title: Activities of multiple cancer-related pathways are associated with BRAF mutation and predict the resistance to BRAF/MEK inhibitors in melanoma cells.
abstract: Drug resistance is a major obstacle in the targeted therapy of melanoma using BRAF/MEK inhibitors. This study was to identify BRAF V600E-associated oncogenic pathways that predict resistance of BRAF-mutated melanoma to BRAF/MEK inhibitors. We took in silico approaches to analyze the activities of 24 cancer-related pathways in melanoma cells and identify those whose activation was associated with BRAF V600E and used the support vector machine (SVM) algorithm to predict the resistance of BRAF-mutated melanoma cells to BRAF/MEK inhibitors. We then experimentally confirmed the in silico findings. In a microarray gene expression dataset of 63 melanoma cell lines, we found that activation of multiple oncogenic pathways preferentially occurred in BRAF-mutated melanoma cells. This finding was reproduced in 5 additional independent melanoma datasets. Further analysis of 46 melanoma cell lines that harbored BRAF mutation showed that 7 pathways, including TNFα, EGFR, IFNα, hypoxia, IFNγ, STAT3, and MYC, were significantly differently expressed in AZD6244-resistant compared with responsive melanoma cells. A SVM classifier built on this 7-pathway activation pattern correctly predicted the response of 10 BRAF-mutated melanoma cell lines to the MEK inhibitor AZD6244 in our experiments. We experimentally showed that TNFα, EGFR, IFNα, and IFNγ pathway activities were also upregulated in melanoma cell A375 compared with its sub-line DRO, while DRO was much more sensitive to AZD6244 than A375. In conclusion, we have identified specific oncogenic pathways preferentially activated in BRAF-mutated melanoma cells and a pathway pattern that predicts resistance of BRAF-mutated melanoma to BRAF/MEK inhibitors, providing novel clinical implications for melanoma therapy.
authors.affiliation: Laboratory for Cellular and Molecular Thyroid Research; Division of Endocrinology and Metabolism; Johns Hopkins University School of Medicine; Baltimore, MD USA.
authors.forename: Dingxie
authors.initials: D
authors.lastname: Liu
authors.affiliation: Department of Electrical and Computer Engineering; Johns Hopkins University; Baltimore, MD USA.
authors.forename: Xuan
authors.initials: X
authors.lastname: Liu
authors.affiliation: Laboratory for Cellular and Molecular Thyroid Research; Division of Endocrinology and Metabolism; Johns Hopkins University School of Medicine; Baltimore, MD USA.
authors.forename: Mingzhao
authors.initials: M
authors.lastname: Xing
mesh_terms: D000970:Antineoplastic Agents / Q000494:pharmacology*; D001562:Benzimidazoles / Q000378:metabolism / Q000627:therapeutic use; D045744:Cell Line, Tumor / Q000187:drug effects; D016207:Cytokines / Q000378:metabolism; D019008:Drug Resistance, Neoplasm; D020869:Gene Expression Profiling; D006801:Humans; D008545:Melanoma / Q000188:drug therapy / Q000235:genetics / Q000378:metabolism*; D020928:Mitogen-Activated Protein Kinases / Q000037:antagonists & inhibitors / Q000378:metabolism*; D009154:Mutation; D051059:PTEN Phosphohydrolase / Q000235:genetics; D047428:Protein Kinase Inhibitors / Q000494:pharmacology*; D048493:Proto-Oncogene Proteins B-raf / Q000037:antagonists & inhibitors / Q000235:genetics / Q000378:metabolism*; D015398:Signal Transduction
chemical_list: C517975:AZD 6244; D000970:Antineoplastic Agents; D001562:Benzimidazoles; D016207:Cytokines; D047428:Protein Kinase Inhibitors; C482119:BRAF protein, human; D048493:Proto-Oncogene Proteins B-raf; D020928:Mitogen-Activated Protein Kinases; D051059:PTEN Phosphohydrolase
keywords: BRAF V600E inhibitor; BRAF mutation; MEK inhibitor; drug resistance; melanoma; oncogenic pathway