Research Paper Volume 15, Issue 14 pp 7187—7218
Identification of TGF-β-related genes in cardiac hypertrophy and heart failure based on single cell RNA sequencing
- 1 Department of Cardiovascular Surgery, Changhai Hospital, Second Military Medical University, Shanghai, China
Received: February 23, 2023 Accepted: June 19, 2023 Published: July 26, 2023
https://doi.org/10.18632/aging.204901How to Cite
Copyright: © 2023 Huang et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Abstract
Background: Heart failure (HF) remains a huge medical burden worldwide. Pathological cardiac hypertrophy is one of the most significant phenotypes of HF. Several studies have reported that the TGF-β pathway plays a double-sided role in HF. Therefore, TGF-β–related genes (TRGs) may be potential therapeutic targets for cardiac hypertrophy and HF. However, the roles of TRGs in HF at the single-cell level remain unclear.
Method: In this study, to analyze the expression pattern of TRGs during the progress of cardiac hypertrophy and HF, we used three public single-cell RNA sequencing datasets for HF (GSE161470, GSE145154, and GSE161153), one HF transcriptome data (GSE57338), and one hypertrophic cardiomyopathy transcriptome data (GSE141910). Weighted gene co-expression network analysis (WGCNA), functional enrichment analysis and machine learning algorithms were used to filter hub genes. Transverse aortic constriction mice model, CCK-8, wound healing assay, quantitative real-time PCR and western blotting were used to validate bioinformatics results.
Results: We observed that cardiac fibroblasts (CFs) and endothelial cells showed high TGF-β activity during the progress of HF. Three modules (royalblue, brown4, and darkturquoize) were identified to be significantly associated with TRGs in HF. Six hub genes (TANC2, ADAMTS2, DYNLL1, MRC2, EGR1, and OTUD1) showed anomaly trend in cardiac hypertrophy. We further validated the regulation of the TGF-β-MYC-ADAMTS2 axis on CFs activation in vitro.
Conclusions: This study identified six hub genes (TANC2, ADAMTS2, DYNLL1, MRC2, EGR1, and OTUD1) by integrating scRNA and transcriptome data. These six hub genes might be therapeutic targets for cardiac hypertrophy and HF.
Abbreviations
HF: heart failure; TRGs: TGF-β–related genes; DEGs: differentially expressed genes; scRNA: single-cell RNA sequencing; WGCNA: weighted gene co-expression network analysis; TAC: transverse aortic constriction; B: B cells; CM: cardiac muscle cells; EC: endothelial cells; EndoC: endocardial endothelial cells; FB: fibroblasts; myeloid: myeloid cells; neuronal: neurogenic cells; NK: natural killer cells; T: T cells; GO: gene ontology annotation; KEGG: Kyoto Encyclopedia of Genes and Genomes; ssGSEA: single-sample gene set enrichment analysis; LASSO: least absolute shrinkage and selection operator; SVM-RFE: support vector machine-recursive feature elimination; TANC2: tetratricopeptide repeat, ankyrin repeat, and coiled-coil containing 2; ADAMTS2: ADAM metallopeptidase with thrombospondin type 1 motif 2; DYNLL1: dynein light chain LC8-type 1; MRC2: mannose receptor C type 2; EGR1: early growth response 1; OTUD1: OTU deubiquitinase 1; t-SNE: t-distributed stochastic neighbor embedding.