AT/RT is an aggressive pediatric tumor of the CNS. Because of the limited available treatments and poor prognosis of AT/RT, there is an urgent need to identify novel therapeutic targets and develop innovative treatment strategies for this disease [25,26,27]. Mutations and/or deletions of the SMARCB1 (BAF47/INI1/SNF5) gene are hallmarks of AT/RT tumors, and so far no other recurrent genetic abnormalities have been identified [2, 28]. Previous studies showed that HMGA2, LIN28, RPL5, RPL10 and SUN2 are crucial regulators in AT/RT [29, 30]. However, the precise molecular mechanism of AT/RT remains largely unknown.
miRNAs play crucial roles in regulating gene expression at the transcriptional, post-transcriptional and epigenetic levels. Previous studies have established that miRNAs participate in a wide variety of biological processes including genomic imprinting, cell cycle, cell differentiation, invasion and migration [31,32,33,34]. Hsiehet et al. showed that miR-221/222 represents a promising new target in AT/RT . Our multi-omics analysis identified five upregulated miRNAs (hsa-miR-301a-3p, hsa-miR-18a-5p, hsa-miR-335-3p, hsa-miR-18b-5p, hsa-miR-17-5p) and 16 downregulated miRNAs (hsa-miR-129–1-3p, hsa-miR-128-3p, hsa-miR-656-3p, hsa-miR-329-3p, hsa-miR-1224-5p, hsa-miR-668-3p, hsa-miR-488-5p, hsa-miR-29c-5p, etc.) in AT/RT. Hsa-miR-129–1-3p was the most-downregulated in AT/RT while hsa-miR-17-5p was the most up-regulated miRNA in AT/RT.
We further found that 179 mRNAs were up-regulated and 402 mRNAs were down-regulated, which could be the result of the dysregulated miRNA networks in AT/RT, as miRNAs regulate the levels and functions of their target mRNAs. GO analyses revealed that these mRNAs are involved in critical pathways such as the regulation of synaptic plasticity, modulation of chemical synaptic transmission, neurotransmitter transportation and secretion. KEGG pathway analysis showed that “Synaptic vesicle cycle,” “GABAergic synapse” and “Glutamatergic synapse” were related to the DEGs, which is consistent with GO enrichment analysis. These findings suggest that altered synaptogenesis and synaptic dysfunction could contribute to the formation and clinical manifestation of AT/RT. Additionally, DEGs were involved in the canonical pathways such as cAMP signaling pathway, which may contribute to the stemness of the AT/RT tumor cells.
Several recent studies have analyzed the influence of the host immune system on cancer prognosis . We performed analyses using CIBERSORT, a computational method for high-throughput characterization of different types of immune cells in complex tissues. Our results demonstrated there was no difference in immune-related cells in AT/RT.
MiRTarBase database is a database that predict targets for miRNAs . Seventeen DEmiRNAs were found to have at least one negatively regulated miRNA-mRNA pair in the DEmRNAs. Notably, over 30 mRNAs were predicted to be regulated by hsa-miR-17-5p. To further probe the negative correlations between hsa-miR-17-5p and its target mRNAs, we calculated the Pearson values using R software. A total of 15 mRNAs were negatively correlated with hsa-miR-17-5p. In addition to the protein–protein interaction networks constructed between DEmiRNAs and DEmRNAs, we also further verified the expression of hsa-miR-17-5p, hsa-miR-18a-5p, hsa-miR-488-5p, hsa-miR-128-3p, hsa-miR-495-3p, hsa-miR-668-3p, and hsa-miR-874-3p using qPCR . These results further demonstrated the importance of hsa-miR-17-5p in AT/RT.
Zeng et al. previously reported that miRNA-17-5p expression is upregulated in glioblastoma and is a potential marker for the proneural subtype . However, the mechanisms by which miRNA-17-5p expression regulates tumorigenesis are not well elucidated. We screened and identified possible targets of miRNA-17-5p and the results suggested that CCND1, THBS1, WEE1, SIRPA, SOX4, UBE2C, MDK, KIF5C, PTBP1, GPM6A, DPYSL2, PTTG1, TPRG1L, KIAA0513, SCAMP5, RAPGEF4, NRIP3, MAP7, RAB11FIP1, BTG3, MELK, TSPAN6, PEA15, PPP3R1, PGM2L1, LAMC1, IER3, GABBR1, CD47, and ABCA1 genes may play important roles in the pathogenesis of AT/RT. qPCR experiments verified that the expressions of MAP7, CDK1, PPP3R1, PRKC1, CCND1 and HDAC1 genes were indeed altered in AT/RT tumor tissue. Interestingly, CCND1, which encodes a crucial regulator of the cell cycle , was upregulated in AT/RT. We hypothesize that miRNA-17-5p promotes tumorigenesis in AT/RT by promoting CCND1 expression and cell cycle entry and progression. In addition, we reported that MAP7 mRNA showed the greatest down-regulation in AT/RT among all identified mRNAs. Together, these studies point to a potential role of miR-17-5p in AT/RT tumorigenesis.
This study has several limitations Future studies are required to determine the effect of miRNA-17-5p in AT/RT cell lines. RNA-seq and brain imaging using large-scale sample sizes would fully represent AT/RT tumorigenesis. Additional studies on the mechanism related to miRNA-17-5p will provide a better understanding of AT/RT therapy.