engleski

Genes for competing endogenous RNAs as targets of transcription factors GLI in melanoma cell lines

Hedgehog-GLI (HH-GLI) signaling is a conserved signaling pathway reported to be aberrantly activated in various human cancers, including melanoma. Beside its canonical signaling, HH-GLI can also be activated noncanonically through interactions with other signaling pathways like MAPK. Both result in activation of GLI transcription factors. Our previous studies demonstrated that BRAF and NRAS mutated melanoma cell lines have different response following HH- GLI inhibition, which indicates that HH-GLI potentially has a different role in BRAF and NRAS mutated melanoma. To identify GLI transcriptional targets, we performed ChIP-Seq. Firstly, 14 collected melanoma cell lines were sequenced and divided into categories based on their BRAF and NRAS mutation background. Three cell lines with the strongest basal GLI protein expression were selected (A375 BRAFmut, CHL-1 wt and MEL224 NRASmut). Selected target genes were analyzed in silico and validated by qPCR. ChIP-seq analysis revealed 603 potential GLI targets of which 30% have GLI1, 66% GLI2 and 21% GLI3 binding sites. Only 3.8% were mutual for all three GLI proteins. Besides protein coding genes, 20 miRNAs and 29 lncRNAs were identified. miRNA analysis revealed that 50% of identified miRNAs regulate genes related to MAPK signaling. Validation included selected 23 protein coding genes, 9 miRNAs and 3 lncRNAs involved in regulation of MAPK signaling pathway. We validated 4 miRNAs and 2 lncRNAs and constructed a potential GLI-lncRNA-miRNA interactome which will further be examined. Future analysis can potentially bring new insights into miRNA-lncRNA regulatory networks involved in HH- GLI and MAPK interplay.

ChIP-Seq ; lncRNAs ; MAP3 Kinase ; melanoma ; miRNAs

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