Abstract: Objective To explore the applicability of single-cell RNA sequencing (scRNA-seq) technology in TCM research given the current challenges to precise characterization of the therapeutic efficacy and toxicological profiles of Traditional Chinese Medicine (TCM). Methods Recent research advances in utilizing scRNA-seq to investigate the efficacy and toxicity mechanisms of TCM were reviewed in general and related disease treatments and toxicity in particular. The functional positioning and key findings of scRNA-seq in various studies were also analyzed. Results A standardized research paradigm known as "component analysis-cellular localization-target screening-mechanism validation" was established to explore the efficacy and toxicity of TCM using scRNA-seq that could overcome the limitations of traditional organ-level observations and reveal the microscopic essence of TCM’s pharmacological and toxicological actions by enabling precise identification of cellular subpopulation-specific responses and dynamic gene expression changes. Based on these insights, we proposed a single-cell network pharmacological or toxicological strategy for systematic elucidation of mechanisms. Conclusion scRNA-seq has emerged as a pivotal methodology for deciphering what is underlying the pharmacology and toxicology of TCM. Research strategies in TCM using this technology can provide novel perspectives and references for advancing the modernization of TCM.

Key words: Traditional Chinese Medicine (TCM), Single-Cell Transcriptome Sequencing (scRNA-seq), Pharmacodynamics of Traditional Chinese Medicine, Toxicity of Traditional Chinese Medicine, Mechanisms of Action of Traditional Chinese Medicine, Pharmacodynamics and Toxicity