Zhuyu pill relieves cholestasis in rats by modulating the expression of lncRNAs and circRNAs

Zhuyu pill (ZYP), a traditional Chinese medicine (TCM) formula composed of Coptis chinensis Franch and Tetradium ruticarpum (A. Jussieu) T. G. Hartley, exhibiting potential anti-cholestatic effects. However, its specific mechanism remains unclear. Long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) are critical gene expression regulators and promising direction for exploring the mechanism.

This study aims to validate the anti-cholestatic effects of ZYP and explore its potential biological mechanisms through lncRNAs and circRNAs.

Rats with alpha-naphthyl isothiocyanate (ANIT)-induced cholestasis were treated with low-dose (0.6 g/kg) or high-dose (1.2 g/kg) ZYP. Efficacy was assessed by serum biochemistry and histopathology. Differentially expressed lncRNAs (DElncRNAs) and circRNAs (DEcircRNAs) in liver tissues were identified via RNA sequencing, followed by GO and KEGG enrichment analysis. MiRanda was used to predict DElncRNAs/DEcircRNAs-miRNA interactions and construct interaction networks. Subsequently, trend analysis was used to screen lncRNA/circRNA-miRNA pairs with expression patterns consistent with the competing endogenous RNA (ceRNA) regulatory mechanism.

Both high- and low-dose ZYP significantly improved biochemical and histopathological parameters, with the high-dose group showing superior effects. Enrichment analysis showed that DElncRNA-related functions were mainly concentrated in lipid metabolism pathways ("Bile secretion", "Adipocytokine signaling pathway", "Arachidonic acid metabolism") and inflammation-related pathways ("NF-κB", "TNF", "MAPK", and "Inflammatory bowel disease (IBD)"), suggesting their roles in alleviating inflammatory injury and lipid metabolism disorders. Among these, core lncRNAs altered by ANIT and reversed by ZYP included TCONS_00032614, TCONS_00018259, TCONS_00025702, TCONS_00012591, and TCONS_00003751, with qRT-PCR results largely consistent with sequencing data. Further lncRNA-miRNA binding prediction and expression trend analysis identified candidate pairs with potential competing ceRNA characteristics: TCONS_00003751/rno-miR-328b-3p, TCONS_00003751/rno-miR-328a-3p, and TCONS_00032614/rno-miR-149-5p. Similarly, DEcircRNA-associated pathways were enriched in inflammatory and immune responses ("Cell adhesion molecules (CAMs)", "Antigen processing and presentation", and "Cytochrome P450 metabolism of xenobiotics"). Candidate circRNAs included circRNA_1402 and circRNA_1452, and Candidate pairs with potential competing ceRNA characteristics included circRNA_1402/rno-miR-1306-5p and circRNA_1452/rno-miR-23a-5p.

ZYP dose-dependently improved biochemical and histopathological parameters in cholestatic rats. This effect is closely related to the roles of lncRNAs and circRNAs in regulating lipid metabolism and inflammation-related pathways. Several candidate ceRNA pairs were preliminarily screened, yet further experimental validation is warranted.