Related Experiment Video
Updated: Apr 30, 2026
Studying the Effects of Matrix Stiffness on Cellular Function using Acrylamide-based Hydrogels
Published on: August 11, 2010
Identification of extracellular matrix stiffness-related genes in human scleral fibroblasts through bioinformatics
Chengcheng Zhu1, Changhui Liu2, Jing Wang2
1Department of Ophthalmology, Qilu Hospital of Shandong University Dezhou Hospital, Dezhou, China; Medical Integration and Practice Center, Cheeloo College of Medicine, Shandong University, Jinan, China.
Background:
Scleral extracellular matrix (ECM) remodeling plays a key role in myopia development. This study aims to identify ECM stiffness-related genes in human scleral fibroblasts (HSFs) using RNA sequencing, bioinformatics analysis, and machine learning.
Methods:
HSFs were cultured on soft and stiff polyacrylamide hydrogels (mimics myopic and normal extracellular matrix). RNA sequencing was performed on HSFs, and differentially expressed genes (DEGs) were identified. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, gene set enrichment analysis (GSEA), protein-protein interaction (PPI) network, and machine learning algorithms were used to explore the ECM stiffness-related key genes. Nomogram and receiver operating characteristic curve were constructed to assess the diagnostic value in HSF sequencing dataset from myopia patients. Differential microRNAs (miRNAs) between myopia and normal samples in GSE131831 were analyzed, and miRNA-messenger RNA network was also developed.
Results:
The dataset included 1368 upregulated and 1481 downregulated DEGs, which were primarily associated with change of scleral ECM stiffness. Five key genes (LDLR, DNM1, DUSP15, NES, and PPL) were identified. DNM1 was the best marker for myopia diagnosis.
Conclusion:
LDLR, DNM1, DUSP15, NES, and PPL were identified as ECM stiffness-related genes in HSFs, of which DNM1 was the optimal diagnostic marker for myopia. The association of these five genes with myopia and scleral remodeling warrants further investigation.
