Unraveling Traditional Chinese Medicine with single-cell RNA sequencing: Current applications and future frontiers

Single-cell RNA sequencing (scRNA-seq) has emerged as a transformative tool in biomedical research, overcoming the limitations of bulk RNA sequencing by resolving cellular heterogeneity, identifying rare cell subtypes, and reconstructing dynamic regulatory networks. This technology holds unprecedented potential for advancing Traditional Chinese Medicine (TCM) research, which faces challenges in deciphering the multi-component, multi-target mechanisms and heterogeneous syndromes using conventional methods.

Relevant studies were retrieved from PubMed, Web of Science, Google Scholar, and CNKI up to June 2025. Search keywords included "single-cell RNA sequencing", "Traditional Chinese Medicine", "tumor", "inflammatory and autoimmune", and "cardiovascular, cerebrovascular". The inclusion criteria were as follows: (a) original research articles; (b) the application of scRNA-seq in TCM-related research, mainly for TCM in research related to tumors, inflammatory and autoimmune diseases, cardiovascular and cerebrovascular diseases, safety evaluation of TCM, and TCM Syndrome Research. The exclusion criteria comprised: (a) studies irrelevant to the review topic; (b) studies that utilized public datasets solely for data mining.

scRNA-seq enables precise identification of bioactive targets of herbal compounds, dissection of synergistic modulation of cellular networks by TCM formulas, and construction of syndrome-associated molecular atlases. Its applications span diverse fields: unraveling immune regulation mechanisms of TCM in tumor therapy, elucidating immunomodulatory effects in inflammatory and autoimmune diseases, clarifying cardioprotective mechanisms in cardiovascular and cerebrovascular disorders, and facilitating safety evaluation of TCM. Additionally, scRNA-seq bridges TCM's holistic syndrome differentiation with molecular medicine by revealing dynamic correlations between TCM syndromes and cellular heterogeneity. By comparing with Western medical research paradigms, scRNA-seq highlights TCM's distinctive focus on network-driven regulation and holistic balance.

This review summarizes cutting-edge studies and future directions, emphasizing scRNA-seq's role as a critical bridge in integrating TCM's systemic principles with molecular insights, thereby accelerating TCM and its integration into precision medicine.