Naslov
RNA sequencing reveals unique and overlapping transcriptional targets of GLI1, GLI2 and GLI3 in melanoma cell lines

Autori
Kurtović, Matea ; Bartoniček, Nenad ; Piteša, Nikolina ; Ozretić, Petar ; Musani, Vesna ; Petrić, Tina ; Čonkaš, Josipa ; Sabol, Maja

Vrsta, podvrsta i kategorija rada
Sažeci sa skupova, ostalo, znanstveni

Izvornik
EACR 2022 Congress Abstracts / - , 2022

Skup
28th Congress of the European Association for Cancer Research - "Innovative Cancer Science: Translating Biology to Medicine"

Mjesto i datum
Sevilla, Španjolska, 20.06.2022. - 23.06.2022

Vrsta sudjelovanja
Poster

Vrsta recenzije
Nije recenziran

Ključne riječi
HH-GLI, RNA-seq, melanoma

Sažetak
Introduction Melanoma is known as the most aggressive and deadliest of all skin cancers. Understanding the interplay of different molecular pathways leading to development and progression of melanoma is important for developing new therapeutic strategies. One of the recent approaches in cancer therapy is targeting the Hedgehog-GLI (HH-GLI) signaling pathway. This pathway has an important role during cellular proliferation, differentiation and stem cell maintenance. The HH-GLI signaling pathway has been associated with skin tumors, but its mechanism differs between melanoma and non-melanoma tumors. In order to elucidate the role of GLI proteins in melanoma, we performed RNA sequencing on human melanoma cell lines with overexpressed GLI1, GLI2 or GLI3. Materials and methods Melanoma cell lines A375 (BRAF V600E), MEL-224 (NRASQ61R) and CHL-1 (no mutation in BRAF or NRAS) were transfected with GLI1, GLI2 or GLI3 plasmids. Non-transfected cell lines were used as controls. Total RNA was isolated 48 hours post transfection and sample quality was checked on Agilent 2100 Bioanalyser. RNA sequencing was performed on Ilumina Novaseq 6000 instrument. The quality of sequencing reads was checked with FastQC tool and reads were mapped to the human reference genome (hg38) with STAR. Mapped reads were quantified with RSEM. Differential gene expression was computed using edgeR package in R software. In order to select GLI target genes for further validation, a list of differentially expressed genes (DEGs) was filtered according to FDR values and logFc. After performing KEGG pathway analysis, genes were selected for further investigation according to their role in diseases, role in different signaling pathways and their importance in melanoma. 12 genes were chosen for validation by qPCR. The validation was performed on three cell lines used for RNA sequencing and on 11 additional melanoma cell lines. Results and discussion After DEGs according to FDR < 0, 01 and logFC >1, we have found 807 DEGs as targets of GLI1, 941 DEGs as targets of GLI2 and 58 DEGs as targets of GLI3. Our results confirmed GLI1 and PTCH1 as known targets of HH-GLI pathway. None of the 12 chosen targets are yet reported as GLI targets, and only half of them are recently reported to have a role in melanoma pathogenesis. Also, we found that majority of the genes are overlapping targets of GLI1 and GLI2 which is to be expected, as GLI1 is a known transcriptional target of GLI2. GLI3 regulates a small number of separate gene targets compared to GLI1 and GLI2. Conclusion In this study we have identified unique and overlapping targets of GLI1, GLI2 and GLI3 in melanoma cell lines and confirmed 12 of them by qPCR on an expanded set of melanoma cell lines, suggesting these genes are novel targets of HH-GLI signaling in melanoma.

Izvorni jezik
Engleski

Znanstvena područja
Biologija, Biotehnologija, Biotehnologija u biomedicini (prirodno područje, biomedicina i zdravstvo, biotehničko područje)

POVEZANOST RADA