Integrated transcriptomic analysis identifies gene–miRNA regulatory networks associated with major chicory root bioactive compounds

Cichorium intybus L. (chicory) is a globally utilized medicinal plant whose root contains bioactive compounds such as inulin, fructose, chlorogenic acids (CGA), and sesquiterpene lactones (STL). These metabolites are central to its health-promoting properties. This study employed an integrated transcriptomic analysis to elucidate the genetic and molecular mechanisms underlying the effects of these compounds in mice. Microarray datasets (GSE150218 and GSE190056) were analyzed to identify differentially expressed genes (DEGs), hub genes, and associated microRNAs (miRNAs). Gene ontology (GO) enrichment, KEGG pathway analysis, and protein–protein interaction (PPI) networks were applied to characterize functional relevance. Distinct hub genes were identified: Rps28 and Rps2 (inulin), Rplp0 , Cct2 , and Rps20 (fructose), Mki67 , Egfr , and Pparg (STL), and Socs2 , Six2 , Smtnl2 , and Gcsh (CGA). Pathway enrichment revealed significant associations with mRNA surveillance, PPAR signaling, AMPK signaling, ribosome, and coronavirus-related pathways. Furthermore, miRNA analysis highlighted strong predicted regulatory interactions between miRNAs and hub genes, including mmu-miR-204-3p (inulin), mmu-miR-17-5p (fructose), mmu-miR-15a-5p (STL), and mmu-miR-142a-5p (CGA). Collectively, these findings identify molecular pathways and regulatory interactions associated with major chicory root bioactive compounds and provide a basis for future mechanistic studies. Experimental validation is required to confirm these predicted regulatory networks.