Journal Article

Integrated analysis of single-cell RNA sequencing and bulk RNA data reveals gene regulatory networks and targets in dilated cardiomyopathy

Zhang, Xin, Niu, Jiayin, Hua, Cuncun, Zhong, Guangzhen, Liu, Pengfei, Zhang, Min

2024

Overview

Dilated cardiomyopathy (DCM) is a common cause of heart failure, thromboembolism, arrhythmias, and sudden cardiac death. The quality of life and long-term survival rates of patients with dilated DCM have greatly improved in recent decades. Nevertheless, the clinical prognosis for DCM patients remains unfavorable. The primary driving factors underlying the pathogenesis of DCM remain incompletely understood. The present study aimed to identify driving factors underlying the pathogenesis of DCM from the perspective of gene regulatory networks. Single-cell RNA sequencing data and bulk RNA data were obtained from the Gene Expression Omnibus (GEO) database. Differential gene analysis, single-cell genomics analysis, and functional enrichment analysis were conducted using R software. The construction of Gene Regulatory Networks was performed using Python. We used the pySCENIC method to analyze the single-cell data and identified 401 regulons. Through variance decomposition, we selected 19 regulons that showed significant responsiveness to DCM. Next, we employed the ssGSEA method to assess regulons in two bulk RNA datasets. Significant statistical differences were observed in 9 and 13 regulons in each dataset. By intersecting these differentiated regulons and identifying shared targets that appeared at least twice, we successfully pinpointed three differentially expressed targets across both datasets. In this study, we assessed and identified 19 gene regulatory networks that were responsive to the disease. Furthermore, we validated these networks using two bulk RNA datasets of DCM. The elucidation of dysregulated regulons and targets (CDKN1A, SAT1, ZFP36) enhances the molecular understanding of DCM, aiding in the development of tailored therapies for patients.

• Publisher: Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
• Subject: 631/208/212 / 692/4019/592 / Cardiomyopathy / Cardiomyopathy, Dilated - genetics / Computational Biology - methods / Congestive heart failure / Datasets / Dilated cardiomyopathy / Gene expression / Gene Expression Profiling / Gene Expression Regulation / Gene Regulatory Networks / Gene set enrichment analysis / Genomic analysis / Humanities and Social Sciences / Humans / Medical prognosis / multidisciplinary / Pathogenesis / Quality of life / Regulon / Ribonucleic acid / RNA / RNA - genetics / RNA - metabolism / Science / Science (multidisciplinary) / Sequence Analysis, RNA - methods / Single-Cell Analysis - methods / Single‑cell sequencing / Statistical analysis / Survival / Targets / Thromboembolism