1
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Zhao H, Baudis M. labelSeg: segment annotation for tumor copy number alteration profiles. Brief Bioinform 2024; 25:bbad541. [PMID: 38300514 PMCID: PMC10833088 DOI: 10.1093/bib/bbad541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/09/2023] [Accepted: 12/28/2024] [Indexed: 02/02/2024] Open
Abstract
Somatic copy number alterations (SCNAs) are a predominant type of oncogenomic alterations that affect a large proportion of the genome in the majority of cancer samples. Current technologies allow high-throughput measurement of such copy number aberrations, generating results consisting of frequently large sets of SCNA segments. However, the automated annotation and integration of such data are particularly challenging because the measured signals reflect biased, relative copy number ratios. In this study, we introduce labelSeg, an algorithm designed for rapid and accurate annotation of CNA segments, with the aim of enhancing the interpretation of tumor SCNA profiles. Leveraging density-based clustering and exploiting the length-amplitude relationships of SCNA, our algorithm proficiently identifies distinct relative copy number states from individual segment profiles. Its compatibility with most CNA measurement platforms makes it suitable for large-scale integrative data analysis. We confirmed its performance on both simulated and sample-derived data from The Cancer Genome Atlas reference dataset, and we demonstrated its utility in integrating heterogeneous segment profiles from different data sources and measurement platforms. Our comparative and integrative analysis revealed common SCNA patterns in cancer and protein-coding genes with a strong correlation between SCNA and messenger RNA expression, promoting the investigation into the role of SCNA in cancer development.
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Affiliation(s)
- Hangjia Zhao
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
- Computational Oncogenomics Group, Swiss Institute of Bioinformatics, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Michael Baudis
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
- Computational Oncogenomics Group, Swiss Institute of Bioinformatics, Winterthurerstrasse 190, 8057, Zurich, Switzerland
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2
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Teo YX, Haw WY, Vallejo A, McGuire C, Woo J, Friedmann PS, Polak ME, Ardern-Jones MR. Potential Biomarker Identification by RNA-seq analysis in Antibiotic-related Drug Reaction with Eosinophilia and Systemic Symptoms (DRESS): a Pilot Study. Toxicol Sci 2022; 189:20-31. [PMID: 35703984 PMCID: PMC9412178 DOI: 10.1093/toxsci/kfac062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
One of the most severe forms of cutaneous adverse drug reactions is 'drug reaction with eosinophilia and systemic symptoms' (DRESS), hence subsequent avoidance of the causal drug is imperative. However, attribution of drug culpability in DRESS is challenging and standard skin allergy tests are not recommended due to patient safety reasons. Whilst incidence of DRESS is relatively low, between 1:1000 to 1:10,000 drug exposures, antibiotics are a commoner cause of DRESS and absence of confirmatory diagnostic test can result in unnecessary avoidance of efficacious treatment. We therefore sought to identify potential biomarkers for development of a diagnostic test in antibiotic-associated DRESS. Peripheral blood mononuclear cells (PBMCs) from a 'discovery' cohort (n = 5) challenged to causative antibiotic or control were analysed for transcriptomic profile. A panel of genes was then tested in a validation cohort (n = 6) and compared to tolerant controls and other inflammatory conditions which can clinically mimic DRESS. A scoring system to identify presence of drug hypersensitivity was developed based on gene expression alterations of this panel. The DRESS transcriptomic panel identified antibiotic-DRESS cases in a validation cohort but was not altered in other inflammatory conditions. Machine learning or differential expression selection of a biomarker panel consisting of six genes (STAC, GPR183, CD40, CISH, CD4, and CCL8) showed high sensitivity and specificity (100% and 85.7-100% respectively) for identification of the culprit drug in these cohorts of antibiotic-associated DRESS. Further work is required to determine whether the same panel can be repeated for larger cohorts, different medications, and other T cell mediated drug hypersensitivity reactions.
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Affiliation(s)
- Ying Xin Teo
- Clinical Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, United Kingdom.,Department of Dermatology, Southampton General Hospital, University Hospitals Southampton NHS Foundation Trust
| | - Wei Yann Haw
- Clinical Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, United Kingdom
| | - Andreas Vallejo
- Clinical Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, United Kingdom
| | - Carolann McGuire
- Clinical Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, United Kingdom
| | - Jeongmin Woo
- Clinical Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, United Kingdom
| | - Peter Simon Friedmann
- Clinical Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, United Kingdom
| | - Marta Ewa Polak
- Clinical Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, United Kingdom
| | - Michael Roger Ardern-Jones
- Clinical Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, United Kingdom.,Department of Dermatology, Southampton General Hospital, University Hospitals Southampton NHS Foundation Trust
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3
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Zou S, Zhang Y, Zhang L, Wang D, Xu S. Construction and validation of a prognostic risk model of angiogenesis factors in skin cutaneous melanoma. Aging (Albany NY) 2022; 14:1529-1548. [PMID: 35157610 PMCID: PMC8876895 DOI: 10.18632/aging.203895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 02/08/2022] [Indexed: 12/24/2022]
Abstract
Melanoma can secrete tumor angiogenesis factors, which is the essential factor for tumor growth and metastasis. However, there are few reports on the relationship between angiogenesis factors and prognosis risk in melanoma. This study aimed to develop a prognostic risk model of angiogenesis for melanoma. Forty-nine differentially expressed angiogenesis were identified from the TCGA database, which were mainly involved in PI3K/Akt pathway, focal adhesion, and MAPK signaling pathway. We then establish an eleven-gene signature. The model indicated a strong prognostic capability in both the discovery cohort and the validation cohort. Patients of smaller height (<170 cm) and lower weight (<80 kg) and those with advanced-stage and ulcerated melanoma had higher risk scores. The risk score was positively correlated with mutation load, homologous recombination defect, neoantigen load and chromosome instability. In addition, the high-risk group had a higher degree of immune cell infiltration, better response to immunotherapy and lower immune score. Therefore, these results indicate that the risk model is an effective method to predict the prognosis of melanoma.
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Affiliation(s)
- Songyun Zou
- Department of Burn and Plastic Surgery, Shenzhen Longhua District Central Hospital, Shenzhen, Guangdong, China
| | - Yonggang Zhang
- Department of Clinical Laboratory, Shenzhen Longhua District Central Hospital, Shenzhen, Guangdong, China
| | - Limei Zhang
- Oncology Department, Shenzhen Longhua District Central Hospital, Shenzhen, Guangdong, China
| | - Dengchuan Wang
- Office of Medical Ethics, Shenzhen Longhua District Central Hospital, Shenzhen, Guangdong, China
| | - Shi Xu
- Department of Burn and Plastic Surgery, Shenzhen Longhua District Central Hospital, Shenzhen, Guangdong, China
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4
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Zhang J, Chen Y, Yan L, Zhang X, Zheng X, Qi J, Yang F, Li J. EphA3 deficiency in hypothalamus promotes high fat diet-induced obesity in mice. J Biomed Res 2022; 37:179-193. [PMID: 37013864 DOI: 10.7555/jbr.36.20220168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Erythropoietin-producing hepatocellular carcinoma A3 (EphA3) is a member of the largest subfamily of tyrosine kinase receptors-Eph receptors. Previous studies have shown that EphA3 is associated with tissue development. Recently, we have found that the expression of EphA3 is elevated in the hypothalamus of mice with diet-induced obesity (DIO). However, the role of EphA3 in hypothalamic-controlled energy metabolism remains unclear. In the current study, we demonstrated that the deletion of EphA3 in the hypothalamus by CRISPR/Cas9-mediated gene editing promotes obesity in male mice with high-fat diet feeding rather than those with normal chow diet feeding. Moreover, the deletion of hypothalamic EphA3 promotes high-fat DIO by increasing food intake and reducing energy expenditure. Knockdown of EphA3 leads to smaller intracellular vesicles in GT1-7 cells. The current study reveals that hypothalamic EphA3 plays important roles in promoting DIO.
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Affiliation(s)
- Jubiao Zhang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- The Affiliated Eye Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Yang Chen
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- The Affiliated Eye Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Lihong Yan
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- The Affiliated Eye Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Xin Zhang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- The Affiliated Eye Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Xiaoyan Zheng
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Junxia Qi
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Fen Yang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Juxue Li
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- The Affiliated Eye Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
- The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210011, China
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5
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Chatterjee D, Chowdhury UF, Shohan MUS, Mohasin M, Kabir Y. In-silico predictions of deleterious SNPs in human ephrin type-A receptor 3 (EPHA3) gene. INFORMATICS IN MEDICINE UNLOCKED 2021. [DOI: 10.1016/j.imu.2021.100728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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6
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Shen Y, Chu Q, Yin X, He Y, Bai P, Wang Y, Fang W, Timko MP, Fan L, Jiang W. TOD-CUP: a gene expression rank-based majority vote algorithm for tissue origin diagnosis of cancers of unknown primary. Brief Bioinform 2020; 22:2106-2118. [PMID: 32266390 DOI: 10.1093/bib/bbaa031] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 01/19/2020] [Accepted: 02/19/2020] [Indexed: 12/14/2022] Open
Abstract
Gene expression profiling holds great potential as a new approach to histological diagnosis and precision medicine of cancers of unknown primary (CUP). Batch effects and different data types greatly decrease the predictive performance of biomarker-based algorithms, and few methods have been widely applied to identify tissue origin of CUP up to now. To address this problem and assist in more precise diagnosis, we have developed a gene expression rank-based majority vote algorithm for tissue origin diagnosis of CUP (TOD-CUP) of most common cancer types. Based on massive tissue-specific RNA-seq data sets (10 553) found in The Cancer Genome Atlas (TCGA), 538 feature genes (biomarkers) were selected based on their gene expression ranks and used to predict tissue types. The top scoring pairs (TSPs) classifier of the tumor type was optimized by the TCGA training samples. To test the prediction accuracy of our TOD-CUP algorithm, we analyzed (1) two microarray data sets (1029 Agilent and 2277 Affymetrix/Illumina chips) and found 91% and 94% prediction accuracy, respectively, (2) RNA-seq data from five cancer types derived from 141 public metastatic cancer tumor samples and achieved 94% accuracy and (3) a total of 25 clinical cancer samples (including 14 metastatic cancer samples) were able to classify 24/25 samples correctly (96.0% accuracy). Taken together, the TOD-CUP algorithm provides a powerful and robust means to accurately identify the tissue origin of 24 cancer types across different data platforms. To make the TOD-CUP algorithm easily accessible for clinical application, we established a Web-based server for tumor tissue origin diagnosis (http://ibi. zju.edu.cn/todcup/).
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Affiliation(s)
- Yifei Shen
- Department of Medical Oncology, First Affiliated Hospital, Zhejiang University and the Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, USA
| | - Qinjie Chu
- Institute of Bioinformatics, Zhejiang University, China
| | - Xinxin Yin
- Institute of Bioinformatics, Zhejiang University, China
| | - Yinjun He
- College of Medicine, Zhejiang University, China
| | - Panpan Bai
- Institute of Bioinformatics, Zhejiang University, China
| | - Yunfei Wang
- Zhejiang Sheng Ting Biotechnology Co., China
| | - Weijia Fang
- Department of Medical Oncology, First Affiliated Hospital, Zhejiang University, China
| | - Michael P Timko
- Department of Biology & Public Health Sciences, University of Virginia, USA
| | - Longjiang Fan
- Department of Medical Oncology, First Affiliated Hospital, Zhejiang University, China
| | - Weiqin Jiang
- Department of Medical Oncology, First Affiliated Hospital, Zhejiang University, China
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7
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Neubert NJ, Schmittnaegel M, Bordry N, Nassiri S, Wald N, Martignier C, Tillé L, Homicsko K, Damsky W, Maby-El Hajjami H, Klaman I, Danenberg E, Ioannidou K, Kandalaft L, Coukos G, Hoves S, Ries CH, Fuertes Marraco SA, Foukas PG, De Palma M, Speiser DE. T cell-induced CSF1 promotes melanoma resistance to PD1 blockade. Sci Transl Med 2019; 10:10/436/eaan3311. [PMID: 29643229 DOI: 10.1126/scitranslmed.aan3311] [Citation(s) in RCA: 209] [Impact Index Per Article: 41.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 12/15/2017] [Accepted: 02/21/2018] [Indexed: 12/12/2022]
Abstract
Colony-stimulating factor 1 (CSF1) is a key regulator of monocyte/macrophage differentiation that sustains the protumorigenic functions of tumor-associated macrophages (TAMs). We show that CSF1 is expressed in human melanoma, and patients with metastatic melanoma have increased CSF1 in blood compared to healthy subjects. In tumors, CSF1 expression correlated with the abundance of CD8+ T cells and CD163+ TAMs. Human melanoma cell lines consistently produced CSF1 after exposure to melanoma-specific CD8+ T cells or T cell-derived cytokines in vitro, reflecting a broadly conserved mechanism of CSF1 induction by activated CD8+ T cells. Mining of publicly available transcriptomic data sets suggested co-enrichment of CD8+ T cells with CSF1 or various TAM-specific markers in human melanoma, which was associated with nonresponsiveness to programmed cell death protein 1 (PD1) checkpoint blockade in a smaller patient cohort. Combination of anti-PD1 and anti-CSF1 receptor (CSF1R) antibodies induced the regression of BRAFV600E -driven, transplant mouse melanomas, a result that was dependent on the effective elimination of TAMs. Collectively, these data implicate CSF1 induction as a CD8+ T cell-dependent adaptive resistance mechanism and show that simultaneous CSF1R targeting may be beneficial in melanomas refractory to immune checkpoint blockade and, possibly, other T cell-based therapies.
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Affiliation(s)
- Natalie J Neubert
- Ludwig Cancer Research Center and Department of Oncology, University of Lausanne (UNIL), CH-1066 Epalinges, Switzerland
| | - Martina Schmittnaegel
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Natacha Bordry
- Ludwig Cancer Research Center and Department of Oncology, University of Lausanne (UNIL), CH-1066 Epalinges, Switzerland
| | - Sina Nassiri
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Noémie Wald
- Ludwig Cancer Research Center and Department of Oncology, University of Lausanne (UNIL), CH-1066 Epalinges, Switzerland
| | - Christophe Martignier
- Ludwig Cancer Research Center and Department of Oncology, University of Lausanne (UNIL), CH-1066 Epalinges, Switzerland
| | - Laure Tillé
- Ludwig Cancer Research Center and Department of Oncology, University of Lausanne (UNIL), CH-1066 Epalinges, Switzerland
| | - Krisztian Homicsko
- Ludwig Cancer Research Center and Department of Oncology, University of Lausanne (UNIL), CH-1066 Epalinges, Switzerland.,Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - William Damsky
- Departments of Dermatology and Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Hélène Maby-El Hajjami
- Ludwig Cancer Research Center and Department of Oncology, University of Lausanne (UNIL), CH-1066 Epalinges, Switzerland
| | - Irina Klaman
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Munich, Nonnenwald 2, D-82377 Penzberg, Germany
| | - Esther Danenberg
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital (CHUV), CH-1005 Lausanne, Switzerland
| | - Kalliopi Ioannidou
- Ludwig Cancer Research Center and Department of Oncology, University of Lausanne (UNIL), CH-1066 Epalinges, Switzerland
| | - Lana Kandalaft
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital (CHUV), CH-1005 Lausanne, Switzerland
| | - George Coukos
- Ludwig Cancer Research Center and Department of Oncology, University of Lausanne (UNIL), CH-1066 Epalinges, Switzerland.,Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital (CHUV), CH-1005 Lausanne, Switzerland
| | - Sabine Hoves
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Munich, Nonnenwald 2, D-82377 Penzberg, Germany
| | - Carola H Ries
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Munich, Nonnenwald 2, D-82377 Penzberg, Germany
| | - Silvia A Fuertes Marraco
- Ludwig Cancer Research Center and Department of Oncology, University of Lausanne (UNIL), CH-1066 Epalinges, Switzerland
| | - Periklis G Foukas
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital (CHUV), CH-1005 Lausanne, Switzerland
| | - Michele De Palma
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.
| | - Daniel E Speiser
- Ludwig Cancer Research Center and Department of Oncology, University of Lausanne (UNIL), CH-1066 Epalinges, Switzerland.
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8
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Fibroblast Growth Factor Receptor Signaling in Skin Cancers. Cells 2019; 8:cells8060540. [PMID: 31167513 PMCID: PMC6628025 DOI: 10.3390/cells8060540] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 05/31/2019] [Accepted: 06/03/2019] [Indexed: 12/19/2022] Open
Abstract
Fibroblast growth factor (FGF)/Fibroblast growth factor receptor (FGFR) signaling regulates various cellular processes during the embryonic development and in the adult organism. In the skin, fibroblasts and keratinocytes control proliferation and survival of melanocytes in a paracrine manner via several signaling molecules, including FGFs. FGF/FGFR signaling contributes to the skin surface expansion in childhood or during wound healing, and skin protection from UV light damage. Aberrant FGF/FGFR signaling has been implicated in many disorders, including cancer. In melanoma cells, the FGFR expression is low, probably because of the strong endogenous mutation-driven constitutive activation of the downstream mitogen-activated protein kinase-extracellular signal-regulated kinase (MAPK-ERK) signaling pathway. FGFR1 is exceptional as it is expressed in the majority of melanomas at a high level. Melanoma cells that acquired the capacity to synthesize FGFs can influence the neighboring cells in the tumor niche, such as endothelial cells, fibroblasts, or other melanoma cells. In this way, FGF/FGFR signaling contributes to intratumoral angiogenesis, melanoma cell survival, and development of resistance to therapeutics. Therefore, inhibitors of aberrant FGF/FGFR signaling are considered as drugs in combination treatment. The ongoing LOGIC-2 phase II clinical trial aims to find out whether targeting the FGF/FGFR signaling pathway with BGJ398 may be a good therapeutic strategy in melanoma patients who develop resistance to v-Raf murine sarcoma viral oncogene homolog B (BRAF)/MEK inhibitors.
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9
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Wei D. A multigene support vector machine predictor for metastasis of cutaneous melanoma. Mol Med Rep 2018; 17:2907-2914. [PMID: 29257259 PMCID: PMC5783509 DOI: 10.3892/mmr.2017.8219] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 11/21/2017] [Indexed: 12/21/2022] Open
Abstract
Gene expression profiles of cutaneous melanoma were analyzed to identify critical genes associated with metastasis. Two gene expression datasets were downloaded from Gene Expression Omnibus (GEO) and another dataset was obtained from The Cancer Genome Atlas (TCGA). Differentially expression genes (DEGs) between metastatic and non‑metastatic melanoma were identified by meta‑analysis. A protein‑protein interaction (PPI) network was constructed for the DEGs using information from BioGRID, HPRD and DIP. Betweenness centrality (BC) was calculated for each node in the network and the top feature genes ranked by BC were selected to construct the support vector machine (SVM) classifier using the training set. The SVM classifier was then validated in another independent dataset. Pathway enrichment analysis was performed for the feature genes using Fisher's exact test. A total of 798 DEGs were identified and a PPI network including 337 nodes and 466 edges was then constructed. Top 110 feature genes ranked by BC were included in the SVM classifier. The prediction accuracies for the three datasets were 96.8, 100 and 94.4%, respectively. A total of 11 KEGG pathways and 13 GO biological pathways were significantly over‑represented in the 110 feature genes, including endometrial cancer, regulation of actin cytoskeleton, focal adhesion, ubiquitin mediated proteolysis, regulation of apoptosis and regulation of cell proliferation. A SVM classifier of high prediction accuracy was acquired. Several critical genes implicated in melanoms metastasis were also revealed. These results may advance understanding of the molecular mechanisms underlying metastasis, and also provide potential therapeutic targets.
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Affiliation(s)
- Dong Wei
- Department of Plastic and Esthetic Surgeries, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan 610072, P.R. China
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10
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11
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Abstract
Differences between genomes can be due to single nucleotide variants (SNPs), translocations, inversions and copy number variants (CNVs, gain or loss of DNA). The latter can range from sub-microscopic events to complete chromosomal aneuploidies. Small CNVs are often benign but those larger than 250 kb are strongly associated with morbid consequences such as developmental disorders and cancer. Detecting CNVs within and between populations is essential to better understand the plasticity of our genome and to elucidate its possible contribution to disease or phenotypic traits.While the link between SNPs and disease susceptibility has been well studied, to date there are still very few published CNV genome-wide association studies; probably owing to the fact that CNV analysis remains a slightly more complex task than SNP analysis (both in term of bioinformatics workflow and uncertainty in the CNV calling leading to high false positive rates and unknown false negative rates). This chapter aims at explaining computational methods for the analysis of CNVs, ranging from study design, data processing and quality control, up to genome-wide association study with clinical traits.
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Affiliation(s)
- Aurélien Macé
- Institute of Social and Preventive Medicine, University Hospital of Lausanne, Lausanne, Switzerland.,Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Zoltán Kutalik
- Institute of Social and Preventive Medicine, University Hospital of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
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12
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Wang X, Xu H, Cao G, Wu Z, Wang J. Loss of EphA3 Protein Expression Is Associated With Advanced TNM Stage in Clear-Cell Renal Cell Carcinoma. Clin Genitourin Cancer 2016; 15:e169-e173. [PMID: 27591824 DOI: 10.1016/j.clgc.2016.07.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 07/25/2016] [Accepted: 07/30/2016] [Indexed: 01/11/2023]
Abstract
BACKGROUND Erythropoietin-producing hepatocellular carcinoma (Eph) receptors constitute the largest family of receptor tyrosine kinases. Ephs and their ligands ephrins play an important role in development and carcinogenesis. The expression of EphA3, an Eph family member, has been investigated in a variety of human cancers, with mixed results. High levels of EphA3 protein expression have been reported in colorectal, prostate, and gastric cancers, whereas loss of protein expression has been reported in lung and hematopoietic cancers. EphA3 expression in clear-cell renal cell carcinoma (ccRCC) and its association with clinicopathological parameters has not previously been examined. The aim of this study was to determine the cancerous value of EphA3 protein expression in patients with ccRCC. MATERIALS AND METHODS This study included 68 patients with ccRCC. EphA3 protein expression was examined in ccRCC tissue samples using immunohistochemistry and a specific polyclonal antibody, and the correlation between EphA3 expression and clinicopathological parameters was subsequently evaluated. RESULTS High EphA3 protein expression was observed in all normal renal tubules. In the 68 ccRCC patient samples examined, EphA3 protein expression was detected in 19 cases (27.9%) and undetectable in 49 cases (72.1%). EphA3 protein expression was significantly associated with tumor diameter (P = .016) and tumor, node metastases stage (P = .029). No significant association between protein expression and sex (P = .387), age (P = .727), or nuclear grade (P = .243) was found. CONCLUSION Ourdata indicate that EphA3 protein expression is reduced in ccRCC, suggesting the possibility that this receptor functions as a tumor suppressor in this disease.
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Affiliation(s)
- Xiaolin Wang
- Department of Urology, Nantong Tumor Hospital, Nantong, Jiangsu, China
| | - Haifei Xu
- Department of Urology, Nantong Tumor Hospital, Nantong, Jiangsu, China
| | - Guangxin Cao
- Department of Urology, Nantong Tumor Hospital, Nantong, Jiangsu, China
| | - Zhijun Wu
- Department of Radiotherapy, Nantong Tumor Hospital, Nantong, Jiangsu, China.
| | - Jiandong Wang
- Department of Pathology, Jinling Hospital, Nanjing, China.
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13
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Afasizheva A, Devine A, Tillman H, Fung KL, Vieira WD, Blehm BH, Kotobuki Y, Busby B, Chen EI, Tanner K. Mitogen-activated protein kinase signaling causes malignant melanoma cells to differentially alter extracellular matrix biosynthesis to promote cell survival. BMC Cancer 2016; 16:186. [PMID: 26944546 PMCID: PMC4779217 DOI: 10.1186/s12885-016-2211-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Accepted: 02/22/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Intrinsic and acquired resistance to drug therapies remains a challenge for malignant melanoma patients. Intratumoral heterogeneities within the tumor microenvironment contribute additional complexity to the determinants of drug efficacy and acquired resistance. METHODS We use 3D biomimetic platforms to understand dynamics in extracellular matrix (ECM) biogenesis following pharmaceutical intervention against mitogen-activated protein kinases (MAPK) signaling. We further determined temporal evolution of secreted ECM components by isogenic melanoma cell clones. RESULTS We found that the cell clones differentially secrete and assemble a myriad of ECM molecules into dense fibrillar and globular networks. We show that cells can modulate their ECM biosynthesis in response to external insults. Fibronectin (FN) is one of the key architectural components, modulating the efficacy of a broad spectrum of drug therapies. Stable cell lines engineered to secrete minimal levels of FN showed a concomitant increase in secretion of Tenascin-C and became sensitive to BRAF(V600E) and ERK inhibition as clonally- derived 3D tumor aggregates. These cells failed to assemble exogenous FN despite maintaining the integrin machinery to facilitate cell- ECM cross-talk. We determined that only clones that increased FN production via p38 MAPK and β1 integrin survived drug treatment. CONCLUSIONS These data suggest that tumor cells engineer drug resistance by altering their ECM biosynthesis. Therefore, drug treatment may induce ECM biosynthesis, contributing to de novo resistance.
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Affiliation(s)
- Anna Afasizheva
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Dr., Bethesda, MD, 20892, USA.
| | - Alexus Devine
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Dr., Bethesda, MD, 20892, USA.
| | - Heather Tillman
- Laboratories of Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Dr., Bethesda, 20892, MD, USA.
| | - King Leung Fung
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Dr., Bethesda, MD, 20892, USA.
| | - Wilfred D Vieira
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Dr., Bethesda, MD, 20892, USA.
| | - Benjamin H Blehm
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Dr., Bethesda, MD, 20892, USA.
| | - Yorihisa Kotobuki
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Dr., Bethesda, MD, 20892, USA.
| | - Ben Busby
- National Centers for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, 20892, MD, USA.
| | - Emily I Chen
- Proteomics Shared Resource at the Herbert Irving Comprehensive Cancer Center & Department of Pharmacology, Columbia University Medical Center, New York, 10032, NY, USA.
| | - Kandice Tanner
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Dr., Bethesda, MD, 20892, USA.
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14
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Hood G, Laufer-Amorim R, Fonseca-Alves CE, Palmieri C. Overexpression of Ephrin A3 Receptor in Canine Prostatic Carcinoma. J Comp Pathol 2016; 154:180-5. [PMID: 26895888 DOI: 10.1016/j.jcpa.2016.01.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 12/21/2015] [Accepted: 01/05/2016] [Indexed: 11/29/2022]
Abstract
Ephrin A3 (EphA3), a member of the ephrin receptor tyrosine kinase family, is involved in a variety of functions in normal cells, especially during embryonic development, and alterations in its expression profile have been observed in several human cancers. However, there are no reports of the expression of EphA3 in normal, hyperplastic or neoplastic canine prostate tissue or in other types of canine tumours. Six normal, 15 hyperplastic and 21 neoplastic canine prostates were examined immunohistochemically with a polyclonal antibody specific for human EphA3. The percentage of positive cells in all prostatic carcinomas was increased, with a mean of 89.28 ± 5.18% compared with normal (9.17 ± 6.72%) and hyperplastic prostates (20.00 ± 8.28%). EphA3 expression was not correlated with the histological subtypes of prostate cancer or with the Gleason score. The increase in EphA3 expression in canine prostatic carcinomas suggests the involvement of this receptor in prostatic carcinogenesis and its potential use as a target for new therapeutic strategies.
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Affiliation(s)
- G Hood
- School of Veterinary Science, The University of Queensland, Gatton Campus, Gatton, Queensland, Australia
| | - R Laufer-Amorim
- School of Veterinary Medicine and Animal Science, University Estadual Paulista, Botucatu, São Paulo, Brazil
| | - C E Fonseca-Alves
- School of Veterinary Medicine and Animal Science, University Estadual Paulista, Botucatu, São Paulo, Brazil
| | - C Palmieri
- School of Veterinary Science, The University of Queensland, Gatton Campus, Gatton, Queensland, Australia.
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15
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MITF drives endolysosomal biogenesis and potentiates Wnt signaling in melanoma cells. Proc Natl Acad Sci U S A 2015; 112:E420-9. [PMID: 25605940 DOI: 10.1073/pnas.1424576112] [Citation(s) in RCA: 176] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Canonical Wnt signaling plays an important role in development and disease, regulating transcription of target genes and stabilizing many proteins phosphorylated by glycogen synthase kinase 3 (GSK3). We observed that the MiT family of transcription factors, which includes the melanoma oncogene MITF (micropthalmia-associated transcription factor) and the lysosomal master regulator TFEB, had the highest phylogenetic conservation of three consecutive putative GSK3 phosphorylation sites in animal proteomes. This finding prompted us to examine the relationship between MITF, endolysosomal biogenesis, and Wnt signaling. Here we report that MITF expression levels correlated with the expression of a large subset of lysosomal genes in melanoma cell lines. MITF expression in the tetracycline-inducible C32 melanoma model caused a marked increase in vesicular structures, and increased expression of late endosomal proteins, such as Rab7, LAMP1, and CD63. These late endosomes were not functional lysosomes as they were less active in proteolysis, yet were able to concentrate Axin1, phospho-LRP6, phospho-β-catenin, and GSK3 in the presence of Wnt ligands. This relocalization significantly enhanced Wnt signaling by increasing the number of multivesicular bodies into which the Wnt signalosome/destruction complex becomes localized upon Wnt signaling. We also show that the MITF protein was stabilized by Wnt signaling, through the novel C-terminal GSK3 phosphorylations identified here. MITF stabilization caused an increase in multivesicular body biosynthesis, which in turn increased Wnt signaling, generating a positive-feedback loop that may function during the proliferative stages of melanoma. The results underscore the importance of misregulated endolysosomal biogenesis in Wnt signaling and cancer.
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16
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Abstract
Eph receptor tyrosine kinases control cell-cell interactions during normal and oncogenic development, and are implicated in a range of processes including angiogenesis, stem cell maintenance and metastasis. They are thus of great interest as targets for cancer therapy. EphA3, originally isolated from leukemic and melanoma cells, is presently one of the most promising therapeutic targets, with multiple tumor-promoting roles in a variety of cancer types. This review focuses on EphA3, its functions in controlling cellular behavior, both in normal and pathological development, and most particularly in cancer.
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Affiliation(s)
- Peter W Janes
- Department of Biochemistry and Molecular Biology, Monash University , Victoria , Australia and
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17
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Feala JD, Abdulhameed MDM, Yu C, Dutta B, Yu X, Schmid K, Dave J, Tortella F, Reifman J. Systems biology approaches for discovering biomarkers for traumatic brain injury. J Neurotrauma 2014; 30:1101-16. [PMID: 23510232 DOI: 10.1089/neu.2012.2631] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The rate of traumatic brain injury (TBI) in service members with wartime injuries has risen rapidly in recent years, and complex, variable links have emerged between TBI and long-term neurological disorders. The multifactorial nature of TBI secondary cellular response has confounded attempts to find cellular biomarkers for its diagnosis and prognosis or for guiding therapy for brain injury. One possibility is to apply emerging systems biology strategies to holistically probe and analyze the complex interweaving molecular pathways and networks that mediate the secondary cellular response through computational models that integrate these diverse data sets. Here, we review available systems biology strategies, databases, and tools. In addition, we describe opportunities for applying this methodology to existing TBI data sets to identify new biomarker candidates and gain insights about the underlying molecular mechanisms of TBI response. As an exemplar, we apply network and pathway analysis to a manually compiled list of 32 protein biomarker candidates from the literature, recover known TBI-related mechanisms, and generate hypothetical new biomarker candidates.
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Affiliation(s)
- Jacob D Feala
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, Maryland, USA
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18
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Kakazu N, Yamane H, Miyachi M, Shiwaku K, Hosoi H. Identification of the 12q15 amplicon within the homogeneously staining regions in the embryonal rhabdomyosarcoma cell line RMS-YM. Cytogenet Genome Res 2014; 142:167-73. [PMID: 24480864 DOI: 10.1159/000357930] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2013] [Indexed: 11/19/2022] Open
Abstract
Gene amplification represents one of the molecular mechanisms of oncogene overexpression in many types of tumors. Homogeneously staining regions (HSRs) are cytogenetic hallmarks of gene amplification. Rhabdomyosarcoma is the most common malignant soft-tissue tumor in children. RMS-YM is an embryonal rhabdomyosarcoma cell line that possesses 3 HSRs. This cytogenetic finding suggests the presence of gene amplifications associated with tumor development or progression in RMS-YM. Here, using fluorescence in situ hybridization, we detected high amplification of the MDM2 gene in the HSRs of RMS-YM. We also refined the region of the amplicon and identified that the FRS2 gene and others are amplified in RMS-YM. MDM2 and FRS2 play important roles as a regulator of p53 and a mediator of FGF signaling, respectively, and thus are potential molecular targets for therapy in many different tumors. RMS-YM may be useful for studies of the molecular pathways of tumorigenesis and tumor progression in rhabdomyosarcoma and for in vitro evaluation of newly developed therapeutic agents that target MDM2 or FRS2.
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Affiliation(s)
- N Kakazu
- Department of Environmental and Preventive Medicine, Shimane University School of Medicine, Izumo, Japan
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19
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Kunz M. Oncogenes in melanoma: an update. Eur J Cell Biol 2013; 93:1-10. [PMID: 24468268 DOI: 10.1016/j.ejcb.2013.12.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 12/16/2013] [Accepted: 12/17/2013] [Indexed: 12/13/2022] Open
Abstract
Melanoma is a highly aggressive tumour with poor prognosis in the metastatic stage. BRAF, NRAS, and KIT are three well-known oncogenes involved in melanoma pathogenesis. Targeting of mutated BRAF kinase has recently been shown to significantly improve overall survival of metastatic melanoma patients, underscoring the particular role of this oncogene in melanoma biology. However, recurrences regularly occur within several months, which supposedly involve further oncogenes. Moreover, oncogenic driver mutations have not been described for up to 30% of all melanomas. In order to obtain a more complete picture of the mutational landscape of melanoma, more recent studies used high-throughput DNA sequencing technologies. A number of new oncogene candidates such as MAPK1/2, ERBB4, GRIN2A, GRM3, RAC1, and PREX2 were identified. Their particular role in melanoma biology is currently under investigation. Evidence for the functional relevance of some of these new oncogene candidates has been provided in in vitro and in vivo experiments. However, these findings await further validation in clinical studies. This review provides an overview on well-known melanoma oncogenes and new oncogene candidates, based on recent high-throughput sequencing studies. The list of genes discussed herein is of course not complete but highlights some of the most significant of recent findings in this area. The new candidates may support more individualized treatment approaches for metastatic melanoma patients in the future.
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Affiliation(s)
- Manfred Kunz
- Department of Dermatology, Venereology and Allergology, University of Leipzig, 04103 Leipzig, Germany.
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20
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Sailani MR, Makrythanasis P, Valsesia A, Santoni FA, Deutsch S, Popadin K, Borel C, Migliavacca E, Sharp AJ, Duriaux Sail G, Falconnet E, Rabionet K, Serra-Juhé C, Vicari S, Laux D, Grattau Y, Dembour G, Megarbane A, Touraine R, Stora S, Kitsiou S, Fryssira H, Chatzisevastou-Loukidou C, Kanavakis E, Merla G, Bonnet D, Pérez-Jurado LA, Estivill X, Delabar JM, Antonarakis SE. The complex SNP and CNV genetic architecture of the increased risk of congenital heart defects in Down syndrome. Genome Res 2013; 23:1410-21. [PMID: 23783273 PMCID: PMC3759718 DOI: 10.1101/gr.147991.112] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Congenital heart defect (CHD) occurs in 40% of Down syndrome (DS) cases. While carrying three copies of chromosome 21 increases the risk for CHD, trisomy 21 itself is not sufficient to cause CHD. Thus, additional genetic variation and/or environmental factors could contribute to the CHD risk. Here we report genomic variations that in concert with trisomy 21, determine the risk for CHD in DS. This case-control GWAS includes 187 DS with CHD (AVSD = 69, ASD = 53, VSD = 65) as cases, and 151 DS without CHD as controls. Chromosome 21–specific association studies revealed rs2832616 and rs1943950 as CHD risk alleles (adjusted genotypic P-values <0.05). These signals were confirmed in a replication cohort of 92 DS-CHD cases and 80 DS-without CHD (nominal P-value 0.0022). Furthermore, CNV analyses using a customized chromosome 21 aCGH of 135K probes in 55 DS-AVSD and 53 DS-without CHD revealed three CNV regions associated with AVSD risk (FDR ≤ 0.05). Two of these regions that are located within the previously identified CHD region on chromosome 21 were further confirmed in a replication study of 49 DS-AVSD and 45 DS- without CHD (FDR ≤ 0.05). One of these CNVs maps near the RIPK4 gene, and the second includes the ZBTB21 (previously ZNF295) gene, highlighting the potential role of these genes in the pathogenesis of CHD in DS. We propose that the genetic architecture of the CHD risk of DS is complex and includes trisomy 21, and SNP and CNV variations in chromosome 21. In addition, a yet-unidentified genetic variation in the rest of the genome may contribute to this complex genetic architecture.
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Affiliation(s)
- M Reza Sailani
- Department of Genetic Medicine and Development, University of Geneva, Geneva 1211, Switzerland
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21
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Damsky WE, Theodosakis N, Bosenberg M. Melanoma metastasis: new concepts and evolving paradigms. Oncogene 2013; 33:2413-22. [PMID: 23728340 DOI: 10.1038/onc.2013.194] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2013] [Revised: 04/22/2013] [Accepted: 04/22/2013] [Indexed: 12/25/2022]
Abstract
Melanoma progression is typically depicted as a linear and stepwise process in which metastasis occurs relatively late in disease progression. Significant evidence suggests that in a subset of melanomas, progression is much more complex and less linear in nature. Epidemiologic and experimental observations in melanoma metastasis are reviewed here and are incorporated into a comprehensive model for melanoma metastasis, which takes into account the varied natural history of melanoma formation and progression.
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Affiliation(s)
- W E Damsky
- 1] Department of Dermatology, Yale University School of Medicine, New Haven, CT, USA [2] Department of Pathology, University of Vermont College of Medicine, Burlington, VT, USA
| | - N Theodosakis
- Department of Dermatology, Yale University School of Medicine, New Haven, CT, USA
| | - M Bosenberg
- Department of Dermatology, Yale University School of Medicine, New Haven, CT, USA
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22
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Valsesia A, Macé A, Jacquemont S, Beckmann JS, Kutalik Z. The Growing Importance of CNVs: New Insights for Detection and Clinical Interpretation. Front Genet 2013; 4:92. [PMID: 23750167 PMCID: PMC3667386 DOI: 10.3389/fgene.2013.00092] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2013] [Accepted: 05/04/2013] [Indexed: 02/03/2023] Open
Abstract
Differences between genomes can be due to single nucleotide variants, translocations, inversions, and copy number variants (CNVs, gain or loss of DNA). The latter can range from sub-microscopic events to complete chromosomal aneuploidies. Small CNVs are often benign but those larger than 500 kb are strongly associated with morbid consequences such as developmental disorders and cancer. Detecting CNVs within and between populations is essential to better understand the plasticity of our genome and to elucidate its possible contribution to disease. Hence there is a need for better-tailored and more robust tools for the detection and genome-wide analyses of CNVs. While a link between a given CNV and a disease may have often been established, the relative CNV contribution to disease progression and impact on drug response is not necessarily understood. In this review we discuss the progress, challenges, and limitations that occur at different stages of CNV analysis from the detection (using DNA microarrays and next-generation sequencing) and identification of recurrent CNVs to the association with phenotypes. We emphasize the importance of germline CNVs and propose strategies to aid clinicians to better interpret structural variations and assess their clinical implications.
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Affiliation(s)
- Armand Valsesia
- Genetics Core, Nestlé Institute of Health Sciences Lausanne, Switzerland
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23
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Huber F, Lang HP, Backmann N, Rimoldi D, Gerber C. Direct detection of a BRAF mutation in total RNA from melanoma cells using cantilever arrays. NATURE NANOTECHNOLOGY 2013; 8:125-129. [PMID: 23377457 DOI: 10.1038/nnano.2012.263] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Accepted: 12/18/2012] [Indexed: 05/27/2023]
Abstract
Malignant melanoma, the deadliest form of skin cancer, is characterized by a predominant mutation in the BRAF gene. Drugs that target tumours carrying this mutation have recently entered the clinic. Accordingly, patients are routinely screened for mutations in this gene to determine whether they can benefit from this type of treatment. The current gold standard for mutation screening uses real-time polymerase chain reaction and sequencing methods. Here we show that an assay based on microcantilever arrays can detect the mutation nanomechanically without amplification in total RNA samples isolated from melanoma cells. The assay is based on a BRAF-specific oligonucleotide probe. We detected mutant BRAF at a concentration of 500 pM in a 50-fold excess of the wild-type sequence. The method was able to distinguish melanoma cells carrying the mutation from wild-type cells using as little as 20 ng µl(-1) of RNA material, without prior PCR amplification and use of labels.
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Affiliation(s)
- F Huber
- Swiss Nano Institute, University of Basel, Klingelbergstrasse 82, 4056 Basel, Switzerland.
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24
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Rakosy Z, Ecsedi S, Toth R, Vizkeleti L, Herandez-Vargas H, Lazar V, Emri G, Szatmari I, Herceg Z, Adany R, Balazs M. Integrative genomics identifies gene signature associated with melanoma ulceration. PLoS One 2013; 8:e54958. [PMID: 23383013 PMCID: PMC3559846 DOI: 10.1371/journal.pone.0054958] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 12/18/2012] [Indexed: 12/31/2022] Open
Abstract
Background Despite the extensive research approaches applied to characterise malignant melanoma, no specific molecular markers are available that are clearly related to the progression of this disease. In this study, our aims were to define a gene expression signature associated with the clinical outcome of melanoma patients and to provide an integrative interpretation of the gene expression -, copy number alterations -, and promoter methylation patterns that contribute to clinically relevant molecular functional alterations. Methods Gene expression profiles were determined using the Affymetrix U133 Plus2.0 array. The NimbleGen Human CGH Whole-Genome Tiling array was used to define CNAs, and the Illumina GoldenGate Methylation platform was applied to characterise the methylation patterns of overlapping genes. Results We identified two subclasses of primary melanoma: one representing patients with better prognoses and the other being characteristic of patients with unfavourable outcomes. We assigned 1,080 genes as being significantly correlated with ulceration, 987 genes were downregulated and significantly enriched in the p53, Nf-kappaB, and WNT/beta-catenin pathways. Through integrated genome analysis, we defined 150 downregulated genes whose expression correlated with copy number losses in ulcerated samples. These genes were significantly enriched on chromosome 6q and 10q, which contained a total of 36 genes. Ten of these genes were downregulated and involved in cell-cell and cell-matrix adhesion or apoptosis. The expression and methylation patterns of additional genes exhibited an inverse correlation, suggesting that transcriptional silencing of these genes is driven by epigenetic events. Conclusion Using an integrative genomic approach, we were able to identify functionally relevant molecular hotspots characterised by copy number losses and promoter hypermethylation in distinct molecular subtypes of melanoma that contribute to specific transcriptomic silencing and might indicate a poor clinical outcome of melanoma.
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Affiliation(s)
- Zsuzsa Rakosy
- Department of Preventive Medicine, Faculty of Public Health, Medical and Health Science Center, University of Debrecen, Debrecen, Hungary
- Public Health Research Group of the Hungarian Academy of Sciences, University of Debrecen, Debrecen, Hungary
| | - Szilvia Ecsedi
- Department of Preventive Medicine, Faculty of Public Health, Medical and Health Science Center, University of Debrecen, Debrecen, Hungary
- Public Health Research Group of the Hungarian Academy of Sciences, University of Debrecen, Debrecen, Hungary
| | - Reka Toth
- Department of Preventive Medicine, Faculty of Public Health, Medical and Health Science Center, University of Debrecen, Debrecen, Hungary
| | - Laura Vizkeleti
- Department of Preventive Medicine, Faculty of Public Health, Medical and Health Science Center, University of Debrecen, Debrecen, Hungary
- Public Health Research Group of the Hungarian Academy of Sciences, University of Debrecen, Debrecen, Hungary
| | - Hector Herandez-Vargas
- World Health Organization International Agency for Research on Cancer, Epigenetics Group, Lyon, France
| | - Viktoria Lazar
- Department of Preventive Medicine, Faculty of Public Health, Medical and Health Science Center, University of Debrecen, Debrecen, Hungary
| | - Gabriella Emri
- Department of Dermatology, Faculty of Medicine, Medical and Health Science Center, University of Debrecen, Debrecen, Hungary
| | - Istvan Szatmari
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Medical and Health Science Center, University of Debrecen, Debrecen, Hungary
| | - Zdenko Herceg
- World Health Organization International Agency for Research on Cancer, Epigenetics Group, Lyon, France
| | - Roza Adany
- Department of Preventive Medicine, Faculty of Public Health, Medical and Health Science Center, University of Debrecen, Debrecen, Hungary
- Public Health Research Group of the Hungarian Academy of Sciences, University of Debrecen, Debrecen, Hungary
| | - Margit Balazs
- Department of Preventive Medicine, Faculty of Public Health, Medical and Health Science Center, University of Debrecen, Debrecen, Hungary
- Public Health Research Group of the Hungarian Academy of Sciences, University of Debrecen, Debrecen, Hungary
- * E-mail:
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25
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Abstract
Mutations in the human mitochondrial genome are known to cause an array of diverse disorders, most of which are maternally inherited, and all of which are associated with defects in oxidative energy metabolism. It is now emerging that somatic mutations in mitochondrial DNA (mtDNA) are also linked to other complex traits, including neurodegenerative diseases, ageing and cancer. Here we discuss insights into the roles of mtDNA mutations in a wide variety of diseases, highlighting the interesting genetic characteristics of the mitochondrial genome and challenges in studying its contribution to pathogenesis.
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26
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Zufferey A, Ibberson M, Reny JL, Xenarios I, Sanchez JC, Fontana P. Unraveling modulators of platelet reactivity in cardiovascular patients using omics strategies: Towards a network biology paradigm. TRANSLATIONAL PROTEOMICS 2013. [DOI: 10.1016/j.trprot.2013.04.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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27
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Yang PT, Anastas JN, Toroni RA, Shinohara MM, Goodson JM, Bosserhoff AK, Chien AJ, Moon RT. WLS inhibits melanoma cell proliferation through the β-catenin signalling pathway and induces spontaneous metastasis. EMBO Mol Med 2012; 4:1294-307. [PMID: 23129487 PMCID: PMC3531604 DOI: 10.1002/emmm.201201486] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Revised: 09/20/2012] [Accepted: 09/24/2012] [Indexed: 12/20/2022] Open
Abstract
Elevated levels of nuclear β-catenin are associated with higher rates of survival in patients with melanoma, raising questions as to how ß-catenin is regulated in this context. In the present study, we investigated the formal possibility that the secretion of WNT ligands that stabilize ß-catenin may be regulated in melanoma and thus contributes to differences in ß-catenin levels. We find that WLS, a conserved transmembrane protein necessary for WNT secretion, is decreased in both melanoma cell lines and in patient tumours relative to skin and to benign nevi. Unexpectedly, reducing endogenous WLS with shRNAs in human melanoma cell lines promotes spontaneous lung metastasis in xenografts in mice and promotes cell proliferation in vitro. Conversely, overexpression of WLS inhibits cell proliferation in vitro. Activating β-catenin downstream of WNT secretion blocks the increased cell migration and proliferation observed in the presence of WLS shRNAs, while inhibiting WNT signalling rescues the growth defects induced by excess WLS. These data suggest that WLS functions as a negative regulator of melanoma proliferation and spontaneous metastasis by activating WNT/β-catenin signalling.
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Affiliation(s)
- Pei-Tzu Yang
- Department of Pharmacology, Howard Hughes Medical Institute, Institute for Stem Cell and Regenerative Medicine, University of Washington School of MedicineSeattle, WA, USA
| | - Jamie N Anastas
- Department of Pharmacology, Howard Hughes Medical Institute, Institute for Stem Cell and Regenerative Medicine, University of Washington School of MedicineSeattle, WA, USA
| | - Rachel A Toroni
- Division of Dermatology, Department of Medicine, University of Washington School of MedicineSeattle, WA, USA
| | - Michi M Shinohara
- Division of Dermatology, Department of Medicine, University of Washington School of MedicineSeattle, WA, USA
| | - Jamie M Goodson
- Department of Biology, University of WashingtonSeattle, WA, USA
| | - Anja K Bosserhoff
- Department of Pathology, University of RegensburgRegensburg, Germany
| | - Andy J Chien
- Department of Pharmacology, Howard Hughes Medical Institute, Institute for Stem Cell and Regenerative Medicine, University of Washington School of MedicineSeattle, WA, USA
- Division of Dermatology, Department of Medicine, University of Washington School of MedicineSeattle, WA, USA
| | - Randall T Moon
- Department of Pharmacology, Howard Hughes Medical Institute, Institute for Stem Cell and Regenerative Medicine, University of Washington School of MedicineSeattle, WA, USA
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28
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Kunz M, Dannemann M, Kelso J. High-throughput sequencing of the melanoma genome. Exp Dermatol 2012; 22:10-7. [PMID: 23174022 DOI: 10.1111/exd.12054] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/19/2012] [Indexed: 12/16/2022]
Abstract
Next-generation sequencing technologies are now common for whole-genome, whole-exome and whole-transcriptome sequencing (RNA-seq) of tumors to identify point mutations, structural or copy number alterations and changes in gene expression. A substantial number of studies have already been performed for melanoma. One study analysed eight melanoma cell lines with RNA-Seq technology and identified 11 novel melanoma gene fusions. Whole-exome sequencing of seven melanoma cell lines identified overlapping gain of function mutations in MAP2K1 (MEK1) and MAP2K2 (MEK2) genes. Integrative sequencing of cutaneous melanoma metastases using different sequencing platforms revealed a new somatic point mutation in HRAS and a structural rearrangement affecting CDKN2C (a CDK4 inhibitor). These latter sequencing-based discoveries may be used to motivate the inclusion of the affected patients into clinical trials with specific signalling pathway inhibitors. Taken together, we are at the beginning of an era with new sequencing technologies providing a more comprehensive view of cancer mutational landscapes and hereby a better understanding of their pathogenesis. This will also open interesting perspectives for new treatment approaches and clinical trial designs.
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Affiliation(s)
- Manfred Kunz
- Department of Dermatology, Venereology and Allergology, University of Leipzig, Leipzig, Germany.
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Qidwai MT, Jamal F, Singh D, Sharma RK. Factors modifying transcriptional regulation of signaling genes have putative role in tumor development and progression in humans. Med Hypotheses 2012; 79:805-12. [PMID: 23026707 DOI: 10.1016/j.mehy.2012.08.033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Revised: 08/17/2012] [Accepted: 08/30/2012] [Indexed: 10/27/2022]
Abstract
Genes involved in signaling are highly regulated at the level of transcription. Several factors have been known to play role in transcriptional modification of genes. Among these DNA sequence variations present in the regulatory region and aberrant methylation of CpG Iceland in promoter region are the most important factors modifying transcriptional regulation of genes. DNA sequence variation interferes with assembling of regulatory protein TF (transcription factor) on the cis elements TFBS (transcription factor binding site). Presence of variations in regulatory region may alter the level of gene product via interaction of TF to TFBS (transcriptional modification). Promoter hypermethylation causes gene silencing and responsible for transcriptional dysregulation of gene. JAK-1, STAT-3, IL-6, MAPK and AR genes participate in signaling pathway and are tightly regulated. Overexpression of IL-6 and activated STAT3 may contribute to the development of prostate cancer and possibly other human cancers. Indeed, constitutively activated STAT3 have been found in a growing number of human tumors. In the present work, we have predicted 34 regulatory polymorphisms that lies in TFBS of 5 (JAK-1, STAT-3, IL-6, MAPK and AR) signaling genes and compare the methylation of CpG Iceland in promoter region of above motioned genes. On the basis of these predictions, it has been hypothesized that transcriptional modification of gene resulting from the DNA sequence variations in regulatory region or promoter hypermethylation increases the susceptibility to diseases such as cancer by alteration in the level of signaling genes product. Presence of DNA sequence variations may also influence the response to a particular drug.
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Liu YY, Chen HY, Zhang ML, Tian D, Li S, Lee JY. Loss of fragile histidine triad and amplification of 1p36.22 and 11p15.5 in primary gastric adenocarcinomas. World J Gastroenterol 2012; 18:4522-32. [PMID: 22969225 PMCID: PMC3435777 DOI: 10.3748/wjg.v18.i33.4522] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Revised: 02/01/2012] [Accepted: 04/13/2012] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate the genomic copy number alterations that may harbor key driver genes in gastric tumorigenesis.
METHODS: Using high-resolution array comparative genomic hybridization (CGH), we investigated the genomic alterations of 20 advanced primary gastric adenocarcinomas (seventeen tubular and three mucinous) of Chinese patients from the Jilin province. Ten matching adjacent normal regions from the same patients were also studied.
RESULTS: The most frequent imbalances detected in these cancer samples were gains of 3q26.31-q27.2, 5p, 8q, 11p, 18p, 19q and 20q and losses of 3p, 4p, 18q and 21q. The use of high-resolution array CGH increased the resolution and sensitivity of the observed genomic changes and identified focal genetic imbalances, which included 54 gains and 16 losses that were smaller than 1 Mb in size. The most interesting focal imbalances were the intergenic loss/homozygous deletion of the fragile histidine triad gene and the amplicons 11q13, 18q11.2 and 19q12, as well as the novel amplicons 1p36.22 and 11p15.5.
CONCLUSION: These regions, especially the focal amplicons, may harbor key driver genes that will serve as biomarkers for either the diagnosis or the prognosis of gastric cancer, and therefore, a large-scale investigation is recommended.
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Standfuss C, Pospisil H, Klein A. SNP microarray analyses reveal copy number alterations and progressive genome reorganization during tumor development in SVT/t driven mice breast cancer. BMC Cancer 2012; 12:380. [PMID: 22935085 PMCID: PMC3534550 DOI: 10.1186/1471-2407-12-380] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Accepted: 08/08/2012] [Indexed: 11/21/2022] Open
Abstract
Background Tumor development is known to be a stepwise process involving dynamic changes that affect cellular integrity and cellular behavior. This complex interaction between genomic organization and gene, as well as protein expression is not yet fully understood. Tumor characterization by gene expression analyses is not sufficient, since expression levels are only available as a snapshot of the cell status. So far, research has mainly focused on gene expression profiling or alterations in oncogenes, even though DNA microarray platforms would allow for high-throughput analyses of copy number alterations (CNAs). Methods We analyzed DNA from mouse mammary gland epithelial cells using the Affymetrix Mouse Diversity Genotyping array (MOUSEDIVm520650) and calculated the CNAs. Segmental copy number alterations were computed based on the probeset CNAs using the circular binary segmentation algorithm. Motif search was performed in breakpoint regions (inter-segment regions) with the MEME suite to identify common motif sequences. Results Here we present a four stage mouse model addressing copy number alterations in tumorigenesis. No considerable changes in CNA were identified for non-transgenic mice, but a stepwise increase in CNA was found during tumor development. The segmental copy number alteration revealed informative chromosomal fragmentation patterns. In inter-segment regions (hypothetical breakpoint sides) unique motifs were found. Conclusions Our analyses suggest genome reorganization as a stepwise process that involves amplifications and deletions of chromosomal regions. We conclude from distinctive fragmentation patterns that conserved as well as individual breakpoints exist which promote tumorigenesis.
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Affiliation(s)
- Christoph Standfuss
- Bioinformatics, Technical University of Applied Sciences Wildau, 15745 Wildau, Bahnhofstrasse, Germany.
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Restored expression of the atypical heat shock protein H11/HspB8 inhibits the growth of genetically diverse melanoma tumors through activation of novel TAK1-dependent death pathways. Cell Death Dis 2012; 3:e371. [PMID: 22898869 PMCID: PMC3434666 DOI: 10.1038/cddis.2012.108] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Melanoma is an aggressive and drug-resistant cancer in need of improved therapeutic strategies. Restored expression of transcriptionally silenced genes is a potential approach, but it is limited by the genetic diversity of the melanoma tumors. The atypical heat shock protein H11/HspB8 has kinase activity and is silenced in melanoma through aberrant DNA methylation. We report that its restored expression induces the death of genetically diverse melanoma lines and inhibits tumor growth through the activation of novel TAK1-dependent death pathways. These include (i) caspase-1 activation independent of the inflammasome through upregulation of apoptosis-associated speck-like protein containing a CARD (ASC), (ii) Beclin-1 upregulation through phosphorylation of mammalian target of rapamycin (mTOR) at S2481 and (iii) apoptosis caused by caspase-1-mediated Beclin-1 cleavage. These data extend current understanding of cell death-associated functions, underscore the strong therapeutic promise of H11/HspB8 and identify TAK1 as a potential intervention target in melanoma.
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Zhuang G, Song W, Amato K, Hwang Y, Lee K, Boothby M, Ye F, Guo Y, Shyr Y, Lin L, Carbone DP, Brantley-Sieders DM, Chen J. Effects of cancer-associated EPHA3 mutations on lung cancer. J Natl Cancer Inst 2012; 104:1182-97. [PMID: 22829656 DOI: 10.1093/jnci/djs297] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Cancer genome sequencing efforts recently identified EPHA3, which encodes the EPHA3 receptor tyrosine kinase, as one of the most frequently mutated genes in lung cancer. Although receptor tyrosine kinase mutations often drive oncogenic conversion and tumorigenesis, the oncogenic potential of the EPHA3 mutations in lung cancer remains unknown. METHODS We used immunoprecipitation, western blotting, and kinase assays to determine the activity and signaling of mutant EPHA3 receptors. A mutation-associated gene signature was generated from one large dataset, mapped to another training dataset with survival information, and tested in a third independent dataset. EPHA3 expression levels were determined by quantitative reverse transcription-polymerase chain reaction in paired normal-tumor clinical specimens and by immunohistochemistry in human lung cancer tissue microarrays. We assessed tumor growth in vivo using A549 and H1299 human lung carcinoma cell xenografts in mice (n = 7-8 mice per group). Tumor cell proliferation was measured by bromodeoxyuridine incorporation and apoptosis by multiple assays. All P values are from two-sided tests. RESULTS At least two cancer-associated EPHA3 somatic mutations functioned as dominant inhibitors of the normal (wild type) EPHA3 protein. An EPHA3 mutation-associated gene signature that was associated with poor patient survival was identified. Moreover, EPHA3 gene copy numbers and/or expression levels were decreased in tumors from large cohorts of patients with lung cancer (eg, the gene was deleted in 157 of 371 [42%] primary lung adenocarcinomas). Reexpression of wild-type EPHA3 in human lung cancer lines increased apoptosis by suppression of AKT activation in vitro and inhibited the growth of tumor xenografts (eg, for H1299 cells, mean tumor volume with wild-type EPHA3 = 437.4 mm(3) vs control = 774.7 mm(3), P < .001). Tumor-suppressive effects of wild-type EPHA3 could be overridden in trans by dominant negative EPHA3 somatic mutations discovered in patients with lung cancer. CONCLUSION Cancer-associated EPHA3 mutations attenuate the tumor-suppressive effects of normal EPHA3 in lung cancer.
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Affiliation(s)
- Guanglei Zhuang
- Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
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34
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Stepanenko AA, Kavsan VM. Evolutionary karyotypic theory of cancer versus conventional cancer gene mutation theory. ACTA ACUST UNITED AC 2012. [DOI: 10.7124/bc.000059] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- A. A. Stepanenko
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
| | - V. M. Kavsan
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
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RNA-Seq and human complex diseases: recent accomplishments and future perspectives. Eur J Hum Genet 2012; 21:134-42. [PMID: 22739340 DOI: 10.1038/ejhg.2012.129] [Citation(s) in RCA: 151] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The availability of the human genome sequence has allowed identification of disease-causing mutations in many Mendelian disorders, and detection of significant associations of nucleotide polymorphisms to complex diseases and traits. Despite these progresses, finding the causative variations for most of the common diseases remains a complex task. Several studies have shown gene expression analyses provide a quite unbiased way to investigate complex traits and common disorders' pathogenesis. Therefore, whole-transcriptome analysis is increasingly acquiring a key role in the knowledge of mechanisms responsible for complex diseases. Hybridization- and tag-based technologies have elucidated the involvement of multiple genes and pathways in pathological conditions, providing insights into the expression of thousand of coding and noncoding RNAs, such as microRNAs. However, the introduction of Next-Generation Sequencing, particularly of RNA-Seq, has overcome some drawbacks of previously used technologies. Identifying, in a single experiment, potentially novel genes/exons and splice isoforms, RNA editing, fusion transcripts and allele-specific expression are some of its advantages. RNA-Seq has been fruitfully applied to study cancer and host-pathogens interactions, and it is taking first steps for studying neurodegenerative diseases (ND) as well as neuropsychiatric diseases. In addition, it is emerging as a very powerful tool to study quantitative trait loci associated with gene expression in complex diseases. This paper provides an overview on gene expression profiling of complex diseases, with emphasis on RNA-Seq, its advantages over conventional technologies for studying cancer and ND, and for linking nucleotide variations to gene expression changes, also discussing its limitations.
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Valsesia A, Stevenson BJ, Waterworth D, Mooser V, Vollenweider P, Waeber G, Jongeneel CV, Beckmann JS, Kutalik Z, Bergmann S. Identification and validation of copy number variants using SNP genotyping arrays from a large clinical cohort. BMC Genomics 2012; 13:241. [PMID: 22702538 PMCID: PMC3464625 DOI: 10.1186/1471-2164-13-241] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Accepted: 06/15/2012] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Genotypes obtained with commercial SNP arrays have been extensively used in many large case-control or population-based cohorts for SNP-based genome-wide association studies for a multitude of traits. Yet, these genotypes capture only a small fraction of the variance of the studied traits. Genomic structural variants (GSV) such as Copy Number Variation (CNV) may account for part of the missing heritability, but their comprehensive detection requires either next-generation arrays or sequencing. Sophisticated algorithms that infer CNVs by combining the intensities from SNP-probes for the two alleles can already be used to extract a partial view of such GSV from existing data sets. RESULTS Here we present several advances to facilitate the latter approach. First, we introduce a novel CNV detection method based on a Gaussian Mixture Model. Second, we propose a new algorithm, PCA merge, for combining copy-number profiles from many individuals into consensus regions. We applied both our new methods as well as existing ones to data from 5612 individuals from the CoLaus study who were genotyped on Affymetrix 500K arrays. We developed a number of procedures in order to evaluate the performance of the different methods. This includes comparison with previously published CNVs as well as using a replication sample of 239 individuals, genotyped with Illumina 550K arrays. We also established a new evaluation procedure that employs the fact that related individuals are expected to share their CNVs more frequently than randomly selected individuals. The ability to detect both rare and common CNVs provides a valuable resource that will facilitate association studies exploring potential phenotypic associations with CNVs. CONCLUSION Our new methodologies for CNV detection and their evaluation will help in extracting additional information from the large amount of SNP-genotyping data on various cohorts and use this to explore structural variants and their impact on complex traits.
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Affiliation(s)
- Armand Valsesia
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
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38
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Gilmore SJ. High throughput investigative Dermatology in 2012 and beyond: A new era beckons. Australas J Dermatol 2012; 54:1-8. [PMID: 22506776 DOI: 10.1111/j.1440-0960.2012.00883.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
High throughput molecular biology began around the mid-1990s with the introduction of microarrays - a technology that enabled investigators to quantify the cellular expression levels of tens of thousands of mRNA transcripts simultaneously. To date, a large number of microarray experiments have been performed in the investigation of RNA expression signatures in normal and pathological tissues. This review focuses on a next generation tool in high throughput investigation: RNA sequencing or RNA-Seq, highlighting its advantages over traditional microarray investigation and discussing its utility in investigative dermatology. In contrast with the results obtained from microarray experiments, RNA-Seq generates mRNA abundance counts, can identify novel transcripts and splice variants, and provides sequence resolution at the level of single base-pairs. Implementing RNA-Seq in the investigation of skin disease will yield novel insights into the pathogenesis of disease, will facilitate the discovery of new diseases and new mechanisms of disease, and will allow researchers to probe genetic disease in high resolution and with unprecedented efficiency.
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Affiliation(s)
- Stephen J Gilmore
- Dermatology Research Centre, University of Queensland, School of Medicine, Princess Alexandra Hospital, Brisbane, Australia.
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39
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Functional sphere profiling reveals the complexity of neuroblastoma tumor-initiating cell model. Neoplasia 2012; 13:991-1004. [PMID: 22028624 DOI: 10.1593/neo.11800] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Revised: 08/30/2011] [Accepted: 09/06/2011] [Indexed: 01/06/2023] Open
Abstract
Neuroblastoma (NB) is a neural crest-derived childhood tumor characterized by a remarkable phenotypic diversity, ranging from spontaneous regression to fatal metastatic disease. Although the cancer stem cell (CSC) model provides a trail to characterize the cells responsible for tumor onset, the NB tumor-initiating cell (TIC) has not been identified. In this study, the relevance of the CSC model in NB was investigated by taking advantage of typical functional stem cell characteristics. A predictive association was established between self-renewal, as assessed by serial sphere formation, and clinical aggressiveness in primary tumors. Moreover, cell subsets gradually selected during serial sphere culture harbored increased in vivo tumorigenicity, only highlighted in an orthotopic microenvironment. A microarray time course analysis of serial spheres passages from metastatic cells allowed us to specifically "profile" the NB stem cell-like phenotype and to identify CD133, ABC transporter, and WNT and NOTCH genes as spheres markers. On the basis of combined sphere markers expression, at least two distinct tumorigenic cell subpopulations were identified, also shown to preexist in primary NB. However, sphere markers-mediated cell sorting of parental tumor failed to recapitulate the TIC phenotype in the orthotopic model, highlighting the complexity of the CSC model. Our data support the NB stem-like cells as a dynamic and heterogeneous cell population strongly dependent on microenvironmental signals and add novel candidate genes as potential therapeutic targets in the control of high-risk NB.
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Baitsch L, Legat A, Barba L, Fuertes Marraco SA, Rivals JP, Baumgaertner P, Christiansen-Jucht C, Bouzourene H, Rimoldi D, Pircher H, Rufer N, Matter M, Michielin O, Speiser DE. Extended co-expression of inhibitory receptors by human CD8 T-cells depending on differentiation, antigen-specificity and anatomical localization. PLoS One 2012; 7:e30852. [PMID: 22347406 PMCID: PMC3275569 DOI: 10.1371/journal.pone.0030852] [Citation(s) in RCA: 149] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Accepted: 12/21/2011] [Indexed: 12/26/2022] Open
Abstract
Inhibitory receptors mediate CD8 T-cell hyporesponsiveness against cancer and infectious diseases. PD-1 and CTLA-4 have been extensively studied, and blocking antibodies have already shown clinical benefit for cancer patients. Only little is known on extended co-expression of inhibitory receptors and their ligands. Here we analyzed the expression of eight inhibitory receptors by tumor-antigen specific CD8 T-cells. We found that the majority of effector T-cells simultaneously expressed four or more of the inhibitory receptors BTLA, TIM-3, LAG-3, KRLG-1, 2B4, CD160, PD-1 and CTLA-4. There were major differences depending on antigen-specificity, differentiation and anatomical localization of T-cells. On the other hand, naive T-cells were only single or double positive for BTLA and TIM-3. Extended co-expression is likely relevant for effector T-cells, as we found expression of multiple ligands in metastatic lesions of melanoma patients. Together, our data suggest that naive T-cells are primarily regulated by BTLA and TIM-3, whereas effector cells interact via larger numbers of inhibitory receptors. Blocking multiple inhibitory receptors simultaneously or sequentially may improve T-cell based therapies, but further studies are necessary to clarify the role of each receptor-ligand pair.
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Affiliation(s)
- Lukas Baitsch
- Clinical Tumor Biology and Immunotherapy Unit, Ludwig Center, University of Lausanne, Lausanne, Switzerland
| | - Amandine Legat
- Clinical Tumor Biology and Immunotherapy Unit, Ludwig Center, University of Lausanne, Lausanne, Switzerland
| | - Leticia Barba
- Clinical Tumor Biology and Immunotherapy Unit, Ludwig Center, University of Lausanne, Lausanne, Switzerland
| | - Silvia A. Fuertes Marraco
- Clinical Tumor Biology and Immunotherapy Unit, Ludwig Center, University of Lausanne, Lausanne, Switzerland
| | - Jean-Paul Rivals
- University Hospital Center, University of Lausanne, Lausanne, Switzerland
| | - Petra Baumgaertner
- Clinical Tumor Biology and Immunotherapy Unit, Ludwig Center, University of Lausanne, Lausanne, Switzerland
| | - Céline Christiansen-Jucht
- Clinical Tumor Biology and Immunotherapy Unit, Ludwig Center, University of Lausanne, Lausanne, Switzerland
| | - Hanifa Bouzourene
- University Hospital Center, University of Lausanne, Lausanne, Switzerland
| | - Donata Rimoldi
- Clinical Tumor Biology and Immunotherapy Unit, Ludwig Center, University of Lausanne, Lausanne, Switzerland
| | - Hanspeter Pircher
- Department of Immunology, Institute of Medical Microbiology and Hygiene, University of Freiburg, Freiburg, Germany
| | - Nathalie Rufer
- Clinical Tumor Biology and Immunotherapy Unit, Ludwig Center, University of Lausanne, Lausanne, Switzerland
- University Hospital Center, University of Lausanne, Lausanne, Switzerland
| | - Maurice Matter
- University Hospital Center, University of Lausanne, Lausanne, Switzerland
| | - Olivier Michielin
- Clinical Tumor Biology and Immunotherapy Unit, Ludwig Center, University of Lausanne, Lausanne, Switzerland
- University Hospital Center, University of Lausanne, Lausanne, Switzerland
| | - Daniel E. Speiser
- Clinical Tumor Biology and Immunotherapy Unit, Ludwig Center, University of Lausanne, Lausanne, Switzerland
- Service of Radiation Oncology, Lausanne University Hospital, Lausanne, Switzerland
- * E-mail:
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Lisabeth EM, Fernandez C, Pasquale EB. Cancer somatic mutations disrupt functions of the EphA3 receptor tyrosine kinase through multiple mechanisms. Biochemistry 2012; 51:1464-75. [PMID: 22242939 DOI: 10.1021/bi2014079] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The Eph receptor tyrosine kinases make up an important family of signal transduction molecules that control many cellular processes, including cell adhesion and movement, cell shape, and cell growth. All of these are important aspects of cancer progression, but the relationship between Eph receptors and cancer is complex and not fully understood. Genetic screens of tumor specimens from cancer patients have revealed somatic mutations in many Eph receptors. The most highly mutated Eph receptor is EphA3, but its functional role in cancer is currently not well established. Here we show that many EphA3 mutations identified in lung, colorectal, and hepatocellular cancers, melanoma, and glioblastoma impair kinase activity or ephrin ligand binding and/or decrease the level of receptor cell surface localization. These results suggest that EphA3 has ephrin- and kinase-dependent tumor suppressing activities, which are disrupted by somatic cancer mutations.
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Affiliation(s)
- Erika M Lisabeth
- Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
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42
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Baitsch L, Legat A, Barba L, Fuertes Marraco SA, Rivals JP, Baumgaertner P, Christiansen-Jucht C, Bouzourene H, Rimoldi D, Pircher H, Rufer N, Matter M, Michielin O, Speiser DE. Extended co-expression of inhibitory receptors by human CD8 T-cells depending on differentiation, antigen-specificity and anatomical localization. PLoS One 2012. [PMID: 22347406 DOI: 10.1371/journal.pone.0030852.s006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Inhibitory receptors mediate CD8 T-cell hyporesponsiveness against cancer and infectious diseases. PD-1 and CTLA-4 have been extensively studied, and blocking antibodies have already shown clinical benefit for cancer patients. Only little is known on extended co-expression of inhibitory receptors and their ligands. Here we analyzed the expression of eight inhibitory receptors by tumor-antigen specific CD8 T-cells. We found that the majority of effector T-cells simultaneously expressed four or more of the inhibitory receptors BTLA, TIM-3, LAG-3, KRLG-1, 2B4, CD160, PD-1 and CTLA-4. There were major differences depending on antigen-specificity, differentiation and anatomical localization of T-cells. On the other hand, naive T-cells were only single or double positive for BTLA and TIM-3. Extended co-expression is likely relevant for effector T-cells, as we found expression of multiple ligands in metastatic lesions of melanoma patients. Together, our data suggest that naive T-cells are primarily regulated by BTLA and TIM-3, whereas effector cells interact via larger numbers of inhibitory receptors. Blocking multiple inhibitory receptors simultaneously or sequentially may improve T-cell based therapies, but further studies are necessary to clarify the role of each receptor-ligand pair.
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Affiliation(s)
- Lukas Baitsch
- Clinical Tumor Biology and Immunotherapy Unit, Ludwig Center, University of Lausanne, Lausanne, Switzerland
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Nikolaev SI, Rimoldi D, Iseli C, Valsesia A, Robyr D, Gehrig C, Harshman K, Guipponi M, Bukach O, Zoete V, Michielin O, Muehlethaler K, Speiser D, Beckmann JS, Xenarios I, Halazonetis TD, Jongeneel CV, Stevenson BJ, Antonarakis SE. Exome sequencing identifies recurrent somatic MAP2K1 and MAP2K2 mutations in melanoma. Nat Genet 2011; 44:133-9. [PMID: 22197931 DOI: 10.1038/ng.1026] [Citation(s) in RCA: 313] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Accepted: 11/04/2011] [Indexed: 12/14/2022]
Abstract
We performed exome sequencing to detect somatic mutations in protein-coding regions in seven melanoma cell lines and donor-matched germline cells. All melanoma samples had high numbers of somatic mutations, which showed the hallmark of UV-induced DNA repair. Such a hallmark was absent in tumor sample-specific mutations in two metastases derived from the same individual. Two melanomas with non-canonical BRAF mutations harbored gain-of-function MAP2K1 and MAP2K2 (MEK1 and MEK2, respectively) mutations, resulting in constitutive ERK phosphorylation and higher resistance to MEK inhibitors. Screening a larger cohort of individuals with melanoma revealed the presence of recurring somatic MAP2K1 and MAP2K2 mutations, which occurred at an overall frequency of 8%. Furthermore, missense and nonsense somatic mutations were frequently found in three candidate melanoma genes, FAT4, LRP1B and DSC1.
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Affiliation(s)
- Sergey I Nikolaev
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
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