Metabolomics is an expanding field dedicated to elucidating metabolic disorders by analyzing endogenous small molecules in biological samples. With the rapid advancement of metabolomics, researchers are investigating the influence of metabolites on metabolic phenotypes. The emergence of functional metabolomics provides a methodological framework to address this issue. This approach focuses on the biological functions of metabolites and their corresponding enzymes while validating the potential mechanisms of differential metabolites through in vivo and in vitro experiments. Despite numerous research findings, a systematic compilation of case studies remains absent. Therefore, this review systematically summarizes and evaluates functional metabolomics, covering its historical development, current state, and future directions, with the aim of fostering its advancement and offering solutions for further research.

Adverse reactions to traditional Chinese medicine have hindered the healthy development and internationalization process of the traditional Chinese medicine industry. The critical issue that needs to be solved urgently is to evaluate the safety of traditional Chinese medicine systematically and effectively. Podophyllotoxin (PPT) is a highly active compound extracted from plants of the genus Podophyllum such as Dysosma versipellis (DV). However, its high toxicity and toxicity to multiple target organs affect the clinical application, such as the liver and kidney. Based on the concurrent effects of PPT's medicinal activity and toxicity, it would be a good example to conduct a systematic review of its safety. Therefore, this study revolves around the Toxicological Evidence Chain (TEC) concept. Based on PPT as the main toxic constituent in DV, observe the objective toxicity impairment phenotype of animals. Evaluate the serum biochemical indicators and pathological tissue sections for substantial toxic damage results. Using metabolomics, lipidomics, and network toxicology to evaluate the nephrotoxicity of PPT from multiple perspectives systematically. The results showed that PPT-induced nephrotoxicity manifested as renal tubular damage, mainly affecting metabolic pathways such as glycerophospholipid metabolism and sphingolipid metabolism. PPT inhibits the autophagy process of kidney cells through the PI3K/Akt/mTOR and Nrf2/HO1 pathways and induces the activation of oxidative stress in the body, thereby causing nephrotoxic injury. This study fully verified the feasibility of the TEC concept for the safety and toxicity evaluation of traditional Chinese medicine. Provide a research template for systematically evaluating the safety of traditional Chinese medicine.