Progress and applications of single-cell RNA sequencing and spatial transcriptome technology in acute kidney injury research

Chunyan Cui; Feifei Cui; Quan Zou; Zilong Zhang; Linpei Jia

doi:10.1016/j.omtn.2025.102583

Progress and applications of single-cell RNA sequencing and spatial transcriptome technology in acute kidney injury research

Mol Ther Nucleic Acids. 2025 May 30;36(3):102583. doi: 10.1016/j.omtn.2025.102583. eCollection 2025 Sep 9.

Authors

Chunyan Cui^{1

2}, Feifei Cui¹, Quan Zou³, Zilong Zhang¹, Linpei Jia⁴

Affiliations

¹ School of Computer Science and Technology, Hainan University, Haikou 570228, China.
² The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou 646000, China.
³ Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China.
⁴ Department of Nephrology, Xuanwu Hospital, Capital Medical University, No. 45 Changchun Street, Beijing 100053, China.

Abstract

Acute kidney injury (AKI) is a critical syndrome characterized by rapid decline in renal function. During the previous ten years, single-cell RNA sequencing (scRNA-seq) technology has evolved from a groundbreaking method to a fundamental tool in life science research. By integrating data from cellular spatial positioning with molecular omics, single-cell spatial omics offers unparalleled insight into how heterogeneous cells assemble and interact, illuminating complex networks governing cellular behavior in tissues and organs and uncovering dynamic processes of cell-cell communication. Single-cell sequencing and spatial transcriptomics have not only facilitated investigations of fundamental biological questions such as developmental differentiation but also enabled exploration of clinical issues such as cardiovascular diseases and tumor microenvironments, fundamentally transforming biomedical research paradigms. This review outlines the progression of sequencing methods, with emphasis on bulk RNA-seq, scRNA-seq, and spatially resolved transcriptomics. Additionally, we review relevant published studies to discuss the ongoing cutting-edge applications of single-cell transcriptomic profiling coupled with spatial omics in AKI research, focusing on cellular heterogeneity, personalized treatment, and other related research directions. Finally, we discuss current constraints of scRNA-seq coupled with spatial omics in AKI research. From a multi-dimensional analysis perspective, we studied scRNA-seq and spatial transcriptomics, highlighting their critical role in advancing AKI understanding.

Keywords: MT: Oligonucleotides: Bioinformatics; acute kidney injury; biomarker; bulk RNA sequencing; single-cell RNA sequencing; spatial transcriptome technology.

Publication types

Review