1
|
Kańduła MM, Aldoshin AD, Singh S, Kolaczyk ED, Kreil D. ViLoN-a multi-layer network approach to data integration demonstrated for patient stratification. Nucleic Acids Res 2022; 51:e6. [PMID: 36395816 PMCID: PMC9841426 DOI: 10.1093/nar/gkac988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 10/11/2022] [Accepted: 11/02/2022] [Indexed: 11/19/2022] Open
Abstract
With more and more data being collected, modern network representations exploit the complementary nature of different data sources as well as similarities across patients. We here introduce the Variation of information fused Layers of Networks algorithm (ViLoN), a novel network-based approach for the integration of multiple molecular profiles. As a key innovation, it directly incorporates prior functional knowledge (KEGG, GO). In the constructed network of patients, patients are represented by networks of pathways, comprising genes that are linked by common functions and joint regulation in the disease. Patient stratification remains a key challenge both in the clinic and for research on disease mechanisms and treatments. We thus validated ViLoN for patient stratification on multiple data type combinations (gene expression, methylation, copy number), showing substantial improvements and consistently competitive performance for all. Notably, the incorporation of prior functional knowledge was critical for good results in the smaller cohorts (rectum adenocarcinoma: 90, esophageal carcinoma: 180), where alternative methods failed.
Collapse
Affiliation(s)
- Maciej M Kańduła
- Institute of Molecular Biotechnology, Boku University Vienna, Austria,Janssen Pharmaceutica NV, Beerse, Belgium
| | | | - Swati Singh
- Institute of Molecular Biotechnology, Boku University Vienna, Austria,Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, India
| | - Eric D Kolaczyk
- Correspondence may also be addressed to Eric D. Kolaczyk. Tel: +1 514 398 3805;
| | - David P Kreil
- To whom correspondence should be addressed. Tel: +43 1 47654 79009;
| |
Collapse
|
2
|
Why Is Aneuploidy Associated with Favorable Outcome in Neuroblastoma? Biomolecules 2021; 11:biom11081116. [PMID: 34439783 PMCID: PMC8391846 DOI: 10.3390/biom11081116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/23/2021] [Accepted: 07/26/2021] [Indexed: 11/17/2022] Open
Abstract
Neuroblastoma is a pediatric cancer, onset with localized as well as metastatic disease. Localized tumors usually show a high content of aneuploid cells. It is suggested that aneuploid cells with numerical copy number variation (CNV) are generated by chromosome instability (CIN). Patients with a localized tumor respond well to the therapy and show a good outcome. On the contrary, patients with a metastatic tumor have worse outcomes and the cells with structural CNV show high levels of CIN. It is proposed that a favorable outcome in patients with localized disease is associated to the grade of CIN.
Collapse
|
3
|
Abstract
Neuroblastoma (NB) is a pediatric tumor of embryonic origin. About 1-2% of all NBs are familial cases, and genetic predisposition is suspected for the remaining cases. During the last decade, genome-wide association studies (GWAS) and high-throughput sequencing approaches have been used to identify associations among common and rare genetic variants and NB risk. Substantial data has been produced by large patient cohorts that implicate various genes in NB tumorigenesis, such as CASC15, BARD1, CHEK2, LMO1, LIN28B, AXIN2, BRCA1, TP53, SMARCA4, and CDK1NB. NB, as well as other pediatric cancers, has few recurrent mutations but several copy number variations (CNVs). Almost all NBs show both numerical and structural CNVs. The proportion between numerical and structural CNVs differs between localized and metastatic tumors, with a greater prevalence of structural CNVs in metastatic NB. This genomic chaos frequently identified in NBs suggests that chromosome instability (CIN) could be one of the major actors in NB oncogenesis. Interestingly, many NB-predisposing variants occur in genes involved in the control of genome stability, mitosis, and normal chromosome separation. Here, we discuss the relationship between genetic predisposition and CIN in NB.
Collapse
Affiliation(s)
- Gian Paolo Tonini
- Neuroblastoma Laboratory, Pediatric Research Institute, Città della Speranza, Corso Stati Uniti 4, 35127, Padova, Italy.
| | - Mario Capasso
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Univeristà degli Studi di Napoli Federico II, Naples, Italy. .,CEINGE Biotecnologie Avanzate, Naples, Italy.
| |
Collapse
|
4
|
Ambros IM, Tonini GP, Pötschger U, Gross N, Mosseri V, Beiske K, Berbegall AP, Bénard J, Bown N, Caron H, Combaret V, Couturier J, Defferrari R, Delattre O, Jeison M, Kogner P, Lunec J, Marques B, Martinsson T, Mazzocco K, Noguera R, Schleiermacher G, Valent A, Van Roy N, Villamon E, Janousek D, Pribill I, Glogova E, Attiyeh EF, Hogarty MD, Monclair TF, Holmes K, Valteau-Couanet D, Castel V, Tweddle DA, Park JR, Cohn S, Ladenstein R, Beck-Popovic M, De Bernardi B, Michon J, Pearson ADJ, Ambros PF. Age Dependency of the Prognostic Impact of Tumor Genomics in Localized Resectable MYCN-Nonamplified Neuroblastomas. Report From the SIOPEN Biology Group on the LNESG Trials and a COG Validation Group. J Clin Oncol 2020; 38:3685-3697. [PMID: 32903140 PMCID: PMC7605396 DOI: 10.1200/jco.18.02132] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
For localized, resectable neuroblastoma without MYCN amplification, surgery only is recommended even if incomplete. However, it is not known whether the genomic background of these tumors may influence outcome.
Collapse
Affiliation(s)
- Inge M Ambros
- Children's Cancer Research Institute, St Anna Kinderkrebsforschung, Vienna, Austria
| | - Gian-Paolo Tonini
- Paediatric Research Institute, Fondazione Città della Speranza, Neuroblastoma Laboratory, Padua, Italy
| | - Ulrike Pötschger
- Children's Cancer Research Institute, St Anna Kinderkrebsforschung, Vienna, Austria
| | - Nicole Gross
- Pediatric Oncology Research, Department of Pediatrics, University Hospital, Lausanne, Switzerland
| | | | - Klaus Beiske
- Department of Pathology, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Ana P Berbegall
- Department of Pathology, Medical School, University of Valencia-Fundación de Investigación del Hospital Clínico Universitario de Valencia, Valencia, Spain.,Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
| | - Jean Bénard
- Département de Biologie et de Pathologie Médicales, Service de Pathologie Moléculaire, Institut Gustave Roussy, Villejuif, France
| | - Nick Bown
- Northern Genetics Service, Newcastle upon Tyne, United Kingdom
| | - Huib Caron
- Department of Pediatric Oncology, Emma Children's Hospital, Academic Medical Center, Amsterdam, the Netherlands
| | - Valérie Combaret
- Centre Léon Bérard, Laboratoire de Recherche Translationnelle, Lyon, France
| | - Jerome Couturier
- Unité de Génétique Somatique et Cytogénétique, Institut Curie, Paris, France
| | | | - Olivier Delattre
- INSERM U830, Laboratoire de Génétique et Biologie des Cancers, Paris, France
| | - Marta Jeison
- Ca-Cytogenetic Laboratory, Pediatric Hematology Oncology Department, Schneider Children's Medical Center of Israel, Petah Tikvah, Israel
| | - Per Kogner
- Childhood Cancer Research Unit, Karolinska Institutet, Astrid Lindgren Children's Hospital, Stockholm, Sweden
| | - John Lunec
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Barbara Marques
- Centro de Genética Humana, Instituto Nacional de Saude doutor Ricardo Jorge, Lisbon, Portugal
| | - Tommy Martinsson
- Department of Clinical Genetics, Institute of Biomedicine, University of Gothenburg, Sahlgrenska University Hospital, Göteborg, Sweden
| | - Katia Mazzocco
- Department of Pathology, Istituto G. Gaslini, Genoa, Italy
| | - Rosa Noguera
- Department of Pathology, Medical School, University of Valencia-Fundación de Investigación del Hospital Clínico Universitario de Valencia, Valencia, Spain.,Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
| | - Gudrun Schleiermacher
- INSERM U830, Laboratoire de Génétique et Biologie des Cancers, Paris, France.,Département de Pédiatrie, Institut Curie, Paris, France
| | - Alexander Valent
- Département de Biologie et de Pathologie Médicales, Service de Pathologie Moléculaire, Institut Gustave Roussy, Villejuif, France
| | - Nadine Van Roy
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Eva Villamon
- Department of Pathology, Medical School, University of Valencia-Fundación de Investigación del Hospital Clínico Universitario de Valencia, Valencia, Spain.,Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
| | - Dasa Janousek
- Children's Cancer Research Institute, St Anna Kinderkrebsforschung, Vienna, Austria
| | - Ingrid Pribill
- Children's Cancer Research Institute, St Anna Kinderkrebsforschung, Vienna, Austria
| | - Evgenia Glogova
- Children's Cancer Research Institute, St Anna Kinderkrebsforschung, Vienna, Austria
| | - Edward F Attiyeh
- Division of Oncology, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Michael D Hogarty
- Division of Oncology, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Tom F Monclair
- Section for Paediatric Surgery, Division of Surgery, Rikshospitalet University Hospital, Oslo, Norway
| | - Keith Holmes
- Department of Paediatric Surgery, St George's Hospital, London, UK
| | | | - Victoria Castel
- Unidad de Oncologia Pediatrica Hospital Universitario La Fe, Valencia, Spain
| | - Deborah A Tweddle
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Julie R Park
- Seattle Children's Hospital and University of Washington School of Medicine, Seattle, WA
| | - Sue Cohn
- Department of Pediatrics, The University of Chicago, Chicago, IL
| | - Ruth Ladenstein
- Children's Cancer Research Institute, St Anna Kinderkrebsforschung, Vienna, Austria.,Department of Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Maja Beck-Popovic
- Pediatric Hematology Oncology Unit, University Hospital of Lausanne, Lausanne, Switzerland
| | - Bruno De Bernardi
- Department of Paediatric Haematology and Oncology, Giannina Gaslini Children's Hospital, Genova, Italy
| | - Jean Michon
- Département de Pédiatrie, Institut Curie, Paris, France
| | - Andrew D J Pearson
- Institute of Cancer Research, Royal Marsden Hospital, Sutton, Surrey, United Kingdom
| | - Peter F Ambros
- Children's Cancer Research Institute, St Anna Kinderkrebsforschung, Vienna, Austria.,Department of Pediatrics, Medical University of Vienna, Vienna, Austria
| |
Collapse
|
5
|
Hormones Secretion and Rho GTPases in Neuroendocrine Tumors. Cancers (Basel) 2020; 12:cancers12071859. [PMID: 32664294 PMCID: PMC7408961 DOI: 10.3390/cancers12071859] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/03/2020] [Accepted: 07/06/2020] [Indexed: 12/14/2022] Open
Abstract
Neuroendocrine tumors (NETs) belong to a heterogeneous group of neoplasms arising from hormone secreting cells. These tumors are often associated with a dysfunction of their secretory activity. Neuroendocrine secretion occurs through calcium-regulated exocytosis, a process that is tightly controlled by Rho GTPases family members. In this review, we compiled the numerous mutations and modification of expression levels of Rho GTPases or their regulators (Rho guanine nucleotide-exchange factors and Rho GTPase-activating proteins) that have been identified in NETs. We discussed how they might regulate neuroendocrine secretion.
Collapse
|
6
|
Krzhizhanovskaya VV, Závodszky G, Lees MH, Dongarra JJ, Sloot PMA, Brissos S, Teixeira J. Bootstrap Bias Corrected Cross Validation Applied to Super Learning. LECTURE NOTES IN COMPUTER SCIENCE 2020. [PMCID: PMC7304018 DOI: 10.1007/978-3-030-50420-5_41] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Super learner algorithm can be applied to combine results of multiple base learners to improve quality of predictions. The default method for verification of super learner results is by nested cross validation; however, this technique is very expensive computationally. It has been proposed by Tsamardinos et al., that nested cross validation can be replaced by resampling for tuning hyper-parameters of the learning algorithms. The main contribution of this study is to apply this idea to verification of super learner. We compare the new method with other verification methods, including nested cross validation. Tests were performed on artificial data sets of diverse size and on seven real, biomedical data sets. The resampling method, called Bootstrap Bias Correction, proved to be a reasonably precise and very cost-efficient alternative for nested cross validation.
Collapse
|
7
|
Ackermann S, Fischer M. Telomere Maintenance in Pediatric Cancer. Int J Mol Sci 2019; 20:E5836. [PMID: 31757062 PMCID: PMC6928840 DOI: 10.3390/ijms20235836] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/15/2019] [Accepted: 11/18/2019] [Indexed: 02/06/2023] Open
Abstract
Telomere length has been proposed as a biomarker of biological age and a risk factor for age-related diseases and cancer. Substantial progress has been made in recent decades in understanding the complex molecular relationships in this research field. However, the majority of telomere studies have been conducted in adults. The data on telomere dynamics in pediatric cancers is limited, and interpretation can be challenging, especially in cases where results are contrasting to those in adult entities. This review describes recent advances in the molecular characterization of structure and function of telomeres, regulation of telomerase activity in cancer pathogenesis in general, and highlights the key advances that have expanded our views on telomere biology in pediatric cancer, with special emphasis on the central role of telomere maintenance in neuroblastoma. Furthermore, open questions in the field of telomere maintenance research are discussed in the context of recently published literature.
Collapse
Affiliation(s)
- Sandra Ackermann
- Department of Experimental Pediatric Oncology, University Children’s Hospital of Cologne, Faculty of Medicine and University Hospital of Cologne, Kerpener Straße 62, 50937 Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Robert-Koch-Straße 21, 50931 Cologne, Germany
| | - Matthias Fischer
- Department of Experimental Pediatric Oncology, University Children’s Hospital of Cologne, Faculty of Medicine and University Hospital of Cologne, Kerpener Straße 62, 50937 Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Robert-Koch-Straße 21, 50931 Cologne, Germany
| |
Collapse
|
8
|
Yue ZX, Xing TY, Gao C, Liu SG, Zhao W, Zhao Q, Wang XS, Jin M, Ma XL. Chromosome band 11q23 deletion predicts poor prognosis in bone marrow metastatic neuroblastoma patients without MYCN amplification. Cancer Commun (Lond) 2019; 39:68. [PMID: 31685009 PMCID: PMC6829843 DOI: 10.1186/s40880-019-0409-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 10/16/2019] [Indexed: 12/16/2022] Open
Abstract
Background Interphase fluorescence in situ hybridization (FISH) of bone marrow cells has been confirmed to be a direct and valid method to assess the v-myc avian myelocytomatosis viral oncogene neuroblastoma derived homolog (MYCN) amplification in patients with bone marrow metastatic neuroblastoma. MYCN amplification alone, however, is insufficient for pretreatment risk stratification. Chromosome band 11q23 deletion has recently been included in the risk stratification of neuroblastoma. In the present study, we aimed to evaluate the biological characteristics and prognostic impact of 11q23 deletion and MYCN amplification in patients with bone marrow metastatic neuroblastoma. Methods We analyzed the MYCN and 11q23 statuses of 101 patients with bone marrow metastatic neuroblastoma using interphase FISH of bone marrow cells. We specifically compared the biological characteristics and prognostic impact of both aberrations. Results MYCN amplification and 11q23 deletion were seen in 12 (11.9%) and 40 (39.6%) patients. The two markers were mutually exclusive. MYCN amplification occurred mainly in patients with high lactate dehydrogenase (LDH) and high neuron-specific enolase (NSE) levels (both P < 0.001), and MYCN-amplified patients had more events (tumor relapse, progression, or death) than MYCN-normal patients (P = 0.004). 11q23 deletion was associated only with age (P = 0.001). Patients with MYCN amplification had poorer outcomes than those with normal MYCN (3-year event-free survival [EFS] rate: 8.3 ± 8.0% vs. 43.8 ± 8.5%, P < 0.001; 3-year overall survival [OS] rate: 10.4 ± 9.7% vs. 63.5% ± 5.7%, P < 0.001). 11q23 deletion reflected a poor prognosis only for patients with normal MYCN (3-year EFS rate: 34.3 ± 9.5% vs. 53.4 ± 10.3%, P = 0.037; 3-year OS rate: 42.9 ± 10.4% vs. 75.9 ± 6.1%, P = 0.048). Those with both MYCN amplification and 11q23 deletion had the worst outcome (P < 0.001). Conclusions Chromosome band 11q23 deletion predicts poor prognosis only in bone marrow metastatic neuroblastoma patients without MYCN amplification. Combined assessment of the two markers was much superior to single-marker assessment in recognizing the patients at a high risk of disease progression.
Collapse
Affiliation(s)
- Zhi-Xia Yue
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, 56 Nanlishi Road, Beijing, 100045, People's Republic of China
| | - Tian-Yu Xing
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, 56 Nanlishi Road, Beijing, 100045, People's Republic of China
| | - Chao Gao
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, 56 Nanlishi Road, Beijing, 100045, People's Republic of China
| | - Shu-Guang Liu
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, 56 Nanlishi Road, Beijing, 100045, People's Republic of China
| | - Wen Zhao
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, 56 Nanlishi Road, Beijing, 100045, People's Republic of China
| | - Qian Zhao
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, 56 Nanlishi Road, Beijing, 100045, People's Republic of China
| | - Xi-Si Wang
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, 56 Nanlishi Road, Beijing, 100045, People's Republic of China
| | - Mei Jin
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, 56 Nanlishi Road, Beijing, 100045, People's Republic of China
| | - Xiao-Li Ma
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, 56 Nanlishi Road, Beijing, 100045, People's Republic of China.
| |
Collapse
|
9
|
Fusco P, Parisatto B, Rampazzo E, Persano L, Frasson C, Di Meglio A, Leslz A, Santoro L, Cafferata B, Zin A, Cimetta E, Basso G, Esposito MR, Tonini GP. Patient-derived organoids (PDOs) as a novel in vitro model for neuroblastoma tumours. BMC Cancer 2019; 19:970. [PMID: 31638925 PMCID: PMC6802324 DOI: 10.1186/s12885-019-6149-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 09/10/2019] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Neuroblastoma (NB) is a paediatric tumour of the sympathetic nervous system. Half of all cases are defined high-risk with an overall survival less than 40% at 5 years from diagnosis. The lack of in vitro models able to recapitulate the intrinsic heterogeneity of primary NB tumours has hindered progress in understanding disease pathogenesis and therapy response. METHODS Here we describe the establishment of 6 patient-derived organoids (PDOs) from cells of NB tumour biopsies capable of self-organising in a structure resembling the tissue of origin. RESULTS PDOs recapitulate the histological architecture typical of the NB tumour. Moreover, PDOs expressed NB specific markers such as neural cell adhesion molecules, NB84 antigen, synaptophysin (SYP), chromogranin A (CHGA) and neural cell adhesion molecule NCAM (CD56). Analyses of whole genome genotyping array revealed that PDOs maintained patient-specific chromosomal aberrations such as MYCN amplification, deletion of 1p and gain of chromosome 17q. Furthermore, the PDOs showed stemness features and retained cellular heterogeneity reflecting the high heterogeneity of NB tumours. CONCLUSIONS We were able to create a novel preclinical model for NB exhibiting self-renewal property and allowing to obtain a reservoir of NB patients' biological material useful for the study of NB molecular pathogenesis and to test drugs for personalised treatments.
Collapse
Affiliation(s)
- P Fusco
- Fondazione Istituto di Ricerca Pediatrica Città della Speranza (IRP) - Neuroblastoma Laboratory Corso Stati Uniti 4, 35127, Padova, Italy
| | - B Parisatto
- Fondazione Istituto di Ricerca Pediatrica Città della Speranza (IRP) - Neuroblastoma Laboratory Corso Stati Uniti 4, 35127, Padova, Italy
| | - E Rampazzo
- Fondazione Istituto di Ricerca Pediatrica Città della Speranza (IRP) - Corso Stati Uniti 4, 35127, Padova, Italy.,University of Padova, Department of Women's and Children's Health, 35128, Padova, Italy
| | - L Persano
- Fondazione Istituto di Ricerca Pediatrica Città della Speranza (IRP) - Corso Stati Uniti 4, 35127, Padova, Italy
| | - C Frasson
- Fondazione Istituto di Ricerca Pediatrica Città della Speranza (IRP) - Corso Stati Uniti 4, 35127, Padova, Italy
| | - A Di Meglio
- University of Padova, Department of Women's and Children's Health, 35128, Padova, Italy
| | - A Leslz
- University of Padova, Department of Women's and Children's Health, 35128, Padova, Italy
| | - L Santoro
- Department of Medicine DIMED, Pathology and Cytopathology Unit, University of Padua, 35127, Padova, Italy
| | - B Cafferata
- Department of Medicine DIMED, Pathology and Cytopathology Unit, University of Padua, 35127, Padova, Italy
| | - A Zin
- Fondazione Istituto di Ricerca Pediatrica Città della Speranza (IRP) - Corso Stati Uniti 4, 35127, Padova, Italy
| | - E Cimetta
- Fondazione Istituto di Ricerca Pediatrica Città della Speranza (IRP) - Corso Stati Uniti 4, 35127, Padova, Italy.,University of Padua, Department of Industrial Engineering (DII), 35127, Padova, Italy
| | - G Basso
- Fondazione Istituto di Ricerca Pediatrica Città della Speranza (IRP) - Corso Stati Uniti 4, 35127, Padova, Italy.,University of Padova, Department of Women's and Children's Health, 35128, Padova, Italy
| | - M R Esposito
- Fondazione Istituto di Ricerca Pediatrica Città della Speranza (IRP) - Neuroblastoma Laboratory Corso Stati Uniti 4, 35127, Padova, Italy.
| | - G P Tonini
- Fondazione Istituto di Ricerca Pediatrica Città della Speranza (IRP) - Neuroblastoma Laboratory Corso Stati Uniti 4, 35127, Padova, Italy
| |
Collapse
|
10
|
Depuydt P, Boeva V, Hocking TD, Cannoodt R, Ambros IM, Ambros PF, Asgharzadeh S, Attiyeh EF, Combaret V, Defferrari R, Fischer M, Hero B, Hogarty MD, Irwin MS, Koster J, Kreissman S, Ladenstein R, Lapouble E, Laureys G, London WB, Mazzocco K, Nakagawara A, Noguera R, Ohira M, Park JR, Pötschger U, Theissen J, Tonini GP, Valteau-Couanet D, Varesio L, Versteeg R, Speleman F, Maris JM, Schleiermacher G, De Preter K. Genomic Amplifications and Distal 6q Loss: Novel Markers for Poor Survival in High-risk Neuroblastoma Patients. J Natl Cancer Inst 2019. [PMID: 29514301 PMCID: PMC6186524 DOI: 10.1093/jnci/djy022] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Background Neuroblastoma is characterized by substantial clinical heterogeneity. Despite intensive treatment, the survival rates of high-risk neuroblastoma patients are still disappointingly low. Somatic chromosomal copy number aberrations have been shown to be associated with patient outcome, particularly in low- and intermediate-risk neuroblastoma patients. To improve outcome prediction in high-risk neuroblastoma, we aimed to design a prognostic classification method based on copy number aberrations. Methods In an international collaboration, normalized high-resolution DNA copy number data (arrayCGH and SNP arrays) from 556 high-risk neuroblastomas obtained at diagnosis were collected from nine collaborative groups and segmented using the same method. We applied logistic and Cox proportional hazard regression to identify genomic aberrations associated with poor outcome. Results In this study, we identified two types of copy number aberrations that are associated with extremely poor outcome. Distal 6q losses were detected in 5.9% of patients and were associated with a 10-year survival probability of only 3.4% (95% confidence interval [CI] = 0.5% to 23.3%, two-sided P = .002). Amplifications of regions not encompassing the MYCN locus were detected in 18.1% of patients and were associated with a 10-year survival probability of only 5.8% (95% CI = 1.5% to 22.2%, two-sided P < .001). Conclusions Using a unique large copy number data set of high-risk neuroblastoma cases, we identified a small subset of high-risk neuroblastoma patients with extremely low survival probability that might be eligible for inclusion in clinical trials of new therapeutics. The amplicons may also nominate alternative treatments that target the amplified genes.
Collapse
Affiliation(s)
- Pauline Depuydt
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent, Belgium
| | - Valentina Boeva
- Institut Cochin, Inserm U1016, CNRS UMR 8104, Université Paris Descartes UMR-S1016, Paris, France.,Institut Curie, Inserm U900, Mines ParisTech, PSL Research University, Paris, France
| | - Toby D Hocking
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Robrecht Cannoodt
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent, Belgium.,Data Mining and Modelling for Biomedicine Group, VIB Center for Inflammation Research, Ghent, Belgium
| | - Inge M Ambros
- Children's Cancer Research Institute, Austria.,Department of Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Peter F Ambros
- Children's Cancer Research Institute, Austria.,Department of Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Shahab Asgharzadeh
- Division of Hematology/Oncology, Children's Hospital Los Angeles, University of Southern California Keck School of Medicine, Los Angeles, CA
| | - Edward F Attiyeh
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA.,Center for Childhood Cancer Research, University of Pennsylvania, Philadelphia, PA.,Department of Pediatrics, University of Pennsylvania, Philadelphia, PA
| | - Valérie Combaret
- Centre Léon-Bérard, Laboratoire de Recherche Translationnelle, Lyon, France
| | | | - Matthias Fischer
- Department of Experimental Pediatric Oncology, University of Cologne, Cologne, Germany.,University Children's Hospital Cologne, Medical Faculty, and Center for Molecular Medicine Cologne
| | - Barbara Hero
- Department of Pediatric Oncology and Hematology, University of Cologne, Cologne, Germany
| | - Michael D Hogarty
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA.,Perelman School of Medicine (MDH), University of Pennsylvania, Philadelphia, PA
| | - Meredith S Irwin
- Division of Hematology-Oncology, Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Jan Koster
- Department of Oncogenomics, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Susan Kreissman
- Department of Pediatrics, Duke University School of Medicine, Durham, NC
| | - Ruth Ladenstein
- Children's Cancer Research Institute, Austria.,Department of Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Eve Lapouble
- Genetic Somatic Unit.,Institut Curie, Paris, France
| | - Geneviève Laureys
- Department of Pediatric Hematology and Oncology, Ghent University Hospital, De Pintelaan, Ghent, Belgium
| | - Wendy B London
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA
| | - Katia Mazzocco
- Department of Pathology, Istituto Giannina Gaslini, Genova, Italy
| | | | - Rosa Noguera
- Pathology Department, Medical School, University of Valencia, Valencia, Spain.,Medical Research Foundation INCLIVA, Valencia, Spain.,CIBERONC, Madrid, Spain
| | - Miki Ohira
- Research Institute for Clinical Oncology Saitama Cancer Center, Saitama, Japan
| | - Julie R Park
- Seattle Children's Hospital and University of Washington, Seattle, WA
| | | | - Jessica Theissen
- Department of Experimental Pediatric Oncology, University of Cologne, Cologne, Germany
| | - Gian Paolo Tonini
- Laboratory of Neuroblastoma, Onco/Haematology Laboratory, University of Padua, Pediatric Research Institute (IRP)-Città della Speranza, Padova, Italy
| | | | - Luigi Varesio
- Laboratory of Molecular Biology (LV), Istituto Giannina Gaslini, Genova, Italy
| | - Rogier Versteeg
- Department of Oncogenomics, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Frank Speleman
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent, Belgium
| | - John M Maris
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA.,Center for Childhood Cancer Research, University of Pennsylvania, Philadelphia, PA.,Department of Pediatrics, University of Pennsylvania, Philadelphia, PA.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA.,Abramson Family Cancer Research Institute, Philadelphia, PA
| | - Gudrun Schleiermacher
- U830 INSERM, Recherche Translationelle en Oncologie Pédiatrique (RTOP) and Department of Pediatric Oncology
| | - Katleen De Preter
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent, Belgium
| |
Collapse
|
11
|
Newton R, Wernisch L. A meta-analysis of multiple matched aCGH/expression cancer datasets reveals regulatory relationships and pathway enrichment of potential oncogenes. PLoS One 2019; 14:e0213221. [PMID: 31335867 PMCID: PMC6650054 DOI: 10.1371/journal.pone.0213221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 07/05/2019] [Indexed: 12/12/2022] Open
Abstract
The copy numbers of genes in cancer samples are often highly disrupted and form a natural amplification/deletion experiment encompassing multiple genes. Matched array comparative genomics and transcriptomics datasets from such samples can be used to predict inter-chromosomal gene regulatory relationships. Previously we published the database METAMATCHED, comprising the results from such an analysis of a large number of publically available cancer datasets. Here we investigate genes in the database which are unusual in that their copy number exhibits consistent heterogeneous disruption in a high proportion of the cancer datasets. We assess the potential relevance of these genes to the pathology of the cancer samples, in light of their predicted regulatory relationships and enriched biological pathways. A network-based method was used to identify enriched pathways from the genes’ inferred targets. The analysis predicts both known and new regulator-target interactions and pathway memberships. We examine examples in detail, in particular the gene POGZ, which is disrupted in many of the cancer datasets and has an unusually large number of predicted targets, from which the network analysis predicts membership of cancer related pathways. The results suggest close involvement in known cancer pathways of genes exhibiting consistent heterogeneous copy number disruption. Further experimental work would clarify their relevance to tumor biology. The results of the analysis presented in the database METAMATCHED, and included here as an R archive file, constitute a large number of predicted regulatory relationships and pathway memberships which we anticipate will be useful in informing such experiments.
Collapse
Affiliation(s)
- Richard Newton
- MRC Biostatistics Unit, Cambridge University, Cambridge, United Kingdom
- * E-mail:
| | - Lorenz Wernisch
- MRC Biostatistics Unit, Cambridge University, Cambridge, United Kingdom
| |
Collapse
|
12
|
Abstract
Neuroblastoma is a pediatric cancer of embryonic origin from neural crest cells. Neuroblastoma has a great medical and social impact because it is occurring with major frequency in pre-scholar age with metastatic disease showing less than 40% of survival at 5-years. In children, metastatic neuroblastoma has very few recurrent mutations but several chromosome structural copy variations. The tumorigenesis of neuroblastoma is still largely unknown; however recently, genomic wide association studies have shown that several gene allelic variants are associated with neuroblastoma predisposition. Many of these gene variants are related to maintaining the chromatin and mitosis integrity. In the present report, I suggest that neuroblastoma predisposing alleles may match by chance influencing the chromatin structure already during the early phases of embryonic life and inducing chromosome instability and structural damages.
Collapse
Affiliation(s)
- Gian Paolo Tonini
- Laboratory of Neuroblastoma, Pediatric Research Institute, Città della Speranza, Corso Stati Uniti 4, 35127 Padova, Italy
| |
Collapse
|
13
|
The presence of Y674/Y675 phosphorylated NTRK1 via TP53 repression of PTPN6 expression as a potential prognostic marker in neuroblastoma. Hum Pathol 2018; 86:182-192. [PMID: 30594749 DOI: 10.1016/j.humpath.2018.12.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 12/05/2018] [Accepted: 12/06/2018] [Indexed: 01/18/2023]
Abstract
The tumor suppressor TP53 promotes nerve growth factor receptor (NTRK1) -Y674/Y675 phosphorylation (NTRK1-pY674/pY675) via repression of the NTRK1 phosphatase PTPN6 in a ligand-independent manner, resulting in suppression of breast cancer cell proliferation. Moreover, NTRK1-pY674/pY675 together with low levels of PTPN6 and TP53 expression is associated with favorable disease-free survival of breast cancer patients. We determined whether in neuroblastoma this protein expression pattern impacts relapse-free survival (RFS). NTRK1-pY674/pY675, PTPN6, and TP53 expression was assessed in 98 neuroblastoma samples by immunohistochemistry. Association between expression levels and RFS was investigated by multivariate and Kaplan-Meier analysis. Mutant or wild-type TP53 was identified by sequencing tumor DNA. Tumors expressing NTRK1-pY674/pY675 and low or undetectable levels of PTPN6 and TP53 were significantly associated with 5-year RFS (P = .014) when the dataset was stratified by MYCN amplification, segmental chromosomal abnormalities and histology. Similar results were observed with tumors expressing wild-type TP53, NTRK1-pY674/pY675 and low or undetectable levels of PTPN6. Kaplan-Meier analysis demonstrated a significant correlation (P = .004), with a 50% probability of RFS (median survival 4.73 years) when present compared with 19.51% (median survival 11.63 months) when absent. Similar results were seen with non-amplified MYCN or unfavorable/undifferentiating samples and tumors from patients aged 18 months or less. Importantly, NTRK1-pY674/pY675 is an independent predictor of improved RFS. These results strongly suggest that NTRK1-pY674/pY675 together with wild-type TP53 and undetectable or low levels of PTPN6 expression is a potential biomarker of improved RFS of neuroblastoma patients. The predictive value of NTRK1-pY674/pY675 together with wild-type TP53 and low PTPN6 expression could contribute to neuroblastoma patient prognosis.
Collapse
|
14
|
Fusco P, Esposito MR, Tonini GP. Chromosome instability in neuroblastoma. Oncol Lett 2018; 16:6887-6894. [PMID: 30546420 PMCID: PMC6256707 DOI: 10.3892/ol.2018.9545] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 08/30/2018] [Indexed: 12/28/2022] Open
Abstract
Neuroblastoma is a neural crest-derived tumor that accounts for 7-10% of all malignancies in children and ~15% of all childhood cancer-associated mortalities. Approximately 50% of patients are characterized as high-risk (HR) and have an overall survival of <40% at 5 years from diagnosis. HR patients with unfavorable prognosis exhibit several structural copy number variations (CNVs), whereas localized tumors belonging to patients in the low- and intermediate-risk classes, have favorable outcomes and display several numerical CNVs. Taken together these results are indicative of chromosome instability (CIN) in neuroblastoma tumor cells. The present review discusses multiple aspects of CIN including methods of measuring CIN, CIN targeting as a therapeutic strategy in cancer and the effects of CIN in neuroblastoma development and aggressiveness with particular emphasis on the CIN gene signature associated with HR neuroblastoma patients.
Collapse
Affiliation(s)
- Pina Fusco
- Neuroblastoma Laboratory, Fondazione Istituto di Ricerca Pediatrica Città della Speranza, I-35127 Padua, Italy
| | - Maria Rosaria Esposito
- Neuroblastoma Laboratory, Fondazione Istituto di Ricerca Pediatrica Città della Speranza, I-35127 Padua, Italy
| | - Gian Paolo Tonini
- Neuroblastoma Laboratory, Fondazione Istituto di Ricerca Pediatrica Città della Speranza, I-35127 Padua, Italy
| |
Collapse
|
15
|
Twist CJ, Naranjo A, Schmidt ML, Tenney SC, Cohn SL, Meany HJ, Mattei P, Adkins ES, Shimada H, London WB, Park JR, Matthay KK, Maris JM. Defining Risk Factors for Chemotherapeutic Intervention in Infants With Stage 4S Neuroblastoma: A Report From Children's Oncology Group Study ANBL0531. J Clin Oncol 2018; 37:115-124. [PMID: 30444686 DOI: 10.1200/jco.18.00419] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
PURPOSE Infants with stage 4S neuroblastoma usually have favorable outcomes with observation or minimal chemotherapy. However, young infants with symptoms secondary to massive hepatomegaly or with unfavorable tumor biology are at high risk of death. Our aim was to improve outcomes for patients with symptomatic and/or unfavorable biology 4S neuroblastoma with a uniform treatment approach using a biology- and response-based algorithm. PATIENTS AND METHODS The subset of patients with 4S disease with MYCN-not amplified tumors with impaired or impending organ dysfunction, or with unfavorable histology and/or diploid DNA index, were eligible. Patients were assigned to receive two, four, or eight cycles of chemotherapy on the basis of histology, diploid DNA index, chromosome arm 1p or 11q loss of heterozygosity (LOH) status, and symptoms. RESULTS Forty-nine eligible patients were enrolled: 41 were symptomatic and 28 had unfavorable biology. Seventeen patients (symptomatic, favorable biology) were assigned two cycles, 21 patients (any unfavorable biologic feature without 1p or 11q LOH) were assigned four cycles, and 11 patients (unfavorable biology including 1p and/or 11q LOH [n = 7] or symptomatic with unknown biology [n = 4]), were assigned eight cycles. The 3-year overall survival was 81.4% ± 5.8%. Eight of nine deaths were in patients younger than 2 months of age at diagnosis (median, 9 days [range, 1 to 68 days]): five acute deaths were a result of hepatomegaly and associated toxicities; two were a result of late relapse in patients with unfavorable biology; and two were a result of treatment complications. No deaths occurred after protocol-mandated pre-emptive treatment of infants younger than 2 months with hepatomegaly, regardless of symptoms. A new scoring algorithm for emergent chemotherapy in patients with 4S disease was developed on the basis of this experience. CONCLUSION The outcome for 4S neuroblastoma can be improved with pre-emptive chemotherapy for evolving hepatomegaly or other baseline comorbidities in infants younger than 2 months of age.
Collapse
Affiliation(s)
| | | | - Mary Lou Schmidt
- 3 University of Illinois at Chicago College of Medicine, Chicago, IL
| | | | | | - Holly J Meany
- 5 Children's National Medical Center, Washington, DC
| | - Peter Mattei
- 6 Children's Hospital of Philadelphia, Philadelphia, PA
| | | | | | - Wendy B London
- 9 Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA
| | | | - Katherine K Matthay
- 11 University of California San Francisco School of Medicine and UCSF Benioff Children's Hospital, San Francisco, CA
| | - John M Maris
- 6 Children's Hospital of Philadelphia, Philadelphia, PA.,12 Perelman School of Medicine, Philadelphia, PA
| |
Collapse
|
16
|
Depuydt P, Koster J, Boeva V, Hocking TD, Speleman F, Schleiermacher G, De Preter K. Meta-mining of copy number profiles of high-risk neuroblastoma tumors. Sci Data 2018; 5:180240. [PMID: 30375995 PMCID: PMC6207068 DOI: 10.1038/sdata.2018.240] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 09/10/2018] [Indexed: 02/01/2023] Open
Abstract
Neuroblastoma, a pediatric tumor of the sympathetic nervous system, is predominantly driven by copy number aberrations, which predict survival outcome in global neuroblastoma cohorts and in low-risk cases. For high-risk patients there is still a need for better prognostic biomarkers. Via an international collaboration, we collected copy number profiles of 556 high-risk neuroblastomas generated on different array platforms. This manuscript describes the composition of the dataset, the methods used to process the data, including segmentation and aberration calling, and data validation. t-SNE analysis shows that samples cluster according to MYCN status, and shows a difference between array platforms. 97.3% of samples are characterized by the presence of segmental aberrations, in regions frequently affected in neuroblastoma. Focal aberrations affect genes known to be involved in neuroblastoma, such as ALK and LIN28B. To conclude, we compiled a unique large copy number dataset of high-risk neuroblastoma tumors, available via R2 and a Shiny web application. The availability of patient survival data allows to further investigate the prognostic value of copy number aberrations.
Collapse
Affiliation(s)
- Pauline Depuydt
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Jan Koster
- Department of Oncogenomics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Valentina Boeva
- Institut Cochin, Inserm U1016, CNRS UMR 8104, Université Paris Descartes UMR-S1016, F-75014 Paris, France.,Institut Curie, Inserm U900, Mines ParisTech, PSL Research University, F-75005 Paris, France
| | - Toby D Hocking
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Frank Speleman
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Gudrun Schleiermacher
- Recherche Translationelle en Oncologie Pédiatrique (RTOP) and Department of Pediatric Oncology, Institut Curie, Paris, France.,U830, INSERM, Paris, France
| | - Katleen De Preter
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| |
Collapse
|
17
|
Polewko-Klim A, Lesiński W, Mnich K, Piliszek R, Rudnicki WR. Integration of multiple types of genetic markers for neuroblastoma may contribute to improved prediction of the overall survival. Biol Direct 2018; 13:17. [PMID: 30236139 PMCID: PMC6148774 DOI: 10.1186/s13062-018-0222-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 08/22/2018] [Indexed: 12/14/2022] Open
Abstract
Background Modern experimental techniques deliver data sets containing profiles of tens of thousands of potential molecular and genetic markers that can be used to improve medical diagnostics. Previous studies performed with three different experimental methods for the same set of neuroblastoma patients create opportunity to examine whether augmenting gene expression profiles with information on copy number variation can lead to improved predictions of patients survival. We propose methodology based on comprehensive cross-validation protocol, that includes feature selection within cross-validation loop and classification using machine learning. We also test dependence of results on the feature selection process using four different feature selection methods. Results The models utilising features selected based on information entropy are slightly, but significantly, better than those using features obtained with t-test. The synergy between data on genetic variation and gene expression is possible, but not confirmed. A slight, but statistically significant, increase of the predictive power of machine learning models has been observed for models built on combined data sets. It was found while using both out of bag estimate and in cross-validation performed on a single set of variables. However, the improvement was smaller and non-significant when models were built within full cross-validation procedure that included feature selection within cross-validation loop. Good correlation between performance of the models in the internal and external cross-validation was observed, confirming the robustness of the proposed protocol and results. Conclusions We have developed a protocol for building predictive machine learning models. The protocol can provide robust estimates of the model performance on unseen data. It is particularly well-suited for small data sets. We have applied this protocol to develop prognostic models for neuroblastoma, using data on copy number variation and gene expression. We have shown that combining these two sources of information may increase the quality of the models. Nevertheless, the increase is small and larger samples are required to reduce noise and bias arising due to overfitting. Reviewers This article was reviewed by Lan Hu, Tim Beissbarth and Dimitar Vassilev.
Collapse
Affiliation(s)
- Aneta Polewko-Klim
- Institute of Informatics, University of Białystok, Konstantego Ciołkowskiego 1M, Białystok, 15-245, Poland.
| | - Wojciech Lesiński
- Institute of Informatics, University of Białystok, Konstantego Ciołkowskiego 1M, Białystok, 15-245, Poland
| | - Krzysztof Mnich
- Computational Centre, University of Białystok, Konstantego Ciołkowskiego 1M, Białystok, 15-245, Poland
| | - Radosław Piliszek
- Computational Centre, University of Białystok, Konstantego Ciołkowskiego 1M, Białystok, 15-245, Poland
| | - Witold R Rudnicki
- Institute of Informatics, University of Białystok, Konstantego Ciołkowskiego 1M, Białystok, 15-245, Poland.,Computational Centre, University of Białystok, Konstantego Ciołkowskiego 1M, Białystok, 15-245, Poland.,Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Pawlińskiego 5A, Warsaw, 02-106, Poland
| |
Collapse
|
18
|
Esposito MR, Binatti A, Pantile M, Coppe A, Mazzocco K, Longo L, Capasso M, Lasorsa VA, Luksch R, Bortoluzzi S, Tonini GP. Somatic mutations in specific and connected subpathways are associated with short neuroblastoma patients' survival and indicate proteins targetable at onset of disease. Int J Cancer 2018; 143:2525-2536. [PMID: 29992558 DOI: 10.1002/ijc.31748] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 05/24/2018] [Accepted: 06/21/2018] [Indexed: 12/29/2022]
Abstract
Neuroblastoma (NB) is an embryonic malignancy of the sympathetic nervous system with heterogeneous biological, morphological, genetic and clinical characteristics. Although genomic studies revealed the specific biological features of NB pathogenesis useful for new therapeutic approaches, the improvement of high-risk (HR)-NB patients overall survival remains unsatisfactory. To further clarify the biological basis of disease aggressiveness, we used whole-exome sequencing to examine the genomic landscape of HR-NB patients at stage M with short survival (SS) and long survival (LS). Only a few genes, including SMARCA4, SMO, ZNF44 and CHD2, were recurrently and specifically mutated in the SS group, confirming the low recurrence of common mutations in this tumor. A systems biology approach revealed that in the two patient groups, mutations occurred in different pathways. Mutated genes (ARHGEF11, CACNA1G, FGF4, PTPRA, PTK2, ANK3, SMO, NTNG2, VCL and NID2) regulate the MAPK pathway associated with the organization of the extracellular matrix, cell motility through PTK2 signaling and matrix metalloproteinase activity. Moreover, we detected mutations in LAMA2, PTK2, LAMA4, and MMP14 genes, impairing MET signaling, in SFI1 and CHD2 involved in centrosome maturation and chromosome remodeling, in AK7 and SPTLC2, which regulate the metabolism of nucleotides and lipoproteins, and in NALCN, SLC12A1, SLC9A9, which are involved in the transport of small molecules. Notably, connected networks of somatically mutated genes specific for SS patients were identified. The detection of mutated genes present at the onset of disease may help to address an early treatment of HR-NB patients using FDA-approved compounds targeting the deregulated pathways.
Collapse
Affiliation(s)
- Maria Rosaria Esposito
- Neuroblastoma Laboratory, Fondazione Istituto di Ricerca Pediatrica Città della Speranza, Padua, Italy
| | - Andrea Binatti
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Marcella Pantile
- Neuroblastoma Laboratory, Fondazione Istituto di Ricerca Pediatrica Città della Speranza, Padua, Italy
| | - Alessandro Coppe
- Department of Women's and Children's Health, University of Padova, Padua, Italy
| | - Katia Mazzocco
- Translational Research Department, Laboratory Medicine, Diagnostics and Services U.O.C. Pathological Anatomy, IRCCS Giannina Gaslini Institute, Genoa, Italy
| | - Luca Longo
- U.O.C. Bioterapie, Ospedale Policlinico San Martino, Genoa, Italy
| | - Mario Capasso
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy.,CEINGE Biotecnologie Avanzate, Naples, Italy.,IRCCS SDN, Istituto di Ricerca Diagnostica e Nucleare, Naples, Italy
| | | | - Roberto Luksch
- Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | | | - Gian Paolo Tonini
- Neuroblastoma Laboratory, Fondazione Istituto di Ricerca Pediatrica Città della Speranza, Padua, Italy
| |
Collapse
|
19
|
Tranchevent LC, Nazarov PV, Kaoma T, Schmartz GP, Muller A, Kim SY, Rajapakse JC, Azuaje F. Predicting clinical outcome of neuroblastoma patients using an integrative network-based approach. Biol Direct 2018; 13:12. [PMID: 29880025 PMCID: PMC5992838 DOI: 10.1186/s13062-018-0214-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 05/04/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND One of the main current challenges in computational biology is to make sense of the huge amounts of multidimensional experimental data that are being produced. For instance, large cohorts of patients are often screened using different high-throughput technologies, effectively producing multiple patient-specific molecular profiles for hundreds or thousands of patients. RESULTS We propose and implement a network-based method that integrates such patient omics data into Patient Similarity Networks. Topological features derived from these networks were then used to predict relevant clinical features. As part of the 2017 CAMDA challenge, we have successfully applied this strategy to a neuroblastoma dataset, consisting of genomic and transcriptomic data. In particular, we observe that models built on our network-based approach perform at least as well as state of the art models. We furthermore explore the effectiveness of various topological features and observe, for instance, that redundant centrality metrics can be combined to build more powerful models. CONCLUSION We demonstrate that the networks inferred from omics data contain clinically relevant information and that patient clinical outcomes can be predicted using only network topological data. REVIEWERS This article was reviewed by Yang-Yu Liu, Tomislav Smuc and Isabel Nepomuceno.
Collapse
Affiliation(s)
- Léon-Charles Tranchevent
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, 1A-B, rue Thomas Edison, Strassen, L-1445 Luxembourg
| | - Petr V. Nazarov
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, 1A-B, rue Thomas Edison, Strassen, L-1445 Luxembourg
| | - Tony Kaoma
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, 1A-B, rue Thomas Edison, Strassen, L-1445 Luxembourg
| | - Georges P. Schmartz
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, 1A-B, rue Thomas Edison, Strassen, L-1445 Luxembourg
- Bioinformatics bachelor program, Universität des Saarlandes, Saarbrücken, Germany
| | - Arnaud Muller
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, 1A-B, rue Thomas Edison, Strassen, L-1445 Luxembourg
| | - Sang-Yoon Kim
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, 1A-B, rue Thomas Edison, Strassen, L-1445 Luxembourg
| | - Jagath C. Rajapakse
- Bioinformatics Research Center, School of Computer Science and Engineering, Nanyang Technological University, Singapore, Singapore
| | - Francisco Azuaje
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, 1A-B, rue Thomas Edison, Strassen, L-1445 Luxembourg
| |
Collapse
|
20
|
Francescatto M, Chierici M, Rezvan Dezfooli S, Zandonà A, Jurman G, Furlanello C. Multi-omics integration for neuroblastoma clinical endpoint prediction. Biol Direct 2018; 13:5. [PMID: 29615097 PMCID: PMC5907722 DOI: 10.1186/s13062-018-0207-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Accepted: 03/09/2018] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND High-throughput methodologies such as microarrays and next-generation sequencing are routinely used in cancer research, generating complex data at different omics layers. The effective integration of omics data could provide a broader insight into the mechanisms of cancer biology, helping researchers and clinicians to develop personalized therapies. RESULTS In the context of CAMDA 2017 Neuroblastoma Data Integration challenge, we explore the use of Integrative Network Fusion (INF), a bioinformatics framework combining a similarity network fusion with machine learning for the integration of multiple omics data. We apply the INF framework for the prediction of neuroblastoma patient outcome, integrating RNA-Seq, microarray and array comparative genomic hybridization data. We additionally explore the use of autoencoders as a method to integrate microarray expression and copy number data. CONCLUSIONS The INF method is effective for the integration of multiple data sources providing compact feature signatures for patient classification with performances comparable to other methods. Latent space representation of the integrated data provided by the autoencoder approach gives promising results, both by improving classification on survival endpoints and by providing means to discover two groups of patients characterized by distinct overall survival (OS) curves. REVIEWERS This article was reviewed by Djork-Arné Clevert and Tieliu Shi.
Collapse
Affiliation(s)
| | - Marco Chierici
- Fondazione Bruno Kessler, Via Sommarive 18, Trento, 38123, Italy
| | | | - Alessandro Zandonà
- Fondazione Bruno Kessler, Via Sommarive 18, Trento, 38123, Italy.,Centre for Integrative Biology, University of Trento, Via Sommarive 9, Trento, 38123, Italy.,Department of Information Engineering, University of Padova, Padova, Italy
| | - Giuseppe Jurman
- Fondazione Bruno Kessler, Via Sommarive 18, Trento, 38123, Italy
| | | |
Collapse
|
21
|
Zanon C, Tonini GP. Transcription instability in high-risk neuroblastoma is associated with a global perturbation of chromatin domains. Mol Oncol 2017; 11:1646-1658. [PMID: 28941026 PMCID: PMC5664000 DOI: 10.1002/1878-0261.12139] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 09/07/2017] [Accepted: 09/13/2017] [Indexed: 12/16/2022] Open
Abstract
Chromosome instability has a pivotal role among the hallmarks of cancer, but its transcriptional counterpart is rarely considered a relevant factor in cell destabilization. To examine transcription instability (TIN), we first devised a metric we named TIN index and used it to evaluate TIN on a dataset containing more than 500 neuroblastoma samples. We found that metastatic tumors from high-risk (HR) patients are characterized by significantly different TIN index values compared to low/intermediate-risk patients. Our results indicate that the TIN index is a good predictor of neuroblastoma patient's outcome, and a related TIN index gene signature (TIN-signature) is also able to predict the neuroblastoma patient's outcome with high confidence. Interestingly, we find that TIN-signature genes have a strong positional association with superenhancers in neuroblastoma tumors. Finally, we show that TIN is linked to chromatin structural domains and interferes with their integrity in HR neuroblastoma patients. This novel approach to gene expression analysis broadens the perspective of genome instability investigations to include functional aspects.
Collapse
Affiliation(s)
- Carlo Zanon
- Neuroblastoma Laboratory, Pediatric Research Institute, Citta' della Speranza, Padua, Italy
| | - Gian Paolo Tonini
- Neuroblastoma Laboratory, Pediatric Research Institute, Citta' della Speranza, Padua, Italy
| |
Collapse
|
22
|
Mlakar V, Jurkovic Mlakar S, Lopez G, Maris JM, Ansari M, Gumy-Pause F. 11q deletion in neuroblastoma: a review of biological and clinical implications. Mol Cancer 2017; 16:114. [PMID: 28662712 PMCID: PMC5492892 DOI: 10.1186/s12943-017-0686-8] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 06/25/2017] [Indexed: 12/12/2022] Open
Abstract
Deletion of the long arm of chromosome 11 (11q deletion) is one of the most frequent events that occur during the development of aggressive neuroblastoma. Clinically, 11q deletion is associated with higher disease stage and decreased survival probability. During the last 25 years, extensive efforts have been invested to identify the precise frequency of 11q aberrations in neuroblastoma, the recurrently involved genes, and to understand the molecular mechanisms of 11q deletion, but definitive answers are still unclear. In this review, it is our intent to compile and review the evidence acquired to date on 11q deletion in neuroblastoma.
Collapse
Affiliation(s)
- Vid Mlakar
- CANSEARCH Research Laboratory, Geneva University Medical School, Avenue de la Roseraie 64, 1205, Geneva, Switzerland
| | - Simona Jurkovic Mlakar
- CANSEARCH Research Laboratory, Geneva University Medical School, Avenue de la Roseraie 64, 1205, Geneva, Switzerland
| | - Gonzalo Lopez
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - John M Maris
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Marc Ansari
- CANSEARCH Research Laboratory, Geneva University Medical School, Avenue de la Roseraie 64, 1205, Geneva, Switzerland.,Department of Pediatrics, Onco-Hematology Unit, Geneva University Hospitals, Rue Willy-Donzé 6, 1205, Geneva, Switzerland
| | - Fabienne Gumy-Pause
- CANSEARCH Research Laboratory, Geneva University Medical School, Avenue de la Roseraie 64, 1205, Geneva, Switzerland. .,Department of Pediatrics, Onco-Hematology Unit, Geneva University Hospitals, Rue Willy-Donzé 6, 1205, Geneva, Switzerland.
| |
Collapse
|
23
|
Tonini GP. Growth, progression and chromosome instability of Neuroblastoma: a new scenario of tumorigenesis? BMC Cancer 2017; 17:20. [PMID: 28056863 PMCID: PMC5217541 DOI: 10.1186/s12885-016-2986-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 12/08/2016] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Neuroblastoma is a pediatric cancer with a low survival rate of patients with metastatic stage 4 disease. Tumor aggressiveness and progression have been associated with structural copy number variations (CNVs) that are observed in malignant cells. In contrast, localized Neuroblastomas, which are associated with a low number of structural CNVs but frequent numerical CNVs, are less aggressive, and patients have good outcomes. Finally, whole-genome and whole-exome sequencing of Neuroblastoma tissues have shown few damaging mutations in these tumors. CONCLUSIONS In the present report it is proposed that chromosome instability (CIN) plays a major role in Neuroblastoma tumorigenesis and that CIN is already present in the early phases of tumor development. High CIN can promote several types of chromosomal damage including chromothripsis, gene deletion, amplification and rearrangements, which deregulate gene expression. Indeed, gene rearrangements have been reported as a new scenario in the development of Neuroblastoma, which supports the hypothesis that CIN is an early step preliminary to the late catastrophic events leading to tumor development.
Collapse
Affiliation(s)
- Gian Paolo Tonini
- Neuroblastoma Laboratory, Italian Neuroblastoma Foundation, Pediatric Research Institute, Fondazione Città della Speranza, Corso Stati Uniti, 4, 35127, Padua, Italy.
| |
Collapse
|
24
|
Luksch R, Castellani MR, Collini P, De Bernardi B, Conte M, Gambini C, Gandola L, Garaventa A, Biasoni D, Podda M, Sementa AR, Gatta G, Tonini GP. Neuroblastoma (Peripheral neuroblastic tumours). Crit Rev Oncol Hematol 2016; 107:163-181. [PMID: 27823645 DOI: 10.1016/j.critrevonc.2016.10.001] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 09/05/2016] [Accepted: 10/03/2016] [Indexed: 02/07/2023] Open
Abstract
Peripheral neuroblastic tumours (PNTs), a family of tumours arising in the embryonal remnants of the sympathetic nervous system, account for 7-10% of all tumours in children. In two-thirds of cases, PNTs originate in the adrenal glands or the retroperitoneal ganglia. At least one third present metastases at onset, with bone and bone marrow being the most frequent metastatic sites. Disease extension, MYCN oncogene status and age are the most relevant prognostic factors, and their influence on outcome have been considered in the design of the recent treatment protocols. Consequently, the probability of cure has increased significantly in the last two decades. In children with localised operable disease, surgical resection alone is usually a sufficient treatment, with 3-year event-free survival (EFS) being greater than 85%. For locally advanced disease, primary chemotherapy followed by surgery and/or radiotherapy yields an EFS of around 75%. The greatest problem is posed by children with metastatic disease or amplified MYCN gene, who continue to do badly despite intensive treatments. Ongoing trials are exploring the efficacy of new drugs and novel immunological approaches in order to save a greater number of these patients.
Collapse
Affiliation(s)
- Roberto Luksch
- Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy.
| | | | - Paola Collini
- Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | | | - Massimo Conte
- Giannina Gaslini Children's Research Hospital, Genoa, Italy
| | | | - Lorenza Gandola
- Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | | | - Davide Biasoni
- Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Marta Podda
- Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | | | - Gemma Gatta
- Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Gian Paolo Tonini
- Neuroblastoma Laboratory, Paediatric Research Institute, Padua, Italy
| |
Collapse
|
25
|
Newman EA, Nuchtern JG. Recent biologic and genetic advances in neuroblastoma: Implications for diagnostic, risk stratification, and treatment strategies. Semin Pediatr Surg 2016; 25:257-264. [PMID: 27955728 DOI: 10.1053/j.sempedsurg.2016.09.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Neuroblastoma is an embryonic cancer of neural crest cell lineage, accounting for up to 10% of all pediatric cancer. The clinical course is heterogeneous ranging from spontaneous regression in neonates to life-threatening metastatic disease in older children. Much of this clinical variance is thought to result from distinct pathologic characteristics that predict patient outcomes. Consequently, many research efforts have been focused on identifying the underlying biologic and genetic features of neuroblastoma tumors in order to more clearly define prognostic subgroups for treatment stratification. Recent technological advances have placed emphasis on the integration of genetic alterations and predictive biologic variables into targeted treatment approaches to improve patient survival outcomes. This review will focus on these recent advances and the implications they have on the diagnostic, staging, and treatment approaches in modern neuroblastoma clinical management.
Collapse
Affiliation(s)
- Erika A Newman
- Section of Pediatric Surgery, Department of Surgery, The University of Michigan, Ann Arbor, Michigan.
| | - Jed G Nuchtern
- Division of Pediatric Surgery, Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, Texas
| |
Collapse
|
26
|
Kuzyk A, Gartner J, Mai S. Identification of Neuroblastoma Subgroups Based on Three-Dimensional Telomere Organization. Transl Oncol 2016; 9:348-56. [PMID: 27567959 PMCID: PMC5006808 DOI: 10.1016/j.tranon.2016.07.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 07/05/2016] [Indexed: 12/19/2022] Open
Abstract
Using 3D telomere quantitative fluorescence in situ hybridization, we determined the 3D telomere organization of 74 neuroblastoma tissue samples. Hierarchical cluster analysis of the measured telomere parameters identified three subgroups from our patient cohort. These subgroups have unique telomere profiles based on telomere length and nuclear architecture. Subgroups with higher levels of telomere dysfunction were comprised of tumors with greater numbers of telomeres, telomeric aggregates, and short telomeres (P<.0001). Tumors with greater telomere dysfunction were associated with unfavorable tumor characteristics (greater age at diagnosis, unfavorable histology, higher stage of disease, MYCN amplification, and higher MYCN expression) and poor prognostic risk (P<.001). Subgroups with greater telomere dysfunction also had higher intratumor heterogeneity. MYCN overexpression in two neuroblastoma cell lines with constitutively low MYCN expression induced changes in their telomere profile that were consistent with increased telomere dysfunction; this illustrates a functional relationship between MYCN and 3D telomere organization. This study demonstrates the ability to classify neuroblastomas based on the level of telomere dysfunction, which is a novel approach for this cancer.
Collapse
Affiliation(s)
- Alexandra Kuzyk
- Manitoba Institute of Cell Biology/The Research Institute of Oncology and Hematology, Department of Biochemistry and Medical Genetics, Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - John Gartner
- Departments of Pathology and Immunology, Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Sabine Mai
- Manitoba Institute of Cell Biology/The Research Institute of Oncology and Hematology, Department of Biochemistry and Medical Genetics, Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada.
| |
Collapse
|
27
|
Nicolai S, Pieraccioli M, Peschiaroli A, Melino G, Raschellà G. Neuroblastoma: oncogenic mechanisms and therapeutic exploitation of necroptosis. Cell Death Dis 2015; 6:e2010. [PMID: 26633716 PMCID: PMC4720889 DOI: 10.1038/cddis.2015.354] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 10/17/2015] [Accepted: 10/19/2015] [Indexed: 12/20/2022]
Abstract
Neuroblastoma (NB) is the most common extracranial childhood tumor classified in five stages (1, 2, 3, 4 and 4S), two of which (3 and 4) identify chemotherapy-resistant, highly aggressive disease. High-risk NB frequently displays MYCN amplification, mutations in ALK and ATRX, and genomic rearrangements in TERT genes. These NB subtypes are also characterized by reduced susceptibility to programmed cell death induced by chemotherapeutic drugs. The latter feature is a major cause of failure in the treatment of advanced NB patients. Thus, proper reactivation of apoptosis or of other types of programmed cell death pathways in response to treatment is relevant for the clinical management of aggressive forms of NB. In this short review, we will discuss the most relevant genomic rearrangements that define high-risk NB and the role that destabilization of p53 and p73 can have in NB aggressiveness. In addition, we will propose a strategy to stabilize p53 and p73 by using specific inhibitors of their ubiquitin-dependent degradation. Finally, we will introduce necroptosis as an alternative strategy to kill NB cells and increase tumor immunogenicity.
Collapse
Affiliation(s)
- S Nicolai
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier 1, Rome 00133, Italy
| | - M Pieraccioli
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier 1, Rome 00133, Italy
| | - A Peschiaroli
- Institute of Cell Biology and Neurobiology (IBCN), CNR, Via E. Ramarini 32, Rome 00015, Italy
| | - G Melino
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier 1, Rome 00133, Italy.,Medical Research Council, Toxicology Unit, Hodgkin Building, Leicester University, Lancaster Road, PO Box 138, Leicester LE1 9HN, UK
| | - G Raschellà
- ENEA Research Center Casaccia, Laboratory of Biosafety and Risk Assessment, Via Anguillarese, 301, Rome 00123, Italy
| |
Collapse
|
28
|
Investigating inter-chromosomal regulatory relationships through a comprehensive meta-analysis of matched copy number and transcriptomics data sets. BMC Genomics 2015; 16:967. [PMID: 26581858 PMCID: PMC4650296 DOI: 10.1186/s12864-015-2100-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 10/15/2015] [Indexed: 12/16/2022] Open
Abstract
Background Gene regulatory relationships can be inferred using matched array comparative genomics and transcriptomics data sets from cancer samples. The way in which copy numbers of genes in cancer samples are often greatly disrupted works like a natural gene amplification/deletion experiment. There are now a large number of such data sets publicly available making a meta-analysis of the data possible. Results We infer inter-chromosomal acting gene regulatory relationships from a meta-analysis of 31 publicly available matched array comparative genomics and transcriptomics data sets in humans. We obtained statistically significant predictions of target genes for 1430 potential regulatory genes. The regulatory relationships being inferred are either direct relationships, of a transcription factor on its target, or indirect ones, through pathways containing intermediate steps. We analyse the predictions in terms of cocitations, both publications which cite a regulator with any of its inferred targets and cocitations of any genes in a target list. Conclusions The most striking observation from the results is the greater number of inter-chromosomal regulatory relationships involving repression compared to those involving activation. The complete results of the meta-analysis are presented in the database METAMATCHED. We anticipate that the predictions contained in the database will be useful in informing experiments and in helping to construct networks of regulatory relationships. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2100-5) contains supplementary material, which is available to authorized users.
Collapse
|
29
|
Mazzocco K, Defferrari R, Sementa AR, Garaventa A, Longo L, De Mariano M, Esposito MR, Negri F, Ircolò D, Viscardi E, Luksch R, D'Angelo P, Prete A, Castellano A, Massirio P, Erminio G, Gigliotti AR, Tonini GP, Conte M. Genetic abnormalities in adolescents and young adults with neuroblastoma: A report from the Italian Neuroblastoma group. Pediatr Blood Cancer 2015; 62:1725-32. [PMID: 25925003 DOI: 10.1002/pbc.25552] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 03/19/2015] [Indexed: 02/06/2023]
Abstract
BACKGROUND Less than 5% of neuroblastomas (NB) occur in adolescents and young adults (AYA), in whom the disease has an indolent and fatal course. PROCEDURE We studied the genomic profile and histological characteristics of 34 NBs from AYA patients enrolled in the Italian Neuroblastoma Registry (INBR) between 1979 and 2009. RESULTS Disease was disseminated in 20 patients and localized in 14; 30/34 tumors were classified as NB and 4/34 as nodular ganglioneuroblastoma (nGNB). Segmental Chromosome Aberrations (SCAs) were observed in 29 tumors (85%) namely 1p imbalance (58%), 17q gain (52%), 9p loss (32%), 11q loss (30%), 1q gain (17%), 7q gain (17%), 2p gain (14%), 3p loss (14%), and 4p loss (7%). MYCN amplification and MYCN gain were detected in 3 (10%) and 2 cases (7%) respectively. An anaplastic lymphoma receptor tyrosine kinase (ALK) gene mutation study on the available cases from this cohort revealed 4/25 (16%) mutated cases. In parallel, alpha thalassaemia/mental retardation syndrome X linked (ATRX) gene mutations were also sought, a novel mutation being detected in 1/21 (4,7%) cases. CONCLUSION This study confirmed the low incidence of MYCN amplification in AYA and recorded a high frequency of 17q gain and 9p and 11q loss independently from the stage of the disease. The presence of 1q gain, which identifies patients with particularly aggressive disease, relapse and poor survival, was also detected. Furthermore, the frequency of ALK mutations suggests that a target-based therapy with ALK inhibitors might be effective in this subset of patients.
Collapse
Affiliation(s)
- Katia Mazzocco
- Department of Pathology, Istituto Giannina Gaslini, Genova, Italy
| | | | | | - Alberto Garaventa
- Department of Hematology-Oncology, Istituto Giannina Gaslini, Genova, Italy
| | - Luca Longo
- U.O.C. Bioterapie IRCSS A.O.U. San Martino-IST, Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy
| | - Marilena De Mariano
- U.O.C. Bioterapie IRCSS A.O.U. San Martino-IST, Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy
| | - Maria Rosaria Esposito
- Neuroblastoma Laboratory, Onco/Hematology Laboratory, SDB Department, University of Padova, Pediatric Research Institute, Fondazione Città della Speranza, Padova, Italy
| | - Francesca Negri
- Department of Pathology, Istituto Giannina Gaslini, Genova, Italy
| | - Davide Ircolò
- Department of Pathology, Istituto Giannina Gaslini, Genova, Italy
| | | | - Roberto Luksch
- Department of Pediatric Oncology, National Cancer Institute, Milano, Italy
| | - Paolo D'Angelo
- Department of Pediatric Hematology and Oncology, ARNAS Civico Di Cristina Benfratelli Hospital, Palermo, Italy
| | - Arcangelo Prete
- Pediatric Oncology and Hematology Unit "Lalla Seràgnoli", University of Bologna Sant'Orsola-Malpighi Hospital, Bologna, Italy
| | - Aurora Castellano
- Department of Pediatric Hematology-Oncology, IRCCS, Ospedale Bambino Gesù, Rome, Italy
| | - Paolo Massirio
- Department of Hematology-Oncology, Istituto Giannina Gaslini, Genova, Italy
| | - Giovanni Erminio
- Department of Epidemiology and Biostatistics, Istituto Giannina Gaslini, Genova, Italy
| | | | - Gian Paolo Tonini
- Neuroblastoma Laboratory, Onco/Hematology Laboratory, SDB Department, University of Padova, Pediatric Research Institute, Fondazione Città della Speranza, Padova, Italy
| | - Massimo Conte
- Department of Hematology-Oncology, Istituto Giannina Gaslini, Genova, Italy
| |
Collapse
|
30
|
Masecchia S, Coco S, Barla A, Verri A, Tonini GP. Genome instability model of metastatic neuroblastoma tumorigenesis by a dictionary learning algorithm. BMC Med Genomics 2015; 8:57. [PMID: 26358114 PMCID: PMC4566396 DOI: 10.1186/s12920-015-0132-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 08/28/2015] [Indexed: 12/21/2022] Open
Abstract
Background Metastatic neuroblastoma (NB) occurs in pediatric patients as stage 4S or stage 4 and it is characterized by heterogeneous clinical behavior associated with diverse genotypes. Tumors of stage 4 contain several structural copy number aberrations (CNAs) rarely found in stage 4S. To date, the NB tumorigenesis is not still elucidated, although it is evident that genomic instability plays a critical role in the genesis of the tumor. Here we propose a mathematical approach to decipher genomic data and we provide a new model of NB metastatic tumorigenesis. Method We elucidate NB tumorigenesis using Enhanced Fused Lasso Latent Feature Model (E-FLLat) modeling the array comparative chromosome hybridization (aCGH) data of 190 metastatic NBs (63 stage 4S and 127 stage 4). This model for aCGH segmentation, based on the minimization of functional dictionary learning (DL), combines several penalties tailored to the specificities of aCGH data. In DL, the original signal is approximated by a linear weighted combination of atoms: the elements of the learned dictionary. Results The hierarchical structures for stage 4S shows at the first level of the oncogenetic tree several whole chromosome gains except to the unbalanced gains of 17q, 2p and 2q. Conversely, the high CNA complexity found in stage 4 tumors, requires two different trees. Both stage 4 oncogenetic trees are marked diverged, up to five sublevels and the 17q gain is the most common event at the first level (2/3 nodes). Moreover the 11q deletion, one of the major unfavorable marker of disease progression, occurs before 3p loss indicating that critical chromosome aberrations appear at early stages of tumorigenesis. Finally, we also observed a significant (p = 0.025) association between patient age and chromosome loss in stage 4 cases. Conclusion These results led us to propose a genome instability progressive model in which NB cells initiate with a DNA synthesis uncoupled from cell division, that leads to stage 4S tumors, primarily characterized by numerical aberrations, or stage 4 tumors with high levels of genome instability resulting in complex chromosome rearrangements associated with high tumor aggressiveness and rapid disease progression. Electronic supplementary material The online version of this article (doi:10.1186/s12920-015-0132-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
| | - Simona Coco
- Lung Cancer Unit; IRCCS A.O.U. San Martino - IST, Genova, Italy.
| | - Annalisa Barla
- DIBRIS, Università degli Studi di Genova, Genova, Italy.
| | | | - Gian Paolo Tonini
- Neuroblastoma Laboratory, Onco/Hematology Laboratory, Department of Woman and Child Health, University of Padua, Pediatric Research Institute, Fondazione Città della Speranza, Padua, Corso Stati Uniti, 4, 35127, Padua, Italy.
| |
Collapse
|
31
|
Comparative genetic study of intratumoral heterogenous MYCN amplified neuroblastoma versus aggressive genetic profile neuroblastic tumors. Oncogene 2015; 35:1423-32. [PMID: 26119945 DOI: 10.1038/onc.2015.200] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 04/08/2015] [Accepted: 05/10/2015] [Indexed: 12/18/2022]
Abstract
Intratumoral heterogeneous MYCN amplification (hetMNA) is an unusual event in neuroblastoma with unascertained biological and clinical implications. Diagnosis is based on the detection of MYCN amplification surrounded by non-amplified tumor cells by fluorescence in situ hybridization (FISH). To better define the genetic features of hetMNA tumors, we studied the Spanish cohort of neuroblastic tumors by FISH and single nucleotide polymorphism arrays. We compared hetMNA tumors with homogeneous MNA (homMNA) and nonMNA tumors with 11q deletion (nonMNA w11q-). Of 1091 primary tumors, 28 were hetMNA by FISH. Intratumoral heterogeneity of 1p, 2p, 11q and 17q was closely associated with hetMNA tumors when analyzing different pieces for each case. For chromosome 2, 16 cases showed 2p intact, 4 focal gain at 2p24.3 and 8 MNA. The lengths of the smallest regions of overlap (SROs) for 2p gains and 1p deletions were between the SRO lengths observed in homMNA and nonMNA w11q- tumors. Co-occurrence of 11q- and +17q was frequently found with the largest SROs for both aberrations. The evidence for and frequency of different genetic subpopulations representing a hallmark of the hetMNA subgroup of NB indicates, on one hand, the presence of a considerable genetic instability with different SRO of either gains and losses compared with those of the other NB groups and highlights and, on the other hand, the need for multiple sampling from distant and macroscopically and microscopically distinct tumor areas. Narrowing down the different SRO for both deletions and gains in NB groups would be crucial to pinpointing the candidate gene(s) and the critical gene dosage with prognostic and therapeutic significance. This complexity of segmental chromosomal aberration patterns reinforces the necessity for a larger cohort study using FISH and pangenomic techniques to develop a suitable therapeutic strategy for these patients.
Collapse
|
32
|
Berbegall AP, Villamón E, Tadeo I, Martinsson T, Cañete A, Castel V, Navarro S, Noguera R. Neuroblastoma after childhood: prognostic relevance of segmental chromosome aberrations, ATRX protein status, and immune cell infiltration. Neoplasia 2015; 16:471-80. [PMID: 25077701 PMCID: PMC4198743 DOI: 10.1016/j.neo.2014.05.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 05/09/2014] [Accepted: 05/16/2014] [Indexed: 01/08/2023] Open
Abstract
Neuroblastoma (NB) is a common malignancy in children but rarely occurs during adolescence or adulthood. This subgroup is characterized by an indolent disease course, almost uniformly fatal, yet little is known about the biologic characteristics. The aim of this study was to identify differential features regarding DNA copy number alterations, α-thalassemia/mental retardation syndrome X-linked (ATRX) protein expression, and the presence of tumor-associated inflammatory cells. Thirty-one NB patients older than 10 years who were included in the Spanish NB Registry were considered for the current study; seven young and middle-aged adult patients (range 18-60 years) formed part of the cohort. We performed single nucleotide polymorphism arrays, immunohistochemistry for immune markers (CD4, CD8, CD20, CD11b, CD11c, and CD68), and ATRX protein expression. Assorted genetic profiles were found with a predominant presence of a segmental chromosome aberration (SCA) profile. Preadolescent and adolescent NB tumors showed a higher number of SCA, including 17q gain and 11q deletion. There was also a marked infiltration of immune cells, mainly high and heterogeneous, in young and middle-aged adult tumors. ATRX negative expression was present in the tumors. The characteristics of preadolescent, adolescent, young adult, and middle-aged adult NB tumors are different, not only from childhood NB tumors but also from each other. Similar examinations of a larger number of such tumor tissues from cooperative groups should lead to a better older age–dependent tumor pattern and to innovative, individual risk-adapted therapeutic approaches for these patients.
Collapse
Affiliation(s)
- Ana P Berbegall
- Pathology Department, Medical School, University of Valencia, INCLIVA, Valencia, Spain; Medical Research Foundation INCLIVA, Hospital Clínico, INCLIVA, Valencia, Spain
| | - Eva Villamón
- Pathology Department, Medical School, University of Valencia, INCLIVA, Valencia, Spain
| | - Irene Tadeo
- Pathology Department, Medical School, University of Valencia, INCLIVA, Valencia, Spain; Medical Research Foundation INCLIVA, Hospital Clínico, INCLIVA, Valencia, Spain
| | - Tommy Martinsson
- Department of Clinical Genetics, Göteborg University, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Adela Cañete
- Pediatric Oncology Unit, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Victoria Castel
- Pediatric Oncology Unit, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Samuel Navarro
- Pathology Department, Medical School, University of Valencia, INCLIVA, Valencia, Spain
| | - Rosa Noguera
- Pathology Department, Medical School, University of Valencia, INCLIVA, Valencia, Spain.
| |
Collapse
|
33
|
Defferrari R, Mazzocco K, Ambros IM, Ambros PF, Bedwell C, Beiske K, Bénard J, Berbegall AP, Bown N, Combaret V, Couturier J, Erminio G, Gambini C, Garaventa A, Gross N, Haupt R, Kohler J, Jeison M, Lunec J, Marques B, Martinsson T, Noguera R, Parodi S, Schleiermacher G, Tweddle DA, Valent A, Van Roy N, Vicha A, Villamon E, Tonini GP. Influence of segmental chromosome abnormalities on survival in children over the age of 12 months with unresectable localised peripheral neuroblastic tumours without MYCN amplification. Br J Cancer 2014; 112:290-5. [PMID: 25356804 PMCID: PMC4453444 DOI: 10.1038/bjc.2014.557] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 09/22/2014] [Accepted: 10/04/2014] [Indexed: 01/06/2023] Open
Abstract
Background: The prognostic impact of segmental chromosome alterations (SCAs) in children older than 1 year, diagnosed with localised unresectable neuroblastoma (NB) without MYCN amplification enrolled in the European Unresectable Neuroblastoma (EUNB) protocol is still to be clarified, while, for other group of patients, the presence of SCAs is associated with poor prognosis. Methods: To understand the role of SCAs we performed multilocus/pangenomic analysis of 98 tumour samples from patients enrolled in the EUNB protocol. Results: Age at diagnosis was categorised into two groups using 18 months as the age cutoff. Significant difference in the presence of SCAs was seen in tumours of patients between 12 and 18 months and over 18 months of age at diagnosis, respectively (P=0.04). A significant correlation (P=0.03) was observed between number of SCAs per tumour and age. Event-free (EFS) and overall survival (OS) were calculated in both age groups, according to both the presence and number of SCAs. In older patients, a poorer survival was associated with the presence of SCAs (EFS=46% vs 75%, P=0.023; OS=66.8% vs 100%, P=0.003). Moreover, OS of older patients inversely correlated with number of SCAs (P=0.002). Finally, SCAs provided additional prognostic information beyond histoprognosis, as their presence was associated with poorer OS in patients over 18 months with unfavourable International Neuroblastoma Pathology Classification (INPC) histopathology (P=0.018). Conclusions: The presence of SCAs is a negative prognostic marker that impairs outcome of patients over the age of 18 months with localised unresectable NB without MYCN amplification, especially when more than one SCA is present. Moreover, in older patients with unfavourable INPC tumour histoprognosis, the presence of SCAs significantly affects OS.
Collapse
Affiliation(s)
- R Defferrari
- Department of Pathology, Istituto Giannina Gaslini, Genova 16148, Italy
| | - K Mazzocco
- Department of Pathology, Istituto Giannina Gaslini, Genova 16148, Italy
| | - I M Ambros
- Children's Cancer Research Institute, St Anna Kinderkrebsforschung, Vienna 1090, Austria
| | - P F Ambros
- Children's Cancer Research Institute, St Anna Kinderkrebsforschung, Vienna 1090, Austria
| | - C Bedwell
- Northern Genetics Service, Newcastle upon Tyne NEI 3 BZ, UK
| | - K Beiske
- Department of Pathology, Oslo University Hospital Rikshopitalet, Oslo 0424, Norway
| | - J Bénard
- Département de Biologie et de Pathologie Médicales, Gustave Roussy Cancer Campus, Villejuif 94800, France
| | - A P Berbegall
- Department of Pathology, Medical School of Valencia, University of Valencia, Valencia 46010, Spain
| | - N Bown
- Northern Genetics Service, Newcastle upon Tyne NEI 3 BZ, UK
| | - V Combaret
- Laboratoire de Recherche Translationnelle, Centre Léon-Bérard, Lyon 69008, France
| | - J Couturier
- Unité de Génétique Somatique et Cytogénétique, Institut Curie, Paris Cedex 05 75248, France
| | - G Erminio
- Epidemiology, Biostatistics and Committees Unit, Istituto Giannina Gaslini, Genova 16148, Italy
| | - C Gambini
- Department of Pathology, Istituto Giannina Gaslini, Genova 16148, Italy
| | - A Garaventa
- Department of Haematology-Oncology, Istituto Giannina Gaslini, Genova 16148, Italy
| | - N Gross
- Pediatric Oncology Research Unit, Lausanne University Hospital (CHUV), Lausanne 1011, Switzerland
| | - R Haupt
- Epidemiology, Biostatistics and Committees Unit, Istituto Giannina Gaslini, Genova 16148, Italy
| | - J Kohler
- Department of Paediatric Oncology, Southampton General Hospital, Southampton S016 6YD, UK
| | - M Jeison
- Cancer Cytogenetique and Molecular Cytogenetique Laboratory, Schneider Children's Medical Center of Israel, Petah Tikva, Israel
| | - J Lunec
- Northern Institute for Cancer Research, Newcastle University, Newcastle NE2 4HH, UK
| | - B Marques
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, Lisbon 1649-016, Portugal
| | - T Martinsson
- Department of Clinical Genetics, Göteborg University, Sahlgrenska University Hospital, Göteborg 413 45, Sweden
| | - R Noguera
- Department of Pathology, Medical School of Valencia, University of Valencia, Valencia 46010, Spain
| | - S Parodi
- Institute of Electronics, Computer and Telecommunication Engineering, National Research Council, Genova 16149, Italy
| | - G Schleiermacher
- 1] INSERM U830, Laboratoire de Génétique et Biologie des Cancers, Paris Cedex 05 75248, France [2] Département d'Oncologie Pédiatrique, Institut Curie, Paris Cedex 05 75248, France
| | - D A Tweddle
- Northern Institute for Cancer Research, Newcastle University, Newcastle NE2 4HH, UK
| | - A Valent
- Département de Biologie et de Pathologie Médicales, Gustave Roussy Cancer Campus, Villejuif 94800, France
| | - N Van Roy
- Center for Medical Genetics, Ghent University Hospital, Ghent 9000, Belgium
| | - A Vicha
- Department of Paediatric Haematology and Oncology, Charles University and University Hospital Motol, Prague 15008, Czech Republic
| | - E Villamon
- Department of Hematology, Hospital Universitari i Politècnic La Fe, Valencia 46009, Spain
| | - G P Tonini
- Laboratory of Neuroblastoma, Onco/Haematology Laboratory, University of Padua, Pediatric Research Institute (IRP)-Città della Speranza, Corso Stati Uniti 4, Padova 35127, Italy
| |
Collapse
|
34
|
Abbasi MR, Rifatbegovic F, Brunner C, Ladenstein R, Ambros IM, Ambros PF. Bone marrows from neuroblastoma patients: an excellent source for tumor genome analyses. Mol Oncol 2014; 9:545-54. [PMID: 25467309 PMCID: PMC5528711 DOI: 10.1016/j.molonc.2014.10.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 10/22/2014] [Accepted: 10/22/2014] [Indexed: 02/01/2023] Open
Abstract
Neuroblastoma is the most common extra‐cranial solid tumor in childhood. Presence of disseminated tumor cells (DTCs) in the bone marrow (BM) at diagnosis and at relapse is a common event in stage M neuroblastomas. Although the clinical heterogeneity of disseminated neuroblastomas is frequently associated with genomic diversity, so far, only little information exists about the genomic status of DTCs. This lack of knowledge is mainly due to the varying amount of BM infiltrating tumor cells, which is usually below 30% even at diagnosis thereby hampering systematic analyses. Thus, a valuable chance to analyze metastatic and relapse clones is, so far, completely unexploited. In this study, we show that the enrichment of tumor cells in fresh or DMSO frozen BM samples with a minimum of 0.05% or 0.1% infiltration rate, respectively, by applying magnetic bead‐based technique increased the DTC content to a sufficient level to allow SNP array analyses in 49 out of 69 samples. In addition, we successfully used non‐enriched BM samples with ≥30% DTCs including non‐stained and immunostained cytospin and BM smear slides for SNP array analyses in 44 cases. We analyzed the genomic profile of DTCs by an ultra‐high density SNP array technique with highest performance detecting all segmental chromosomal aberrations, amplified regions, acquired loss of heterozygosity events and minor aberrations affecting single genes or parts thereof. Genomic analysis of bone marrow micrometastases by ultra‐high density SNP array. Routinely processed bone marrow (BM) samples allow detailed genomic studies. Enrichment of BM samples with >0.05% tumor cells allows detailed genomic analyses.
Collapse
Affiliation(s)
- M Reza Abbasi
- Tumor Biology, Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria.
| | - Fikret Rifatbegovic
- Tumor Biology, Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Clemens Brunner
- Tumor Biology, Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Ruth Ladenstein
- SiRP, Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria; Department of Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Inge M Ambros
- Tumor Biology, Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Peter F Ambros
- Tumor Biology, Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria; Department of Pediatrics, Medical University of Vienna, Vienna, Austria.
| |
Collapse
|
35
|
Coco S, Truini A, Alama A, Dal Bello MG, Venè R, Garuti A, Carminati E, Rijavec E, Genova C, Barletta G, Sini C, Ballestrero A, Boccardo F, Grossi F. Afatinib resistance in non-small cell lung cancer involves the PI3K/AKT and MAPK/ERK signalling pathways and epithelial-to-mesenchymal transition. Target Oncol 2014; 10:393-404. [PMID: 25341405 DOI: 10.1007/s11523-014-0344-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 10/13/2014] [Indexed: 12/22/2022]
Abstract
The epidermal growth factor receptor (EGFR) signalling is one of the most deregulated pathways in non-small cell lung cancer (NSCLC). Recently, the development of novel irreversible tyrosine kinase inhibitors (TKI), such as afatinib, has significantly improved the survival of advanced NSCLC patients harbouring activated EGFR mutations. However, treatment with TKI is not always curative due to the development of resistance. In the present study, we investigated the sensitivity to afatinib in two NSCLC EGFR mutated cell lines (NCI-H1650 and NCI-H1975) by expression profile analysis of 92 genes involved in the EGF pathway. Thereafter, the established afatinib resistant clones were evaluated at different biological levels: genomic, by array comparative genomic hybridisation (aCGH) and deep sequencing; transcriptomic, by quantitative polymerase chain reaction (qPCR) and proteomic, by Western blot and immunofluorescence. The baseline gene expression of the two cell lines revealed that NCI-H1650, the less afatinib-responsive cell, showed activation of two main EGFR downstream pathways such as PI3K/AKT and PLCγ/PKC axes. Analysis of the afatinib-resistant cells showed PI3K/AKT and MAPK/ERK pathways activation together with a biological switch from an epithelial-to-mesenchymal phenotype might confer afatinib-resistant properties to this cell line. Our data suggest that the activation of EGFR-dependent downstream pathways might be involved in the occurrence of resistance to afatinib assuming that the EGFR mutational status should not be exclusively considered when selecting TKI treatments. In particular, the epithelial-to-mesenchymal transition might provide a new basis for understanding afatinib resistance.
Collapse
Affiliation(s)
- Simona Coco
- Lung Cancer Unit, IRCCS AOU San Martino-IST, L.go R. Benzi 10, 16132, Genoa, Italy,
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
36
|
Newton R, Wernisch L. A meta-analysis of multiple matched copy number and transcriptomics data sets for inferring gene regulatory relationships. PLoS One 2014; 9:e105522. [PMID: 25148247 PMCID: PMC4141782 DOI: 10.1371/journal.pone.0105522] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 07/21/2014] [Indexed: 12/25/2022] Open
Abstract
Inferring gene regulatory relationships from observational data is challenging. Manipulation and intervention is often required to unravel causal relationships unambiguously. However, gene copy number changes, as they frequently occur in cancer cells, might be considered natural manipulation experiments on gene expression. An increasing number of data sets on matched array comparative genomic hybridisation and transcriptomics experiments from a variety of cancer pathologies are becoming publicly available. Here we explore the potential of a meta-analysis of thirty such data sets. The aim of our analysis was to assess the potential of in silico inference of trans-acting gene regulatory relationships from this type of data. We found sufficient correlation signal in the data to infer gene regulatory relationships, with interesting similarities between data sets. A number of genes had highly correlated copy number and expression changes in many of the data sets and we present predicted potential trans-acted regulatory relationships for each of these genes. The study also investigates to what extent heterogeneity between cell types and between pathologies determines the number of statistically significant predictions available from a meta-analysis of experiments.
Collapse
Affiliation(s)
- Richard Newton
- Biostatistics Unit, Medical Research Council, Cambridge, United Kingdom
- * E-mail:
| | - Lorenz Wernisch
- Biostatistics Unit, Medical Research Council, Cambridge, United Kingdom
| |
Collapse
|
37
|
Schleiermacher G, Janoueix-Lerosey I, Delattre O. Recent insights into the biology of neuroblastoma. Int J Cancer 2014; 135:2249-61. [PMID: 25124476 DOI: 10.1002/ijc.29077] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 05/08/2014] [Indexed: 01/24/2023]
Abstract
Neuroblastoma (NB) is an embryonal tumor of the sympathetic nervous system which accounts for 8-10% of pediatric cancers. It is characterized by a broad spectrum of clinical behaviors from spontaneous regression to fatal outcome despite aggressive therapies. Considerable progress has been made recently in the germline and somatic genetic characterization of patients and tumors. Indeed, predisposition genes that account for a significant proportion of familial and syndromic cases have been identified and genome-wide association studies have retrieved a number of susceptibility loci. In addition, genome-wide sequencing, copy-number and expression studies have been conducted on tumors and have detected important gene modifications, profiles and signatures that have strong implications for the therapeutic stratification of patients. The identification of major players in NB oncogenesis, including MYCN, ALK, PHOX2B and LIN28B, has enabled the development of new animal models. Our review focuses on these recent advances, on the insights they provide on the mechanisms involved in NB development and their applications for the clinical management of patients.
Collapse
Affiliation(s)
- Gudrun Schleiermacher
- Equipe SIRIC Recherche Translationnelle en Oncologie Pédiatrique, Département de Recherche Translationnelle et Inserm U830, Centre de Recherche, Paris Cedex, 05, France; Département de pédiatrie, Institut Curie, Paris Cedex, 05, France; Unité Génétique et Biologie des Cancers, Inserm U830, Centre de Recherche, Institut Curie, Paris Cedex, 05, France
| | | | | |
Collapse
|
38
|
Cobrinik D, Ostrovnaya I, Hassimi M, Tickoo SK, Cheung IY, Cheung NKV. Recurrent pre-existing and acquired DNA copy number alterations, including focal TERT gains, in neuroblastoma central nervous system metastases. Genes Chromosomes Cancer 2013; 52:1150-66. [PMID: 24123354 DOI: 10.1002/gcc.22110] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 08/14/2013] [Indexed: 12/13/2022] Open
Abstract
Stage 4 neuroblastomas have a high rate of local and metastatic relapse and associated disease mortality. The central nervous system (CNS) is currently one of the most common isolated relapse sites, yet the genomic alterations that contribute to these metastases are unknown. This study sought to identify recurrent DNA copy number alterations (CNAs) and target genes relating to neuroblastoma CNS metastases by studying 19 pre-CNS primary tumors and 27 CNS metastases, including 12 matched pairs. SNP microarray analyses revealed that MYCN amplified (MYCNA) tumors had recurrent CNAs different from non-MYCNA cohorts. Several CNAs known to be prevalent among primary neuroblastomas occurred more frequently in CNS metastases, including 4p-, 7q+, 12q+, and 19q- in non-MYCNA metastases, and 9p- and 14q- irrespective of MYCNA status. In addition, novel CNS metastases-related CNAs included 18q22.1 gains in non-MYCNA pre-CNS primaries and 5p15.33 gains and 15q26.1→tel losses in non-MYCNA CNS metastases. Based on minimal common regions, gene expression, and biological properties, TERT (5p), NR2F2 (15q), ALDH1A3 (15q), CDKN2A (9p), and possibly CDH7 and CDH19 (18q) were candidate genes associated with the CNS metastatic process. Notably, the 5p15 minimal common region contained only TERT, and non-MYCNA CNS metastases with focal 5p15 gains had increased TERT expression, similar to MYCNA tumors. These findings suggest that a specific genomic lesion (18q22.1 gain) predisposes to CNS metastases and that distinct lesions are recurrently acquired during metastatic progression. Among the acquired lesions, increased TERT copy number and expression appears likely to function in lieu of MYCNA to promote CNS metastasis.
Collapse
Affiliation(s)
- David Cobrinik
- Department of Pediatrics, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065
| | | | | | | | | | | |
Collapse
|
39
|
Abstract
Neuroblastoma is a solid tumour that arises from the developing sympathetic nervous system. Over the past decade, our understanding of this disease has advanced tremendously. The future challenge is to apply the knowledge gained to developing risk-based therapies and, ultimately, improving outcome. In this Review we discuss the key discoveries in the developmental biology, molecular genetics and immunology of neuroblastoma, as well as new translational tools for bringing these promising scientific advances into the clinic.
Collapse
Affiliation(s)
- Nai-Kong V. Cheung
- Department of Pediatrics, Memorial Sloan-Kettering Cancer Center, New York, NY 10065
| | - Michael A. Dyer
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105
- Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, TN 38163
- Howard Hughes Medical Institute, Chevy Chase, MD 20815
| |
Collapse
|
40
|
Kocak H, Ackermann S, Hero B, Kahlert Y, Oberthuer A, Juraeva D, Roels F, Theissen J, Westermann F, Deubzer H, Ehemann V, Brors B, Odenthal M, Berthold F, Fischer M. Hox-C9 activates the intrinsic pathway of apoptosis and is associated with spontaneous regression in neuroblastoma. Cell Death Dis 2013; 4:e586. [PMID: 23579273 PMCID: PMC3668636 DOI: 10.1038/cddis.2013.84] [Citation(s) in RCA: 163] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Neuroblastoma is an embryonal malignancy of the sympathetic nervous system. Spontaneous regression and differentiation of neuroblastoma is observed in a subset of patients, and has been suggested to represent delayed activation of physiologic molecular programs of fetal neuroblasts. Homeobox genes constitute an important family of transcription factors, which play a fundamental role in morphogenesis and cell differentiation during embryogenesis. In this study, we demonstrate that expression of the majority of the human HOX class I homeobox genes is significantly associated with clinical covariates in neuroblastoma using microarray expression data of 649 primary tumors. Moreover, a HOX gene expression-based classifier predicted neuroblastoma patient outcome independently of age, stage and MYCN amplification status. Among all HOX genes, HOXC9 expression was most prominently associated with favorable prognostic markers. Most notably, elevated HOXC9 expression was significantly associated with spontaneous regression in infant neuroblastoma. Re-expression of HOXC9 in three neuroblastoma cell lines led to a significant reduction in cell viability, and abrogated tumor growth almost completely in neuroblastoma xenografts. Neuroblastoma growth arrest was related to the induction of programmed cell death, as indicated by an increase in the sub-G1 fraction and translocation of phosphatidylserine to the outer membrane. Programmed cell death was associated with the release of cytochrome c from the mitochondria into the cytosol and activation of the intrinsic cascade of caspases, indicating that HOXC9 re-expression triggers the intrinsic apoptotic pathway. Collectively, our results show a strong prognostic impact of HOX gene expression in neuroblastoma, and may point towards a role of Hox-C9 in neuroblastoma spontaneous regression.
Collapse
Affiliation(s)
- H Kocak
- Children's Hospital, Department of Pediatric Oncology and Hematology and Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
41
|
High genomic instability predicts survival in metastatic high-risk neuroblastoma. Neoplasia 2013; 14:823-32. [PMID: 23019414 DOI: 10.1593/neo.121114] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 07/17/2012] [Accepted: 07/30/2012] [Indexed: 12/13/2022] Open
Abstract
We aimed to identify novel molecular prognostic markers to better predict relapse risk estimate for children with high-risk (HR) metastatic neuroblastoma (NB). We performed genome- and/or transcriptome-wide analyses of 129 stage 4 HR NBs. Children older than 1 year of age were categorized as "short survivors" (dead of disease within 5 years from diagnosis) and "long survivors" (alive with an overall survival time ≥ 5 years). We reported that patients with less than three segmental copy number aberrations in their tumor represent a molecularly defined subgroup with a high survival probability within the current HR group of patients. The complex genomic pattern is a prognostic marker independent of NB-associated chromosomal aberrations, i.e., MYCN amplification, 1p and 11q losses, and 17q gain. Integrative analysis of genomic and expression signatures demonstrated that fatal outcome is mainly associated with loss of cell cycle control and deregulation of Rho guanosine triphosphates (GTPases) functioning in neuritogenesis. Tumors with MYCN amplification show a lower chromosome instability compared to MYCN single-copy NBs (P = .0008), dominated by 17q gain and 1p loss. Moreover, our results suggest that the MYCN amplification mainly drives disruption of neuronal differentiation and reduction of cell adhesion process involved in tumor invasion and metastasis. Further validation studies are warranted to establish this as a risk stratification for patients.
Collapse
|
42
|
Villamón E, Berbegall AP, Piqueras M, Tadeo I, Castel V, Djos A, Martinsson T, Navarro S, Noguera R. Genetic instability and intratumoral heterogeneity in neuroblastoma with MYCN amplification plus 11q deletion. PLoS One 2013; 8:e53740. [PMID: 23341988 PMCID: PMC3544899 DOI: 10.1371/journal.pone.0053740] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 12/03/2012] [Indexed: 12/14/2022] Open
Abstract
Background/Aim Genetic analysis in neuroblastoma has identified the profound influence of MYCN amplification and 11q deletion in patients’ prognosis. These two features of high-risk neuroblastoma usually occur as mutually exclusive genetic markers, although in rare cases both are present in the same tumor. The purpose of this study was to characterize the genetic profile of these uncommon neuroblastomas harboring both these high-risk features. Methods We selected 18 neuroblastomas with MNA plus 11q loss detected by FISH. Chromosomal aberrations were analyzed using Multiplex Ligation-dependent Probe Amplification and Single Nucleotide Polymorphism array techniques. Results and Conclusion This group of tumors has approximately the same high frequency of aberrations as found earlier for 11q deleted tumors. In some cases, DNA instability generates genetic heterogeneity, and must be taken into account in routine genetic diagnosis.
Collapse
Affiliation(s)
- Eva Villamón
- Department of Pathology, Medical School, University of Valencia, Valencia, Spain
| | - Ana P. Berbegall
- Department of Pathology, Medical School, University of Valencia, Valencia, Spain
| | - Marta Piqueras
- Department of Pathology, Medical School, University of Valencia, Valencia, Spain
| | - Irene Tadeo
- Research Foundation of Hospital Clínico Universitario of Valencia, Valencia, Spain
| | - Victoria Castel
- Pediatric Oncology Unit, Hospital Universitario La Fe, Valencia, Spain
| | - Anna Djos
- Department of Clinical Genetics, The Sahlgrenska Academy, University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Tommy Martinsson
- Department of Clinical Genetics, The Sahlgrenska Academy, University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Samuel Navarro
- Department of Pathology, Medical School, University of Valencia, Valencia, Spain
| | - Rosa Noguera
- Department of Pathology, Medical School, University of Valencia, Valencia, Spain
- * E-mail:
| |
Collapse
|
43
|
Cangemi G, Reggiardo G, Barco S, Barbagallo L, Conte M, D'Angelo P, Bianchi M, Favre C, Galleni B, Melioli G, Haupt R, Garaventa A, Corrias MV. Prognostic value of ferritin, neuron-specific enolase, lactate dehydrogenase, and urinary and plasmatic catecholamine metabolites in children with neuroblastoma. Onco Targets Ther 2012; 5:417-23. [PMID: 23226699 PMCID: PMC3514851 DOI: 10.2147/ott.s36366] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Different plasma and urinary parameters have been tested as valuable prognostic markers for children with neuroblastoma (NB), but conclusive results from multivariate analyses are still lacking. Samples collected at diagnosis from 505 patients diagnosed in Italy between June 1994 and November 2010 were analyzed at the Italian reference laboratory according to standard methodologies. Patient clinical data were retrieved from the Italian NB Registry. For statistical analysis, patients were grouped according to stage, age, MYCN status, and outcome. Cumulative survival was calculated by the Kaplan-Meier procedure using the first quartile of the marker distribution as a cut-off value to stratify the patients. Multivariate analysis was performed by the Cox regression model by considering only the significant variables. When the entire cohort of patients was considered, none of the different parameters had an independent prognostic value. However, in patients with localized disease without MYCN amplification the significant positive associations between urinary and plasmatic vanillylmandelic acid (VMA)/homovanillic acid (HVA) ratio and a better prognosis remained significant (P < 0.05 and P < 0.01, respectively), as well as, the positive association between high lactate dehydrogenase (LDH) values and a worse prognosis (P < 0.001). Moreover, in stage 4 patients without MYCN amplification, neuron-specific enolase levels above 200 ng/mL and LDH levels above 2500 IU/mL maintained their significant association with a worse outcome (P = 0.01 and P = 0.0001, respectively). In conclusion, LDH had an independent prognostic value in patients of all stages without MYCN amplification. Moreover, the urinary and plasmatic VMA/HVA ratio was an independent predictor of prognosis in patients with localized disease without MYCN amplification. Since LDH and catecholamine metabolites are measured in all patients at diagnosis, these findings may be helpful for an easy, cost-effective, patient risk stratification.
Collapse
Affiliation(s)
- Giuliana Cangemi
- Clinical Pathology Laboratory Unit, Giannina Gaslini Institute, Genoa, Italy
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Schleiermacher G, Mosseri V, London WB, Maris JM, Brodeur GM, Attiyeh E, Haber M, Khan J, Nakagawara A, Speleman F, Noguera R, Tonini GP, Fischer M, Ambros I, Monclair T, Matthay KK, Ambros P, Cohn SL, Pearson ADJ. Segmental chromosomal alterations have prognostic impact in neuroblastoma: a report from the INRG project. Br J Cancer 2012; 107:1418-22. [PMID: 22976801 PMCID: PMC3494425 DOI: 10.1038/bjc.2012.375] [Citation(s) in RCA: 123] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Background: In the INRG dataset, the hypothesis that any segmental chromosomal alteration might be of prognostic impact in neuroblastoma without MYCN amplification (MNA) was tested. Methods: The presence of any segmental chromosomal alteration (chromosome 1p deletion, 11q deletion and/or chromosome 17q gain) defined a segmental genomic profile. Only tumours with a confirmed unaltered status for all three chromosome arms were considered as having no segmental chromosomal alterations. Results: Among the 8800 patients in the INRG database, a genomic type could be attributed for 505 patients without MNA: 397 cases had a segmental genomic type, whereas 108 cases had an absence of any segmental alteration. A segmental genomic type was more frequent in patients >18 months and in stage 4 disease (P<0.0001). In univariate analysis, 11q deletion, 17q gain and a segmental genomic type were associated with a poorer event-free survival (EFS) (P<0.0001, P=0.0002 and P<0.0001, respectively). In multivariate analysis modelling EFS, the parameters age, stage and a segmental genomic type were retained in the model, whereas the individual genetic markers were not (P<0.0001 and RR=2.56; P=0.0002 and RR=1.8; P=0.01 and RR=1.7, respectively). Conclusion: A segmental genomic profile, rather than the single genetic markers, adds prognostic information to the clinical markers age and stage in neuroblastoma patients without MNA, underlining the importance of pangenomic studies.
Collapse
Affiliation(s)
- G Schleiermacher
- INSERM U, Laboratoire de Génétique et Biologie des Cancers, Institut Curie, Paris, France.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Tonini GP, Nakagawara A, Berthold F. Towards a turning point of neuroblastoma therapy. Cancer Lett 2012; 326:128-34. [PMID: 22922304 DOI: 10.1016/j.canlet.2012.08.017] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Revised: 08/15/2012] [Accepted: 08/16/2012] [Indexed: 12/31/2022]
Abstract
In 1983, the MYCN oncogene amplification was discovered in neuroblastoma cells and few years later its prognostic role was clearly demonstrated. The first European study, in which MYCN gene status is taken as prognostic factor for therapeutic decision, was released by SIOPEN and GPOH in 1995. Afterward, other trials were released by SIOPEN, GPOH, COG, and JNBSG in which MYCN gene amplification was employed as prognostic risk factor. However, since MYCN is abnormal in about 20% of tumors and is a reliable prognostic marker for only some subgroups of patients, additional chromosomal abnormalities have been introduced for clinical decisions: 1p deletions/imbalances (GPOH), 11q deletions/imbalances (COG), and structural copy number aberrations (SIOPEN). MYCN gene status and chromosome aberrations improved patients' risk evaluation and helped to develop tailored therapy for diverse subgroups of patients. Unfortunately, high risk patients still have an unfavorable prognosis and are the major challenge for oncologists. In the last decade, the advent of genome-wide analysis and the next generation sequencing technique have given the opportunity to deeply investigate the genome of neuroblastoma to identify both candidate genes associated with tumor progression and druggable target genes. ALK gene is an actual candidate for the therapy with small molecule inhibitors, but others as mTOR, Aurora, and TRK, are suitable targets for subgroups of high risk patients. The huge amount of clinical and biological information collected in the last 20 years suggests that it is time to turn on for new and more personalized therapies of neuroblastoma.
Collapse
Affiliation(s)
- Gian Paolo Tonini
- Italian Neuroblastoma Foundation, IRCCS A.O.U. San Martino-IST, National Cancer Research Institute, Genoa, Italy.
| | | | | |
Collapse
|