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Updated: Jul 29, 2026
Transcriptome Analysis of Single Cells
Published on: April 25, 2011
Combined analysis of single-cell and bulk transcriptome sequencing data identifies critical glycolysis genes in
Xuan Gao1,2, Youli Fan1,2, Guijia Wang1
1Department of Cardiology, The Key Laboratory of Myocardial Ischemia, Ministry of Education, The Second Affiliated Hospital of Harbin Medical University, NO.246 Xuefu Road, Nangang District, Harbin, 150086, China.
Background:
Abnormal glycolytic metabolism plays a significant role in pulmonary vascular remodeling in idiopathic pulmonary arterial hypertension (IPAH), yet the specific mechanisms remain unclear. The primary objective of this study is to investigate the key regulatory mechanisms of glycolysis in IPAH.
Methods:
Bulk and single-cell sequencing data obtained from IPAH patient tissue samples were downloaded from the GEO database. scMetabolism and AUCcell analyses of the IPAH single-cell sequencing data were carried out to quantify the glycolytic metabolic activity and identify the main cell types regulating glycolysis, respectively. The ssGSEA method was used to assess the glycolytic activity in each bulk sample within the bulk sequencing data. Differential analysis, weighted gene co-expression network analysis (WGCNA), and protein-protein interaction (PPI) network analysis were conducted to identify key genes associated with glycolysis in IPAH samples. Single-cell sequencing and a monocrotaline (MCT)-induced model of PH in rats were utilized to validate the expression of these key genes.
Results:
Single-cell sequencing data indicated that IPAH patients displayed increased glycolytic activity, which was primarily regulated by fibroblasts. Similarly, bulk transcriptomic data revealed a significant increase in glycolytic activity in IPAH patients. Differential analysis, WGCNA, PPI network analysis, and integrated single-cell analysis further identified insulin-like growth factor-1 (IGF1), lysyl-tRNA synthetase (KARS), caspase-3 (CASP3), and cyclin-dependent kinase inhibitor 2 A (CDKN2A) as key genes associated with fibroblast-mediated glycolysis in IPAH patients. Differential expression of IGF1, KARS, CASP3, and CDKN2A was also observed in our in vivo model of PH.
Conclusion:
Our study identifies IGF1, KARS, CASP3, and CDKN2A as key regulatory genes in glycolysis in IPAH, which provides the basis for the development of targeted therapies.
