Molecular mechanisms of miRNA expression dysregulation in SHH-activated subtype medulloblastoma

doi:10.3969/j.issn.1674-8115.2026.01.001

Abstract

Abstract:

Objective ·To investigate the role of miRNA expression dysregulation in sonic hedgehog-activated subtype medulloblastoma (SHH-MB), and to compare the dysregulated miRNA features between subcutaneous xenograft models in nude mice and patients with solid tumors. Methods ·Mouse SHH-MB cell lines (SmoWT and SMB56) were used to establish subcutaneous xenograft models in nude mice. For each model, mice were randomly divided into groups treated with the smoothened inhibitor (SMOi) GDC-0449 (SmoWT experimental group and SMB56 experimental group) or dimethyl sulfoxide (DMSO) (SmoWT control group and SMB56 control group), and tumor samples from these 4 groups were collected. Cerebellar tissues from normal P7 (postnatal day 7) and P60 nude mice were collected as controls (P7 normal cerebellum group and P60 normal cerebellum group). Following the same procedure, cerebellar tissues were also collected from P7 normal nude mice treated with GDC-0449 (P7 cerebellum treatment group) or DMSO (P7 cerebellum control group). mRNA sequencing (mRNA-seq) and microRNA sequencing (miRNA-seq) were performed on these eight sample groups to obtain mRNA and miRNA expression profiles. Subsequently, differential expression analysis was systematically employed to elucidate: ① the core transcriptomic features of tumors in mouse SHH-MB models; ② transcriptomic features associated with normal cerebellar development; ③ Hedgehog (Hh)-dependent and Hh-independent transcriptomic features in both tumors and developing cerebellum. Target genes of key differentially expressed miRNAs were predicted by integrating data from the miRDB, TargetScan, and miRTarBase databases, combined with mRNA differential expression results. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was then performed to identify core signaling pathways involving these target genes. Specifically, for the Hh-dependent miRNA miR-204-5p identified in the P7 developing cerebellum, target genes were predicted and subjected to KEGG pathway enrichment analysis. Finally, mRNA and miRNA expression profiles from SHH-MB patient tumors and healthy control cerebella were obtained from the R2 and Gene Expression Omnibus (GEO). Conservation of differentially expressed miRNAs/mRNAs and their regulatory relationships between humans and mice was then systematically assessed through differential expression and Venn analysis. Results ·Analysis of mRNA expression profile correlations revealed a high correlation between the SmoWT control and SMB56 control groups. Both tumor control groups showed higher correlation with the P7 normal cerebellum group than with the P60 normal cerebellum group. Treatment with GDC-0449 did not significantly alter the overall transcriptomic profiles of either control group. The miRNA expression profile correlation results were consistent with those observed in the mRNA profiles. Differential expression analysis comparing the SmoWT control and SMB56 control groups with the P7 and P60 normal cerebellum groups identified 95 commonly upregulated and 126 commonly downregulated miRNAs in the two control groups. Among these, 50 upregulated and 38 downregulated miRNAs showed the same expression trends in the P7 and P60 normal cerebellum comparison. Differential expression analysis between the SmoWT experimental and control groups and between the SMB56 experimental and control groups identified Hh-dependent and Hh-independent differentially expressed miRNAs in each model. Venn diagram showed that the Hh-dependent miRNAs (accounting for 10%-20% of all differentially expressed miRNAs) showed minimal overlap between mouse SHH-MB models, whereas Hh-independent miRNAs were highly conserved across models. KEGG pathway enrichment analysis of the target genes of Hh-dependent differentially expressed miRNAs showed significant enrichment in the phosphoinositide 3-kinase/protein kinase B (PI3K/AKT) pathway, phospholipase D (PLD) pathway, RAS/mitogen-activated protein kinase (RAS/MAPK) pathway, and DNA replication pathways. Comparison between the P7 cerebellum treatment group and the P7 cerebellum control group identified 7 miRNAs and 285 mRNAs whose expression was promoted by the Hh pathway, and 1 miRNA and 72 mRNAs whose expression was inhibited by the Hh pathway in the P7 cerebellum. The target genes of miR-204-5p were enriched in the cell cycle pathway. Differential expression analysis of SHH-MB patient tumors vs healthy cerebellar controls identified 22 conserved human‑mouse miRNAs, with their target genes enriched in the cyclic adenosine monophosphate (cAMP) signaling pathway and the cell cycle pathway. Conclusion ·Mouse SHH-MB models exhibit extensive miRNA expression dysregulation. However, SMOi treatment reverses only a small subset of these dysregulated miRNAs, indicating a limited effect of the Hh pathway on miRNA dysregulation. Only Hh-independent dysregulated miRNAs show partial overlap between mouse SHH-MB models. Furthermore, there are conserved dysregulated miRNA features between mouse SHH-MB models and patients with solid tumors.

Key words: sonic hedgehog-activated subtype medulloblastoma (SHH-MB), Hedgehog pathway, miRNA expression dysregulation, cerebellar development

CLC Number:

R739.41

Zhu Ying, Sui Yi, Tang Yujie. Molecular mechanisms of miRNA expression dysregulation in SHH-activated subtype medulloblastoma[J]. Journal of Shanghai Jiao Tong University (Medical Science), 2026, 46(1): 1-14.

Figures/Tables 6

Fig 1 Dependency analysis of miRNA biogenesis genes in mouse SHH-MB models

Fig 2 Comparison of mRNA transcriptomes between mouse SHH-MB models and normal nude mouse cerebellum, and mRNA expression levels of Hh pathway transcription factors and miRNA biogenesis genes

Fig 3 Comparison of miRNA transcriptomes between mouse SHH-MB models and normal nude mouse cerebellum, and DO enrichment analysis of differentially expressed miRNAs

Fig 4 Hh pathway dependence of differentially expressed miRNAs/mRNAs and KEGG pathway enrichment in mouse SHH-MB models

Fig 5 Hh pathway dependence of differentially expressed miRNAs/mRNAs in the developing cerebellum, comparison with SHH-MB models, and KEGG pathway enrichment of target genes

Fig 6 Expression characteristics of miRNAs/mRNAs in tumor tissues from SHH-MB patients and human-mouse conservation analysis

TrendMD

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