Showing papers by "Katleen De Preter published in 2014"

Activated Alk triggers prolonged neurogenesis and Ret upregulation providing a therapeutic target in ALK-mutated neuroblastoma

Abstract: // Alex Cazes 1,2 , Lucille Lopez-Delisle 1,2 , Konstantina Tsarovina 3 , Cecile Pierre-Eugene 1,2 , Katleen De Preter 4 , Michel Peuchmaur 5,6 , Andre Nicolas 7 , Claire Provost 8 , Caroline Louis-Brennetot 1,2 , Romain Daveau 1,2 , Candy Kumps 4 , Ilaria Cascone 9 , Gudrun Schleiermacher 1,2,10 , Aurelie Prignon 8 , Frank Speleman 4 , Hermann Rohrer 3 , Olivier Delattre 1,2 and Isabelle Janoueix-Lerosey 1,2 1 Inserm U830, 26 rue d’Ulm, 75005 Paris, France. 2 Institut Curie, Centre de Recherche, 26 rue d’Ulm, 75005 Paris, France. 3 Research Group Developmental Neurobiology, Max Planck Institute for Brain Research, Max-von-Laue-Str. 4, 60438 Frankfurt/M, Germany. 4 Center for Medical Genetics, Ghent University Hospital, De Pintelaan 185, B-9000 Ghent, Belgium. 5 Departement of Pathology, AP-HP, Hopital Universitaire Robert Debre, 48 boulevard Serurier, 75019 Paris, France. 6 Universite Diderot Paris 7, Paris Sorbonne Cite, Paris, France. 7 Platform of Experimental Pathology, Institut Curie, 26 rue d’Ulm, 75005 Paris, France. 8 LIMP (Laboratoire d’Imagerie Moleculaire Positonique), Hopital Tenon, 4 rue de la Chine, 75020 Paris, France. 9 Laboratoire CRRET, EAC CNRS 7149, Universite Paris 12-Val de Marne, 61, avenue du General de Gaulle, 94010 Creteil, France. 10 Institut Curie, Departement de Pediatrie, 26 rue d’Ulm, 75005 Paris, France. Correspondence: Isabelle Janoueix-Lerosey, email: // Keywords : Neuroblastoma, ALK, neurogenesis, therapeutic target, RET Received : March 24, 2014 Accepted : April 01, 2014 Published : April 02, 2014 Abstract Activating mutations of the ALK (Anaplastic lymphoma Kinase) gene have been identified in sporadic and familial cases of neuroblastoma, a cancer of early childhood arising from the sympathetic nervous system (SNS). To decipher ALK function in neuroblastoma predisposition and oncogenesis, we have characterized knock-in (KI) mice bearing the two most frequent mutations observed in neuroblastoma patients. A dramatic enlargement of sympathetic ganglia is observed in Alk F1178L mice from embryonic to adult stages associated with an increased proliferation of sympathetic neuroblasts from E14.5 to birth. In a MYCN transgenic context, the F1178L mutation displays a higher oncogenic potential than the R1279Q mutation as evident from a shorter latency of tumor onset. We show that tumors expressing the R1279Q mutation are sensitive to ALK inhibition upon crizotinib treatment. Furthermore, our data provide evidence that activated ALK triggers RET upregulation in mouse sympathetic ganglia at birth as well as in murine and human neuroblastoma. Using vandetanib, we show that RET inhibition strongly impairs tumor growth in vivo in both MYCN /KI Alk R1279Q and MYCN /KI Alk F1178L mice. Altogether, our findings demonstrate the critical role of activated ALK in SNS development and pathogenesis and identify RET as a therapeutic target in ALK mutated neuroblastoma.

Histone chaperone CHAF1A inhibits differentiation and promotes aggressive neuroblastoma.

Abstract: Neuroblastoma arises from the embryonal neural crest secondary to a block in differentiation. Long-term patient survival correlates inversely with the extent of differentiation, and treatment with retinoic acid or other prodifferentiation agents improves survival modestly. In this study, we show the histone chaperone and epigenetic regulator CHAF1A functions in maintaining the highly dedifferentiated state of this aggressive malignancy. CHAF1A is a subunit of the chromatin modifier chromatin assembly factor 1 and it regulates H3K9 trimethylation of key target genes regulating proliferation, survival, and differentiation. Elevated CHAF1A expression strongly correlated with poor prognosis. Conversely, CHAF1A loss-of-function was sufficient to drive neuronal differentiation in vitro and in vivo. Transcriptome analysis of cells lacking CHAF1A revealed repression of oncogenic signaling pathways and a normalization of glycolytic metabolism. Our findings demonstrate that CHAF1A restricts neural crest differentiation and contributes to the pathogenesis of high-risk neuroblastoma.

ViVar: a comprehensive platform for the analysis and visualization of structural genomic variation.

Abstract: Structural genomic variations play an important role in human disease and phenotypic diversity. With the rise of high-throughput sequencing tools, mate-pair/paired-end/single-read sequencing has become an important technique for the detection and exploration of structural variation. Several analysis tools exist to handle different parts and aspects of such sequencing based structural variation analyses pipelines. A comprehensive analysis platform to handle all steps, from processing the sequencing data, to the discovery and visualization of structural variants, is missing. The ViVar platform is built to handle the discovery of structural variants, from Depth Of Coverage analysis, aberrant read pair clustering to split read analysis. ViVar provides you with powerful visualization options, enables easy reporting of results and better usability and data management. The platform facilitates the processing, analysis and visualization, of structural variation based on massive parallel sequencing data, enabling the rapid identification of disease loci or genes. ViVar allows you to scale your analysis with your work load over multiple (cloud) servers, has user access control to keep your data safe and is easy expandable as analysis techniques advance. URL: https://www.cmgg.be/vivar/

Robust Selection of Cancer Survival Signatures from High-Throughput Genomic Data Using Two-Fold Subsampling

Abstract: Identifying relevant signatures for clinical patient outcome is a fundamental task in high-throughput studies. Signatures, composed of features such as mRNAs, miRNAs, SNPs or other molecular variables, are often non-overlapping, even though they have been identified from similar experiments considering samples with the same type of disease. The lack of a consensus is mostly due to the fact that sample sizes are far smaller than the numbers of candidate features to be considered, and therefore signature selection suffers from large variation. We propose a robust signature selection method that enhances the selection stability of penalized regression algorithms for predicting survival risk. Our method is based on an aggregation of multiple, possibly unstable, signatures obtained with the preconditioned lasso algorithm applied to random (internal) subsamples of a given cohort data, where the aggregated signature is shrunken by a simple thresholding strategy. The resulting method, RS-PL, is conceptually simple and easy to apply, relying on parameters automatically tuned by cross validation. Robust signature selection using RS-PL operates within an (external) subsampling framework to estimate the selection probabilities of features in multiple trials of RS-PL. These probabilities are used for identifying reliable features to be included in a signature. Our method was evaluated on microarray data sets from neuroblastoma, lung adenocarcinoma, and breast cancer patients, extracting robust and relevant signatures for predicting survival risk. Signatures obtained by our method achieved high prediction performance and robustness, consistently over the three data sets. Genes with high selection probability in our robust signatures have been reported as cancer-relevant. The ordering of predictor coefficients associated with signatures was well-preserved across multiple trials of RS-PL, demonstrating the capability of our method for identifying a transferable consensus signature. The software is available as an R package rsig at CRAN (http://cran.r-project.org).

The MYCN/miR-26a-5p/LIN28B regulatory axis controls MYCN-driven LIN28B upregulation in neuroblastoma

Abstract: The RNA binding protein LIN28B is an essential regulator of stem cell self-renewal and has been identified as a bona fide oncogene in neuroblastoma. LIN28B is known to enhance MYCN expression through downregulation of let-7 microRNAs (miRNAs). As part of a broader study of dynamic miRNA/mRNA regulation during neuroblastoma development, we observed unexpected dynamic upregulation of LIN28B in MYCN-driven hyperplasia and tumors in mice. Hence, we hypothesized that MYCN and LIN28B are involved in a positive feedback loop through one or more miRNAs that are acting as regulatory switches between the hubs in this regulatory network. In order to fully explore this putative network, we experimentally studied all possible LIN28B-miRNA interactions through an unbiased LIN28B 3’UTR-miRNA library screen for a total of 470 miRNAs. This LIN28B 3’UTR-miRNA library screen identified 30 miRNAs potentially targeting LIN28B. Subsequently, integrated analyses with miRNA expression profiles of a large cohort of primary neuroblastoma tumors, yielded miR-26a-5p as top candidate miRNA for LIN28B targeting in neuroblastoma. Importantly, miR-26a-5p is directly downregulated by MYCN in the MYCN-inducible MYCN3 cell line, thus providing strong evidence for MYCN-driven LIN28B upregulation. In vivo assessment using xenograft experiments with miR-26a-5p modulated neuroblastoma cell lines is currently ongoing. The discovery of this MYCN/ miR-26a-5p/ LIN28B regulatory axis marks LIN28B as an important effector of the MYCN oncogenic phenotype and underlines once more the importance of MYCN-regulated miRNAs in establishing the MYCN-driven oncogenic process. Consequently, LIN28B can be regarded as a prominent therapeutic target for MYCN-driven neuroblastoma tumors. Finally, given the role of both MYCN and LIN28B as bona fide stem cell markers, these novel findings are of broader significance for normal development and cancer biology.

Genetisch geïnspireerde toekomstperspectieven voor de therapie van het neuroblastoom

Abstract: Recente genoomwijde mutatieanalysen van verschillende tumorentiteiten hebben een schat aan nieuwe informatie en vele verrassende ontdekkingen opgeleverd met vaak een directe impact op het therapeutische beleid. Voor pediatrische maligniteiten is echter gebleken dat de mutatiefre- quentie een stuk lager ligt dan bij tumoren bij volwassenen. Nochtans leiden deze nieuwe gegevens ook tot nieuwe inzichten in het ontstaansproces van tumoren bij kinderen en duiken er nieuwe mogelijkheden op voor therapeutisch ingrijpen. Het neuroblastoom, een vaste tumor van het ont- wikkelende sympathische zenuwstelsel, neemt hierbij een bijzondere plaats in. De prognose is immers – ondanks zeer intensieve multimodale therapie – nog steeds ongunstig voor kinderen met een hoogrisicotumor die ouder dan achttien maanden zijn bij de diagnose. De laatste jaren zijn er belangrijke nieuwe inzichten verworven in de genetische defecten die aan de basis liggen van het ontstaan van het neuroblastoom en werden ook op genoomwijde schaal de DNA-mutaties in kaart gebracht. Naast de reeds lang gekende amplificatie van het MYCN-gen en de typische patronen van structurele chromosomale afwijkingen blijken activerende mutaties in het ALK-gen de enige vaak voorkomende afwijkingen te zijn in het neuroblastoomgenoom. Andere, minder vaak voorkomende mutaties lijken zich echter te concentreren in een aantal biologische signaalwegen die belangrijk zijn voor de ontwikkelende zenuwcel. In dit artikel wordt er een over- zicht gegeven van de meest recente stand van zaken, alsook van de nieuwe perspectieven voor klinische interventie en therapie.

Differential module analysis in neuroblastoma regulatory networks

Abstract: In most expression data studies, differential gene expression analyses are carried out in order to identify the genes which are most differentially expressed between two conditions. This methodology has already proven its use in many studies. However, by comparing expression values on a gene-to-gene basis this method is able to detect gene-specific patterns, but is insensitive for patterns which are only detectable at pathway-level. Recent approaches are based on inferring and comparing interaction networks for the different biological conditions. Such methods are called Differential Network (DN) methods. In one of the DN approaches [1], strongly related genes within each network are grouped together in modules. The modular organisation gives a high-level overview of the biological mechanisms present in a biological system under the different conditions. Finally, the most differential modules are selected, that is, the modules which are most characteristic for a specific condition. The mechanism which is represented by the module is then predicted to be uniquely present in that condition. We developed and optimised a DN technique in order to identify regulatory modules in neuroblastoma (NB) patients for the different NB subtypes. Its innovative features are the use of state-of-the-art network inference and module inference methods, as well as a statistical validation for each of the retrieved modules by performing permutation tests. We enriched each of the modules with Gene Ontology terms in order to assign biological process functions. We compared the results with previous NB studies and found that the modules were enriched for known mechanisms in NB, and were commonly enriched for neurogenesis and tumorigenesis mechanisms. Some NB subtype 2A specific modules were found to be enriched for regulation of the Wnt signalling pathway, a pathway known to be strongly expressed in NB 2A patients but not in NB 2B patients [2]. Other NB modules were enriched for regulation of TRP receptor signalling pathway, another pathway known to be associated with survivability of patients [3, 4]. REFERENCES 1) Ryan Gill, Somnath Datta and Susmita Datta. “A statistical framework for differential network analysis from microarray data.” In: BMC bioinformatics 11 (Jan 2010), pg. 95. 2) X Liu et al. “Deregulated Wnt/beta-catenin program in high-risk neuroblastomas without MYCN amplification.” In: Oncogene 27.10 (Feb 2008), p. 1478–88. 3) Akira Nakagawara. “Association between high levels of expression of the TRK gene and favorable outcome in human neuroblastoma”. In: The New England Journal of Medicine (1993). 4) Akira Nakagawara et al. “Expression and function of TRK-B and BDNF in human neuroblastomas.” In: Molecular and cellular biology 14.1 (Jan 1994), pg. 759–67.