LncRNA-mRNA co-expression network in the mechanism of butylphthalide treatment for ischemic stroke

BACKGROUND

Butylphthalide has shown significant potential in the treatment of ischemic stroke, but its precise mechanisms of action remain unclear. Long non-coding RNAs (lncRNAs) and messenger RNAs (mRNAs) play crucial roles in the pathogenesis of ischemic stroke and may serve as potential therapeutic targets. This study investigated the effects of butylphthalide treatment on the lncRNA-mRNA co-expression network in ischemic stroke patients.

METHODS

Peripheral blood samples were collected from ischemic stroke patients treated with butylphthalide and from control subjects. mRNA and lncRNA expression profiles were obtained using microarray scanning, and differentially expressed lncRNAs (DElncRNAs) were validated by qRT-PCR. Target genes interacting with DElncRNAs were predicted using the miRTargetLink database. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed on both DElncRNAs and differentially expressed mRNAs (DEmRNAs). A protein-protein interaction (PPI) network was constructed for proteins encoded by DEmRNAs. Co-expression analysis, based on Pearson correlation coefficients, identified the top five mRNAs and lncRNAs with high connectivity. Finally, molecular docking was performed to investigate the binding interaction between butylphthalide and key mRNAs.

RESULTS

A total of 86 differentially expressed mRNAs (69 upregulated, 17 downregulated) and 35 DElncRNAs (all upregulated) were identified. DEmRNAs were primarily associated with pathways related to cell receptors, signal transduction, cell proliferation, migration, and glucose metabolism, while DElncRNAs were involved in processes such as embryonic development, neuronal connectivity, and energy metabolism. Co-expression analysis identified key mRNA nodes (SETD9, ZNF718, AOC2, MPND, ODF1) and lncRNA nodes (IDH2-DT, CLEC12A-AS1, CARD8-AS1, LINC01275, ZNF436-AS1). Molecular docking analysis suggested that MT-CO1, SETD9, and ZNF718 could be potential targets of butylphthalide.

CONCLUSION

Butylphthalide may exert its therapeutic effects by regulating the LncRNA-mRNA co-expression network, influencing energy metabolism and neuronal development. This provides new insights into its mechanism of action and potential therapeutic targets.

Triterpenes from Ganoderma lucidum inhibit hepatocellular carcinoma by regulating enhancer-associated lncRNA in vivo

ETHNOPHARMACOLOGICAL RELEVANCE

Ganoderma lucidum (G. lucidum) has been widely used as adjuvant of anti-tumor therapy for variety tumors. The bioactive ingredients of G. lucidum mainly include triterpenes, such as Ganoderic acid A, Ganoderic acid B, Ganoderenic acid A, Ganoderenic acid B, Ganoderenic acid D, and Ganoderic acid X. However, the effects and underlying mechanisms of G. lucidum are often challenging in hepatocellular carcinoma (HCC) treatment.

AIM OF THE STUDY

To explore the potential role and mechanism of enhancer-associated lncRNAs (en-lncRNAs) in G. lucidum treated HCC through the in vivo and in vitro experiments.

MATERIALS AND METHODS

Hepa1-6-bearing C57 BL/6 mice model were established to evaluate the therapeutic efficacy of G. lucidum treated HCC. Ki67 and TUNEL staining were used to detect the tumor cell proliferation and apoptosis in vivo. The Mouse lncRNA 4*180K array was implemented to identify the differentially expressed (DE) lncRNAs and mRNAs of G. lucidum treated tumor mice. The constructed lncRNA-mRNA co-expression network and bioinformatics analysis were used to selected core en-lncRNAs and its neighboring genes. The UPLC-MS method was used to identify the triterpenes of G. lucidum, and the in vitro experiments were used to verify which triterpene monomers regulated en-lncRNAs in tumor cells. Finally, a stable knockdown/overexpression cell lines were used to confirm the relationship between en-lncRNA and neighboring gene.

RESULTS

Ki67 and TUNEL staining demonstrated G. lucidum significantly inhibited tumor growth, suppressed cell proliferation and induced apoptosis in vivo. Transcriptomic analysis revealed the existence of 126 DE lncRNAs high correlated with 454 co-expressed mRNAs in G. lucidum treated tumor mice. Based on lncRNA-mRNA network and qRT-PCR validation, 6 core lncRNAs were selected and considered high correlated with G. lucidum treatment. Bioinformatics analysis revealed FR036820 and FR121302 might act as enhancers, and qRT-PCR results suggested FR121302 might enhance Popdc2 mRNA level in HCC. Furthermore, 6 main triterpene monomers of G. lucidum were identified by UPLC-MS method, and in vitro experiments showed FR121302 and Popdc2 were significantly suppressed by Ganoderenic acid A and Ganoderenic acid B, respectively. The knock/overexpression results demonstrated that FR121302 activating and enhancing Popdc2 expression levels, and Ganoderenic acid A and Ganoderenic acid B dramatically suppressed FR121302 and decreased Popdc2 level in Hepa1-6 cells.

CONCLUSIONS

Enhancer-associated lncRNA plays a crucial role as an enhancer during hepatocarcinogenesis, and triterpenes of G. lucidum significantly inhibited tumor cell proliferation and induced apoptosis by regulating en-lncRNAs. Our study demonstrated Ganoderenic acid A and Ganoderenic acid B suppressed en-lncRNA FR121302 may be one of the critical strategies of G. lucidum inhibit hepatocellular carcinoma growth.