Transcriptome Inference and Systematic Approaches to Investigate TCM Compounds With Beneficial Metabolic Effects

Obesity is a major risk factor for type 2 diabetes. Some traditional Chinese medicine (TCM) compounds can improve obesity by increasing energy consumption. This study aimed to identify and verify TCM compounds that promote adipose thermogenesis to alleviate obesity via transcriptomic analysis, molecular docking, network pharmacology, and Connectivity Map (CMap) analysis. Thirty-six TCMs related to adipose tissue thermogenesis were first collected to generate transcriptomic data. Then a ranking method based on integrated transcriptomic data was used to select emodin from the TCM Da Huang for network pharmacology to explore its potential mechanisms and further experimental validation. CMap analysis of thermogenesis signature genes from ProFAT and GEO datasets identified triptolide as another compound for improving obesity through enhanced thermogenesis. In vitro experiments with 3T3-L1 cells and in vivo experiments with zebrafish were conducted. The results showed that both emodin and triptolide could upregulate the NAD⁺/NADH ratio, increase AMPK and SIRT1 expression, suppress lipid accumulation, and promote lipolysis, as verified by both in vitro and in vivo experiments. They also upregulated thermogenesis-related genes (e.g., UCP1, PGC1α, and PRDM16), lipolysis-related genes (e.g., PKA, ATGL, and HSL), mitochondrial biogenesis-related genes (e.g., NRF1, NRF2, and TFAM), and β-oxidation-related genes (e.g., CPT1α and CPT1β). Meanwhile, they downregulated lipogenesis-related genes such as FASN, SREBP1, and ACC. These results provide a basis for understanding the effects of emodin and triptolide on obesity. The findings highlight the effectiveness of combined screening approaches in exploring compounds with beneficial metabolic effects.