Bulk transcriptome and single-nucleus RNA sequencing analyses highlight the role of recombination activating 1 in non-alcoholic fatty liver disease

Xiaohua Luo; Hongbo Deng; Qiang Li; Miao Zhao; Yu Zhang; Junjie Guo; Yifan Wen; Guangshun Chen; Jiequn Li

doi:10.1016/j.ijbiomac.2025.141919

Bulk transcriptome and single-nucleus RNA sequencing analyses highlight the role of recombination activating 1 in non-alcoholic fatty liver disease

Int J Biol Macromol. 2025 Mar 10;307(Pt 1):141919. doi: 10.1016/j.ijbiomac.2025.141919. Online ahead of print.

Authors

Xiaohua Luo¹, Hongbo Deng¹, Qiang Li¹, Miao Zhao², Yu Zhang¹, Junjie Guo¹, Yifan Wen¹, Guangshun Chen³, Jiequn Li⁴

Affiliations

¹ Department of Liver Transplant, The Second Xiangya Hospital of Central South University, 410011 Changsha, China.
² Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Science, Central South University, 410078 Changsha, China.
³ Department of Liver Transplant, The Second Xiangya Hospital of Central South University, 410011 Changsha, China. Electronic address: chenguangshun1323@csu.edu.cn.
⁴ Department of Liver Transplant, The Second Xiangya Hospital of Central South University, 410011 Changsha, China. Electronic address: leejiequn@csu.edu.cn.

PMID: 40074128
DOI: 10.1016/j.ijbiomac.2025.141919

Abstract

Non-alcoholic fatty liver disease (NAFLD) is a prevalent chronic condition with an incompletely understood pathogenesis. In this study, five candidate genes-RAG1, CKAP2, CENPK, TYMS, and BUB1-were identified as being associated with NAFLD progression through integrative bioinformatics analyses. A predictive model incorporating these genes demonstrated strong robustness and diagnostic accuracy. Single-nucleus RNA sequencing analysis further revealed that RAG1 plays a potential role in hepatocytes of NAFLD patients. Functional experiments using RNA interference to suppress RAG1 expression in HepG2 cells treated with oleic and palmitic acids showed reduced total glyceride and cholesterol levels, mitigated lipid accumulation, and alterations in pathways related to lipid metabolism, inflammation, and fibrosis. Furthermore, adeno-associated virus-specific knockdown of RAG1 in hepatocytes attenuated hepatic steatosis in high-fat diet-fed mice. These findings suggest that investigating the molecular mechanisms of hub genes like RAG1 may advance our understanding of NAFLD pathogenesis and inform therapeutic development.

Keywords: Bioinformatics; Machine learning algorithms; NAFLD; RAG1; Transcriptomics; snRNA-seq analysis.