkers for preeclampsia (PE) diagnosis by integrating Weighted Gene Co-expression Network Analysis (WGCNA) with machine learning techniques.
PATIENTS AND METHODS: We obtained the PE dataset GSE25906 from the gene expression omnibus (GEO) database. Analysis of differentially expressed genes (DEGs) and module genes with Limma and Weighted Gene Co-expression Network analysis (WGCNA). Candidate hub genes for PE were identified using machine learning. Subsequently, we used western-blotting (WB) and real-time fluorescence quantitative (qPCR) to verify the expression of F13A1 and SCCPDH in preeclampsia patients. Finally, we estimated the extent of immune cell infiltration in PE samples by employing the CIBERSORT algorithms.
RESULTS: Our findings revealed that F13A1 and SCCPDH were the hub genes of PE. The nomogram and two candidate hub genes had high diagnostic values (AUC: 0.90 and 0.88, respectively). The expression levels of F13A1 and SCCPDH were verified by WB and qPCR. CIBERSORT analysis confirmed that the PE group had a significantly larger proportion of plasma cells and activated dendritic cells and a lower portion of resting memory CD4 + T cells.
CONCLUSION: The study proposes F13A1 and SCCPDH as potential biomarkers for diagnosing PE and points to an improvement in early detection. Integration of WGCNA with machine learning could enhance biomarker discovery in complex conditions like PE and offer a path toward more precise and reliable diagnostic tools.
PATIENTS AND METHODS: We obtained the PE dataset GSE25906 from the gene expression omnibus (GEO) database. Analysis of differentially expressed genes (DEGs) and module genes with Limma and Weighted Gene Co-expression Network analysis (WGCNA). Candidate hub genes for PE were identified using machine learning. Subsequently, we used western-blotting (WB) and real-time fluorescence quantitative (qPCR) to verify the expression of F13A1 and SCCPDH in preeclampsia patients. Finally, we estimated the extent of immune cell infiltration in PE samples by employing the CIBERSORT algorithms.
RESULTS: Our findings revealed that F13A1 and SCCPDH were the hub genes of PE. The nomogram and two candidate hub genes had high diagnostic values (AUC: 0.90 and 0.88, respectively). The expression levels of F13A1 and SCCPDH were verified by WB and qPCR. CIBERSORT analysis confirmed that the PE group had a significantly larger proportion of plasma cells and activated dendritic cells and a lower portion of resting memory CD4 + T cells.
CONCLUSION: The study proposes F13A1 and SCCPDH as potential biomarkers for diagnosing PE and points to an improvement in early detection. Integration of WGCNA with machine learning could enhance biomarker discovery in complex conditions like PE and offer a path toward more precise and reliable diagnostic tools.