26 results on '"Thomas Botton"'
Search Results
2. Discovery of a new molecule inducing melanoma cell death: dual AMPK/MELK targeting for novel melanoma therapies
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Emilie Jaune, Elisa Cavazza, Cyril Ronco, Oleksandr Grytsai, Patricia Abbe, Nedra Tekaya, Marwa Zerhouni, Guillaume Beranger, Lisa Kaminski, Frédéric Bost, Maeva Gesson, Meri Tulic, Paul Hofman, Robert Ballotti, Thierry Passeron, Thomas Botton, Rachid Benhida, and Stéphane Rocchi
- Subjects
Cytology ,QH573-671 - Abstract
Abstract In the search of biguanide-derived molecules against melanoma, we have discovered and developed a series of bioactive products and identified the promising new compound CRO15. This molecule exerted anti-melanoma effects on cells lines and cells isolated from patients including the ones derived from tumors resistant to BRAF inhibitors. Moreover, CRO15 was able to decrease viability of cells lines from a broad range of cancer types. This compound acts by two distinct mechanisms. First by activating the AMPK pathway induced by a mitochondrial disorder. Second by inhibition of MELK kinase activity, which induces cell cycle arrest and activation of DNA damage repair pathways by p53 and REDD1 activation. All of these mechanisms activate autophagic and apoptotic processes resulting in melanoma cell death. The strong efficacy of CRO15 to reduce the growth of melanoma xenograft sensitive or resistant to BRAF inhibitors opens interesting perspective.
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- 2021
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- View/download PDF
3. Genetic Heterogeneity of BRAF Fusion Kinases in Melanoma Affects Drug Responses
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Thomas Botton, Eric Talevich, Vivek Kumar Mishra, Tongwu Zhang, A. Hunter Shain, Céline Berquet, Alexander Gagnon, Robert L. Judson, Robert Ballotti, Antoni Ribas, Meenhard Herlyn, Stéphane Rocchi, Kevin M. Brown, Nicholas K. Hayward, Iwei Yeh, and Boris C. Bastian
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Biology (General) ,QH301-705.5 - Abstract
Summary: BRAF fusions are detected in numerous neoplasms, but their clinical management remains unresolved. We identified six melanoma lines harboring BRAF fusions representative of the clinical cases reported in the literature. Their unexpected heterogeneous responses to RAF and MEK inhibitors could be categorized upon specific features of the fusion kinases. Higher expression level correlated with resistance, and fusion partners containing a dimerization domain promoted paradoxical activation of the mitogen-activated protein kinase (MAPK) pathway and hyperproliferation in response to first- and second-generation RAF inhibitors. By contrast, next-generation αC-IN/DFG-OUT RAF inhibitors blunted paradoxical activation across all lines and had their therapeutic efficacy further increased in vitro and in vivo by combination with MEK inhibitors, opening perspectives in the clinical management of tumors harboring BRAF fusions. : Botton et al. shed light on the heterogeneity of BRAF fusions encountered in melanocytic tumors and characterize features influencing their signaling and drug response. These findings unveil the singularities of BRAF fusions and establish general principles to guide their clinical management in melanoma and other malignancies. Keywords: BRAF fusion, melanoma, paradoxical activation, RAF inhibitor, MEK inhibitor, sequencing, rearrangement, translocation, kinase, pre-clinical
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- 2019
- Full Text
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4. CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing.
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Eric Talevich, A Hunter Shain, Thomas Botton, and Boris C Bastian
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Biology (General) ,QH301-705.5 - Abstract
Germline copy number variants (CNVs) and somatic copy number alterations (SCNAs) are of significant importance in syndromic conditions and cancer. Massively parallel sequencing is increasingly used to infer copy number information from variations in the read depth in sequencing data. However, this approach has limitations in the case of targeted re-sequencing, which leaves gaps in coverage between the regions chosen for enrichment and introduces biases related to the efficiency of target capture and library preparation. We present a method for copy number detection, implemented in the software package CNVkit, that uses both the targeted reads and the nonspecifically captured off-target reads to infer copy number evenly across the genome. This combination achieves both exon-level resolution in targeted regions and sufficient resolution in the larger intronic and intergenic regions to identify copy number changes. In particular, we successfully inferred copy number at equivalent to 100-kilobase resolution genome-wide from a platform targeting as few as 293 genes. After normalizing read counts to a pooled reference, we evaluated and corrected for three sources of bias that explain most of the extraneous variability in the sequencing read depth: GC content, target footprint size and spacing, and repetitive sequences. We compared the performance of CNVkit to copy number changes identified by array comparative genomic hybridization. We packaged the components of CNVkit so that it is straightforward to use and provides visualizations, detailed reporting of significant features, and export options for integration into existing analysis pipelines. CNVkit is freely available from https://github.com/etal/cnvkit.
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- 2016
- Full Text
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5. Rac1 dynamics in the human opportunistic fungal pathogen Candida albicans.
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Romain Vauchelles, Danièle Stalder, Thomas Botton, Robert A Arkowitz, and Martine Bassilana
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Medicine ,Science - Abstract
The small Rho G-protein Rac1 is highly conserved from fungi to humans, with approximately 65% overall sequence identity in Candida albicans. As observed with human Rac1, we show that C. albicans Rac1 can accumulate in the nucleus, and fluorescence recovery after photobleaching (FRAP) together with fluorescence loss in photobleaching (FLIP) studies indicate that this Rho G-protein undergoes nucleo-cytoplasmic shuttling. Analyses of different chimeras revealed that nuclear accumulation of C. albicans Rac1 requires the NLS-motifs at its carboxyl-terminus, which are blocked by prenylation of the adjacent cysteine residue. Furthermore, we show that C. albicans Rac1 dynamics, both at the plasma membrane and in the nucleus, are dependent on its activation state and in particular that the inactive form accumulates faster in the nucleus. Heterologous expression of human Rac1 in C. albicans also results in nuclear accumulation, yet accumulation is more rapid than that of C. albicans Rac1. Taken together our results indicate that Rac1 nuclear accumulation is an inherent property of this G-protein and suggest that the requirements for its nucleo-cytoplasmic shuttling are conserved from fungi to humans.
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- 2010
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6. Genetic Heterogeneity of BRAF Fusion Kinases in Melanoma Affects Drug Responses
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Tongwu Zhang, Nicholas K. Hayward, Boris C. Bastian, Kevin M. Brown, Iwei Yeh, Meenhard Herlyn, A. Hunter Shain, Robert L. Judson, Céline Berquet, Thomas Botton, Eric Talevich, Vivek Mishra, Antoni Ribas, Alexander Gagnon, Robert Ballotti, and Stéphane Rocchi
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0301 basic medicine ,MAPK/ERK pathway ,paradoxical activation ,Oncogene Proteins, Fusion ,Nude ,Medical Physiology ,Drug Resistance ,translocation ,Chromosomal translocation ,Mice ,0302 clinical medicine ,Protein Isoforms ,RNA, Small Interfering ,Melanoma ,lcsh:QH301-705.5 ,RAF inhibitor ,media_common ,Cancer ,Oncogene Proteins ,Kinase ,MEK inhibitor ,Intracellular Signaling Peptides and Proteins ,sequencing ,Gene Expression Regulation, Neoplastic ,5.1 Pharmaceuticals ,Female ,RNA Interference ,Development of treatments and therapeutic interventions ,Mitogen-Activated Protein Kinases ,Dimerization ,Signal Transduction ,Drug ,Proto-Oncogene Proteins B-raf ,pre-clinical ,kinase ,media_common.quotation_subject ,rearrangement ,BRAF fusion ,Mice, Nude ,Biology ,Small Interfering ,General Biochemistry, Genetics and Molecular Biology ,Article ,03 medical and health sciences ,medicine ,melanoma ,Animals ,Humans ,Protein kinase A ,Fusion ,Protein Kinase Inhibitors ,neoplasms ,Neoplastic ,Genetic heterogeneity ,medicine.disease ,030104 developmental biology ,Gene Expression Regulation ,Vemurafenib ,lcsh:Biology (General) ,Drug Resistance, Neoplasm ,Cancer research ,ras Proteins ,RNA ,Neoplasm ,Biochemistry and Cell Biology ,030217 neurology & neurosurgery - Abstract
Summary: BRAF fusions are detected in numerous neoplasms, but their clinical management remains unresolved. We identified six melanoma lines harboring BRAF fusions representative of the clinical cases reported in the literature. Their unexpected heterogeneous responses to RAF and MEK inhibitors could be categorized upon specific features of the fusion kinases. Higher expression level correlated with resistance, and fusion partners containing a dimerization domain promoted paradoxical activation of the mitogen-activated protein kinase (MAPK) pathway and hyperproliferation in response to first- and second-generation RAF inhibitors. By contrast, next-generation αC-IN/DFG-OUT RAF inhibitors blunted paradoxical activation across all lines and had their therapeutic efficacy further increased in vitro and in vivo by combination with MEK inhibitors, opening perspectives in the clinical management of tumors harboring BRAF fusions. : Botton et al. shed light on the heterogeneity of BRAF fusions encountered in melanocytic tumors and characterize features influencing their signaling and drug response. These findings unveil the singularities of BRAF fusions and establish general principles to guide their clinical management in melanoma and other malignancies. Keywords: BRAF fusion, melanoma, paradoxical activation, RAF inhibitor, MEK inhibitor, sequencing, rearrangement, translocation, kinase, pre-clinical
- Published
- 2019
7. NTRK3 kinase fusions in Spitz tumours
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Takeshi Isoyama, Maria C. Garrido, Alexander Gagnon, Boris C. Bastian, Kenji Nakamaru, A. Hunter Shain, Timothy H. McCalmont, Thomas Botton, Iwei Yeh, Philip E. LeBoit, Swapna S. Vemula, Meng Kian Tee, and Alyssa J. Sparatta
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0301 basic medicine ,biology ,Kinase ,Melanoma ,medicine.disease ,Spitz nevus ,Receptor tyrosine kinase ,Pathology and Forensic Medicine ,03 medical and health sciences ,030104 developmental biology ,0302 clinical medicine ,030220 oncology & carcinogenesis ,Trk receptor ,Immunology ,medicine ,ROS1 ,biology.protein ,Cancer research ,Oncogene Fusion ,Protein kinase A - Abstract
Oncogenic fusions in TRK family receptor tyrosine kinases have been identified in several cancers and can serve as therapeutic targets. We identified ETV6-NTRK3, MYO5A-NTRK3 and MYH9-NTRK3 fusions in Spitz tumours, and demonstrated that NTRK3 fusions constitutively activate the mitogen-activated protein kinase, phosphoinositide 3-kinase and phospholipase Cγ1 pathways in melanocytes. This signalling was inhibited by DS-6051a, a small-molecule inhibitor of NTRK1/2/3 and ROS1. NTRK3 fusions expand the range of oncogenic kinase fusions in melanocytic neoplasms and offer targets for a small subset of melanomas for which no targeted options currently exist. Copyright © 2016 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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- 2016
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8. Hybrid Capture-Based Tumor Sequencing and Copy Number Analysis to Confirm Origin of Metachronous Metastases in BRCA1-Mutant Cholangiocarcinoma Harboring a Novel YWHAZ-BRAF Fusion
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Eric A. Collisson, Huat Chye Lim, Phil Stephens, Spencer C. Behr, Robin Kate Kelley, Meagan Montesion, John D. Gordan, Thomas Botton, and Sarah E. Umetsu
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0301 basic medicine ,Proto-Oncogene Proteins B-raf ,Liver Cancer ,Cancer Research ,DNA Copy Number Variations ,Oncology and Carcinogenesis ,Copy number analysis ,Genomics ,DNA sequencing ,Germline ,Metastasis ,Cholangiocarcinoma ,03 medical and health sciences ,0302 clinical medicine ,Rare Diseases ,Clinical Research ,Genetics ,Medicine ,Humans ,2.1 Biological and endogenous factors ,Clinical significance ,Oncology & Carcinogenesis ,Neoplasm Metastasis ,Aetiology ,Digestive Diseases - (Gallbladder) ,Cancer ,screening and diagnosis ,business.industry ,BRCA1 Protein ,Liver Disease ,Human Genome ,medicine.disease ,4.1 Discovery and preclinical testing of markers and technologies ,Detection ,030104 developmental biology ,Good Health and Well Being ,Oncology ,030220 oncology & carcinogenesis ,YWHAZ ,Cancer research ,business ,Digestive Diseases ,Biotechnology - Abstract
Biliary tract cancers such as cholangiocarcinoma represent a heterogeneous group of cancers that can be difficult to diagnose. Recent comprehensive genomic analyses in large cholangiocarcinoma cohorts have defined important molecular subgroups within cholangiocarcinoma that may relate to anatomic location and etiology [1-4] and may predict responsiveness to targeted therapies in development [5-7]. These emerging data highlight the potential for tumor genomics to inform diagnosis and treatment options in this challenging tumor type. We report the case of a patient with a germline BRCA1 mutation who presented with a cholangiocarcinoma driven by the novel YWHAZ-BRAF fusion. Hybrid capture-based DNA sequencing and copy number analysis performed as part of clinical care demonstrated that two later-occurring tumors were clonally derived from the primary cholangiocarcinoma rather than distinct new primaries, revealing an unusual pattern of late metachronous metastasis. We discuss the clinical significance of these genetic alterations and their relevance to therapeutic strategies. Key Points Hybrid capture-based next-generation DNA sequencing assays can provide diagnostic clarity in patients with unusual patterns of metastasis and recurrence in which the pathologic diagnosis is ambiguous. To our knowledge, this is the first reported case of a YWHAZ-BRAF fusion in pancreaticobiliary cancer, and a very rare case of cholangiocarcinoma in the setting of a germline BRCA1 mutation. The patient's BRCA1 mutation and YWHAZ-BRAF fusion constitute potential targets for future therapy.
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- 2018
9. Bi-allelic loss of CDKN2A initiates melanoma invasion via BRN2 activation
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Jue Lin, Hanlin Zeng, Aparna Jorapur, Andrew S. McNeal, Matthew Donne, Nancy M. Joseph, Ingmar N. Bastian, Laura B. Pincus, A. Hunter Shain, Thomas Botton, Yuntian Zhang, Rodrigo Torres, Iwei Yeh, Robert L. Judson, Ursula E. Lang, Beth S. Ruben, Boris C. Bastian, Jeffrey P. North, and Richard Yu
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0301 basic medicine ,Male ,Cancer Research ,Skin Neoplasms ,Lung Neoplasms ,Loss of Heterozygosity ,law.invention ,Metastasis ,Mice ,CDKN2A ,law ,Cell Movement ,hemic and lymphatic diseases ,E2F1 ,2.1 Biological and endogenous factors ,Aetiology ,Melanoma ,Cancer ,Tumor ,Genomics ,invasion ,Phenotype ,Oncology ,Female ,Cellular model ,Signal Transduction ,Proto-Oncogene Proteins B-raf ,Transcriptional Activation ,Oncology and Carcinogenesis ,Biology ,BRN2 ,Article ,Cell Line ,03 medical and health sciences ,CRISPR engineering ,medicine ,melanoma ,Animals ,Point Mutation ,Humans ,Neoplasm Invasiveness ,Oncology & Carcinogenesis ,Transcription factor ,neoplasms ,Cyclin-Dependent Kinase Inhibitor p16 ,Homeodomain Proteins ,Neoplastic ,Neurosciences ,medicine.disease ,digestive system diseases ,melanocytes ,stomatognathic diseases ,030104 developmental biology ,Gene Expression Regulation ,POU Domain Factors ,Cancer research ,Suppressor ,Inbred NOD ,E2F1 Transcription Factor - Abstract
Loss of the CDKN2A tumor suppressor is associated with melanoma metastasis, but the mechanisms connecting the phenomena are unknown. Using CRISPR-Cas9 to engineer a cellular model of melanoma initiation from primary human melanocytes, we discovered that a lineage restricted transcription factor, BRN2, is downstream of CDKN2A and directly regulated by E2F1. In a cohort of melanocytic tumors that capture distinct progression stages, we observed that CDKN2A loss coincides with both the onset of invasive behavior and increased BRN2 expression. Loss of the CDKN2A protein product p16(INK4A) permitted metastatic dissemination of human melanoma lines in mice, a phenotype rescued by inhibition of BRN2. These results demonstrate a mechanism by which CDKN2A suppresses the initiation of melanoma invasion through inhibition of BRN2.
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- 2018
10. Comment on ‘Testing for BRAF fusions in patients with advanced BRAF/NRAS/KIT wild-type melanomas permits to identify patients who could benefit of anti-MEK targeted therapy’
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Thomas Botton, Stéphane Rocchi, and Thierry Passeron
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Proto-Oncogene Proteins B-raf ,0301 basic medicine ,Neuroblastoma RAS viral oncogene homolog ,endocrine system diseases ,medicine.medical_treatment ,Immune checkpoint inhibitors ,GTP Phosphohydrolases ,Pathology and Forensic Medicine ,Targeted therapy ,03 medical and health sciences ,0302 clinical medicine ,medicine ,Humans ,In patient ,Melanoma ,neoplasms ,business.industry ,Wild type ,Membrane Proteins ,General Medicine ,Immunotherapy ,medicine.disease ,digestive system diseases ,030104 developmental biology ,030220 oncology & carcinogenesis ,Cancer research ,%22">Fish ,business - Abstract
We read with great interest the article from Le Flahec and colleagues encouraging the testing for BRAF fusions in patients with advanced BRAF/NRAS/KIT wild-type melanomas.1 As emphasised in the article, the only viable therapeutic option currently available for patients lacking BRAF point mutations is immunotherapy. However, despite unprecedented efficacy gain, combined immune checkpoint inhibitors therapy only achieves long-lasting response in a third of the patients.2 Thus, considering that BRAF fusions are the most common oncogenic rearrangements in melanoma and that they are clinically actionable, we agree with the authors that their detection in BRAF/NRAS/KIT wild-type tumours is of theranostic importance. To further support the detection of BRAF fusions in melanoma, we would like to comment on some of the conclusions in the light of our recently published article on the subject.3 Our discovery that the nature of the fusion partner can influence the …
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- 2019
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11. Exome sequencing of desmoplastic melanoma identifies recurrent NFKBIE promoter mutations and diverse activating mutations in the MAPK pathway
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Eric Talevich, Hojabr Kakavand, Iwei Yeh, Thomas Botton, Joe W. Gray, Maria C. Garrido, Jongsuk Chung, Graham J. Mann, Nam Huh, J. Zachary Sanborn, Thomas Wiesner, Adam B. Olshen, Joe S Hur, A. Hunter Shain, Alexander Gagnon, Rajmohan Murali, Raymond J. Cho, Klaus J. Busam, Nicholas J. Wang, Ritu Roy, Richard A. Scolyer, John F. Thompson, and Boris C. Bastian
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Neuroblastoma RAS viral oncogene homolog ,MAP Kinase Signaling System ,Biology ,medicine.disease_cause ,Article ,Proto-Oncogene Proteins ,Genetics ,medicine ,Humans ,Exome ,Promoter Regions, Genetic ,neoplasms ,Melanoma ,Exome sequencing ,Desmoplastic melanoma ,Mutation ,medicine.disease ,NFKBIE ,3. Good health ,PTPN11 ,Cancer research ,I-kappa B Proteins - Abstract
Desmoplastic melanoma is an uncommon variant of melanoma with sarcomatous histology, distinct clinical behavior and unknown pathogenesis. We performed low-coverage genome and high-coverage exome sequencing of 20 desmoplastic melanomas, followed by targeted sequencing of 293 genes in a validation cohort of 42 cases. A high mutation burden (median of 62 mutations/Mb) ranked desmoplastic melanoma among the most highly mutated cancers. Mutation patterns strongly implicate ultraviolet radiation as the dominant mutagen, indicating a superficially located cell of origin. Newly identified alterations included recurrent promoter mutations of NFKBIE, encoding NF-κB inhibitor ɛ (IκBɛ), in 14.5% of samples. Common oncogenic mutations in melanomas, in particular in BRAF (encoding p.Val600Glu) and NRAS (encoding p.Gln61Lys or p.Gln61Arg), were absent. Instead, other genetic alterations known to activate the MAPK and PI3K signaling cascades were identified in 73% of samples, affecting NF1, CBL, ERBB2, MAP2K1, MAP3K1, BRAF, EGFR, PTPN11, MET, RAC1, SOS2, NRAS and PIK3CA, some of which are candidates for targeted therapies.
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- 2015
12. Hybrid Capture-Based Tumor Sequencing and Copy Number Analysis to Confirm Origin of Metachronous Metastases in
- Author
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Huat C, Lim, Meagan, Montesion, Thomas, Botton, Eric A, Collisson, Sarah E, Umetsu, Spencer C, Behr, John D, Gordan, Phil J, Stephens, and Robin K, Kelley
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Cholangiocarcinoma ,Proto-Oncogene Proteins B-raf ,DNA Copy Number Variations ,BRCA1 Protein ,Humans ,Precision Medicine Clinic: Molecular Tumor Board ,Neoplasm Metastasis ,digestive system diseases - Abstract
Biliary tract cancers such as cholangiocarcinoma represent a heterogeneous group of cancers that can be difficult to diagnose. Recent comprehensive genomic analyses in large cholangiocarcinoma cohorts have defined important molecular subgroups within cholangiocarcinoma that may relate to anatomic location and etiology [1], [2], [3], [4] and may predict responsiveness to targeted therapies in development [5], [6], [7]. These emerging data highlight the potential for tumor genomics to inform diagnosis and treatment options in this challenging tumor type. We report the case of a patient with a germline BRCA1 mutation who presented with a cholangiocarcinoma driven by the novel YWHAZ‐BRAF fusion. Hybrid capture‐based DNA sequencing and copy number analysis performed as part of clinical care demonstrated that two later‐occurring tumors were clonally derived from the primary cholangiocarcinoma rather than distinct new primaries, revealing an unusual pattern of late metachronous metastasis. We discuss the clinical significance of these genetic alterations and their relevance to therapeutic strategies. KEY POINTS. Hybrid capture‐based next‐generation DNA sequencing assays can provide diagnostic clarity in patients with unusual patterns of metastasis and recurrence in which the pathologic diagnosis is ambiguous. To our knowledge, this is the first reported case of a YWHAZ‐BRAF fusion in pancreaticobiliary cancer, and a very rare case of cholangiocarcinoma in the setting of a germline BRCA1 mutation. The patient's BRCA1 mutation and YWHAZ‐BRAF fusion constitute potential targets for future therapy.
- Published
- 2017
13. Compounds Triggering ER Stress Exert Anti-Melanoma Effects and Overcome BRAF Inhibitor Resistance
- Author
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Emilie Jaune, Hella Amdouni, Anne-Sophie Dabert-Gay, Jean-Sébastien Annicotte, Magali Plaisant, Solange Moréra, Delphine Debayle, Corine Bertolotto, Patricia Abbe, Thierry Passeron, Abdelali Lehraiki, Laurent Héliot, Robert Ballotti, Philippe Gual, Baharia Mograbi, Cyril Ronco, Mariano Gonzalez-Pisfil, Thomas Botton, Damien Alcor, Caroline Robert, Michael Cerezo, Stéphane Rocchi, Nabil Rabhi, Véronique Hofman, Armelle Vigouroux, Antoine Millet, Rachid Benhida, Maruf M.U. Ali, Paul Hofman, Florian Rouaud, Université Nice Sophia Antipolis - Faculté de Médecine (UNS UFR Médecine), Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA), Centre méditerranéen de médecine moléculaire (C3M), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institutions et Dynamiques Historiques de l'Économie et de la Société (IDHES), École normale supérieure - Cachan (ENS Cachan)-Université Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Institut de Chimie de Nice (ICN), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Service de Dermatologie [Nice], Hôpital Archet 2 [Nice] (CHU), Institut de Recherche sur le Cancer et le Vieillissement (IRCAN), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Nice Sophia Antipolis (... - 2019) (UNS), Institut de pharmacologie moléculaire et cellulaire (IPMC), Centre d'Etudes Lasers Intenses et Applications (CELIA), Université de Bordeaux (UB)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Génomique Intégrative et Modélisation des Maladies Métaboliques (EGID), Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Centre National de la Recherche Scientifique (CNRS)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Laboratoire de Physique des Lasers, Atomes et Molécules - UMR 8523 (PhLAM), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Institut Français de Recherche pour l'Exploitation de la Mer - Brest (IFREMER), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Microbiologie et enzymologie structurale (MESB3S), Département Biochimie, Biophysique et Biologie Structurale (B3S), Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, Laboratoire d'Enzymologie et Biochimie Structurales, Centre National de la Recherche Scientifique (CNRS), University of Stavanger, Laboratoire Chrono-environnement - UFC (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Centre méditérannéen de médecine moléculaire ( C3M ), Université Nice Sophia Antipolis ( UNS ), Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Université Nice Sophia Antipolis - Faculté de Médecine ( UNS UFR Médecine ), Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ), Institut de Chimie de Nice ( ICN ), Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ) -Centre National de la Recherche Scientifique ( CNRS ), Hôpital Archet 2 [Nice] ( CHU ), Institut de Recherche sur le Cancer et le Vieillissement ( IRCAN ), Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Pathologie Clinique et Expérimentale, Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ) -Hôpital pasteur [Colmar]-CHU Nice, Institut de pharmacologie moléculaire et cellulaire ( IPMC ), Génomique Intégrative et Modélisation des Maladies Métaboliques ( EGID ), Institut Pasteur de Lille, Réseau International des Instituts Pasteur ( RIIP ) -Réseau International des Instituts Pasteur ( RIIP ) -Université de Lille-Centre Hospitalier Régional Universitaire [Lille] ( CHRU Lille ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Physique des Lasers, Atomes et Molécules - UMR 8523 ( PhLAM ), Université de Lille-Centre National de la Recherche Scientifique ( CNRS ), Département de médecine oncologique [Gustave Roussy], Institut Gustave Roussy ( IGR ), Microbiologie et enzymologie structurale ( MESB3S ), Département Biochimie, Biophysique et Biologie Structurale ( B3S ), Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ) -Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ), Department of Life Sciences, Imperial College London, Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Côte d'Azur (UCA), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Metabolic functional (epi)genomics and molecular mechanisms involved in type 2 diabetes and related diseases - UMR 8199 - UMR 1283 (EGENODIA (GI3M)), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Hôpital pasteur [Colmar]-Centre Hospitalier Universitaire de Nice (CHU Nice), Institut Gustave Roussy (IGR), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA), Metabolic functional (epi)genomics and molecular mechanisms involved in type 2 diabetes and related diseases - UMR 8199 - UMR 1283 (GI3M), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Bordeaux (UB), Institut Français de Recherche pour l'Exploitation de la Mer - Brest (IFREMER Centre de Bretagne), Institutions et Dynamiques Historiques de l'Économie et de la Société ( IDHES ), École normale supérieure - Cachan ( ENS Cachan ) -Université Panthéon-Sorbonne ( UP1 ) -Université Paris 8 Vincennes-Saint-Denis ( UP8 ) -Université Paris Nanterre ( UPN ) -Université d'Évry-Val-d'Essonne ( UEVE ) -Centre National de la Recherche Scientifique ( CNRS ), Centre d'Etudes Lasers Intenses et Applications ( CELIA ), Université de Bordeaux ( UB ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Centre National de la Recherche Scientifique ( CNRS ), Institut Français de Recherche pour l'Exploitation de la Mer - Brest ( IFREMER ), Institut Français de Recherche pour l'Exploitation de la Mer ( IFREMER ), Centre National de la Recherche Scientifique ( CNRS ), Laboratoire Chrono-environnement ( LCE ), Université Bourgogne Franche-Comté ( UBFC ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Franche-Comté ( UFC ), and Houel, Ludivine
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0301 basic medicine ,Proto-Oncogene Proteins B-raf ,Cancer Research ,Programmed cell death ,[SDV]Life Sciences [q-bio] ,Antineoplastic Agents ,Pharmacology ,Biology ,Transcriptome ,03 medical and health sciences ,Mice ,0302 clinical medicine ,Cell Line, Tumor ,medicine ,Animals ,Humans ,Endoplasmic Reticulum Chaperone BiP ,Melanoma ,Protein Kinase Inhibitors ,neoplasms ,Heat-Shock Proteins ,030304 developmental biology ,Cell Proliferation ,Regulation of gene expression ,0303 health sciences ,Sulfonamides ,[ SDV ] Life Sciences [q-bio] ,Autophagy ,Cell Biology ,medicine.disease ,Endoplasmic Reticulum Stress ,Xenograft Model Antitumor Assays ,[SDV] Life Sciences [q-bio] ,Gene Expression Regulation, Neoplastic ,030104 developmental biology ,Oncology ,Cell culture ,Apoptosis ,Drug Resistance, Neoplasm ,030220 oncology & carcinogenesis ,Unfolded protein response ,Cancer research - Abstract
International audience; Hepatitis B virus (HBV) is a small DNA virus that replicates by reverse transcription of a terminally redundant RNA, the pregenome. Specific packaging of this transcript into viral capsids is mediated by interaction of the reverse transcriptase, P protein, with the 5'-proximal encapsidation signal epsilon, epsilon-function is correlated with the formation of a hairpin structure containing a bulge and a loop, each consisting of 6 nt. To analyse the importance of primary sequence in these regions, we have combined selection of encapsidation competent individuals from pools of randomized epsilon-sequences in transfected cells with in vitro amplification, thus bypassing the current experimental limitations of the HBV system. While no alterations of the authentic loop sequence were detectable, many different sequences were tolerated in the 3'-part of the bulge. However, at the two 5'-proximal bulge positions the wt sequence was strongly selected for, indicating that for RNA packaging close contacts between protein and the 5'- but not the 3'-part of the bulge are important. Such a bipartite organisation provides a structural basis for the recently demonstrated special role of the 3'-part of the bulge as template for the first nucleotides of (-)-strand DNA in HBV reverse transcription.
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- 2016
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14. CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing
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Boris C. Bastian, Eric Talevich, A. Hunter Shain, and Thomas Botton
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0301 basic medicine ,Molecular biology ,Array CGH ,Mathematical Sciences ,Computational biology ,Sequencing techniques ,DNA library construction ,Morphogenesis ,Copy-number variation ,DNA sequencing ,Genome Sequencing ,Biology (General) ,In Situ Hybridization, Fluorescence ,In Situ Hybridization ,Genetics ,Comparative Genomic Hybridization ,Massive parallel sequencing ,Genome ,Ecology ,High-Throughput Nucleotide Sequencing ,Genomics ,Biological Sciences ,Genomic Library Construction ,Computational Theory and Mathematics ,Modeling and Simulation ,Sequence Analysis ,Research Article ,Human ,DNA Copy Number Variations ,QH301-705.5 ,Bioinformatics ,Copy number analysis ,Biology ,DNA construction ,Deep sequencing ,Fluorescence ,03 medical and health sciences ,Cellular and Molecular Neuroscience ,Information and Computing Sciences ,Humans ,Repeated Sequences ,Ecology, Evolution, Behavior and Systematics ,Comparative genomics ,Biology and life sciences ,Genome, Human ,Human Genome ,Computational Biology ,Sequence Analysis, DNA ,Genome analysis ,DNA ,Genomic Libraries ,Morphogenic Segmentation ,Research and analysis methods ,030104 developmental biology ,Molecular biology techniques ,Software ,Comparative genomic hybridization ,Developmental Biology ,Genome-Wide Association Study - Abstract
Germline copy number variants (CNVs) and somatic copy number alterations (SCNAs) are of significant importance in syndromic conditions and cancer. Massively parallel sequencing is increasingly used to infer copy number information from variations in the read depth in sequencing data. However, this approach has limitations in the case of targeted re-sequencing, which leaves gaps in coverage between the regions chosen for enrichment and introduces biases related to the efficiency of target capture and library preparation. We present a method for copy number detection, implemented in the software package CNVkit, that uses both the targeted reads and the nonspecifically captured off-target reads to infer copy number evenly across the genome. This combination achieves both exon-level resolution in targeted regions and sufficient resolution in the larger intronic and intergenic regions to identify copy number changes. In particular, we successfully inferred copy number at equivalent to 100-kilobase resolution genome-wide from a platform targeting as few as 293 genes. After normalizing read counts to a pooled reference, we evaluated and corrected for three sources of bias that explain most of the extraneous variability in the sequencing read depth: GC content, target footprint size and spacing, and repetitive sequences. We compared the performance of CNVkit to copy number changes identified by array comparative genomic hybridization. We packaged the components of CNVkit so that it is straightforward to use and provides visualizations, detailed reporting of significant features, and export options for integration into existing analysis pipelines. CNVkit is freely available from https://github.com/etal/cnvkit.
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- 2016
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15. Abstract 5518: Bi-allelic loss of CDKN2A initiates melanoma invasion and metastasis via E2F1-BRN2 axis
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Matthew Donne, Robert L. Judson, Ursula E. Lang, A. Hunter Shain, Aparna Jorapur, Hanlin Zeng, Yuntian Zhang, Andrew S. McNeal, Nancy M. Joseph, Ingmar N. Bastian, Iwei Ye, Beth S. Ruben, Boris C. Bastian, Laura B. Pincus, Jeffrey P. North, Jue Lin, Rodrigo Torres, Richard Yu, and Thomas Botton
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Cancer Research ,Melanoma ,Cell cycle ,Biology ,medicine.disease ,Metastasis ,Oncology ,CDKN2A ,Cancer research ,medicine ,E2F1 ,Neoplastic transformation ,neoplasms ,Transcription factor ,Loss function - Abstract
CDKN2A acts as a critical tumor suppressor in melanoma, as evidenced by frequent loss of function mutations and deletion. Loss of CDKN2A is believed to permit escape from senescent pre-neoplastic cell populations through relieve of a cell cycle block mediated by its two gene products. We performed a comprehensive analysis of CDKN2A gene status, mRNA and protein expression levels of p16 and p14 in a cohort of melanomas and their adjacent pre-neoplastic lesions and observed that bi-allelic CDKN2A loss coincides with the progression stage when primary melanomas become invasive. In melanoma lines, p16INK4A, one of the protein products of the CDKN2A locus, is a potent barrier to metastasis, independent of its known role inhibiting cell proliferation. We genetically engineered primary human melanocytes to harbor CDKN2A deletions and/or BRAF V600E mutation at their endogenous BRAF locus. Using this physiologic model for the early phases of neoplastic transformation, we found no evidence for BRAF-induced senescence, rather observing that p16INK4A loss activates a master regulator of melanoma invasion, BRN2, through Rb-E2F1 pathway. These results demonstrate that one of the most frequently altered genes across human cancers, CDKN2A, has an unexpected novel role in inhibiting cellular invasion through lineage specific transcription factors and acts as an essential gatekeeper of early metastatic dissemination. Citation Format: Hanlin Zeng, Aparna Jorapur, A. Hunter Shain, Ursula E. Lang, Rodrigo Torres, Yuntian Zhang, Thomas Botton, Jue Lin, Andrew S. Mcneal, Matthew Donne, Ingmar N. Bastian, Jeffrey North, Laura Pincus, Richard Yu, Beth S. Ruben, Nancy Joseph, Iwei Ye, Boris C. Bastian, Robert L. Judson. Bi-allelic loss of CDKN2A initiates melanoma invasion and metastasis via E2F1-BRN2 axis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5518.
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- 2018
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16. Ciglitazone negatively regulates CXCL1 signaling through MITF to suppress melanoma growth
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Tijana Tomic, Corine Bertolotto, Marcel Deckert, Stéphane Rocchi, Sandy Giuliano, Lluis Fajas, Ortonne Jp, Sophie Tartare-Deckert, Alexandre Puissant, Robert Ballotti, Yann Cheli, and Thomas Botton
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Chemokine CXCL1 ,animal diseases ,Cellular differentiation ,Transplantation, Heterologous ,Down-Regulation ,Mice, Nude ,Antineoplastic Agents ,Apoptosis ,Biology ,Mice ,03 medical and health sciences ,0302 clinical medicine ,Melanocyte differentiation ,Cell Line, Tumor ,Ciglitazone ,medicine ,Animals ,Humans ,RNA, Small Interfering ,Melanoma ,Molecular Biology ,Transcription factor ,030304 developmental biology ,Original Paper ,Microphthalmia-Associated Transcription Factor ,0303 health sciences ,Cell Differentiation ,Cell Biology ,respiratory system ,Microphthalmia-associated transcription factor ,medicine.disease ,Recombinant Proteins ,3. Good health ,CXCL1 ,030220 oncology & carcinogenesis ,Cancer research ,RNA Interference ,Thiazolidinediones ,Signal transduction ,Signal Transduction - Abstract
We have previously demonstrated that the thiazolidinedione ciglitazone inhibited, independently of PPARγ activation, melanoma cell growth. Further investigations now show that ciglitazone effects are mediated through the regulation of secreted factors. Q-PCR screening of several genes involved in melanoma biology reveals that ciglitazone inhibits expression of the CXCL1 chemokine gene. CXCL1 is overexpressed in melanoma and contributes to tumorigenicity. We show that ciglitazone induces a diminution of CXCL1 level in different human melanoma cell lines. This effect is mediated by the downregulation of microphthalmia-associated transcription factor, MITF, the master gene in melanocyte differentiation and involved in melanoma development. Further, recombinant CXCL1 protein is sufficient to abrogate thiazolidinedione effects such as apoptosis induction, whereas extinction of the CXCL1 pathway mimics phenotypic changes observed in response to ciglitazone. Finally, inhibition of human melanoma tumor development in nude mice treated with ciglitazone is associated with a strong decrease in MITF and CXCL1 levels. Our results show that anti-melanoma effects of thiazolidinediones involve an inhibition of the MITF/CXCL1 axis and highlight the key role of this specific pathway in melanoma malignancy.
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- 2010
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17. Clinical activity of the MEK inhibitor trametinib in metastatic melanoma containing BRAF kinase fusion
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Boris C. Bastian, Iwei Yeh, Richard A. Scolyer, Georgina V. Long, Alexander M. Menzies, and Thomas Botton
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Trametinib ,Metastatic melanoma ,Oncogene Proteins ,business.industry ,Kinase ,MEK inhibitor ,Treatment outcome ,Disease progression ,Dermatology ,General Biochemistry, Genetics and Molecular Biology ,Article ,Oncology ,Monoclonal ,Cancer research ,Medicine ,business - Published
- 2015
18. CNVkit: Copy number detection and visualization for targeted sequencing using off-target reads
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Thomas Botton, Boris C. Bastian, A. Hunter Shain, and Eric Talevich
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Genetics ,0303 health sciences ,Massive parallel sequencing ,business.industry ,Copy number analysis ,Computational biology ,Biology ,01 natural sciences ,Genome ,Deep sequencing ,010104 statistics & probability ,03 medical and health sciences ,Software ,Copy-number variation ,0101 mathematics ,business ,GC-content ,030304 developmental biology ,Comparative genomic hybridization - Abstract
Germline copy number variants (CNVs) and somatic copy number alterations (SCNAs) are of significant importance in syndromic conditions and cancer. Massive parallel sequencing is increasingly used to infer copy number information from variations in the read depth in sequencing data. However, this approach has limitations in the case of targeted re-sequencing, which leaves gaps in coverage between the regions chosen for enrichment and introduces biases related to the efficiency of target capture and library preparation. We present a method for copy number detection, implemented in the software package CNVkit, that uses both the targeted reads and the nonspecifically captured off-target reads to infer copy number evenly across the genome. This combination achieves both exon-level resolution in targeted regions and sufficient resolution in the larger intronic and intergenic regions to identify copy number changes. In particular, we successfully inferred copy number at equivalent to 100-kilobase resolution genome-wide from a platform targeting as few as 293 genes. After normalizing read counts to a pooled reference, we evaluated and corrected for three sources of bias that explain most of the extraneous variability in the sequencing read depth: GC content, target footprint size and spacing, and repetitive sequences. We compared the performance of CNVkit to copy number changes identified by array comparative genomic hybridization. We packaged the components of CNVkit so that it is straightforward to use and provides visualizations, detailed reporting of significant features, and export options for compatibility with other software. Availability: http://github.com/etal/cnvkit
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- 2014
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19. Kinase fusions are frequent in Spitz tumours and spitzoid melanomas
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Rajmohan Murali, Maria C. Garrido, Rosaura Esteve-Puig, Klaus J. Busam, Thomas Botton, Doron Lipson, Kristina W. Brennan, Lorenzo Cerroni, Jie He, Iwei Yeh, Jeffrey S. Ross, Geoff Otto, Gabriele Palmedo, Roman Yelensky, Heinz Kutzner, Vincent A. Miller, Maureen T. Cronin, Thomas Wiesner, Boris C. Bastian, Michael F. Berger, Philip J. Stephens, and Alyssa J. Sparatta
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Skin Neoplasms ,Oncogene Proteins ,Oncogene Proteins, Fusion ,DNA Mutational Analysis ,Molecular Sequence Data ,General Physics and Astronomy ,Entrectinib ,Biology ,General Biochemistry, Genetics and Molecular Biology ,Article ,Nevus, Epithelioid and Spindle Cell ,medicine ,ROS1 ,Nevus ,Humans ,Pathological ,neoplasms ,Melanoma ,Multidisciplinary ,Base Sequence ,Kinase ,Genome, Human ,Reproducibility of Results ,General Chemistry ,medicine.disease ,Fusion protein ,Xenograft Model Antitumor Assays ,Immunology ,Cancer research ,Protein Kinases - Abstract
Spitzoid neoplasms are a group of melanocytic tumours with distinctive histopathological features. They include benign tumours (Spitz naevi), malignant tumours (spitzoid melanomas) and tumours with borderline histopathological features and uncertain clinical outcome (atypical Spitz tumours). Their genetic underpinnings are poorly understood, and alterations in common melanoma-associated oncogenes are typically absent. Here we show that spitzoid neoplasms harbour kinase fusions of ROS1 (17%), NTRK1 (16%), ALK (10%), BRAF (5%) and RET (3%) in a mutually exclusive pattern. The chimeric proteins are constitutively active, stimulate oncogenic signalling pathways, are tumourigenic and are found in the entire biologic spectrum of spitzoid neoplasms, including 55% of Spitz naevi, 56% of atypical Spitz tumours and 39% of spitzoid melanomas. Kinase inhibitors suppress the oncogenic signalling of the fusion proteins in vitro. In summary, kinase fusions account for the majority of oncogenic aberrations in spitzoid neoplasms and may serve as therapeutic targets for metastatic spitzoid melanomas. Spitzoid neoplasms constitute a spectrum of melanocytic tumours, characterized by distinct clinical, pathological and genetic features. Here, Wiesner et al. show that kinase fusions represent the majority of oncogenic aberrations in spitzoid neoplasms and may serve as therapeutic targets for metastatic spitzoid melanoma.
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- 2013
20. Recurrent BRAF kinase fusions in melanocytic tumors offer an opportunity for targeted therapy
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Stéphane Rocchi, Iwei Yeh, Thomas Botton, Swapna S. Vemula, Elizabeth A. Burton, Maria C. Garrido, Alyssa J. Sparatta, Gideon Bollag, Boris C. Bastian, Maryline Allegra, Philip E. LeBoit, Tyrrell A. Nelson, Robert Ballotti, Timothy H. McCalmont, and Philippe Bahadoran
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MAPK/ERK pathway ,Male ,Indoles ,Skin Neoplasms ,Oncogene Proteins, Fusion ,oncogenes ,medicine.medical_treatment ,translocation ,Medical and Health Sciences ,Targeted therapy ,2.1 Biological and endogenous factors ,Molecular Targeted Therapy ,Aetiology ,Vemurafenib ,Child ,Melanoma ,Cancer ,Oncogene Proteins ,Gene Rearrangement ,Sulfonamides ,Kinase ,Biological Sciences ,Middle Aged ,Sorafenib ,Oncology ,Child, Preschool ,Melanocytes ,Female ,medicine.drug ,Biotechnology ,Adult ,Niacinamide ,Proto-Oncogene Proteins B-raf ,Adolescent ,kinase ,MAP Kinase Signaling System ,Dermatology ,Epithelioid and Spindle Cell ,Biology ,General Biochemistry, Genetics and Molecular Biology ,Article ,BRAF ,Young Adult ,Rare Diseases ,Nevus, Epithelioid and Spindle Cell ,medicine ,melanoma ,Genetics ,Humans ,Fusion ,Preschool ,Nevus ,neoplasms ,Dermatology & Venereal Diseases ,Phenylurea Compounds ,Human Genome ,medicine.disease ,digestive system diseases ,Enzyme Activation ,Orphan Drug ,Protein kinase domain ,Cancer research ,Comparative genomic hybridization - Abstract
BRAF is the most prevalent oncogene and an important therapeutic target in melanoma. In some cancers, BRAF is activated by rearrangements that fuse its kinase domain to 5' partner genes. We examined 848 comparative genomic hybridization profiles of melanocytic tumors and found copy number transitions within BRAF in 10 tumors, of which six could be further characterized by sequencing. In all, the BRAF kinase domain was fused in-frame to six N-terminal partners. No other mutations were identified in melanoma oncogenes. One of the seven melanoma cell lines without known oncogenic mutations harbored a similar BRAF fusion, which constitutively activated the MAP kinase pathway. Sorafenib, but not vemurafenib, could block MAP kinase pathway activation and proliferation of the cell line at clinically relevant concentrations, whereas BRAF(V) (600E) mutant melanoma cell lines were significantly more sensitive to vemurafenib. The patient from whom the cell line was derived showed a durable clinical response to sorafenib.
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- 2013
21. Metformin inhibits melanoma development through autophagy and apoptosis mechanisms
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Tomic T, Pierre Gounon, Sophie Tartare-Deckert, Alexandre Puissant, Philippe Bahadoran, Corine Bertolotto, Patrick Auberger, Frederic Luciano, Michael Cerezo, Maryline Allegra, Stéphane Rocchi, Thomas Botton, Guillaume Robert, Bereder Jm, and Robert Ballotti
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Cancer Research ,medicine.medical_specialty ,autophagy ,Cell cycle checkpoint ,endocrine system diseases ,Immunology ,ATG5 ,Transplantation, Heterologous ,Mice, Nude ,Antineoplastic Agents ,Biology ,Resting Phase, Cell Cycle ,Autophagy-Related Protein 5 ,Cellular and Molecular Neuroscience ,Mice ,Internal medicine ,Cell Line, Tumor ,medicine ,melanoma ,Animals ,Humans ,RNA, Small Interfering ,Melanoma ,Autophagy ,digestive, oral, and skin physiology ,G1 Phase ,apoptosis ,nutritional and metabolic diseases ,Membrane Proteins ,Cell Biology ,Cell cycle ,medicine.disease ,Metformin ,Transplantation ,Endocrinology ,Apoptosis ,Cancer research ,Beclin-1 ,RNA Interference ,Original Article ,Apoptosis Regulatory Proteins ,Microtubule-Associated Proteins ,medicine.drug - Abstract
Metformin is the most widely used antidiabetic drug because of its proven efficacy and limited secondary effects. Interestingly, recent studies have reported that metformin can block the growth of different tumor types. Here, we show that metformin exerts antiproliferative effects on melanoma cells, whereas normal human melanocytes are resistant to these metformin-induced effects. To better understand the basis of this antiproliferative effect of metformin in melanoma, we characterized the sequence of events underlying metformin action. We showed that 24 h metformin treatment induced a cell cycle arrest in G0/G1 phases, while after 72 h, melanoma cells underwent autophagy as demonstrated by electron microscopy, immunochemistry, and by quantification of the autolysosome-associated LC3 and Beclin1 proteins. In addition, 96 h post metformin treatment we observed robust apoptosis of melanoma cells. Interestingly, inhibition of autophagy by knocking down LC3 or ATG5 decreased the extent of apoptosis, and suppressed the antiproliferative effect of metformin on melanoma cells, suggesting that apoptosis is a consequence of autophagy. The relevance of these observations were confirmed in vivo, as we showed that metformin treatment impaired the melanoma tumor growth in mice, and induced autophagy and apoptosis markers. Taken together, our data suggest that metformin has an important impact on melanoma growth, and may therefore be beneficial in patients with melanoma.
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- 2011
22. Mitf is the key molecular switch between mouse or human melanoma initiating cells and their differentiated progeny
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S Guiliano, Véronique Hofman, Stéphane Rocchi, Thomas Botton, Robert Ballotti, Yann Cheli, Paul Hofman, Philippe Bahadoran, Corine Bertolotto, Centre méditérannéen de médecine moléculaire (C3M), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM), ERI-21/EA 4319, Laboratoire de Pathologie Clinique et Expérimentale et CRB INSERM, Institut National de la Santé et de la Recherche Médicale (INSERM)-Hôpital Louis Pasteur [Chartres]-Université de Nice Sophia-Antipolis (UNSA), Service de Dermatologie [Nice], Hôpital Archet 2 [Nice] (CHU), BERTOLOTTO-BALLOTTI, BERTOLOTTO-BALLOTTI, and Université Nice Sophia Antipolis (1965 - 2019) (UNS)
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Homeobox protein NANOG ,Cancer Research ,Skin Neoplasms ,Population ,Melanoma, Experimental ,[SDV.CAN]Life Sciences [q-bio]/Cancer ,Biology ,Stem cell marker ,03 medical and health sciences ,Mice ,0302 clinical medicine ,Melanocyte differentiation ,[SDV.CAN] Life Sciences [q-bio]/Cancer ,Cell Line, Tumor ,Genetics ,medicine ,Animals ,Humans ,Gene Silencing ,education ,Molecular Biology ,Melanoma ,neoplasms ,030304 developmental biology ,0303 health sciences ,education.field_of_study ,Microphthalmia-Associated Transcription Factor ,Cell Differentiation ,Microphthalmia-associated transcription factor ,medicine.disease ,Mice, Inbred C57BL ,030220 oncology & carcinogenesis ,Lymphatic Metastasis ,Immunology ,Cancer cell ,Cell Transdifferentiation ,Cancer research ,Neoplastic Stem Cells ,CDK inhibitor ,Cell Division ,Cyclin-Dependent Kinase Inhibitor p27 ,Neoplasm Transplantation - Abstract
International audience; In melanoma, as well as in other solid tumors, the cells within a given tumor exhibit strong morphological, functional and molecular heterogeneity that might reflect the existence of different cancer cell populations, among which are melanoma-initiating cells (MICs) with 'stemness' properties and their differentiated, fast-growing progeny. The existence of a slow-growing population might explain the resistance of melanoma to classical chemotherapies that target fast growing cells. Therefore, elucidating the biologic properties of MICs and, more importantly, the molecular mechanisms that drive the transition between MICs and their proliferating progeny needs to be addressed to develop an efficient melanoma therapy. Using B16 mouse melanoma cells and syngeneic mice, we show that the inhibition of microphthalmia-associated transcription factor (Mitf), the master regulator of melanocyte differentiation, increases the tumorigenic potential of melanoma cells and upregulates the stem cell markers Oct4 and Nanog. Notably, p27, the CDK inhibitor, is increased in Mitf-depleted cells and is required for exacerbation of the tumorigenic properties of melanoma cells. Further, a slow-growing population with low-Mitf level and high tumorigenic potential exists spontaneously in melanoma. Ablation of this population dramatically decreases tumor formation. Importantly, these data were confirmed using human melanoma cell lines and freshly isolated human melanoma cell from lymph node and skin melanoma metastasis. Taken together our data, identified Mitf and p27 as the key molecular switches that control the transition between MICs and their differentiated progeny. Eradication of low-Mitf cells might be an appealing strategy to cure melanoma.
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- 2011
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23. In vitro and in vivo anti-melanoma effects of ciglitazone
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Thomas Botton, Genevieve Gozzerino, Sophie Tartare-Deckert, Corine Bertolotto, Philippe Bahadoran, Robert Ballotti, Jean-Sébastien Annicotte, Lluis Fajas, Alexandre Puissant, Thamilla Zamoum, Ortonne Jp, Stéphane Rocchi, Institut de Génétique Moléculaire de Montpellier (IGMM), and Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)
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Skin Neoplasms ,Animals Antineoplastic Agents/pharmacology/*therapeutic use Apoptosis/drug effects Cell Cycle/drug effects Cell Line ,Apoptosis ,Biochemistry ,Mice ,0302 clinical medicine ,Melanoma ,Caspase ,0303 health sciences ,biology ,Cell Cycle ,Drug Humans Melanoma/*drug therapy/metabolism/pathology Mice Mice ,Tumor Cell Proliferation/drug effects Dose-Response Relationship ,3. Good health ,030220 oncology & carcinogenesis ,Nude PPAR gamma/metabolism Signal Transduction/physiology Skin Neoplasms/*drug therapy/metabolism/pathology Thiazolidinediones/pharmacology/*therapeutic use Xenograft Model Antitumor Assays ,Rosiglitazone ,Signal Transduction ,medicine.drug ,medicine.medical_specialty ,Mice, Nude ,Antineoplastic Agents ,Dermatology ,03 medical and health sciences ,Cyclin D1 ,In vivo ,Cell Line, Tumor ,Internal medicine ,Ciglitazone ,medicine ,Animals ,Humans ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,Molecular Biology ,Cell Proliferation ,030304 developmental biology ,Dose-Response Relationship, Drug ,business.industry ,Cell Biology ,medicine.disease ,Xenograft Model Antitumor Assays ,PPAR gamma ,Endocrinology ,Cancer cell ,biology.protein ,Cancer research ,Thiazolidinediones ,business - Abstract
Activation of PPARgamma by synthetic ligands, thiazolidinediones, inhibits the proliferation of cancer cells. In this report, focusing our attention on ciglitazone, we show that ciglitazone inhibits melanoma growth by inducing apoptosis and cell-cycle arrest, whereas normal melanocytes are resistant to ciglitazone. In melanoma cells, ciglitazone-induced apoptosis is associated with caspase activations and a loss of mitochondrial membrane potential. Induction of cell-cycle arrest by ciglitazone is associated with changes in expression of key cell-cycle regulators such as p21, cyclin D1, and pRB hypophosphorylation. Cell-cycle arrest occurs at low ciglitazone concentrations and through a PPARgamma-dependent pathway, whereas the induction of apoptosis is caused by higher ciglitazone concentrations and independently of PPARgamma. These results allow an effective molecular dissociation between proapoptotic effects and growth inhibition evoked by ciglitazone in melanoma cells. Finally, we show that in vivo treatment of nude mice by ciglitazone dramatically inhibits human melanoma xenograft development. The data presented suggest that ciglitazone might be a better candidate for clinical trials in melanoma treatment than the thiazolidinediones currently used in the treatment of type 2 diabetes, such as rosiglitazone, which is devoid of a proapoptotic PPARgamma-independent function.
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- 2009
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24. Abstract 2968: Exome sequencing of desmoplastic melanoma reveals recurrent NFKBIE promoter mutations and diverse MAPK/PI3K pathway activating mutations
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Richard A. Scolyer, Nam Huh, Nicholas J. Wang, Iweh Yeh, Alexander Gagnon, Jongsuk Chung, Rajmohan Murali, Maria C. Garrido, Klaus J. Busam, Thomas Wiesner, Joe W. Gray, Graham J. Mann, Zack Sanborn, John F. Thompson, Thomas Botton, Ritu Roy, Joe Hur, Eric Talevich, Hojabr Kakavand, Raymond J. Cho, Boris C. Bastian, Alan Hunter Shain, and Adam B. Olshen
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Neuroblastoma RAS viral oncogene homolog ,Desmoplastic melanoma ,Genetics ,Cancer Research ,Mutation ,Candidate gene ,Melanoma ,Biology ,medicine.disease_cause ,medicine.disease ,NFKBIE ,Oncology ,CDKN2A ,medicine ,Cancer research ,neoplasms ,Exome sequencing - Abstract
Desmoplastic melanomas (DMs) comprise 4% of the overall melanoma burden and have a 5-year survival rate of 85%. DMs are dermal tumors characterized by spindled melanocytes situated within abundant desomplastic stroma. These unusual histological features commonly lead to misdiagnosis. Currently, there are no known genetic drivers. A better understanding of the underlying biology of desmoplastic melanoma would provide biomarkers and therapeutic opportunities. Towards this goal, we performed low-coverage genome and high-coverage exome sequencing of 20 DMs in a discovery cohort, followed by targeted sequencing of 293 candidate genes on a validation cohort of 42 cases. Additionally, high-resolution aCGH was performed on samples from both cohorts. A high mutation burden (median 62 mutations/Mb) ranked desmoplastic melanoma among the most highly mutated cancers sequenced to date. Mutation patterns strongly indicate that UV-radiation is the dominant mutagen and implicate a superficially located cell of origin despite their predominantly intradermal presentation. Novel alterations included recurrent promoter mutations and amplification of NF-kappa B inhibitor epsilon, NFKBIE (IkBϵ) in 14.5% of samples. The promoter mutations typically affect both alleles and occur over a highly conserved DNA region. The mutations are predicted to disrupt a canonical Ets Like Factor 1 (ELF1) binding site. In total, these data imply aberrant NF-kappa B signaling as a pathogenic feature of desmoplastic melanoma. Commonly mutated oncogenes in melanomas, in particular BRAF V600E and NRAS Q61K/R, were absent. Instead, other genetic alterations known to activate the MAPK and PI3K signaling cascades were identified in 73% of samples, affecting NF1, CBL, ERBB2, MAP2K1, MAP3K1, BRAF, EGFR, PTPN11, MET, RAC1, SOS2, NRAS, and PIK3CA. Rb and p53 pathway alterations occurred respectively in 71% and 66% of tumors, affecting RB1, FBXW7, CDK4, PPP6C, CCND1, CDKN2A, TP53, and MDM2. Finally, TERT promoter mutations or amplifications occurred in 90% of tumors. The consequences of the mutations on protein expression levels was confirmed by immunostaining for NF1, EGFR, Rb, CDK4, CCND1, p16, p53, and Mdm2. Collectively, many of these oncogenic mutations are potentially druggable. In conclusion, desmoplastic melanomas harbor distinct genetic alterations that explain their unique biology, and this study illuminates genetic biomarkers and nominates targets for therapeutic intervention. Citation Format: Alan H. Shain, Maria Garrido, Thomas Botton, Eric Talevich, Iweh Yeh, Zack Sanborn, Jongsuk Chung, Nicholas Wang, Hojabr Kakavand, Graham Mann, John Thompson, Thomas Wiesner, Ritu Roy, Adam Olshen, Alexander Gagnon, Joe Gray, Nam Huh, Joe Hur, Klaus Busam, Richard Scolyer, Raymond Cho, Rajmohan Murali, Boris Bastian. Exome sequencing of desmoplastic melanoma reveals recurrent NFKBIE promoter mutations and diverse MAPK/PI3K pathway activating mutations. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2968. doi:10.1158/1538-7445.AM2015-2968
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- 2015
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25. Activating MET Kinase Rearrangements in Melanoma and Spitz Tumors
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Boris C. Bastian, A. Hunter Shain, Timothy H. McCalmont, Thaddeus W. Mully, Swapna S. Vemula, Iwei Yeh, Alyssa J. Sparatta, Jeffrey P. North, Alexander Gagnon, Thomas Botton, Maria C. Garrido, Philip E. LeBoit, Arnaud de la Fouchardière, and Eric Talevich
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Adult ,Male ,Melanoma, Experimental ,General Physics and Astronomy ,Biology ,General Biochemistry, Genetics and Molecular Biology ,Article ,Cell Line ,Mice ,Nevus, Epithelioid and Spindle Cell ,medicine ,Animals ,Humans ,Oncogene Fusion ,Protein kinase A ,Gene Rearrangement ,Multidisciplinary ,Kinase ,Medullary thyroid cancer ,General Chemistry ,Gene rearrangement ,Middle Aged ,Proto-Oncogene Proteins c-met ,medicine.disease ,Fusion protein ,Molecular biology ,3. Good health ,Protein kinase domain ,Cancer research ,Female - Abstract
Oncogenic gene fusions have been identified in many cancers and many serve as biomarkers or targets for therapy. Here we identify six different melanocytic tumours with genomic rearrangements of MET fusing the kinase domain of MET in-frame to six different N-terminal partners. These tumours lack activating mutations in other established melanoma oncogenes. We functionally characterize two of the identified fusion proteins (TRIM4-MET and ZKSCAN1-MET) and find that they constitutively activate the mitogen-activated protein kinase (MAPK), phosphoinositol-3 kinase (PI3K) and phospholipase C gamma 1 (PLCγ1) pathways. The MET inhibitors cabozantinib (FDA-approved for progressive medullary thyroid cancer) and PF-04217903 block their activity at nanomolar concentrations. MET fusion kinases thus provide a potential therapeutic target for a rare subset of melanoma for which currently no targeted therapeutic options currently exist.
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- 2015
26. Rac1 Dynamics in the Human Opportunistic Fungal Pathogen Candida albicans
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Robert A. Arkowitz, Romain Vauchelles, Martine Bassilana, Thomas Botton, Danièle Stalder, Institute of Developmental Biology and Cancer (IBDC), Université Nice Sophia Antipolis (... - 2019) (UNS), and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)
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rac1 GTP-Binding Protein ,Cytoplasm ,Science ,Signaling in cellular processes ,Yeast and Fungal Models ,Signal transduction ,03 medical and health sciences ,Model Organisms ,Molecular cell biology ,Prenylation ,Candida albicans ,medicine ,Humans ,Biology ,[SDV.BDD]Life Sciences [q-bio]/Development Biology ,GTPase signaling ,030304 developmental biology ,Fluorescence loss in photobleaching ,Cell Nucleus ,0303 health sciences ,Multidisciplinary ,biology ,030302 biochemistry & molecular biology ,Fluorescence recovery after photobleaching ,biology.organism_classification ,Corpus albicans ,Cell biology ,medicine.anatomical_structure ,Medicine ,Heterologous expression ,Nuclear transport ,Nucleus ,Research Article - Abstract
International audience; The small Rho G-protein Rac1 is highly conserved from fungi to humans, with approximately 65% overall sequence identity in Candida albicans. As observed with human Rac1, we show that C. albicans Rac1 can accumulate in the nucleus, and fluorescence recovery after photobleaching (FRAP) together with fluorescence loss in photobleaching (FLIP) studies indicate that this Rho G-protein undergoes nucleo-cytoplasmic shuttling. Analyses of different chimeras revealed that nuclear accumulation of C. albicans Rac1 requires the NLS-motifs at its carboxyl-terminus, which are blocked by prenylation of the adjacent cysteine residue. Furthermore, we show that C. albicans Rac1 dynamics, both at the plasma membrane and in the nucleus, are dependent on its activation state and in particular that the inactive form accumulates faster in the nucleus. Heterologous expression of human Rac1 in C. albicans also results in nuclear accumulation, yet accumulation is more rapid than that of C. albicans Rac1. Taken together our results indicate that Rac1 nuclear accumulation is an inherent property of this G-protein and suggest that the requirements for its nucleo-cytoplasmic shuttling are conserved from fungi to humans.
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- 2010
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