Impact of BRAF kinase inhibitors on the miRNomes and transcriptomes of melanoma cells

Ines Kozar; Giulia Cesi; Christiane Margue; Demetra Philippidou; Stephanie Kreis

doi:10.1016/j.bbagen.2017.04.005

Impact of BRAF kinase inhibitors on the miRNomes and transcriptomes of melanoma cells

Biochim Biophys Acta Gen Subj. 2017 Nov;1861(11 Pt B):2980-2992. doi: 10.1016/j.bbagen.2017.04.005. Epub 2017 Apr 10.

Authors

Ines Kozar¹, Giulia Cesi², Christiane Margue³, Demetra Philippidou⁴, Stephanie Kreis⁵

Affiliations

¹ Life Sciences Research Unit, University of Luxembourg, 6, avenue du Swing, L-4367 Belvaux, Luxembourg. Electronic address: ines.kozar@uni.lu.
² Life Sciences Research Unit, University of Luxembourg, 6, avenue du Swing, L-4367 Belvaux, Luxembourg. Electronic address: giulia.cesi@uni.lu.
³ Life Sciences Research Unit, University of Luxembourg, 6, avenue du Swing, L-4367 Belvaux, Luxembourg. Electronic address: christiane.margue@uni.lu.
⁴ Life Sciences Research Unit, University of Luxembourg, 6, avenue du Swing, L-4367 Belvaux, Luxembourg. Electronic address: demetra.philippidou@uni.lu.
⁵ Life Sciences Research Unit, University of Luxembourg, 6, avenue du Swing, L-4367 Belvaux, Luxembourg. Electronic address: stephanie.kreis@uni.lu.

PMID: 28408301
DOI: 10.1016/j.bbagen.2017.04.005

Abstract

Background: Melanoma is an aggressive skin cancer with increasing incidence worldwide. The development of BRAF kinase inhibitors as targeted treatments for patients with BRAF-mutant tumours contributed profoundly to an improved overall survival of patients with metastatic melanoma. Despite these promising results, the emergence of rapid resistance to targeted therapy remains a serious clinical issue.

Methods: To investigate the impact of BRAF inhibitors on miRNomes and transcriptomes, we used in vitro melanoma models consisting of BRAF inhibitor-sensitive and -resistant cell lines generated in our laboratory. Subsequently, microarray analyses were performed followed by RT-qPCR validations.

Results: Regarding miRNome and transcriptome changes, the long-term effects of BRAF inhibition differed in a cell line-specific manner with the two different BRAF inhibitors inducing comparable responses in three melanoma cell lines. Despite this heterogeneity, several miRNAs (e.g. miR-92a-1-5p, miR-708-5p) and genes (e.g. DOK5, PCSK2) were distinctly differentially expressed in drug-resistant versus -sensitive cell lines. Analyses of coexpressed miRNAs, as well as inversely correlated miRNA-mRNA pairs, revealed a low MITF/AXL ratio in two drug-resistant cell lines that might be regulated by miRNAs.

Conclusion: Several genes and miRNAs were differentially regulated in the drug-resistant and -sensitive cell lines and might be considered as prognostic and/or diagnostic resistance biomarkers in melanoma drug resistance.

General significance: Thus far, only little information is available on the significance and role of miRNAs with respect to kinase inhibitor treatments and emergence of drug resistance. In this study, promising miRNAs and genes were identified and associated to BRAF inhibitor-mediated resistance in melanoma. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue.

Keywords: BRAF inhibitors; Drug resistance; Melanoma; Targeted therapy; miRNA.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Cell Line, Tumor
Drug Resistance, Neoplasm / genetics
Gene Expression Profiling
Gene Expression Regulation, Neoplastic / drug effects
Humans
Melanoma / drug therapy
Melanoma / genetics*
Melanoma / pathology
MicroRNAs / drug effects
MicroRNAs / genetics*
Microarray Analysis
Protein Kinase Inhibitors / pharmacology*
Protein Kinase Inhibitors / therapeutic use
Proto-Oncogene Proteins B-raf / antagonists & inhibitors*
Skin Neoplasms / drug therapy
Skin Neoplasms / genetics*
Skin Neoplasms / pathology
Transcriptome / drug effects*

Substances

MicroRNAs
Protein Kinase Inhibitors
Proto-Oncogene Proteins B-raf