Journal Article

Identification of Immune-Associated Genes in Diagnosing Aortic Valve Calcification With Metabolic Syndrome by Integrated Bioinformatics Analysis and Machine Learning

Zhou, Yufei, Shi, Wenxiang, Wang, Kai, Zhao, Di, Wang, Jing, Xiao, Shengjue

2022

Overview

BackgroundImmune system dysregulation plays a critical role in aortic valve calcification (AVC) and metabolic syndrome (MS) pathogenesis. The study aimed to identify pivotal diagnostic candidate genes for AVC patients with MS.MethodsWe obtained three AVC and one MS dataset from the gene expression omnibus (GEO) database. Identification of differentially expressed genes (DEGs) and module gene via Limma and weighted gene co-expression network analysis (WGCNA), functional enrichment analysis, protein–protein interaction (PPI) network construction, and machine learning algorithms (least absolute shrinkage and selection operator (LASSO) regression and random forest) were used to identify candidate immune-associated hub genes for diagnosing AVC with MS. To assess the diagnostic value, the nomogram and receiver operating characteristic (ROC) curve were developed. Finally, immune cell infiltration was created to investigate immune cell dysregulation in AVC.ResultsThe merged AVC dataset included 587 DEGs, and 1,438 module genes were screened out in MS. MS DEGs were primarily enriched in immune regulation. The intersection of DEGs for AVC and module genes for MS was 50, which were mainly enriched in the immune system as well. Following the development of the PPI network, 26 node genes were filtered, and five candidate hub genes were chosen for nomogram building and diagnostic value evaluation after machine learning. The nomogram and all five candidate hub genes had high diagnostic values (area under the curve from 0.732 to 0.982). Various dysregulated immune cells were observed as well.ConclusionFive immune-associated candidate hub genes ( BEX2 , SPRY2 , CXCL16 , ITGAL , and MORF4L2 ) were identified, and the nomogram was constructed for AVC with MS diagnosis. Our study could provide potential peripheral blood diagnostic candidate genes for AVC in MS patients.

• Publisher: Frontiers Media SA,Frontiers Media S.A
• Subject: Accuracy / Algorithms / Aortic valve / aortic valve calcification / Bioinformatics / Biomarkers / Calcification / Calcification (ectopic) / CXCL16 protein / Datasets / diagnosis / differentially expressed genes / Gene expression / Gene set enrichment analysis / Hyperlipidemia / immune infiltration / Immune system / Immunology / Immunoregulation / Learning algorithms / Machine learning / Metabolic syndrome / Nomograms / Peripheral blood / Proteins / Software