-
Alex Cazes,
Caroline Louis-Brennetot,
Pierre Mazot,
Florent Dingli,
Berangere Lombard,
Valentina Boeva,
Romain Daveau,
Julie Cappo,
Valerie Combaret,
Gudrun Schleiermacher,
Stephanie Jouannet,
Sandrine Ferrand,
Gaelle Pierron,
Emmanuel Barillot,
Damarys Loew,
Marc Vigny,
Olivier Delattre, Isabelle Janoueix-Lerosey
[show abstract]
[hide abstract]
ABSTRACT: Activating mutations of the ALK gene have been identified in sporadic and familial cases of neuroblastoma (NB), a cancer of the peripheral nervous system, and are thought to be the primary mechanism of oncogenic activation of this receptor in this pediatric neoplasm. To address the possibility that ALK activation may occur through genomic rearrangements as detected in other cancers, we first took advantage of high-resolution array-CGH to search for ALK rearrangements in NB samples. Using complementary experiments by capture/paired-end sequencing and FISH experiments, various types of rearrangements were fully characterized, including partial gains or amplifications, in several NB cell lines and primary tumors. In the CLB-Bar cell line, we described a genomic rearrangement associated with an amplification of the ALK locus, leading to the expression of a 170 kDa protein lacking part of the extracellular domain encoded by exons 4 to 11, named ALKdelta4-11. Analysis of genomic DNA from the tumor at diagnosis and relapse revealed that the ALK gene was amplified at diagnosis but that the rearranged ALK allele was observed at the relapse stage only, suggesting that it may be implicated in tumor aggressiveness. Consistently, oncogenic and tumorigenic properties of the ALKdelta4-11 variant were demonstrated after stable expression in NIH3T3 cells. Moreover, we documented an increased constitutive kinase activity of this variant, as well as an impaired maturation and retention into intracellular compartments. These results indicate that genomic rearrangements constitute an alternative mechanism to ALK point mutations resulting in receptor activation.
Cancer Research 11/2012; · 7.86 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: More and more cancer studies use next-generation sequencing (NGS) data to detect various types of genomic variation. However, even when researchers have such data at hand, single-nucleotide polymorphism arrays have been considered necessary to assess copy number alterations and especially loss of heterozygosity (LOH). Here, we present the tool Control-FREEC that enables automatic calculation of copy number and allelic content profiles from NGS data, and consequently predicts regions of genomic alteration such as gains, losses and LOH. Taking as input aligned reads, Control-FREEC constructs copy number and B-allele frequency profiles. The profiles are then normalized, segmented and analyzed in order to assign genotype status (copy number and allelic content) to each genomic region. When a matched normal sample is provided, Control-FREEC discriminates somatic from germline events. Control-FREEC is able to analyze overdiploid tumor samples and samples contaminated by normal cells. Low mappability regions can be excluded from the analysis using provided mappability tracks.
C++ source code is available at: http://bioinfo.curie.fr/projects/freec/
freec@curie.fr
Supplementary data are available at Bioinformatics online.
Bioinformatics 12/2011; 28(3):423-5. · 5.47 Impact Factor
-
Franck Bourdeaut,
Sandrine Ferrand,
Laurence Brugières,
Marjorie Hilbert,
Agnès Ribeiro,
Ludovic Lacroix,
Jean Bénard,
Valérie Combaret,
Jean Michon,
Dominique Valteau-Couanet,
Bertrand Isidor,
Xavier Rialland,
Maryline Poirée,
Anne-Sophie Defachelles,
Michel Peuchmaur,
Gudrun Schleiermacher,
Gaëlle Pierron,
Marion Gauthier-Villars, Isabelle Janoueix-Lerosey,
Olivier Delattre
[show abstract]
[hide abstract]
ABSTRACT: Neuroblastic tumours may occur in a predisposition context. Two main genes are involved: PHOX2B, observed in familial cases and frequently associated with other neurocristopathies (Ondine's and Hirschsprung's disease); and ALK, mostly in familial tumours. We have assessed the frequency of mutations of these two genes in patients with a presumable higher risk of predisposition. We sequenced both genes in 26 perinatal cases (prebirth and <1 month of age, among which 10 were multifocal), 16 multifocal postnatal (>1 month) cases, 3 pairs of affected relatives and 8 patients with multiple malignancies. The whole coding sequences of the two genes were analysed in tumour and/or constitutional DNAs. We found three ALK germline mutations, all in a context of multifocal tumours. Two mutations (T1151R and R1192P) were inherited and shared by several unaffected patients, thus illustrating an incomplete penetrance. Younger age at tumour onset did not seem to offer a relevant selection criterion for ALK analyses. Conversely, multifocal tumours might be the most to benefit from the genetic screening. Finally, no PHOX2B germline mutation was found in this series. In conclusion, ALK deleterious mutations are rare events in patients with a high probability of predisposition. Other predisposing genes remain to be discovered.
European journal of human genetics: EJHG 11/2011; 20(3):291-7. · 3.56 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Neuroblastoma (NB) is the most common extracranial solid tumor in childhood and arises from cells of the developing sympathoadrenergic lineage. Activating mutations in the gene encoding the ALK tyrosine kinase receptor predispose for NB. Here, we focus on the normal function of Alk signaling in the control of sympathetic neuron proliferation, as well as on the effects of mutant ALK. Forced expression of wild-type ALK and NB-related constitutively active ALK mutants in cultures of proliferating immature sympathetic neurons results in a strong proliferation increase, whereas Alk knockdown and pharmacological inhibition of Alk activity decrease proliferation. Alk activation upregulates NMyc and trkB and maintains Alk expression by an autoregulatory mechanism involving Hand2. The Alk-ligand Midkine (Mk) is expressed in immature sympathetic neurons and in vivo inhibition of Alk signaling by virus-mediated shRNA knockdown of Alk and Mk leads to strongly reduced sympathetic neuron proliferation. Taken together, these results demonstrate that the extent and timing of sympathetic neurogenesis is controlled by Mk/Alk signaling. The predisposition for NB caused by activating ALK mutations may thus be explained by aberrations of normal neurogenesis, i.e. elevated and sustained Alk signaling and increased NMyc expression.
Development 11/2011; 138(21):4699-708. · 6.60 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Neuroblastoma, the most frequent solid extracranial tumor of childhood, is characterized by a wide variability of its clinical course. The most important clinical prognostic markers are stage and age at diagnosis, but these markers are insufficient to predict outcome reliably and to determine treatment intensity. Recent evidence indicates that neuroblastoma can be considered as a "genetic disease", firstly by the recent observation that certain alleles of specific genes significantly increase the relative risk to develop neuroblastoma, and the discovery of mutations in genes such as ALK or PHOX2B in rare familial cases. On the other hand, a large number of recurrent genetic somatic alterations have been described in neuroblastoma. Recent technological advances, such as array-CGH (comparative genomic hybridisation), now enable the analysis of these markers in a single step and allow the definition of genomic profiles associated with typical clinical features. Numerical chromosome alterations are observed more frequently in tumors of younger children with localised disease and a good prognosis, whereas segmental chromosome alterations are found more frequently in tumors of older children with advanced stages of disease and a poorer outcome. Future therapeutic stratification schemes can make use of the tumor genomic profile by proposing less intense treatment for infants with a neuroblastoma harboring a favorable tumor genomic profile, while intensifying treatment in case of a defavorable tumor genomic profile. Such approaches require standardisation of the molecular techniques and the interpretation of results for application in international trials.
Bulletin du cancer 05/2011; 98(5):477-88. · 0.67 Impact Factor
-
Loïc de Pontual,
Dania Kettaneh,
Christopher T Gordon,
Myriam Oufadem,
Nathalie Boddaert,
Melissa Lees,
Laurent Balu,
Eric Lachassinne,
Andy Petros,
Julie Mollet,
Louise C Wilson,
Arnold Munnich,
Laurence Brugière,
Olivier Delattre,
Michel Vekemans,
Heather Etchevers,
Stanislas Lyonnet, Isabelle Janoueix-Lerosey,
Jeanne Amiel
[show abstract]
[hide abstract]
ABSTRACT: Neuroblastoma (NB) is a frequent embryonal tumor of sympathetic ganglia and adrenals with extremely variable outcome. Recently, somatic amplification and gain-of-function mutations of the anaplastic lymphoma receptor tyrosine kinase (ALK) gene, either somatic or germline, were identified in a significant proportion of NB cases. Here we report a novel syndromic presentation associating congenital NB with severe encephalopathy and abnormal shape of the brainstem on brain MRI in two unrelated sporadic cases harboring de novo, germline, heterozygous ALK gene mutations. Both mutations are gain-of-function mutations that have been reported in NB and NB cell lines. These observations further illustrate the role of oncogenes in both tumour predisposition and normal development, and shed light on the pleiotropic and activity-dependent role of ALK in humans. More generally, missing germline mutations relative to the spectrum of somatic mutations reported for a given oncogene may be a reflection of severe effects during embryonic development, and may prompt mutation screening in patients with extreme phenotypes.
Human Mutation 03/2011; 32(3):272-6. · 5.69 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: SUMMARY: We present a tool for control-free copy number alteration (CNA) detection using deep-sequencing data, particularly useful for cancer studies. The tool deals with two frequent problems in the analysis of cancer deep-sequencing data: absence of control sample and possible polyploidy of cancer cells. FREEC (control-FREE Copy number caller) automatically normalizes and segments copy number profiles (CNPs) and calls CNAs. If ploidy is known, FREEC assigns absolute copy number to each predicted CNA. To normalize raw CNPs, the user can provide a control dataset if available; otherwise GC content is used. We demonstrate that for Illumina single-end, mate-pair or paired-end sequencing, GC-contentr normalization provides smooth profiles that can be further segmented and analyzed in order to predict CNAs. AVAILABILITY: Source code and sample data are available at http://bioinfo-out.curie.fr/projects/freec/.
Bioinformatics 11/2010; 27(2):268-9. · 5.47 Impact Factor
-
Sara De Brouwer,
Katleen De Preter,
Candy Kumps,
Piotr Zabrocki,
Michaël Porcu,
Ellen M Westerhout,
Arjan Lakeman,
Jo Vandesompele,
Jasmien Hoebeeck,
Tom Van Maerken, [......], Isabelle Janoueix-Lerosey,
Per Kogner,
Tommy Martinsson,
Akira Nakagawara,
Miki Ohira,
Huib Caron,
Angelika Eggert,
Jan Cools,
Rogier Versteeg,
Frank Speleman
[show abstract]
[hide abstract]
ABSTRACT: Activating mutations of the anaplastic lymphoma kinase (ALK) were recently described in neuroblastoma. We carried out a meta-analysis of 709 neuroblastoma tumors to determine their frequency and mutation spectrum in relation to genomic and clinical parameters, and studied the prognostic significance of ALK copy number and expression.
The frequency and type of ALK mutations, copy number gain, and expression were analyzed in a new series of 254 neuroblastoma tumors. Data from 455 published cases were used for further in-depth analysis.
ALK mutations were present in 6.9% of 709 investigated tumors, and mutations were found in similar frequencies in favorable [International Neuroblastoma Staging System (INSS) 1, 2, and 4S; 5.7%] and unfavorable (INSS 3 and 4; 7.5%) neuroblastomas (P = 0.087). Two hotspot mutations, at positions R1275 and F1174, were observed (49% and 34.7% of the mutated cases, respectively). Interestingly, the F1174 mutations occurred in a high proportion of MYCN-amplified cases (P = 0.001), and this combined occurrence was associated with a particular poor outcome, suggesting a positive cooperative effect between both aberrations. Furthermore, the F1174L mutant was characterized by a higher degree of autophosphorylation and a more potent transforming capacity as compared with the R1275Q mutant. Chromosome 2p gains, including the ALK locus (91.8%), were associated with a significantly increased ALK expression, which was also correlated with poor survival.
ALK mutations occur in equal frequencies across all genomic subtypes, but F1174L mutants are observed in a higher frequency of MYCN-amplified tumors and show increased transforming capacity as compared with the R1275Q mutants.
Clinical Cancer Research 09/2010; 16(17):4353-62. · 7.74 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: SUMMARY: We present SVDetect, a program designed to identify genomic structural variations from paired-end and mate-pair next-generation sequencing data produced by the Illumina GA and ABI SOLiD platforms. Applying both sliding-window and clustering strategies, we use anomalously mapped read pairs provided by current short read aligners to localize genomic rearrangements and classify them according to their type, e.g. large insertions-deletions, inversions, duplications and balanced or unbalanced inter-chromosomal translocations. SVDetect outputs predicted structural variants in various file formats for appropriate graphical visualization. AVAILABILITY: Source code and sample data are available at http://svdetect.sourceforge.net/
Bioinformatics 08/2010; 26(15):1895-6. · 5.47 Impact Factor
-
André Oberthuer,
Barbara Hero,
Frank Berthold,
Dilafruz Juraeva,
Andreas Faldum,
Yvonne Kahlert,
Shahab Asgharzadeh,
Robert Seeger,
Paola Scaruffi,
Gian Paolo Tonini, [......],
Manfred Schwab,
Roland Eils,
Patrick Warnat,
Lars Kaderali,
Thorsten Simon,
Boris Decarolis,
Jessica Theissen,
Frank Westermann,
Benedikt Brors,
Matthias Fischer
[show abstract]
[hide abstract]
ABSTRACT: To evaluate the impact of a predefined gene expression-based classifier for clinical risk estimation and cytotoxic treatment decision making in neuroblastoma patients.
Gene expression profiles of 440 internationally collected neuroblastoma specimens were investigated by microarray analysis, 125 of which were examined prospectively. Patients were classified as either favorable or unfavorable by a 144-gene prediction analysis for microarrays (PAM) classifier established previously on a separate set of 77 patients. PAM classification results were compared with those of current prognostic markers and risk estimation strategies.
The PAM classifier reliably distinguished patients with contrasting clinical courses (favorable [n = 249] and unfavorable [n = 191]; 5-year event free survival [EFS] 0.84 +/- 0.03 v 0.38 +/- 0.04; 5-year overall survival [OS] 0.98 +/- 0.01 v 0.56 +/- 0.05, respectively; both P < .001). Moreover, patients with divergent outcome were robustly discriminated in both German and international cohorts and in prospectively analyzed samples (P <or= .001 for both EFS and OS for each). In subgroups with clinical low-, intermediate-, and high-risk of death from disease, the PAM predictor significantly separated patients with divergent outcome (low-risk 5-year OS: 1.0 v 0.75 +/- 0.10, P < .001; intermediate-risk: 1.0 v 0.82 +/- 0.08, P = .042; and high-risk: 0.81 +/- 0.08 v 0.43 +/- 0.05, P = .001). In multivariate Cox regression models based on both EFS and OS, PAM was a significant independent prognostic marker (EFS: hazard ratio [HR], 3.375; 95% CI, 2.075 to 5.492; P < .001; OS: HR, 11.119, 95% CI, 2.487 to 49.701; P < .001). The highest potential clinical impact of the classifier was observed in patients currently considered as non-high-risk (n = 289; 5-year EFS: 0.87 +/- 0.02 v 0.44 +/- 0.07; 5-year OS: 1.0 v 0.80 +/- 0.06; both P < .001).
Gene expression-based classification using the 144-gene PAM predictor can contribute to improved treatment stratification of neuroblastoma patients.
Journal of Clinical Oncology 07/2010; 28(21):3506-15. · 18.37 Impact Factor
-
Gudrun Schleiermacher, Isabelle Janoueix-Lerosey,
Agnès Ribeiro,
Jerzy Klijanienko,
Jérôme Couturier,
Gaëlle Pierron,
Véronique Mosseri,
Alexander Valent,
Nathalie Auger,
Dominique Plantaz,
Hervé Rubie,
Dominique Valteau-Couanet,
Franck Bourdeaut,
Valérie Combaret,
Christophe Bergeron,
Jean Michon,
Olivier Delattre
[show abstract]
[hide abstract]
ABSTRACT: Neuroblastoma is characterized by two distinct types of genetic profiles, consisting of either numerical or segmental chromosome alterations. The latter are associated with a higher risk of relapse, even when occurring together with numerical alterations. We explored the role of segmental alterations in tumor progression and the possibility of evolution from indolent to aggressive genomic types.
Array-based comparative genomic hybridization data of 394 neuroblastoma samples were analyzed and linked to clinical data.
Integration of ploidy and genomic data indicated that pseudotriploid tumors with mixed numerical and segmental profiles may be derived from pseudotriploid tumors with numerical alterations only. This was confirmed by the analysis of paired samples, at diagnosis and at relapse, as in tumors with a purely numerical profile at diagnosis additional segmental alterations at relapse were frequently observed. New segmental alterations at relapse were also seen in patients with segmental alterations at diagnosis. This was not linked to secondary effects of cytotoxic treatments since it occurred even in patients treated with surgery alone. A higher number of chromosome breakpoints were correlated with advanced age at diagnosis, advanced stage of disease, with a higher risk of relapse, and a poorer outcome.
These data provide further evidence of the role of segmental alterations, suggesting that tumor progression is linked to the accumulation of segmental alterations in neuroblastoma. This possibility of genomic evolution should be taken into account in treatment strategies of low- and intermediate-risk neuroblastoma and should warrant biologic reinvestigation at the time of relapse.
Journal of Clinical Oncology 07/2010; 28(19):3122-30. · 18.37 Impact Factor
-
Katleen De Preter,
Joëlle Vermeulen,
Benedikt Brors,
Olivier Delattre,
Angelika Eggert,
Matthias Fischer, Isabelle Janoueix-Lerosey,
Cinzia Lavarino,
John M Maris,
Jaume Mora,
Akira Nakagawara,
André Oberthuer,
Miki Ohira,
Gudrun Schleiermacher,
Alexander Schramm,
Johannes H Schulte,
Qun Wang,
Frank Westermann,
Frank Speleman,
Jo Vandesompele
[show abstract]
[hide abstract]
ABSTRACT: Reliable prognostic stratification remains a challenge for cancer patients, especially for diseases with variable clinical course such as neuroblastoma. Although numerous studies have shown that outcome might be predicted using gene expression signatures, independent cross-platform validation is often lacking.
Using eight independent studies comprising 933 neuroblastoma patients, a prognostic gene expression classifier was developed, trained, tested, and validated. The classifier was established based on reanalysis of four published studies with updated clinical information, reannotation of the probe sequences, common risk definition for training cases, and a single method for gene selection (prediction analysis of microarray) and classification (correlation analysis).
Based on 250 training samples from four published microarray data sets, a correlation signature was built using 42 robust prognostic genes. The resulting classifier was validated on 351 patients from four independent and unpublished data sets and on 129 remaining test samples from the published studies. Patients with divergent outcome in the total cohort, as well as in the different risk groups, were accurately classified (log-rank P < 0.001 for overall and progression-free survival in the four independent data sets). Moreover, the 42-gene classifier was shown to be an independent predictor for survival (odds ratio, >5).
The strength of this 42-gene classifier is its small number of genes and its cross-platform validity in which it outperforms other published prognostic signatures. The robustness and accuracy of the classifier enables prospective assessment of neuroblastoma patient outcome. Most importantly, this gene selection procedure might be an example for development and validation of robust gene expression signatures in other cancer entities.
Clinical Cancer Research 02/2010; 16(5):1532-41. · 7.74 Impact Factor
-
Franck Bourdeaut, Isabelle Janoueix-Lerosey,
Carlo Lucchesi,
Régine Paris,
Agnès Ribeiro,
Loïc de Pontual,
Jeanne Amiel,
Stanislas Lyonnet,
Gaëlle Pierron,
Jean Michon,
Michel Peuchmaur,
Olivier Delattre
[show abstract]
[hide abstract]
ABSTRACT: The morphology of malignant cells distinguishes between undifferentiated, poorly differentiated and differentiating neuroblastomas and constitutes a strong prognostic factor. Spontaneous or treatment-induced maturation characterizes a subset of neuroblastomas. It constitutes the basis of retinoic acid treatment to improve survival in aggressive neuroblastomas. However, the molecular events that drive differentiation are poorly understood. In the present study we have investigated the relationships between gene expression profiles and differentiation criteria in stroma-poor neuroblastomas. This study included three undifferentiated (UN), 20 poorly differentiated (PDN) and 11 differentiating (DN) neuroblastomas. These groups could be clearly separated using unsupervised clustering methods, which further enabled a major classification impact of genes involved in neural development, differentiation and function to be identified. UNs are characterized by high ASCL1, high PHOX2B, low GATA2, low TH and low DBH expressions. Most PDNs harbour a clear adrenergic phenotype, even in the presence of missense PHOX2B mutations. Finally, all DN tumours demonstrate cholinergic features. Depending upon their association with adrenergic characteristics, this enables dual 'cholinergic/adrenergic' and 'fully cholinergic' neuroblastomas to be defined. This suggests that the cholinergic switch, a final specification process that occurs physiologically in a minority of sympathetic neurons, is a critical step of differentiation in some neuroblastic tumours. This switch is associated with a down regulation of DBH that is apparently not strictly dependent upon PHOX2B. Conversely, GATA2 and TFAP2B may play critical roles in maintaining adrenergic features in poorly differentiated tumours.
The Journal of Pathology 08/2009; 219(4):463-72. · 6.32 Impact Factor
-
Joëlle Vermeulen,
Katleen De Preter,
Arlene Naranjo,
Liesbeth Vercruysse,
Nadine Van Roy,
Jan Hellemans,
Katrien Swerts,
Sophie Bravo,
Paola Scaruffi,
Gian Paolo Tonini, [......],
Hervé Rubie,
Janice Kohler,
Ulrike Pötschger,
Ruth Ladenstein,
Michael D Hogarty,
Patrick McGrady,
Wendy B London,
Geneviève Laureys,
Frank Speleman,
Jo Vandesompele
[show abstract]
[hide abstract]
ABSTRACT: More accurate prognostic assessment of patients with neuroblastoma is required to better inform the choice of risk-related therapy. The aim of this study is to develop and validate a gene-expression signature to improve outcome prediction.
59 genes were selected using an innovative data-mining strategy, and were profiled in the largest neuroblastoma patient series (n=579) to date using real-time quantitative PCR starting from only 20 ng of RNA. A multigene-expression signature was built using 30 training samples, tested on 313 test samples, and subsequently validated in a blind study on an independent set of 236 tumours.
The signature has a performance, sensitivity, and specificity of 85.4% (95% CI 77.7-93.2), 84.4% (66.5-94.1), and 86.5% (81.1-90.6), respectively, to predict patient outcome. Multivariate analysis indicates that the signature is a significant independent predictor of overall survival and progression-free survival after controlling for currently used risk factors: patients with high molecular risk have a higher risk of death from disease and higher risk of relapse or progression than patients with low molecular risk (odds ratio 19.32 [95% CI 6.50-57.43] and 3.96 [1.97-7.97] for overall survival and progression-free survival, respectively, both p<0.0001). Patients at an increased risk of an adverse outcome can also be identified in the current treatment groups, showing the potential of this signature for improved clinical management. These results were confirmed in the validation study, in which the signature was also independently statistically significant in a model adjusted for MYCN status, age, International Neuroblastoma Staging System stage, ploidy, International Neuroblastoma Pathology Classification grade of differentiation, and mitosis karyorrhexis index (odds ratios between 4.81 and 10.53 depending on the model for overall survival and 3.68 [95% CI 2.01-6.71] for progression-free survival).
The 59-gene expression signature is an accurate predictor of outcome in patients with neuroblastoma. The signature is an independent risk predictor, identifying patients with an increased risk of poor outcome in the current clinical-risk groups. The method and signature is suitable for routine laboratory testing, and should be evaluated in prospective studies.
The Belgian Foundation Against Cancer, the Children Cancer Fund Ghent, the Belgian Society of Paediatric Haematology and Oncology, the Belgian Kid's Fund and the Fondation Nuovo-Soldati (JV), the Fund for Scientific Research Flanders (KDP, JH), the Fund for Scientific Research Flanders, the Institute for the Promotion of Innovation by Science and Technology in Flanders, Strategisch basisonderzoek, the Fondation Fournier Majoie pour l'Innovation, the Instituto Carlos III, the Italian Neuroblastoma Foundation, the European Community under the FP6, and the Belgian programme of Interuniversity Poles of Attraction.
The lancet oncology 06/2009; 10(7):663-71. · 14.47 Impact Factor
-
Medecine sciences: M/S 05/2009; 25(4):330-2. · 0.64 Impact Factor
-
Isabelle Janoueix-Lerosey,
Gudrun Schleiermacher,
Evi Michels,
Véronique Mosseri,
Agnès Ribeiro,
Delphine Lequin,
Joëlle Vermeulen,
Jérôme Couturier,
Michel Peuchmaur,
Alexander Valent,
Dominique Plantaz,
Hervé Rubie,
Dominique Valteau-Couanet,
Caroline Thomas,
Valérie Combaret,
Raphaël Rousseau,
Angelika Eggert,
Jean Michon,
Frank Speleman,
Olivier Delattre
[show abstract]
[hide abstract]
ABSTRACT: For a comprehensive overview of the genetic alterations of neuroblastoma, their association and clinical significance, we conducted a whole-genome DNA copy number analysis.
A series of 493 neuroblastoma (NB) samples was investigated by array-based comparative genomic hybridization in two consecutive steps (224, then 269 patients).
Genomic analysis identified several types of profiles. Tumors presenting exclusively whole-chromosome copy number variations were associated with excellent survival. No disease-related death was observed in this group. In contrast, tumors with any type of segmental chromosome alterations characterized patients with a high risk of relapse. Patients with both numerical and segmental abnormalities clearly shared the higher risk of relapse of segmental-only patients. In a multivariate analysis, taking into account the genomic profile, but also previously described individual genetic and clinical markers with prognostic significance, the presence of segmental alterations with (HR, 7.3; 95% CI, 3.7 to 14.5; P < .001) or without MYCN amplification (HR, 4.5; 95% CI, 2.4 to 8.4; P < .001) was the strongest predictor of relapse; the other significant variables were age older than 18 months (HR, 1.8; 95% CI, 1.2 to 2.8; P = .004) and stage 4 (HR, 1.8; 95% CI, 1.2 to 2.7; P = .005). Finally, within tumors showing segmental alterations, stage 4, age, MYCN amplification, 1p and 11q deletions, and 1q gain were independent predictors of decreased overall survival.
The analysis of the overall genomic pattern, which probably unravels particular genomic instability mechanisms rather than the analysis of individual markers, is essential to predict relapse in NB patients. It adds critical prognostic information to conventional markers and should be included in future treatment stratification.
Journal of Clinical Oncology 02/2009; 27(7):1026-33. · 18.37 Impact Factor
-
Sarah Fattet,
Christine Haberler,
Patricia Legoix,
Pascale Varlet,
Arielle Lellouch-Tubiana,
Severine Lair,
Elodie Manie,
Marie-Anne Raquin,
Danielle Bours,
Sabrina Carpentier,
Emmanuel Barillot,
Jacques Grill,
Francois Doz,
Stephanie Puget, Isabelle Janoueix-Lerosey,
Olivier Delattre
[show abstract]
[hide abstract]
ABSTRACT: Medulloblastoma is the most frequent malignant paediatric brain tumour. The activation of the Wnt/beta-catenin pathway occurs in 10-15% of medulloblastomas and has been recently described as a marker for favourable patient outcome. We report a series of 72 paediatric medulloblastomas evaluated for beta-catenin protein expression, CTNNB1 mutations, and comparative genomic hybridization. Gene expression profiles were also available in a subset of 40 cases. Immunostaining of beta-catenin showed extensive nuclear staining (>50% of the tumour cells) in six cases and focal nuclear staining (<10% of cells) in three cases. The other cases either exhibited a signal strictly limited to the cytoplasm (58 cases) or were negative (five cases). CTNNB1 mutations were detected in all beta-catenin extensively nucleopositive cases. The expression profiles of these cases documented strong activation of the Wnt/beta-catenin pathway. Remarkably, five out of these six tumours showed a complete loss of chromosome 6. In contrast, cases with focal nuclear beta-catenin staining, as well as tumours with negative or cytoplasmic staining, never demonstrated CTNNB1 mutation, Wnt/beta-catenin pathway activation or chromosome 6 loss. Patients with extensive nuclear staining were significantly older at diagnosis and were in continuous complete remission after a mean follow-up of 75.7 months (range 27.5-121.2 months) from diagnosis. All three patients with focal nuclear staining of beta-catenin died within 36 months from diagnosis. Altogether, these data confirm and extend previous observations that CTNNB1-mutated tumours represent a distinct molecular subgroup of medulloblastomas with favourable outcome, indicating that therapy de-escalation should be considered. International consensus on the definition criteria of this distinct medulloblastoma subgroup should be achieved.
The Journal of Pathology 01/2009; 218(1):86-94. · 6.32 Impact Factor
-
Isabelle Janoueix-Lerosey,
Delphine Lequin,
Laurence Brugières,
Agnès Ribeiro,
Loïc de Pontual,
Valérie Combaret,
Virginie Raynal,
Alain Puisieux,
Gudrun Schleiermacher,
Gaëlle Pierron,
Dominique Valteau-Couanet,
Thierry Frebourg,
Jean Michon,
Stanislas Lyonnet,
Jeanne Amiel,
Olivier Delattre
[show abstract]
[hide abstract]
ABSTRACT: Neuroblastoma, a tumour derived from the peripheral sympathetic nervous system, is one of the most frequent solid tumours in childhood. It usually occurs sporadically but familial cases are observed, with a subset of cases occurring in association with congenital malformations of the neural crest being linked to germline mutations of the PHOX2B gene. Here we conducted genome-wide comparative genomic hybridization analysis on a large series of neuroblastomas. Copy number increase at the locus encoding the anaplastic lymphoma kinase (ALK) tyrosine kinase receptor was observed recurrently. One particularly informative case presented a high-level gene amplification that was strictly limited to ALK, indicating that this gene may contribute on its own to neuroblastoma development. Through subsequent direct sequencing of cell lines and primary tumour DNAs we identified somatic mutations of the ALK kinase domain that mainly clustered in two hotspots. Germline mutations were observed in two neuroblastoma families, indicating that ALK is a neuroblastoma predisposition gene. Mutated ALK proteins were overexpressed, hyperphosphorylated and showed constitutive kinase activity. The knockdown of ALK expression in ALK-mutated cells, but also in cell lines overexpressing a wild-type ALK, led to a marked decrease of cell proliferation. Altogether, these data identify ALK as a critical player in neuroblastoma development that may hence represent a very attractive therapeutic target in this disease that is still frequently fatal with current treatments.
Nature 11/2008; 455(7215):967-70. · 36.28 Impact Factor
-
Isabelle Janoueix-Lerosey,
Delphine Lequin,
Laurence Brugi|[egrave]|res,
Agn|[egrave]|s Ribeiro,
Lo|[iuml]|c de Pontual,
Val|[eacute]|rie Combaret,
Virginie Raynal,
Alain Puisieux,
Gudrun Schleiermacher,
Ga|[euml]|lle Pierron,
Dominique Valteau-Couanet,
Thierry Frebourg,
Jean Michon,
Stanislas Lyonnet,
Jeanne Amiel,
Olivier Delattre
[show abstract]
[hide abstract]
ABSTRACT: Neuroblastoma, a tumour derived from the peripheral sympathetic nervous system, is one of the most frequent solid tumours in childhood
Nature 10/2008; 455(7215):967-970. · 36.28 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Somatically acquired chromosomal imbalances are a key feature of neuroblastoma, a heterogeneous pediatric solid tumor. Among these alterations, genomic amplification targeting the MYCN oncogene and observed in about 25-30% of the cases, strongly correlates with advanced stage and poor outcome. In this work, we have used BAC and SNP arrays as well as gene expression arrays to characterize amplifications in neuroblastoma. Eighty-eight distinct BACs defining high-level amplification events were identified in 65 samples, including 43 tumors and 22 cell lines. Although the highest recurrence was observed on chromosome 2, clones on chromosomes 8, 12, 16, and 17 also revealed genomic amplification in several samples. A detailed analysis of the 2p22-2p25 MYCN containing region indicated highly complex patterns in a number of cases. Coamplifications involving MYCN and other regions were explored by FISH in three cell lines. High-resolution arrays then allowed us to further refine the mapping of 25 amplicons in 19 samples, either reducing the size of a single continuous amplicon or increasing the complexity by highlighting multiple noncontiguous regions of amplification. Combined analysis of gene expression profiling and array-CGH data indicated that 12 to 25% of the genes that are targeted by genomic amplification are actually over-expressed in tumor cells, several of them having already been implicated in cancer. Finally, our results suggest that the presence of amplicons localized outside of chromosome 2, in addition to MYCN amplification, may be linked to a particularly severe outcome in neuroblastoma patients.
Genes Chromosomes and Cancer 07/2008; 47(10):819-34. · 3.31 Impact Factor
