Page 22 - SDIR5 Abstract book 21 12 2021.

CANCER AND METABOLISM

Short talks

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

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Nikolina Piteša , Nenad Bartoniček , Matea Kurtović , Vesna Musani , Diana Trnski , Petar Ozretić , Maja
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Sabol
1 Laboratory for Hereditary Cancer, Department of Molecular Medicine, Ruđer Bošković Institute, Zagreb, Croatia
2 Genome Informatics, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW,
Australia

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.

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