Revolutionizing pharmacological research of traditional Chinese medicine with single-cell omics technologies

Traditional Chinese Medicine (TCM) offers a holistic approach to healthcare, yet its modernization is hindered by the immense complexity of its multi-component formulations and multi-target mechanisms. Conventional bulk-level analyses fail to capture the cellular heterogeneity underlying TCM's therapeutic effects, resulting in a substantial gap between its empirical success and mechanistic understanding. This review aims to systematically summarize the applications of single-cell omics technologies (transcriptomics, proteomics, metabolomics) in TCM pharmacological research. More importantly, we propose that these technologies represent a paradigm shift, providing an unprecedented high-resolution toolkit to deconstruct the holistic principles of TCM into the precise language of cellular and molecular biology. We highlight how single-cell omics are revolutionizing TCM research by: (1) identifying the specific cell subtypes targeted by active compounds and formulas; (2) elucidating the synergistic mechanisms of herbal combinations by revealing coordinated responses across different cell populations; (3) providing a cellular-level basis for TCM concepts such as organotropism and syndrome differentiation; and (4) revealing how TCM achieves homeostatic regulation by rebalancing entire cellular ecosystems. Single-cell omics technologies are powerful drivers for the modernization and globalization of TCM. By bridging the gap between holistic theory and cellular-level evidence, they not only validate the scientific basis of TCM but also pave the way for the discovery of novel therapeutic targets and the development of more precise, personalized treatment strategies. This review lays the groundwork for future breakthroughs, positioning single-cell omics as a cornerstone of next-generation TCM pharmacology.