Work

Hyperlipidemia-associated specific modules and hub genes revealed by integrative methods of WGCNA and MetaDE

Year: 2025

Type: article

Abstract: Background and objectives This study aimed to screen the specific modules and hub genes of hyperlipidemia. Methods Three microarray datasets (GSE3059, GSE1010 and GSE13985) were obtained from the Gene Expression Omnibus database. Weighted Gene Co-expression Network Analysis (WGCNA) was used to screen stable gene modules across the three datasets. The MetaDE method was used to screen differentially expressed genes (DEGs) based on GSE1010 and GSE13985 datasets. The Cytoscape software was utilized for protein-protein interaction (PPI) network visualization, and the DAVID was employed to perform Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathway analysis on the DEG nodes in the interaction network. Results Based on the WGCNA algorithm, eleven hyperlipidemia-related modules were screened, and a total of 1,149 DEGs were screened by the metaDE method. 288 overlapping genes were used to establish a PPI network. Finally, a total of four overlapping KEGG pathways were obtained, including Fc gamma R-mediated phagocytosis ( ARPC1A , GAB2 , LYN , HCK , RAF1 , WAS ), chemokine signalling pathway ( LYN , PTK2B , HCK , GRK6 , GRK3 , RAF1 , CXCR2 , JAK3 , FOXO3 , WAS ), endocytosis ( CHMP2A , CHMP1B , RAB5C , VPS45 , TGFBR2 , GRK6 , GRK3 , CXCR2 ) and natural killer cell-mediated cytotoxicity ( TNFRSF10C , PTK2B , ICAM2 , RAF1 , FCGR3B , SH3BP2 ). The hub genes such as RAF1 , GRK3 and CXCR2, might be potential genetic biomarkers of hyperlipidemia. Discussion This study identified the critical pathways and hub genes associated with hyperlipidemia. In particular, these critical pathways may help clarify the pathogenesis of hyperlipidemia, and the hub genes may become new biomarkers and therapeutic target for hyperlipidemia.

Source: Frontiers in Genetics

DOI: 10.3389/fgene.2025.1592778

Authors: Zhiyi Zhao, Yin Cao, Anna Gu, Hanxin Yao

Institutions: First Hospital of Jilin University, Northeast Normal University

Language: English

Topic: Bioinformatics and Genomic Networks

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

SDG: Good health and well-being

Open Access status: gold

Estimated APC paid: $3,801