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Liu D, Benzaquen J, Morris LGT, Ilié M, Hofman P. Mutations in KMT2C, BCOR and KDM5C Predict Response to Immune Checkpoint Blockade Therapy in Non-Small Cell Lung Cancer. Cancers (Basel) 2022; 14:cancers14112816. [PMID: 35681795 PMCID: PMC9179442 DOI: 10.3390/cancers14112816] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/24/2022] [Accepted: 06/01/2022] [Indexed: 12/22/2022] Open
Abstract
Simple Summary Efficient biomarkers are urgently needed to predict response to immune checkpoint blockade (ICB) therapy for non-small cell lung cancer (NSCLC), particularly NSCLC with low tumor mutational burden (TMB). Here, we show that mutations of three chromatin remodeling-related genes, including KMT2C, BCOR and KDM5C, are associated with the ICB response in NSCLC, including NSCLC with low TMB level. Furthermore, this association is further improved by a combined use of KMT2C/BCOR/KDM5C mutations with TMB or PD-L1 expression. These data suggest that KMT2C/BCOR/KDM5C mutation status has the potential to serve as a predictive biomarker for ICB therapy in NSCLC. Abstract Efficient predictive biomarkers are urgently needed to identify non-small cell lung cancer (NSCLC) patients who could benefit from immune checkpoint blockade (ICB) therapy. Since chromatin remodeling is required for DNA repair process, we asked whether mutations in chromatin remodeling genes could increase tumor mutational burden (TMB) and predict response to ICB therapy in NSCLC. Analysis of seven ICB-treated NSCLC cohorts revealed that mutations of three chromatin remodeling-related genes, including KMT2C, BCOR and KDM5C, were significantly associated with ICB response, and combined mutations of these three genes further enhance this association. NSCLC patients with KMT2C/BCOR/KDM5C mutations had comparable clinical outcomes to TMB-high patients in terms of objective response rate, durable clinical benefit and overall survival. Although KMT2C/BCOR/KDM5C mutations were positively correlated with TMB levels in NSCLC, the association of this mutation with better ICB response was independent of tumor TMB and programmed death-ligand 1 (PD-L1) level, and combination of KMT2C/BCOR/KDM5C mutations with TMB or PD-L1 further improve the prediction of ICB response in NSCLC patients. Cancer Genome Atlas (TCGA) pan-cancer analysis suggested that the association of KMT2C/BCOR/KDM5C mutations with ICB response observed here might not result from DNA repair defects. In conclusion, our data indicate that KMT2C/BCOR/KDM5C mutation has the potential to serve as a predictive biomarker, alone or combined with PD-L1 expression or TMB, for ICB therapy in NSCLC.
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Affiliation(s)
- Dingxie Liu
- Bluewater Biotech LLC, New Providence, NJ 07974, USA
- Correspondence: (D.L.); (P.H.)
| | - Jonathan Benzaquen
- Department of Pneumology, Pasteur Hospital, FHU OncoAge, 06000 Nice, France; (J.B.); (M.I.)
| | - Luc G. T. Morris
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA;
| | - Marius Ilié
- Department of Pneumology, Pasteur Hospital, FHU OncoAge, 06000 Nice, France; (J.B.); (M.I.)
| | - Paul Hofman
- Laboratory of Clinical and Experimental Pathology, CHU Nice, FHU OncoAge, University Côte d’Azur, 06100 Nice, France
- Team 4, IRCAN, UMR 7284/U10181, FHU OncoAge, University Côte d’Azur, 06107 Nice, France
- Hospital-Integrated Biobank (BB-0033-00025), CHU of Nice, FHU OncoAge, University Côte d’Azur, 06100 Nice, France
- Correspondence: (D.L.); (P.H.)
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Wang Y, Wan S, Li Z, Fu Y, Wang G, Zhang J, Wu X. Design, synthesis, biological evaluation and molecular modeling of novel 1H-pyrazolo[3,4-d]pyrimidine derivatives as BRAFV600E and VEGFR-2 dual inhibitors. Eur J Med Chem 2018; 155:210-228. [DOI: 10.1016/j.ejmech.2018.05.054] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 05/30/2018] [Accepted: 05/30/2018] [Indexed: 10/14/2022]
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3
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Li K, Zeng L, Wei H, Hu J, Jiao L, Zhang J, Xiong Y. Identification of gene-specific DNA methylation signature for Colorectal Cancer. Cancer Genet 2018; 228-229:5-11. [PMID: 30553473 DOI: 10.1016/j.cancergen.2018.05.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 04/22/2018] [Accepted: 05/08/2018] [Indexed: 12/28/2022]
Abstract
BACKGROUND Colorectal Cancer (CC), a common disease causing approximately million deaths annually, has been the third most frequent type of malignancy. We aimed to identify gene-specific DNA methylation signature to function as prognostic and predictive markers for CC patient survival. METHODS Expression profiles of gene-specific DNA methylation and the corresponding clinical information of 201 CC patients were downloaded from The Cancer Genome Atlas (TCGA) dataset and differentially expressed gene-specific DNA methylation was identified after tumor subtype classification. A risk score model was further built by analyzing the expression data of these gene-specific DNA methylations from the training dataset of CC patients. RESULTS Totally, 214 gene-specific DNA methylations were found to be expressed significantly between different subtypes of CC, including 150 up-regulated and 64 down-regulated ones. Up-regulated gene-specific DNA methylation accounted for 70.1% and the down-regulated gene-specific DNA methylation accounted for 29.9%. Hereinto, six gene-specific DNA methylations were obtained, including methy_vimentin and methy_ TFPI2, which were found significantly correlated with overall survival status of patients with CC. CONCLUSIONS With the six gene-specific DNA methylation signatures, patients in the training set were divided into low-risk and high- risk groups. What's more, gene-specific DNA methylation target genes were highly associated with protein phosphorylation, which indicated that further research on phosphorylation of target gene-coding protein might provide new sight on the treatment of CC.
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Affiliation(s)
- Kaixue Li
- Department of Gastroenterology, The Second People's Hospital of Shenzhen, the First Affiliated Hospital of Shenzhen University, Shenzhen 518035, China
| | - Li Zeng
- Department of Gastroenterology, The Second People's Hospital of Shenzhen, the First Affiliated Hospital of Shenzhen University, Shenzhen 518035, China
| | - Hong Wei
- Department of Gastroenterology, The Second People's Hospital of Shenzhen, the First Affiliated Hospital of Shenzhen University, Shenzhen 518035, China
| | - Jingjing Hu
- Department of Gastroenterology, The Second People's Hospital of Shenzhen, the First Affiliated Hospital of Shenzhen University, Shenzhen 518035, China
| | - Lu Jiao
- Department of Gastroenterology, The Second People's Hospital of Shenzhen, the First Affiliated Hospital of Shenzhen University, Shenzhen 518035, China
| | - Juan Zhang
- Department of Gastroenterology, The Second People's Hospital of Shenzhen, the First Affiliated Hospital of Shenzhen University, Shenzhen 518035, China
| | - Ying Xiong
- Department of Gastroenterology, The Second People's Hospital of Shenzhen, the First Affiliated Hospital of Shenzhen University, Shenzhen 518035, China.
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4
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REC8 is a novel tumor suppressor gene epigenetically robustly targeted by the PI3K pathway in thyroid cancer. Oncotarget 2016; 6:39211-24. [PMID: 26472282 PMCID: PMC4770767 DOI: 10.18632/oncotarget.5391] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 10/02/2015] [Indexed: 11/25/2022] Open
Abstract
The role of the PI3K pathway in human cancer has been well established, but much of its molecular mechanism, particularly the epigenetic aspect, remains to be defined. We hypothesized that aberrant methylation and hence altered expression of certain unknown important genes induced by the genetically activated PI3K pathway signaling is a major epigenetic mechanism in human tumorigenesis. Through a genome-wide search for such genes that were epigenetically controlled by the PI3K pathway in thyroid cancer cells, we found a wide range of genes with broad functions epigenetically targeted by the PI3K pathway. The most prominent among these genes was REC8, classically known as a meiotic-specific gene, which we found to be robustly down-regulated by the PI3K pathway through hypermethylation. REC8 hypermethylation was strongly associated with genetic alterations and activities of the PI3K pathway in thyroid cancer cell lines, thyroid cancer tumors, and some other human cancers; it was also associated with poor clinicopathological outcomes of thyroid cancer, including advanced disease stages and patient mortality. Demethylating the hypermethylated REC8 gene restored its expression in thyroid cancer cells in which the PI3K pathway was genetically over-activated and induced expression of REC8 protein inhibited the proliferation and colony formation of these cells. These findings are consistent with REC8 being a novel major bona fide tumor suppressor gene and a robust epigenetic target of the PI3K pathway. Aberrant inactivation of REC8 through hypermethylation by the PI3K pathway may represent an important mechanism mediating the oncogenic functions of the PI3K pathway.
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5
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Liu D. Gene signatures of estrogen and progesterone receptor pathways predict the prognosis of colorectal cancer. FEBS J 2016; 283:3115-33. [PMID: 27376509 DOI: 10.1111/febs.13798] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 06/21/2016] [Accepted: 06/30/2016] [Indexed: 12/19/2022]
Abstract
The associations of estrogen receptor (ER) and progesterone receptor (PR) pathways with the prognosis of colorectal cancer (CRC) are still controversial. The aim of this study was to readdress these issues by introducing a gene signature-based approach to semiquantitate pathway activity. In this approach, the ER and PR pathway activities in CRC were computed based on the expression profiles of the signature genes of ER and PR pathways, respectively. The results showed that the ER pathway activity was progressively significantly decreased from normal colorectal mucosa, colorectal adenoma to CRC. ER pathway signaling was a favorable factor for the presence of microsatellite stability (MSS) in CRC in seven cohorts tested, while was an unfavorable factor for cancer recurrence in all four CRC cohorts tested (n = 1122; overall HR: 0.311, 95% CI: 0.199-0.488, P < 0.001). Subset stratification in stage II patients showed that ER pathway remained significantly inversely associated with recurrence. PR pathway was also suppressed in colorectal tumors and inversely associated with recurrence of CRC, but to a much lesser extent than ER pathway. Moreover, the inverse association of PR pathway with cancer recurrence was more likely observed in CRC with high ER pathway activity, suggesting the interactions between the two pathways. PR pathway was not associated with MSS in CRC, but it was more significant than ER pathway associated with advance cancer stages and cancer response to adjuvant chemotherapy. These results suggested the potential application of the gene signatures of ER and PR pathways, especially the former, as novel markers for prognosis and management of CRC.
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Affiliation(s)
- Dingxie Liu
- Division of Endocrinology, Diabetes & Metabolism, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Bluewater Biotech LLC, Berkeley Heights, NJ, USA
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6
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Jiang W, Jia P, Hutchinson KE, Johnson DB, Sosman JA, Zhao Z. Clinically relevant genes and regulatory pathways associated with NRASQ61 mutations in melanoma through an integrative genomics approach. Oncotarget 2016; 6:2496-508. [PMID: 25537510 PMCID: PMC4385866 DOI: 10.18632/oncotarget.2954] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Accepted: 12/09/2015] [Indexed: 12/25/2022] Open
Abstract
Therapies such as BRAF inhibitors have become standard treatment for melanoma patients whose tumors harbor activating BRAFV600 mutations. However, analogous therapies for inhibiting NRAS mutant signaling have not yet been well established. In this study, we performed an integrative analysis of DNA methylation, gene expression, and microRNA expression data to identify potential regulatory pathways associated with the most common driver mutations in NRAS (Q61K/L/R) through comparison of NRASQ61-mutated melanomas with pan-negative melanomas. Surprisingly, we found dominant hypomethylation (98.03%) in NRASQ61-mutated melanomas. We identified 1,150 and 49 differentially expressed genes and microRNAs, respectively. Integrated functional analyses of alterations in all three data types revealed important signaling pathways associated with NRASQ61 mutations, such as the MAPK pathway, as well as other novel cellular processes, such as axon guidance. Further analysis of the relationship between DNA methylation and gene expression changes revealed 9 hypermethylated and down-regulated genes and 112 hypomethylated and up-regulated genes in NRASQ61 melanomas. Finally, we identified 52 downstream regulatory cascades of three hypomethylated and up-regulated genes (PDGFD, ZEB1, and THRB). Collectively, our observation of predominant gene hypomethylation in NRASQ61 melanomas and the identification of NRASQ61-linked pathways will be useful for the development of targeted therapies against melanomas harboring NRASQ61 mutations.
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Affiliation(s)
- Wei Jiang
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Peilin Jia
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.,Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Katherine E Hutchinson
- Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Douglas B Johnson
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.,Department of Medicine/Division of Hematology-Oncology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Jeffrey A Sosman
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.,Department of Medicine/Division of Hematology-Oncology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Zhongming Zhao
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.,Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.,Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.,Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
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7
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Thomas NE, Slater NA, Edmiston SN, Zhou X, Kuan PF, Groben PA, Carson CC, Hao H, Parrish E, Moschos SJ, Berwick M, Ollila DW, Conway K. DNA methylation profiles in primary cutaneous melanomas are associated with clinically significant pathologic features. Pigment Cell Melanoma Res 2014; 27:1097-105. [PMID: 24986547 PMCID: PMC4211983 DOI: 10.1111/pcmr.12289] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 06/20/2014] [Indexed: 12/22/2022]
Abstract
DNA methylation studies have elucidated a methylation signature distinguishing primary melanomas from benign nevi and provided new insights about genes that may be important in melanoma development. However, it is unclear whether methylation differences among primary melanomas are related to tumor pathologic features with known clinical significance. We utilized the Illumina GoldenGate Cancer Panel array to investigate the methylation profiles of 47 primary cutaneous melanomas. Arraywide methylation patterns revealed a positive association of methylation with Breslow thickness and mutated BRAF, a negative association with mitotic rate, and a weak association with ulceration. Hierarchical clustering on CpG sites exhibiting the most variable methylation (n = 235) divided the melanoma samples into three clusters, including a highly methylated cluster that was positively associated with Breslow thickness and an intermediately methylated cluster associated with Breslow thickness and mitotic rate. Our findings provide support for the existence of methylation-defined subsets in melanomas with increased methylation associated with Breslow thickness.
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Affiliation(s)
- Nancy E. Thomas
- Department of Dermatology, University of North Carolina, Chapel
Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North
Carolina, Chapel Hill, NC, USA
| | - Nathaniel A. Slater
- Department of Dermatology, University of North Carolina, Chapel
Hill, NC, USA
| | - Sharon N. Edmiston
- Lineberger Comprehensive Cancer Center, University of North
Carolina, Chapel Hill, NC, USA
| | - Xin Zhou
- Department of Biostatistics, University of North Carolina, Chapel
Hill, NC, USA
| | - Pei-Fen Kuan
- Lineberger Comprehensive Cancer Center, University of North
Carolina, Chapel Hill, NC, USA
- Department of Biostatistics, University of North Carolina, Chapel
Hill, NC, USA
| | - Pamela A. Groben
- Department of Pathology and Laboratory Medicine, University of
North Carolina, Chapel Hill, NC, USA
| | - Craig C. Carson
- Department of Dermatology, University of North Carolina, Chapel
Hill, NC, USA
| | - Honglin Hao
- Department of Dermatology, University of North Carolina, Chapel
Hill, NC, USA
| | - Eloise Parrish
- Lineberger Comprehensive Cancer Center, University of North
Carolina, Chapel Hill, NC, USA
| | - Stergios J. Moschos
- Lineberger Comprehensive Cancer Center, University of North
Carolina, Chapel Hill, NC, USA
- Department of Medicine, University of North Carolina, Chapel
Hill, NC, USA
| | - Marianne Berwick
- Department of Medicine, Division of Epidemiology, University of
New Mexico, Albuquerque, NM, USA
| | - David W. Ollila
- Lineberger Comprehensive Cancer Center, University of North
Carolina, Chapel Hill, NC, USA
- Department of Surgery, University of North Carolina, Chapel Hill,
NC, USA
| | - Kathleen Conway
- Lineberger Comprehensive Cancer Center, University of North
Carolina, Chapel Hill, NC, USA
- Department of Epidemiology, University of North Carolina, Chapel
Hill, NC, USA
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Ecsedi S, Hernandez-Vargas H, Lima SC, Vizkeleti L, Toth R, Lazar V, Koroknai V, Kiss T, Emri G, Herceg Z, Adany R, Balazs M. DNA methylation characteristics of primary melanomas with distinct biological behaviour. PLoS One 2014; 9:e96612. [PMID: 24832207 PMCID: PMC4022506 DOI: 10.1371/journal.pone.0096612] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 04/09/2014] [Indexed: 12/29/2022] Open
Abstract
In melanoma, the presence of promoter related hypermethylation has previously been reported, however, no methylation-based distinction has been drawn among the diverse melanoma subtypes. Here, we investigated DNA methylation changes associated with melanoma progression and links between methylation patterns and other types of somatic alterations, including the most frequent mutations and DNA copy number changes. Our results revealed that the methylome, presenting in early stage samples and associated with the BRAF(V600E) mutation, gradually decreased in the medium and late stages of the disease. An inverse relationship among the other predefined groups and promoter methylation was also revealed except for histologic subtype, whereas the more aggressive, nodular subtype melanomas exhibited hypermethylation as well. The Breslow thickness, which is a continuous variable, allowed for the most precise insight into how promoter methylation decreases from stage to stage. Integrating our methylation results with a high-throughput copy number alteration dataset, local correlations were detected in the MYB and EYA4 genes. With regard to the effects of DNA hypermethylation on melanoma patients' survival, correcting for clinical cofounders, only the KIT gene was associated with a lower overall survival rate. In this study, we demonstrate the strong influence of promoter localized DNA methylation changes on melanoma initiation and show how hypermethylation decreases in melanomas associated with less favourable clinical outcomes. Furthermore, we establish the methylation pattern as part of an integrated apparatus of somatic DNA alterations.
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Affiliation(s)
- Szilvia Ecsedi
- Department of Preventive Medicine, Faculty of Public Health, University of Debrecen, Debrecen, Hungary
- MTA-DE- Public Health Research Group, University of Debrecen, Debrecen, Hungary
| | - Hector Hernandez-Vargas
- International Agency for Research on Cancer, Section of Mechanisms of Carcinogenesis, Epigenetics Group, Lyon, France
| | - Sheila C. Lima
- International Agency for Research on Cancer, Section of Mechanisms of Carcinogenesis, Epigenetics Group, Lyon, France
| | - Laura Vizkeleti
- Department of Preventive Medicine, Faculty of Public Health, University of Debrecen, Debrecen, Hungary
- MTA-DE- Public Health Research Group, University of Debrecen, Debrecen, Hungary
| | - Reka Toth
- Department of Preventive Medicine, Faculty of Public Health, University of Debrecen, Debrecen, Hungary
| | - Viktoria Lazar
- Department of Preventive Medicine, Faculty of Public Health, University of Debrecen, Debrecen, Hungary
| | - Viktoria Koroknai
- Department of Preventive Medicine, Faculty of Public Health, University of Debrecen, Debrecen, Hungary
| | - Timea Kiss
- Department of Preventive Medicine, Faculty of Public Health, University of Debrecen, Debrecen, Hungary
| | - Gabriella Emri
- Department of Dermatology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Zdenko Herceg
- International Agency for Research on Cancer, Section of Mechanisms of Carcinogenesis, Epigenetics Group, Lyon, France
| | - Roza Adany
- Department of Preventive Medicine, Faculty of Public Health, University of Debrecen, Debrecen, Hungary
- MTA-DE- Public Health Research Group, University of Debrecen, Debrecen, Hungary
| | - Margit Balazs
- Department of Preventive Medicine, Faculty of Public Health, University of Debrecen, Debrecen, Hungary
- MTA-DE- Public Health Research Group, University of Debrecen, Debrecen, Hungary
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Liu D, Liu X, Xing M. Activities of multiple cancer-related pathways are associated with BRAF mutation and predict the resistance to BRAF/MEK inhibitors in melanoma cells. Cell Cycle 2013; 13:208-19. [PMID: 24200969 DOI: 10.4161/cc.26971] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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.
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Affiliation(s)
- Dingxie Liu
- Laboratory for Cellular and Molecular Thyroid Research; Division of Endocrinology and Metabolism; Johns Hopkins University School of Medicine; Baltimore, MD USA
| | - Xuan Liu
- Department of Electrical and Computer Engineering; Johns Hopkins University; Baltimore, MD USA
| | - Mingzhao Xing
- Laboratory for Cellular and Molecular Thyroid Research; Division of Endocrinology and Metabolism; Johns Hopkins University School of Medicine; Baltimore, MD USA
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