1
|
Winnicka D, Skowera P, Stelmach M, Styka B, Lejman M. Application of the FISH method and high-density SNP arrays to assess genetic changes in neuroblastoma-research by one institute. Acta Biochim Pol 2024; 71:12821. [PMID: 39049899 PMCID: PMC11267511 DOI: 10.3389/abp.2024.12821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 06/12/2024] [Indexed: 07/27/2024]
Abstract
Neuroblastoma is the most common extracranial solid tumor in children. Amplification of the MYCN gene has been observed in approximately 20%-30% of tumors. It is strongly correlated with advanced-stage disease, rapid tumor progression, resistance to chemotherapy and poor outcomes independent of patient age and stage of advanced disease. MYCN amplification identifies high-risk patients. To assess neuroblastoma tumors with MYCN amplification we used paraffin-embedded tissue sections in 57 patients and intraoperative tumor imprints in 10 patients by fluorescence in situ hybridization (FISH). Positive results for MYCN amplification have been observed in twelve patients' paraffin-embedded tissue sections and in three patients' intraoperative tumor imprints, which represents 22.4% of all patients tested in the analysis. Fluorescence in situ hybridization is a highly sensitive and useful technique for detecting MYCN amplification on paraffin-embedded tissue sections of neuroblastoma tumors and intraoperative tumor imprints thus facilitating therapeutic decisions based on the presence or absence of this important biologic marker. The presence of structural changes, regardless of MYCN gene amplification status, influences the clinical behavior of neuroblastoma. High-Density SNP Arrays have emerged as the perfect tools for detecting these changes due to their exceptional accuracy, sensitivity and ability to analyze copy number and allele information. Consequently, they are proven to be highly valuable in the genomic diagnosis of immature neuroectodermal tumors.
Collapse
Affiliation(s)
| | | | - Magdalena Stelmach
- Independent Laboratory of Genetic Diagnostics, Medical University of Lublin, Lublin, Poland
| | | | | |
Collapse
|
2
|
Allinson LM, Potts A, Goodman A, Bown N, Bashton M, Thompson D, Basta NO, Gabriel AS, McCorkindale M, Ng A, McNally RJQ, Tweddle DA. Loss of ALK hotspot mutations in relapsed neuroblastoma. Genes Chromosomes Cancer 2022; 61:747-753. [PMID: 36029175 PMCID: PMC9826054 DOI: 10.1002/gcc.23093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 08/22/2022] [Accepted: 08/22/2022] [Indexed: 01/11/2023] Open
Abstract
ALK is the most commonly mutated oncogene in neuroblastoma with increased mutation frequency reported at relapse. Here we report the loss of an ALK mutation in two patients at relapse and a paired neuroblastoma cell line at relapse. ALK detection methods including Sanger sequencing, targeted next-generation sequencing and a new ALK Agena MassARRAY technique were used to detect common hotspot ALK variants in tumors at diagnosis and relapse from two high-risk neuroblastoma patients. Copy number analysis including single nucleotide polymorphism array and array comparative genomic hybridization confirmed adequate tumor cell content in DNA used for mutation testing. Case 1 presented with an ALK F1174L mutation at diagnosis with a variant allele frequency (VAF) ranging between 23.5% and 28.5%, but the mutation was undetectable at relapse. Case 2 presented with an ALK R1257Q mutation at diagnosis (VAF = 39%-47.4%) which decreased to <0.01% at relapse. Segmental chromosomal aberrations were maintained between diagnosis and relapse confirming sufficient tumor cell content for mutation detection. The diagnostic SKNBE1n cell line harbors an ALK F1174S mutation, which was lost in the relapsed SKNBE2c cell line. To our knowledge, these are the first reported cases of loss of ALK mutations at relapse in neuroblastoma in the absence of ALK inhibitor therapy, reflecting intra-tumoral spatial and temporal heterogeneity. As ALK inhibitors are increasingly used in the treatment of refractory/relapsed neuroblastoma, our study highlights the importance of confirming whether an ALK mutation detected at diagnosis is still present in clones leading to relapse.
Collapse
Affiliation(s)
- Lisa M. Allinson
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Translational & Clinical Research InstituteNewcastle UniversityNewcastle upon TyneUK
| | - Aaron Potts
- Newcastle Genetics LaboratoryNewcastle upon Tyne Hospitals NHS TrustNewcastle upon TyneUK
| | - Angharad Goodman
- Newcastle Genetics LaboratoryNewcastle upon Tyne Hospitals NHS TrustNewcastle upon TyneUK
| | - Nick Bown
- Newcastle Genetics LaboratoryNewcastle upon Tyne Hospitals NHS TrustNewcastle upon TyneUK
| | - Matthew Bashton
- The Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life SciencesNorthumbria UniversityNewcastle upon TyneUK
| | - Dean Thompson
- Department of Applied Sciences, Faculty of Health and Life SciencesNorthumbria UniversityNewcastle upon TyneUK
| | - Nermine O. Basta
- Population Health Sciences InstituteNewcastle UniversityNewcastle upon TyneUK
| | - Alem S. Gabriel
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Translational & Clinical Research InstituteNewcastle UniversityNewcastle upon TyneUK
| | | | - Antony Ng
- Royal Hospital for Sick ChildrenBristolUK
| | | | - Deborah A. Tweddle
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Translational & Clinical Research InstituteNewcastle UniversityNewcastle upon TyneUK,Great North Children's HospitalNewcastle upon TyneUK
| |
Collapse
|
3
|
Amplification of CDK4 and MDM2: a detailed study of a high-risk neuroblastoma subgroup. Sci Rep 2022; 12:12420. [PMID: 35859155 PMCID: PMC9300649 DOI: 10.1038/s41598-022-16455-1] [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: 08/20/2021] [Accepted: 07/11/2022] [Indexed: 11/08/2022] Open
Abstract
In neuroblastoma, MYCN amplification and 11q-deletion are important, although incomplete, markers of high-risk disease. It is therefore relevant to characterize additional alterations that can function as prognostic and/or predictive markers. Using SNP-microarrays, a group of neuroblastoma patients showing amplification of one or multiple 12q loci was identified. Two loci containing CDK4 and MDM2 were commonly co-amplified, although amplification of either locus in the absence of the other was observed. Pharmacological inhibition of CDK4/6 with ribociclib or abemaciclib decreased proliferation in a broad set of neuroblastoma cell lines, including CDK4/MDM2-amplified, whereas MDM2 inhibition by Nutlin-3a was only effective in p53wild-type cells. Combined CDK4/MDM2 targeting had an additive effect in p53wild-type cell lines, while no or negative additive effect was observed in p53mutated cells. Most 12q-amplified primary tumors were of abdominal origin, including those of intrarenal origin initially suspected of being Wilms' tumor. An atypical metastatic pattern was also observed with low degree of bone marrow involvement, favoring other sites such as the lungs. Here we present detailed biological data of an aggressive neuroblastoma subgroup hallmarked by 12q amplification and atypical clinical presentation for which our in vitro studies indicate that CDK4 and/or MDM2 inhibition also could be beneficial.
Collapse
|
4
|
van Gerven MR, Bozsaky E, Matser YAH, Vosseberg J, Taschner-Mandl S, Koster J, Tytgat GAM, Molenaar JJ, van den Boogaard M. The mutational spectrum of ATRX aberrations in neuroblastoma and the associated patient and tumor characteristics. Cancer Sci 2022; 113:2167-2178. [PMID: 35384159 PMCID: PMC9207354 DOI: 10.1111/cas.15363] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 03/18/2022] [Accepted: 04/02/2022] [Indexed: 11/30/2022] Open
Abstract
Neuroblastoma is the most common extracranial solid tumor in children. The chromatin remodeler ATRX is frequently mutated in high‐risk patients with a poor prognosis. Although many studies have reported ATRX aberrations and the associated clinical characteristics in neuroblastoma, a comprehensive overview is currently lacking. In this study, we extensively characterize the mutational spectrum of ATRX aberrations in neuroblastoma tumors reported in previous studies and present an overview of patient and tumor characteristics. We collected the data of a total of 127 neuroblastoma patients and three cell lines with ATRX aberrations originating from 20 papers. We subdivide the ATRX aberrations into nonsense, missense, and multiexon deletions (MEDs) and show that 68% of them are MEDs. Of these MEDs, 75% are predicted to be in‐frame. Furthermore, we identify a missense mutational hotspot region in the helicase domain. We also confirm that all three ATRX mutation types are more often identified in patients diagnosed at an older age, but still approximately 40% of the patients are aged 5 years or younger at diagnosis. Surprisingly, we found that 11q deletions are enriched in neuroblastomas with ATRX deletions compared to a reference cohort, but not in neuroblastomas with ATRX point mutations. Taken together, our data emphasizes a distinct ATRX mutation spectrum in neuroblastoma, which should be considered when studying molecular phenotypes and therapeutic strategies.
Collapse
Affiliation(s)
| | - Eva Bozsaky
- Tumor biology group, St Anna Children's Cancer Research Institute, Vienna, Austria
| | - Yvette A H Matser
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Julian Vosseberg
- Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | | | - Jan Koster
- Department of Oncogenomics, Amsterdam UMC, location AMC, Amsterdam, the Netherlands
| | | | - Jan J Molenaar
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Department of Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | | |
Collapse
|
5
|
Yamamoto T, Sato Y, Yasuda S, Shikamura M, Tamura T, Takenaka C, Takasu N, Nomura M, Dohi H, Takahashi M, Mandai M, Kanemura Y, Nakamura M, Okano H, Kawamata S. OUP accepted manuscript. Stem Cells Transl Med 2022; 11:527-538. [PMID: 35445254 PMCID: PMC9154342 DOI: 10.1093/stcltm/szac014] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 02/13/2022] [Indexed: 11/15/2022] Open
Abstract
Cell therapy using induced pluripotent stem cell (iPSC) derivatives may result in abnormal tissue generation because the cells undergo numerous cycles of mitosis before clinical application, potentially increasing the accumulation of genetic abnormalities. Therefore, genetic tests may predict abnormal tissue formation after transplantation. Here, we administered iPSC derivatives with or without single-nucleotide variants (SNVs) and deletions in cancer-related genes with various genomic copy number variant (CNV) profiles into immunodeficient mice and examined the relationships between mutations and abnormal tissue formation after transplantation. No positive correlations were found between the presence of SNVs/deletions and the formation of abnormal tissues; the overall predictivity was 29%. However, a copy number higher than 3 was correlated, with an overall predictivity of 86%. Furthermore, we found CNV hotspots at 14q32.33 and 17q12 loci. Thus, CNV analysis may predict abnormal tissue formation after transplantation of iPSC derivatives and reduce the number of tumorigenicity tests.
Collapse
Affiliation(s)
- Takako Yamamoto
- R&D Center for Cell Therapy, Foundation for Biomedical Research and Innovation, Kobe, Japan
| | - Yoji Sato
- Division of Cell-Based Therapeutic Products, National Institute of Health Sciences, Kawasaki, Japan
| | - Satoshi Yasuda
- Division of Cell-Based Therapeutic Products, National Institute of Health Sciences, Kawasaki, Japan
| | - Masayuki Shikamura
- R&D Center for Cell Therapy, Foundation for Biomedical Research and Innovation, Kobe, Japan
| | - Takashi Tamura
- R&D Center for Cell Therapy, Foundation for Biomedical Research and Innovation, Kobe, Japan
| | - Chiemi Takenaka
- R&D Center for Cell Therapy, Foundation for Biomedical Research and Innovation, Kobe, Japan
| | | | | | | | | | | | - Yonehiro Kanemura
- Department of Biomedical Research and Innovation, Institute for Clinical Research, National Hospital Organization Osaka National Hospital, Osaka, Japan
| | - Masaya Nakamura
- Department of Orthopedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Hideyuki Okano
- Department of Physiology, Keio University School of Medicine, Tokyo, Japan
| | - Shin Kawamata
- R&D Center for Cell Therapy, Foundation for Biomedical Research and Innovation, Kobe, Japan
- Riken BDR, Kobe, Japan
- Corresponding author: Shin Kawamata, Minatojima-minamimachi 1-5-4, Chuo-ku Kobe, 650-0047 Japan.
| |
Collapse
|
6
|
Ishii Y, Sato-Otsubo A, Takita J, Morio T, Takagi M. Copy number alteration analysis for neuroblastoma using droplet digital polymerase chain reaction. Pediatr Int 2021; 63:1192-1197. [PMID: 33462952 DOI: 10.1111/ped.14606] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/12/2021] [Accepted: 01/15/2021] [Indexed: 11/28/2022]
Abstract
BACKGROUND Neuroblastoma (NB) is a malignant tumor derived from the neural crest. MYCN amplification is a well-known adverse molecular prognostic factor for NB. Genome copy number alterations (CNAs) such as chromosome (Chr) 11q deletion, 1p deletion, and 17q gain are associated with a poor prognosis. Fluorescence in situ hybridization (FISH) and Southern blotting analysis are frequently used to detect MYCN amplification. Although comparative genomic hybridization (CGH) and single-nucleotide polymorphism (SNP) chip arrays can easily detect CNAs, these methods are impractical for clinical use due to their cost and run time. Consequently, genome copy number analysis using digital droplet PCR has become widely used to monitor CNAs. METHODS In this study, we used digital droplet polymerase chain reaction to detect MYCN amplification and Chr 11q CNA, which was used for risk stratification according to the International Neuroblastoma Risk Group classification system. We compared the results with data from SNP chip arrays in seven NB cell lines and eight primary NB samples. RESULTS Digital droplet PCR assays successfully detected MYCN amplification and 11q CNA. The results were very consistent with those obtained by SNP chip assay. CONCLUSIONS Digital droplet PCR can be conducted more rapidly than FISH or Southern blotting. Accordingly, it should be useful for on-site clinical applications aimed at detecting CNAs in NB and performing risk stratification promptly after diagnosis.
Collapse
Affiliation(s)
- Yuko Ishii
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University (TMDU), Bunkyo-Ku, Tokyo, Japan
| | - Aiko Sato-Otsubo
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Bunkyo-Ku, Tokyo, Japan
| | - Junko Takita
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Sakyo-Ku, Kyoto, Japan
| | - Tomohiro Morio
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University (TMDU), Bunkyo-Ku, Tokyo, Japan
| | - Masatoshi Takagi
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University (TMDU), Bunkyo-Ku, Tokyo, Japan
| |
Collapse
|
7
|
Neuroblastoma Risk Assessment and Treatment Stratification with Hybrid Capture-Based Panel Sequencing. J Pers Med 2021; 11:jpm11080691. [PMID: 34442335 PMCID: PMC8398598 DOI: 10.3390/jpm11080691] [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: 05/14/2021] [Revised: 07/06/2021] [Accepted: 07/09/2021] [Indexed: 11/17/2022] Open
Abstract
For many years, the risk-based therapy stratification of children with neuroblastoma has relied on clinical and molecular covariates. In recent years, genome analysis has revealed further alterations defining risk, tumor biology, and therapeutic targets. The implementation of a robust and scalable method for analyzing traditional and new molecular markers in routine diagnostics is an urgent clinical need. Here, we investigated targeted panel sequencing as a diagnostic approach to analyze all relevant genomic neuroblastoma risk markers in one assay. Our "neuroblastoma hybrid capture sequencing panel" (NB-HCSP) assay employs a technology for the high-coverage sequencing (>1000×) of 55 selected genes and neuroblastoma-relevant genomic regions, which allows for the detection of single nucleotide changes, structural rearrangements, and copy number alterations. We validated our assay by analyzing 15 neuroblastoma cell lines and a cohort of 20 neuroblastomas, for which reference routine diagnostic data and genome sequencing data were available. We observed a high concordance for risk markers identified by the NB-HSCP assay, clinical routine diagnostics, and genome sequencing. Subsequently, we demonstrated clinical applicability of the NB-HCSP assay by analyzing routine clinical samples. We conclude that the NB-HCSP assay may be implemented into routine diagnostics as a single assay that covers all essential covariates for initial neuroblastoma classification, extended risk stratification, and targeted therapy selection.
Collapse
|
8
|
Choi JH, Ro JY. Mediastinal neuroblastoma, ganglioneuroblastoma, and ganglioneuroma: Pathology review and diagnostic approach. Semin Diagn Pathol 2021; 39:120-130. [PMID: 34167847 DOI: 10.1053/j.semdp.2021.06.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 06/10/2021] [Indexed: 12/13/2022]
Abstract
Neuroblastic tumors are a group of tumors of the sympathetic ganglia and adrenal medulla that derive from primordial neural crest cells. These tumors include neuroblastoma, intermixed ganglioneuroblastoma, nodular ganglioneuroblastoma, and ganglioneuroma. Neuroblastomas are the most common extracranial solid tumor arising in childhood and may occur in different anatomic sites. Neuroblastic tumors are common mesenchymal tumors of the mediastinum. Herein, we describe advances in our understanding of neuroblastic tumor biology. Pathologists should be aware of diagnostic challenges associated with these tumors to ensure correct histologic diagnosis and appropriate clinical management. We describe updated mediastinal neuroblastic tumor pathology, focusing on morphological, immunohistochemical, and molecular features and differential diagnoses.
Collapse
Affiliation(s)
- Joon Hyuk Choi
- Department of Pathology, Yeungnam University College of Medicine, 170 Hyeonchung-ro, Namgu, Daegu, 42415, South Korea.
| | - Jae Y Ro
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Medical College of Cornell University, Houston, TX, 77030, USA
| |
Collapse
|
9
|
Bellini A, Pötschger U, Bernard V, Lapouble E, Baulande S, Ambros PF, Auger N, Beiske K, Bernkopf M, Betts DR, Bhalshankar J, Bown N, de Preter K, Clément N, Combaret V, Font de Mora J, George SL, Jiménez I, Jeison M, Marques B, Martinsson T, Mazzocco K, Morini M, Mühlethaler-Mottet A, Noguera R, Pierron G, Rossing M, Taschner-Mandl S, Van Roy N, Vicha A, Chesler L, Balwierz W, Castel V, Elliott M, Kogner P, Laureys G, Luksch R, Malis J, Popovic-Beck M, Ash S, Delattre O, Valteau-Couanet D, Tweddle DA, Ladenstein R, Schleiermacher G. Frequency and Prognostic Impact of ALK Amplifications and Mutations in the European Neuroblastoma Study Group (SIOPEN) High-Risk Neuroblastoma Trial (HR-NBL1). J Clin Oncol 2021; 39:3377-3390. [PMID: 34115544 PMCID: PMC8791815 DOI: 10.1200/jco.21.00086] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
PURPOSE In neuroblastoma (NB), the ALK receptor tyrosine kinase can be constitutively activated through activating point mutations or genomic amplification. We studied ALK genetic alterations in high-risk (HR) patients on the HR-NBL1/SIOPEN trial to determine their frequency, correlation with clinical parameters, and prognostic impact. MATERIALS AND METHODS Diagnostic tumor samples were available from 1,092 HR-NBL1/SIOPEN patients to determine ALK amplification status (n = 330), ALK mutational profile (n = 191), or both (n = 571). RESULTS Genomic ALK amplification (ALKa) was detected in 4.5% of cases (41 out of 901), all except one with MYCN amplification (MNA). ALKa was associated with a significantly poorer overall survival (OS) (5-year OS: ALKa [n = 41] 28% [95% CI, 15 to 42]; no-ALKa [n = 860] 51% [95% CI, 47 to 54], [P < .001]), particularly in cases with metastatic disease. ALK mutations (ALKm) were detected at a clonal level (> 20% mutated allele fraction) in 10% of cases (76 out of 762) and at a subclonal level (mutated allele fraction 0.1%-20%) in 3.9% of patients (30 out of 762), with a strong correlation between the presence of ALKm and MNA (P < .001). Among 571 cases with known ALKa and ALKm status, a statistically significant difference in OS was observed between cases with ALKa or clonal ALKm versus subclonal ALKm or no ALK alterations (5-year OS: ALKa [n = 19], 26% [95% CI, 10 to 47], clonal ALKm [n = 65] 33% [95% CI, 21 to 44], subclonal ALKm (n = 22) 48% [95% CI, 26 to 67], and no alteration [n = 465], 51% [95% CI, 46 to 55], respectively; P = .001). Importantly, in a multivariate model, involvement of more than one metastatic compartment (hazard ratio [HR], 2.87; P < .001), ALKa (HR, 2.38; P = .004), and clonal ALKm (HR, 1.77; P = .001) were independent predictors of poor outcome. CONCLUSION Genetic alterations of ALK (clonal mutations and amplifications) in HR-NB are independent predictors of poorer survival. These data provide a rationale for integration of ALK inhibitors in upfront treatment of HR-NB with ALK alterations.
Collapse
Affiliation(s)
- Angela Bellini
- Equipe SiRIC RTOP Recherche Translationelle en Oncologie Pédiatrique, Institut Curie, Paris, France.,INSERM U830, Laboratoire de Génétique et Biologie des Cancers, Institut Curie, Paris, France.,SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Ulrike Pötschger
- Department for Studies and Statistics and Integrated Research, Vienna, Austria.,St Anna Children's Cancer Research Institute, Vienna, Austria
| | - Virginie Bernard
- Institut Curie Genomics of Excellence (ICGex) Platform, Research Center, Institut Curie, Paris, France
| | - Eve Lapouble
- Unité de Génétique Somatique, Service de Génétique, Hospital Group, Institut Curie, Paris, France
| | - Sylvain Baulande
- Institut Curie Genomics of Excellence (ICGex) Platform, Research Center, Institut Curie, Paris, France
| | - Peter F Ambros
- St Anna Children's Cancer Research Institute, Vienna, Austria
| | - Nathalie Auger
- Service de Génétique des tumeurs; Institut Gustave Roussy, Villejuif, France
| | - Klaus Beiske
- Department of Pathology, Oslo University Hospital, and Medical Faculty, University of Oslo, Oslo, Norway
| | - Marie Bernkopf
- St Anna Children's Cancer Research Institute, Vienna, Austria
| | - David R Betts
- Department of Clinical Genetics, Children's Health Ireland at Crumlin, Dublin, Ireland
| | - Jaydutt Bhalshankar
- Equipe SiRIC RTOP Recherche Translationelle en Oncologie Pédiatrique, Institut Curie, Paris, France.,INSERM U830, Laboratoire de Génétique et Biologie des Cancers, Institut Curie, Paris, France.,SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Nick Bown
- Northern Genetics Service, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | | | - Nathalie Clément
- Equipe SiRIC RTOP Recherche Translationelle en Oncologie Pédiatrique, Institut Curie, Paris, France.,INSERM U830, Laboratoire de Génétique et Biologie des Cancers, Institut Curie, Paris, France.,SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Valérie Combaret
- Translational Research Laboratory, Centre Léon Bérard, Lyon, France
| | | | - Sally L George
- Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
| | - Irene Jiménez
- Equipe SiRIC RTOP Recherche Translationelle en Oncologie Pédiatrique, Institut Curie, Paris, France.,INSERM U830, Laboratoire de Génétique et Biologie des Cancers, Institut Curie, Paris, France.,SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Marta Jeison
- Schneider Children's Medical Center of Israel, Tel Aviv University, Tel Aviv, Israel
| | - Barbara Marques
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal
| | | | - Katia Mazzocco
- Department of Pathology, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Martina Morini
- Laboratory of Molecular Biology, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Annick Mühlethaler-Mottet
- Pediatric Hematology-Oncology Research Laboratory, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Rosa Noguera
- Department of Pathology, Medical School, University of Valencia-Incliva Health Research Institute/CIBERONC, Madrid, Spain
| | - Gaelle Pierron
- Unité de Génétique Somatique, Service de Génétique, Hospital Group, Institut Curie, Paris, France
| | - Maria Rossing
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | | | | | - Ales Vicha
- Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Louis Chesler
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, Sutton, United Kingdom
| | - Walentyna Balwierz
- Department of Pediatric Oncology and Hematology, Institute of Pediatrics, Jagiellonian University Medical College, Krakow, Poland
| | - Victoria Castel
- Clinical and Translational Oncology Research Group, Health Research Institute La Fe, Valencia, Spain
| | - Martin Elliott
- Leeds Children's Hospital, Leeds General Infirmary, Leeds, United Kingdom
| | - Per Kogner
- Karolinska University Hospital, Stockholm, Sweden
| | - Geneviève Laureys
- Department of Paediatric Haematology and Oncology, Princess Elisabeth Children's Hospital, Ghent University Hospital, Ghent, Belgium
| | - Roberto Luksch
- Paediatric Oncology, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milan, Italy
| | - Josef Malis
- Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Maja Popovic-Beck
- Pediatric Hematology-Oncology Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Shifra Ash
- Ruth Rappaport Children's Hospital, Rambam Health Care Campus, Haifa, Israel
| | - Olivier Delattre
- INSERM U830, Laboratoire de Génétique et Biologie des Cancers, Institut Curie, Paris, France.,SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France.,Institut Curie Genomics of Excellence (ICGex) Platform, Research Center, Institut Curie, Paris, France
| | | | - Deborah A Tweddle
- Wolfson Childhood Cancer Research Centre, Newcastle Centre for Cancer, Translational & Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Ruth Ladenstein
- Department for Studies and Statistics and Integrated Research, St Anna Children's Hospital, St Anna Children's Cancer Research Institute, Vienna, Austria.,Department of Paediatrics, Medical University of Vienna, Vienna, Austria
| | - Gudrun Schleiermacher
- Equipe SiRIC RTOP Recherche Translationelle en Oncologie Pédiatrique, Institut Curie, Paris, France.,INSERM U830, Laboratoire de Génétique et Biologie des Cancers, Institut Curie, Paris, France.,SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| |
Collapse
|
10
|
Schwann cell plasticity regulates neuroblastic tumor cell differentiation via epidermal growth factor-like protein 8. Nat Commun 2021; 12:1624. [PMID: 33712610 PMCID: PMC7954855 DOI: 10.1038/s41467-021-21859-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 02/17/2021] [Indexed: 01/31/2023] Open
Abstract
Adult Schwann cells (SCs) possess an inherent plastic potential. This plasticity allows SCs to acquire repair-specific functions essential for peripheral nerve regeneration. Here, we investigate whether stromal SCs in benign-behaving peripheral neuroblastic tumors adopt a similar cellular state. We profile ganglioneuromas and neuroblastomas, rich and poor in SC stroma, respectively, and peripheral nerves after injury, rich in repair SCs. Indeed, stromal SCs in ganglioneuromas and repair SCs share the expression of nerve repair-associated genes. Neuroblastoma cells, derived from aggressive tumors, respond to primary repair-related SCs and their secretome with increased neuronal differentiation and reduced proliferation. Within the pool of secreted stromal and repair SC factors, we identify EGFL8, a matricellular protein with so far undescribed function, to act as neuritogen and to rewire cellular signaling by activating kinases involved in neurogenesis. In summary, we report that human SCs undergo a similar adaptive response in two patho-physiologically distinct situations, peripheral nerve injury and tumor development.
Collapse
|
11
|
Long-Term Outcome and Role of Biology within Risk-Adapted Treatment Strategies: The Austrian Neuroblastoma Trial A-NB94. Cancers (Basel) 2021; 13:cancers13030572. [PMID: 33540616 PMCID: PMC7867286 DOI: 10.3390/cancers13030572] [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: 11/23/2020] [Revised: 01/08/2021] [Accepted: 01/28/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Neuroblastoma, the most common extracranial malignancy of childhood, shows a highly variable course of disease ranging from spontaneous regression or maturation into a benign tumor to an aggressive and intractable cancer in up to 60% of patients. To adapt treatment intensity, risk staging at diagnosis is of utmost importance. The A-NB94 trial was the first in Austria to stratify therapy intensity according to tumor staging, patient’s age, and MYCN amplification status, the latter being a biologic marker turning otherwise low-risk tumors into high-risk disease. Recent publications showed a prognostic impact of various genomic features including segmental chromosomal aberrations (SCAs). We retrospectively investigated the relevance of SCAs within this risk-adapted treatment strategy. The A-NB94 approach resulted in an excellent long-term survival for the majority of patients with acceptable long-term morbidity. An age- and stage-dependent frequency of SCAs was confirmed and SCAs should always be considered in future treatment decision making processes. Abstract We evaluated long-term outcome and genomic profiles in the Austrian Neuroblastoma Trial A-NB94 which applied a risk-adapted strategy of treatment (RAST) using stage, age and MYCN amplification (MNA) status for stratification. RAST ranged from surgery only to intensity-adjusted chemotherapy, single or multiple courses of high-dose chemotherapy (HDT) followed by autologous stem cell rescue depending on response to induction chemotherapy, and irradiation to the primary tumor site. Segmental chromosomal alterations (SCAs) were investigated retrospectively using multi- and pan-genomic techniques. The A-NB94 trial enrolled 163 patients. Patients with localized disease had an excellent ten-year (10y) event free survival (EFS) and overall survival (OS) of 99 ± 1% and 93 ± 2% whilst it was 80 ± 13% and 90 ± 9% for infants with stage 4S and for infants with stage 4 non-MNA disease both 83 ± 15%. Stage 4 patients either >12 months or ≤12 months but with MNA had a 10y-EFS and OS of 45 ± 8% and 47 ± 8%, respectively. SCAs were present in increasing frequencies according to stage and age: in 29% of localized tumors but in 92% of stage 4 tumors (p < 0.001), and in 39% of patients ≤ 12 months but in 63% of patients > 12 months (p < 0.001). RAST successfully reduced chemotherapy exposure in low- and intermediate-risk patients with excellent long-term results while the outcome of high-risk disease met contemporary trials.
Collapse
|
12
|
Szewczyk K. Typical numerical alterations in genome identified by array CGH analysis in neuroblastoma tumors. AIMS MOLECULAR SCIENCE 2021. [DOI: 10.3934/molsci.2021019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
<abstract><sec>
<title>Introduction</title>
<p>The clinical variability in the course of neuroblastoma (NB) is closely linked to diverse genetic changes acquired by tumor cells. Rapid NB progression is associated with oncogene MYCN amplification (MNA) and segmental chromosomal aberrations (SCA). Alternatively, numerical chromosomal alterations (NCA) have positive impact on treatment. So far, no studies have been undertaken to identify NCA that may group NB patients. Therefore, the aim of the study was to identify NCA typical for NB.</p>
</sec><sec>
<title>Materials and methods</title>
<p>Copy number alterations in NB tumor genome (fresh samples N = 94; formalin-fixed paraffin-embedded specimens N = 66) were analyzed with a pangenomic array CGH technique.</p>
</sec><sec>
<title>Results</title>
<p>The profile with NCA was observed in 72 (45%) cases, NCA+SCA in 37 (23%), normal in 35 (22%) and MNA in 16 (10%). Samples with NCA were characterized by whole chromosome gains: 17, 7, 6 (78%, 65%, 51%, respectively) and copy loss of chromosome 14 (57%). Similarly to NCA, patients with a combined NCA and SCA profile were also characterized by gain of whole chromosome 17 and 7 (35% both) and loss of chromosome 14 (38%), but with lower frequency. In the combined NCA and SCA profiles, typical NB changes such as deletion 1p36 (27%) and gain 17q (41%) were observed, as well as deletion 11q (24%). The same alterations were detected in MNA samples (44%, 44%, 19%, respectively). A difference was found in spanning 11q deletion between MNA and NCA+SCA subgroup, which may suggest new prognostic markers in NB. In MNA subgroup specific NCA was not indicated.</p>
</sec><sec>
<title>Conclusions</title>
<p>The hypothesis that NCA in NB tumors are more frequent in younger children with good prognosis was confirmed. To gain new insights into the pathogenesis of NB and to establish molecular targets for diagnosis and therapy, candidate genes in the altered chromosomal regions must be investigated.</p>
</sec></abstract>
Collapse
|
13
|
López-Carrasco A, Martín-Vañó S, Burgos-Panadero R, Monferrer E, Berbegall AP, Fernández-Blanco B, Navarro S, Noguera R. Impact of extracellular matrix stiffness on genomic heterogeneity in MYCN-amplified neuroblastoma cell line. J Exp Clin Cancer Res 2020; 39:226. [PMID: 33109237 PMCID: PMC7592549 DOI: 10.1186/s13046-020-01729-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 10/07/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Increased tissue stiffness is a common feature of malignant solid tumors, often associated with metastasis and poor patient outcomes. Vitronectin, as an extracellular matrix anchorage glycoprotein related to a stiff matrix, is present in a particularly increased quantity and specific distribution in high-risk neuroblastoma. Furthermore, as cells can sense and transform the proprieties of the extracellular matrix into chemical signals through mechanotransduction, genotypic changes related to stiffness are possible. METHODS We applied high density SNPa and NGS techniques to in vivo and in vitro models (orthotropic xenograft vitronectin knock-out mice and 3D bioprinted hydrogels with different stiffness) using two representative neuroblastoma cell lines (the MYCN-amplified SK-N-BE(2) and the ALK-mutated SH-SY5Y), to discern how tumor genomics patterns and clonal heterogeneity of the two cell lines are affected. RESULTS We describe a remarkable subclonal selection of genomic aberrations in SK-N-BE(2) cells grown in knock-out vitronectin xenograft mice that also emerged when cultured for long times in stiff hydrogels. In particular, we detected an enlarged subclonal cell population with chromosome 9 aberrations in both models. Similar abnormalities were found in human high-risk neuroblastoma with MYCN amplification. The genomics of the SH-SY5Y cell line remained stable when cultured in both models. CONCLUSIONS Focus on heterogeneous intratumor segmental chromosome aberrations and mutations, as a mirror image of tumor microenvironment, is a vital area of future research.
Collapse
Affiliation(s)
- Amparo López-Carrasco
- Department of Pathology, Medical School, University of Valencia/INCLIVA, Valencia, Spain
- CIBERONC, Madrid, Spain
| | - Susana Martín-Vañó
- Department of Pathology, Medical School, University of Valencia/INCLIVA, Valencia, Spain
- CIBERONC, Madrid, Spain
| | - Rebeca Burgos-Panadero
- Department of Pathology, Medical School, University of Valencia/INCLIVA, Valencia, Spain
- CIBERONC, Madrid, Spain
| | - Ezequiel Monferrer
- Department of Pathology, Medical School, University of Valencia/INCLIVA, Valencia, Spain
- CIBERONC, Madrid, Spain
| | - Ana P Berbegall
- Department of Pathology, Medical School, University of Valencia/INCLIVA, Valencia, Spain
- CIBERONC, Madrid, Spain
| | | | - Samuel Navarro
- Department of Pathology, Medical School, University of Valencia/INCLIVA, Valencia, Spain
- CIBERONC, Madrid, Spain
| | - Rosa Noguera
- Department of Pathology, Medical School, University of Valencia/INCLIVA, Valencia, Spain.
- CIBERONC, Madrid, Spain.
| |
Collapse
|
14
|
Juan Ribelles A, Gargallo P, Ferriol C, Segura V, Yáñez Y, Juan B, Cañada AJ, Font de Mora J, Cañete A, Castel V. Distribution of segmental chromosomal alterations in neuroblastoma. Clin Transl Oncol 2020; 23:1096-1104. [PMID: 32948984 DOI: 10.1007/s12094-020-02497-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 09/05/2020] [Indexed: 11/26/2022]
Abstract
BACKGROUND Neuroblastoma (NB) is a heterogeneous tumor with extremely diverse prognosis according to clinical and genetic factors such as specific combinations of chromosomal imbalances. METHODS Molecular karyotyping data from a national neuroblastic tumor database of 155 NB samples were analyzed and related to clinical data. RESULTS Segmental chromosomal alterations (SCA) were detected in 102 NB, whereas 45 only displayed numerical alterations. Incidence of SCA was higher in stage M (92%) and MYCN amplified (MNA) NB (96%). Presence of SCA was associated with older age, especially 1q gain and 3p deletion. 96% of the deaths were observed in the SCA group and 85% of the relapsed NB contained SCA. The alteration most commonly associated with a higher number of other segmental rearrangements was 11q deletion, followed by 4p deletion. Whole-chromosome 19 gain was associated with lower stages, absence of SCA and better outcome. CONCLUSIONS SCA are not randomly distributed and are concentrated on recurrent chromosomes. The most frequently affected chromosomes identify prognostic factors in specific risk groups. SCA are associated with older age and MNA. We have identified a small subset of patients with better outcome that share whole-chromosome 19 numeric gain, suggesting its use as a prognostic biomarker in NB.
Collapse
Affiliation(s)
- A Juan Ribelles
- Pediatric Oncology and Hematology Unit, Hospital U i P La Fe, Av. Fernando Abril Martorell, 106, Valencia, Spain.
| | - P Gargallo
- Clinical and Translational Oncology Research Group, Instituto de Investigación La Fe, Valencia, Spain
| | - C Ferriol
- Universitat de València, Valencia, Spain
| | - V Segura
- Clinical and Translational Oncology Research Group, Instituto de Investigación La Fe, Valencia, Spain
| | - Y Yáñez
- Clinical and Translational Oncology Research Group, Instituto de Investigación La Fe, Valencia, Spain
| | - B Juan
- Universitat de València, Valencia, Spain
| | - A J Cañada
- Biostatistics Department, Instituto de Investigación La Fe, Valencia, Spain
| | - J Font de Mora
- Clinical and Translational Oncology Research Group, Instituto de Investigación La Fe, Valencia, Spain
| | - A Cañete
- Pediatric Oncology and Hematology Unit, Hospital U i P La Fe, Av. Fernando Abril Martorell, 106, Valencia, Spain
| | - V Castel
- Clinical and Translational Oncology Research Group, Instituto de Investigación La Fe, Valencia, Spain
| |
Collapse
|
15
|
Abstract
Neuroblastoma is the most common extracranial solid tumor of childhood with a median age of presentation of 17 months. A common theme in high-risk neuroblastoma is maintenance of telomeres, one mechanism for which involves alternate lengthening of telomeres (ALT) associated with ATRX gene mutations. Mutations are believed to result in loss of ATRX protein, and therefore immunohistochemistry is used to detect mutations. We screened 133 cases of neuroblastoma by ATRX immunohistochemistry, and found 9 cases with partial to total absence of ATRX. Sequencing for ATRX mutations detected a mutation in 1 of 9 cases, suggesting immunostaining was not reliable for detecting mutations. To correlate immunostaining with ALT, fluorescence in situ hybridization (FISH) for ALT was performed in 6 of these cases and 5 (from 4 patients) showed ALT, implying impaired ATRX protein function, despite the failure to identify a mutation. Two other cases with large deletions in the ATRX gene showed diffusely positive staining for ATRX protein but showed ALT by FISH. Four of the 6 patients with ALT-positive tumors were over 5 years old. Therefore, 29 additional patients 5 years old and above with ATRX-positive tumors were screened for ALT by FISH and 6 additional cases with ALT were detected, bringing the total to 29% (10/34) of children 5 years old and above, 70% of which showed positive ATRX immunohistochemistry. Patients with ATRX mutations in neuroblastoma tend to have a more chronic and progressive course of disease. Screening neuroblastoma tumors at diagnosis for ATRX mutations may help identify patients who might benefit from personalized therapy directed against ALT. However, relaying on negative immunohistochemistry for ATRX protein to identify ALT in neuroblastoma may miss a significant proportion of patients. The addition of FISH for ALT as part of the diagnostic workup, especially for older children (5 y old and above), would help ensure that patients are correctly identified for anti-ALT therapy.
Collapse
|
16
|
Tsuyukubo T, Ishida K, Osakabe M, Shiomi E, Kato R, Takata R, Obara W, Sugai T. Comprehensive analysis of somatic copy number alterations in clear cell renal cell carcinoma. Mol Carcinog 2020; 59:412-424. [PMID: 32039517 PMCID: PMC7079091 DOI: 10.1002/mc.23164] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 01/07/2020] [Accepted: 01/27/2020] [Indexed: 12/14/2022]
Abstract
Somatic copy number alterations (SCNAs) are important biological characteristics that can identify genome-wide alterations in renal cell carcinoma (RCC). Recent studies have shown that SCNAs have potential value for determining the prognosis of RCC. We examined SCNAs using the Affymetrix platform to analyze samples from 59 patients with clear cell RCCs (ccRCCs) including first cohort (30 cases) and second cohort (validation cohort, 29 cases). We stratified SCNAs in the ccRCCs using a hierarchical cluster analysis based on SCNA types, including gain, loss of heterozygosity (LOH), copy neutral LOH, mosaic, and mixed types. In this way, the examined two cohorts were categorized into two subgroups (1 and 2). Although the frequency of mixed type was higher in subgroup 1 than in subgroup 2 in the two cohorts, the association did not reach statistical significance. There was a significant difference in the frequency of metachronous metastasis between subgroups 1 and 2 (subgroup 2 > 1). In addition, subgroup 2 was retained in multivariate analysis of both cohorts. We examined whether there were specific alleles differing between subgroups 1 and 2 in both cohorts. We found that there was indeed a statistically significant difference in the 3p mixed types. Among the 3p mixed type, we found that 3p24.3 mixed type was inversely correlated with the presence of metachronous metastasis in ccRCC. The association was also retained in multivariate analysis in second cohort. We suggest that the 3p24.3 mixed type may be a novel marker to predict a favorable prognosis in ccRCC.
Collapse
Affiliation(s)
- Takashi Tsuyukubo
- Department of Molecular Diagnostic Pathology, School of Medicine, Iwate Medical University, Morioka, Japan.,Department of Urology, School of Medicine, Iwate Medical University, Morioka, Japan
| | - Kazuyuki Ishida
- Department of Molecular Diagnostic Pathology, School of Medicine, Iwate Medical University, Morioka, Japan
| | - Mitsumasa Osakabe
- Department of Molecular Diagnostic Pathology, School of Medicine, Iwate Medical University, Morioka, Japan
| | - Ei Shiomi
- Department of Molecular Diagnostic Pathology, School of Medicine, Iwate Medical University, Morioka, Japan.,Department of Urology, School of Medicine, Iwate Medical University, Morioka, Japan
| | - Renpei Kato
- Department of Urology, School of Medicine, Iwate Medical University, Morioka, Japan
| | - Ryo Takata
- Department of Urology, School of Medicine, Iwate Medical University, Morioka, Japan
| | - Wataru Obara
- Department of Urology, School of Medicine, Iwate Medical University, Morioka, Japan
| | - Tamotsu Sugai
- Department of Molecular Diagnostic Pathology, School of Medicine, Iwate Medical University, Morioka, Japan
| |
Collapse
|
17
|
Vicente‐Munuera P, Burgos‐Panadero R, Noguera I, Navarro S, Noguera R, Escudero LM. The topology of vitronectin: A complementary feature for neuroblastoma risk classification based on computer-aided detection. Int J Cancer 2020; 146:553-565. [PMID: 31173338 PMCID: PMC6899647 DOI: 10.1002/ijc.32495] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 04/30/2019] [Accepted: 05/27/2019] [Indexed: 12/13/2022]
Abstract
Tumors are complex networks of constantly interacting elements: tumor cells, stromal cells, immune and stem cells, blood/lympathic vessels, nerve fibers and extracellular matrix components. These elements can influence their microenvironment through mechanical and physical signals to promote tumor cell growth. To get a better understanding of tumor biology, cooperation between multidisciplinary fields is needed. Diverse mathematic computations and algorithms have been designed to find prognostic targets and enhance diagnostic assessment. In this work, we use computational digital tools to study the topology of vitronectin, a glycoprotein of the extracellular matrix. Vitronectin is linked to angiogenesis and migration, two processes closely related to tumor cell spread. Here, we investigate whether the distribution of this molecule in the tumor stroma may confer mechanical properties affecting neuroblastoma aggressiveness. Combining image analysis and graph theory, we analyze different topological features that capture the organizational cues of vitronectin in histopathological images taken from human samples. We find that the Euler number and the branching of territorial vitronectin, two topological features, could allow for a more precise pretreatment risk stratification to guide treatment strategies in neuroblastoma patients. A large amount of recently synthesized VN would create migration tracks, pinpointed by both topological features, for malignant neuroblasts, so that dramatic change in the extracellular matrix would increase tumor aggressiveness and worsen patient outcomes.
Collapse
Affiliation(s)
- Pablo Vicente‐Munuera
- Departamento de Biología CelularInstituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Roció/CSIC/Universidad de SevillaSevilleSpain
- Biomedical Network Research Centre on Neurodegenerative Diseases (CIBERNED)MadridSpain
| | - Rebeca Burgos‐Panadero
- Department of Pathology, Medical SchoolUniversity of Valencia/INCLIVAValenciaSpain
- Biomedical Network Research Centre on Oncology (CIBERONC)MadridSpain
| | - Inmaculada Noguera
- Central Support Service for Experimental Research (SCSIE), University of ValenciaValenciaSpain
| | - Samuel Navarro
- Department of Pathology, Medical SchoolUniversity of Valencia/INCLIVAValenciaSpain
- Biomedical Network Research Centre on Oncology (CIBERONC)MadridSpain
| | - Rosa Noguera
- Department of Pathology, Medical SchoolUniversity of Valencia/INCLIVAValenciaSpain
- Biomedical Network Research Centre on Oncology (CIBERONC)MadridSpain
| | - Luis M. Escudero
- Departamento de Biología CelularInstituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Roció/CSIC/Universidad de SevillaSevilleSpain
- Biomedical Network Research Centre on Neurodegenerative Diseases (CIBERNED)MadridSpain
| |
Collapse
|
18
|
Merugu S, Chen L, Gavens E, Gabra H, Brougham M, Makin G, Ng A, Murphy D, Gabriel AS, Robinson ML, Wright JH, Burchill SA, Humphreys A, Bown N, Jamieson D, Tweddle DA. Detection of Circulating and Disseminated Neuroblastoma Cells Using the ImageStream Flow Cytometer for Use as Predictive and Pharmacodynamic Biomarkers. Clin Cancer Res 2019; 26:122-134. [DOI: 10.1158/1078-0432.ccr-19-0656] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 08/13/2019] [Accepted: 10/18/2019] [Indexed: 11/16/2022]
|
19
|
Clinical Features of Neuroblastoma With 11q Deletion: An Increase in Relapse Probabilities In Localized And 4S Stages. Sci Rep 2019; 9:13806. [PMID: 31551474 PMCID: PMC6760233 DOI: 10.1038/s41598-019-50327-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 08/27/2019] [Indexed: 01/15/2023] Open
Abstract
Neuroblastoma (NB) is a heterogeneous tumor with an extremely diverse prognosis according to clinical and genetic factors, such as the presence of an 11q deletion (11q-del). A multicentric study using data from a national neuroblastic tumor database was conducted. This study compared the most important features of NB patients: presence of 11q-del, presence of MYCN amplification (MNA) and remaining cases. A total of 357 patients were followed throughout an 8-year period. 11q-del was found in sixty cases (17%). 11q-del tumors were diagnosed at an older age (median 3.29 years). Overall survival (OS) was lower in 11q-del patients (60% at 5 years), compared to all other cases (76% at 5 years) p = 0.014. Event free survival (EFS) was 35% after 5 years, which is a low number when compared with the remaining cases: 75% after 5 years (p < 0.001). Localized tumors with 11q-del have a higher risk of relapse (HR = 3.312) such as 4 s 11q-del patients (HR 7.581). 11q-del in NB is a dismal prognostic factor. Its presence predicts a bad outcome and increases relapse probability, specially in localized stages and 4 s stages. The presence of 11q aberration should be taken into consideration when stratifying neuroblastoma risk groups.
Collapse
|
20
|
Burgos-Panadero R, Noguera I, Cañete A, Navarro S, Noguera R. Vitronectin as a molecular player of the tumor microenvironment in neuroblastoma. BMC Cancer 2019; 19:479. [PMID: 31117974 PMCID: PMC6532218 DOI: 10.1186/s12885-019-5693-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 05/08/2019] [Indexed: 11/14/2022] Open
Abstract
Background Vitronectin is a multifunctional glycoprotein known in several human tumors for its adhesive role in processes such as cell growth, angiogenesis and metastasis. In this study, we examined vitronectin expression in neuroblastoma to investigate whether this molecule takes part in cell-cell or cell-extracellular matrix interactions that may confer mechanical properties to promote tumor aggressiveness. Methods We used immunohistochemistry and image analysis tools to characterize vitronectin expression and to test its prognostic value in 91 neuroblastoma patients. To better understand the effect of vitronectin, we studied its in vitro expression using commercial neuroblastoma cell lines and in vivo using intra-adrenal gland xenograft models by immunohistochemistry. Results Digital image analysis allowed us to associate vitronectin staining intensity and location discriminating between territorial vitronectin and interterritorial vitronectin expression patterns. High territorial vitronectin expression (strong staining associated with pericellular and intracellular location) was present in tumors from patients with metastatic undifferentiating neuroblastoma, that were MYCN amplified, 11q deleted or with segmental chromosomal profiles, in the high-risk stratification group and with high genetic instability. In vitro studies confirmed that vitronectin is expressed in tumor cells as small cytoplasmic dot drops. In vivo experiments revealed tumor cells with high and dense cytoplasmic vitronectin expression. Conclusions These findings highlight the relevance of vitronectin in neuroblastoma tumor biology and suggest its potential as a future therapeutic target in neuroblastoma. Electronic supplementary material The online version of this article (10.1186/s12885-019-5693-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Rebeca Burgos-Panadero
- Pathology Department, Medical School, University of Valencia-INCLIVA, Valencia, Spain.,CIBERONC, Madrid, Spain
| | - Inmaculada Noguera
- Central Support Service for Experimental Research (SCSIE), University of Valencia, Valencia, Spain
| | - Adela Cañete
- Pediatric Oncology Unit, University and Polytechnic Hospital La Fe, Valencia, Spain
| | - Samuel Navarro
- Pathology Department, Medical School, University of Valencia-INCLIVA, Valencia, Spain.,CIBERONC, Madrid, Spain
| | - Rosa Noguera
- Pathology Department, Medical School, University of Valencia-INCLIVA, Valencia, Spain. .,CIBERONC, Madrid, Spain.
| |
Collapse
|
21
|
Luijten MNH, Lee JXT, Crasta KC. Mutational game changer: Chromothripsis and its emerging relevance to cancer. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2018; 777:29-51. [PMID: 30115429 DOI: 10.1016/j.mrrev.2018.06.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 06/22/2018] [Accepted: 06/28/2018] [Indexed: 12/14/2022]
Abstract
In recent years, the paradigm that genomic abnormalities in cancer cells arise through progressive accumulation of mutational events has been challenged by the discovery of single catastrophic events. One such phenomenon termed chromothripsis, involving massive chromosomal rearrangements arising all at once, has emerged as a major mutational game changer. The strong interest in this process stems from its widespread association with a range of cancer types and its potential as a mutational driver. In this review, we first describe chromothripsis detection and incidence in cancers. We then explore recently proposed underlying mechanistic origins, which explain the curious observations of the highly localised nature of the rearrangements on chromothriptic chromosomes. Detection of chromothriptic patterns following incorporation of single chromosomes into micronuclei or following telomere attrition have greatly contributed to our understanding of the reasons behind this chromosomal restriction. These underlying cellular events have been found to be participants in the tumourigenic process, strongly suggesting a potential role for chromothripsis in cancer development. Thus, we discuss potential implications of chromothripsis for cancer progression and therapy.
Collapse
Affiliation(s)
| | - Jeannie Xue Ting Lee
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, 636921, Singapore.
| | - Karen Carmelina Crasta
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, 636921, Singapore; School of Biological Sciences, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore; Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research, 61 Biopolis Drive, 138673, Singapore; Department of Medicine, Imperial College London, South Kensington Campus, London SW7 2AZ, UK.
| |
Collapse
|
22
|
Berbegall AP, Bogen D, Pötschger U, Beiske K, Bown N, Combaret V, Defferrari R, Jeison M, Mazzocco K, Varesio L, Vicha A, Ash S, Castel V, Coze C, Ladenstein R, Owens C, Papadakis V, Ruud E, Amann G, Sementa AR, Navarro S, Ambros PF, Noguera R, Ambros IM. Heterogeneous MYCN amplification in neuroblastoma: a SIOP Europe Neuroblastoma Study. Br J Cancer 2018; 118:1502-1512. [PMID: 29755120 PMCID: PMC5988829 DOI: 10.1038/s41416-018-0098-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 03/01/2018] [Accepted: 04/06/2018] [Indexed: 12/21/2022] Open
Abstract
Background In neuroblastoma (NB), the most powerful prognostic marker, the MYCN amplification (MNA), occasionally shows intratumoural heterogeneity (ITH), i.e. coexistence of MYCN-amplified and non-MYCN-amplified tumour cell clones, called heterogeneous MNA (hetMNA). Prognostication and therapy allocation are still unsolved issues. Methods The SIOPEN Biology group analysed 99 hetMNA NBs focussing on the prognostic significance of MYCN ITH. Results Patients <18 months (18 m) showed a better outcome in all stages as compared to older patients (5-year OS in localised stages: <18 m: 0.95 ± 0.04, >18 m: 0.67 ± 0.14, p = 0.011; metastatic: <18 m: 0.76 ± 0.15, >18 m: 0.28 ± 0.09, p = 0.084). The genomic 'background’, but not MNA clone sizes, correlated significantly with relapse frequency and OS. No relapses occurred in cases of only numerical chromosomal aberrations. Infiltrated bone marrows and relapse tumour cells mostly displayed no MNA. However, one stage 4s tumour with segmental chromosomal aberrations showed a homogeneous MNA in the relapse. Conclusions This study provides a rationale for the necessary distinction between heterogeneous and homogeneous MNA. HetMNA tumours have to be evaluated individually, taking age, stage and, most importantly, genomic background into account to avoid unnecessary upgrading of risk/overtreatment, especially in infants, as well as in order to identify tumours prone to developing homogeneous MNA.
Collapse
Affiliation(s)
- Ana P Berbegall
- Department of Pathology, Medical School, University of Valencia/INCLIVA Biomedical Research Institute, 46010, Valencia, Spain.,Ciberonc, Madrid, Spain
| | - Dominik Bogen
- Department of Tumour Biology CCRI, Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, 1090, Vienna, Austria
| | - Ulrike Pötschger
- S2IRP: Studies and Statistics for Integrated Research and Projects CCRI, Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, 1090, Vienna, Austria
| | - Klaus Beiske
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo and Department of Pathology, Norwegian Radium Hospital, Oslo University Hospital, 0372, Oslo, Norway
| | - Nick Bown
- Northern Genetics Service, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Institute of Genetic Medicine, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK
| | - Valérie Combaret
- Centre Léon Bérard, Laboratoire de Recherche Translationnelle, 28 rue Laennec, Lyon, 69008, France
| | - Raffaella Defferrari
- Department of Pathology, Gaslini Institute, Largo G. Gaslini 5, 16147, Genoa, Italy
| | - Marta Jeison
- Cancer Cytogenetic and Molecular Cytogenetic Laboratory, Schneider Children's Medical Center of Israel, 49202, Petach Tikva, Israel
| | - Katia Mazzocco
- Department of Pathology, Gaslini Institute, Largo G. Gaslini 5, 16147, Genoa, Italy
| | - Luigi Varesio
- Laboratory of Molecular Biology, Gaslini Institute, Largo G. Gaslini 5, 16147, Genoa, Italy
| | - Ales Vicha
- Department of Pediatric Hematology and Oncology, Charles University in Prague, Second Faculty of Medicine and University Hospital Motol, 15006, Prague, Czech Republic
| | - Shifra Ash
- Department of Paediatric Haematology-Oncology, Schneider Children's Medical Center of Israel, 49202, Petach Tikva, Israel
| | - Victoria Castel
- Pediatric Oncology Unit, Hospital Universitari i Politècnic La Fe, 46026, Valencia, Spain
| | - Carole Coze
- Department of Paediatric Haematology-Oncology, Aix-Marseille University and APHM, Hôpital d' Enfants de La Timone, 13385, Marseille, France
| | - Ruth Ladenstein
- S2IRP: Studies and Statistics for Integrated Research and Projects CCRI, Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, 1090, Vienna, Austria.,St Anna Children's Hospital and Department of Paediatrics of the Medical University, 1090, Vienna, Austria
| | - Cormac Owens
- Our Lady's Children's Hospital, Crumlin, Dublin, D12 N512, Ireland
| | - Vassilios Papadakis
- Department of Paediatric Haematology-Oncology, Agia Sofia Children's Hospital Athens, 11528, Athens, Greece
| | - Ellen Ruud
- Department of Paediatric Medicine, Rikshospitalet, Oslo University Hospital, 0372, Oslo, Norway
| | - Gabriele Amann
- Institute of Clinical Pathology, Medical University Vienna, Vienna, Austria
| | - Angela R Sementa
- Department of Pathology, Gaslini Institute, Largo G. Gaslini 5, 16147, Genoa, Italy
| | - Samuel Navarro
- Department of Pathology, Medical School, University of Valencia/INCLIVA Biomedical Research Institute, 46010, Valencia, Spain.,Ciberonc, Madrid, Spain
| | - Peter F Ambros
- Department of Tumour Biology CCRI, Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, 1090, Vienna, Austria.,Department of Paediatrics, Medical University Vienna, Vienna, Austria
| | - Rosa Noguera
- Department of Pathology, Medical School, University of Valencia/INCLIVA Biomedical Research Institute, 46010, Valencia, Spain. .,Ciberonc, Madrid, Spain.
| | - Inge M Ambros
- Department of Tumour Biology CCRI, Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, 1090, Vienna, Austria.
| |
Collapse
|
23
|
MYCN and HDAC5 transcriptionally repress CD9 to trigger invasion and metastasis in neuroblastoma. Oncotarget 2018; 7:66344-66359. [PMID: 27572323 PMCID: PMC5341807 DOI: 10.18632/oncotarget.11662] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 08/24/2016] [Indexed: 02/07/2023] Open
Abstract
The systemic and resistant nature of metastatic neuroblastoma renders it largely incurable with current multimodal treatment. Clinical progression stems mainly from the increasing burden of metastatic colonization. Therapeutically inhibiting the migration-invasion-metastasis cascade would be of great benefit, but the mechanisms driving this cycle are as yet poorly understood. In-depth transcriptome analyses and ChIP-qPCR identified the cell surface glycoprotein, CD9, as a major downstream player and direct target of the recently described GRHL1 tumor suppressor. CD9 is known to block or facilitate cancer cell motility and metastasis dependent upon entity. High-level CD9 expression in primary neuroblastomas correlated with patient survival and established markers for favorable disease. Low-level CD9 expression was an independent risk factor for adverse outcome. MYCN and HDAC5 colocalized to the CD9 promoter and repressed transcription. CD9 expression diminished with progressive tumor development in the TH-MYCN transgenic mouse model for neuroblastoma, and CD9 expression in neuroblastic tumors was far below that in ganglia from wildtype mice. Primary neuroblastomas lacking MYCN amplifications displayed differential CD9 promoter methylation in methyl-CpG-binding domain sequencing analyses, and high-level methylation was associated with advanced stage disease, supporting epigenetic regulation. Inducing CD9 expression in a SH-EP cell model inhibited migration and invasion in Boyden chamber assays. Enforced CD9 expression in neuroblastoma cells transplanted onto chicken chorioallantoic membranes strongly reduced metastasis to embryonic bone marrow. Combined treatment of neuroblastoma cells with HDAC/DNA methyltransferase inhibitors synergistically induced CD9 expression despite hypoxic, metabolic or cytotoxic stress. Our results show CD9 is a critical and indirectly druggable suppressor of the invasion-metastasis cycle in neuroblastoma.
Collapse
|
24
|
Abstract
Neuroblastomas (NB) are one of the most common extracranial solid tumors in children, and they frequently display high heterogeneity in the disease course. With ongoing research, more information regarding the genetic etiology and molecular mechanisms underlying these contrasting phenotypes is being uncovered. The proto-oncogene MYCN is amplified in approximately 20% of NB cases and is considered a indicator of poor prognosis and an indicator of high-risk NB. The poor prognosis of high risk NB is incompletely explained by MYCN amplification. Recently, massive parallel sequencing studies reported several relatively common gene alterations, such as ATRX mutation and TERT rearrangement that are involved in telomere maintenance through telomerase activity and alternative lengthening of telomeres. Thus, these are important for understanding the etiology and molecular pathogenesis of NB, and hence, for identifying diagnostic and treatment markers. Development of telomerase inhibitors and identification of alternative lengthening of telomeres related targets will contribute to the individualized treatment for high-risk NB. In this mini-review, we will discuss the research progress of TERT-mediated and ATRX-mediated telomere maintenance and NB, especially high-risk tumors.
Collapse
|
25
|
Morscher RJ, Aminzadeh-Gohari S, Hauser-Kronberger C, Feichtinger RG, Sperl W, Kofler B. Combination of metronomic cyclophosphamide and dietary intervention inhibits neuroblastoma growth in a CD1-nu mouse model. Oncotarget 2017; 7:17060-73. [PMID: 26959744 PMCID: PMC4941371 DOI: 10.18632/oncotarget.7929] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 02/05/2016] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND MYCN-amplification in high-grade Neuroblastoma (NB) tumors correlates with increased vascularization and therapy resistance. This study combines an anti-angiogenic approach with targeting NB metabolism for treatment. METHODS AND RESULTS Metronomic cyclophosphamide (MCP) monotherapy significantly inhibited NB growth and prolonged host survival. Growth inhibition was more pronounced in MYCN-amplified xenografts. Immunohistochemical evaluation of this subtype showed significant decrease in blood vessel density and intratumoral hemorrhage accompanied by blood vessel maturation and perivascular fibrosis. Up-regulation of VEGFA was not sufficient to compensate for the effects of the MCP regimen. Reduced Bcl-2 expression and increased caspase-3 cleavage were evident. In contrast non MYCN-amplified tumors developed resistance, which was accompanied by Bcl-2-up-regulation. Combining MCP with a ketogenic diet and/or calorie-restriction significantly enhanced the anti-tumor effect. Calorie-restricted ketogenic diet in combination with MCP resulted in tumor regression in all cases. CONCLUSIONS Our data show efficacy of combining an anti-angiogenic cyclophosphamide dosing regimen with dietary intervention in a preclinical NB model. These findings might open a new front in NB treatment.
Collapse
Affiliation(s)
- Raphael Johannes Morscher
- Laura Bassi Centre of Expertise-THERAPEP, Department of Pediatrics, Paracelsus Medical University, 5020 Salzburg, Austria.,Division of Medical Genetics, Medical University Innsbruck, 6020 Innsbruck, Austria
| | - Sepideh Aminzadeh-Gohari
- Laura Bassi Centre of Expertise-THERAPEP, Department of Pediatrics, Paracelsus Medical University, 5020 Salzburg, Austria
| | | | - René Günther Feichtinger
- Laura Bassi Centre of Expertise-THERAPEP, Department of Pediatrics, Paracelsus Medical University, 5020 Salzburg, Austria
| | - Wolfgang Sperl
- Department of Pediatrics, Paracelsus Medical University, 5020 Salzburg, Austria
| | - Barbara Kofler
- Laura Bassi Centre of Expertise-THERAPEP, Department of Pediatrics, Paracelsus Medical University, 5020 Salzburg, Austria
| |
Collapse
|
26
|
Sanmartín E, Muñoz L, Piqueras M, Sirerol JA, Berlanga P, Cañete A, Castel V, Font de Mora J. Deletion of 11q in Neuroblastomas Drives Sensitivity to PARP Inhibition. Clin Cancer Res 2017; 23:6875-6887. [PMID: 28830922 DOI: 10.1158/1078-0432.ccr-17-0593] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 06/23/2017] [Accepted: 08/16/2017] [Indexed: 11/16/2022]
Abstract
Purpose: Despite advances in multimodal therapy, neuroblastomas with hemizygous deletion in chromosome 11q (20%-30%) undergo consecutive recurrences with poor outcome. We hypothesized that patients with 11q-loss may share a druggable molecular target(s) that can be exploited for a precision medicine strategy to improve treatment outcome.Experimental Design: SNP arrays were combined with next-generation sequencing (NGS) to precisely define the deleted region in 17 primary 11q-loss neuroblastomas and identify allelic variants in genes relevant for neuroblastoma etiology. We assessed PARP inhibitor olaparib in combination with other chemotherapy medications using both in vitro and in vivo models.Results: We detected that ATM haploinsufficiency and ATM allelic variants are common genetic hallmarks of 11q-loss neuroblastomas. On the basis of the distinct DNA repair pathways triggered by ATM and PARP, we postulated that 11q-loss may define a subgroup of neuroblastomas with higher sensitivity to PARP inhibitors. Noteworthy, concomitant treatment with olaparib and DNA alkylating agent temozolomide potently inhibited growth of cell lines harboring 11q-loss. This drug synergism was less potent when temozolomide was exchanged for cisplatin or irinotecan. Intact 11q cells concomitantly treated with ATM inhibitor displayed growth arrest and enhanced apoptosis, revealing a role for ATM in the mechanism that mediates sensitivity to temozolomide-olaparib. Interestingly, functional TP53 is required for efficacy of this treatment. In an in vivo model, coadministration of temozolomide-olaparib resulted in sustained xenograft regression.Conclusions: Our findings reveal a potent synergism between temozolomide and olaparib in treatment of neuroblastomas with 11q-loss and provide a rationale for further clinical investigation. Clin Cancer Res; 23(22); 6875-87. ©2017 AACR.
Collapse
Affiliation(s)
- Elena Sanmartín
- Laboratory of Cellular and Molecular Biology, Instituto de Investigación Sanitaria La Fe, Valencia, Spain.,Clinical and Translational Research in Cancer, Instituto de Investigación Sanitaria La Fe, Valencia, Spain
| | - Lisandra Muñoz
- Laboratory of Cellular and Molecular Biology, Instituto de Investigación Sanitaria La Fe, Valencia, Spain.,Clinical and Translational Research in Cancer, Instituto de Investigación Sanitaria La Fe, Valencia, Spain
| | - Marta Piqueras
- Department of Physiology, School of Medicine, University of Valencia, Valencia, Spain
| | - J Antoni Sirerol
- Laboratory of Cellular and Molecular Biology, Instituto de Investigación Sanitaria La Fe, Valencia, Spain.,Clinical and Translational Research in Cancer, Instituto de Investigación Sanitaria La Fe, Valencia, Spain
| | - Pablo Berlanga
- Clinical and Translational Research in Cancer, Instituto de Investigación Sanitaria La Fe, Valencia, Spain.,Pediatric Oncology Unit, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Adela Cañete
- Clinical and Translational Research in Cancer, Instituto de Investigación Sanitaria La Fe, Valencia, Spain.,Pediatric Oncology Unit, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Victoria Castel
- Clinical and Translational Research in Cancer, Instituto de Investigación Sanitaria La Fe, Valencia, Spain.,Pediatric Oncology Unit, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Jaime Font de Mora
- Laboratory of Cellular and Molecular Biology, Instituto de Investigación Sanitaria La Fe, Valencia, Spain. .,Clinical and Translational Research in Cancer, Instituto de Investigación Sanitaria La Fe, Valencia, Spain
| |
Collapse
|
27
|
Abbasi MR, Rifatbegovic F, Brunner C, Mann G, Ziegler A, Pötschger U, Crazzolara R, Ussowicz M, Benesch M, Ebetsberger-Dachs G, Chan GCF, Jones N, Ladenstein R, Ambros IM, Ambros PF. Impact of Disseminated Neuroblastoma Cells on the Identification of the Relapse-Seeding Clone. Clin Cancer Res 2017; 23:4224-4232. [PMID: 28228384 DOI: 10.1158/1078-0432.ccr-16-2082] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 09/20/2016] [Accepted: 02/12/2017] [Indexed: 02/07/2023]
Abstract
Purpose: Tumor relapse is the most frequent cause of death in stage 4 neuroblastomas. Since genomic information on the relapse precursor cells could guide targeted therapy, our aim was to find the most appropriate tissue for identifying relapse-seeding clones.Experimental design: We analyzed 10 geographically and temporally separated samples of a single patient by SNP array and validated the data in 154 stage 4 patients.Results: In the case study, aberrations unique to certain tissues and time points were evident besides concordant aberrations shared by all samples. Diagnostic bone marrow-derived disseminated tumor cells (DTCs) as well as the metastatic tumor and DTCs at relapse displayed a 1q deletion, not detected in any of the seven primary tumor samples. In the validation cohort, the frequency of 1q deletion was 17.8%, 10%, and 27.5% in the diagnostic DTCs, diagnostic tumors, and DTCs at relapse, respectively. This aberration was significantly associated with 19q and ATRX deletions. We observed a significant increased likelihood of an adverse event in the presence of 19q deletion in the diagnostic DTCs.Conclusions: Different frequencies of 1q and 19q deletions in the primary tumors as compared with DTCs, their relatively high frequency at relapse, and their effect on event-free survival (19q deletion) indicate the relevance of analyzing diagnostic DTCs. Our data support the hypothesis of a branched clonal evolution and a parallel progression of primary and metastatic tumor cells. Therefore, searching for biomarkers to identify the relapse-seeding clone should involve diagnostic DTCs alongside the tumor tissue. Clin Cancer Res; 23(15); 4224-32. ©2017 AACR.
Collapse
Affiliation(s)
- M Reza Abbasi
- CCRI, Children's Cancer Research Institute, Vienna, Austria.
| | | | | | - Georg Mann
- St. Anna Children's Hospital, Vienna, Austria
| | - Andrea Ziegler
- CCRI, Children's Cancer Research Institute, Vienna, Austria
| | | | - Roman Crazzolara
- Department of Pediatrics, Medical University of Innsbruck, Innsbruck, Austria
| | - Marek Ussowicz
- Department of Pediatric Hematology and Oncology, Wroclaw Medical University, Wroclaw, Poland
| | - Martin Benesch
- Department of Pediatrics and Adolescent Medicine, Medical University of Graz, Graz, Austria
| | | | - Godfrey C F Chan
- Department of Pediatrics and Adolescent Medicine, University of Hong Kong, Hong Kong
| | - Neil Jones
- Department of Pediatrics and Adolescent Medicine, Paracelsus Medical University, Salzburg, Austria
| | - Ruth Ladenstein
- CCRI, Children's Cancer Research Institute, Vienna, Austria.,Department of Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Inge M Ambros
- CCRI, Children's Cancer Research Institute, Vienna, Austria
| | - Peter F Ambros
- CCRI, Children's Cancer Research Institute, Vienna, Austria. .,Department of Pediatrics, Medical University of Vienna, Vienna, Austria
| |
Collapse
|
28
|
Taschner-Mandl S, Schwarz M, Blaha J, Kauer M, Kromp F, Frank N, Rifatbegovic F, Weiss T, Ladenstein R, Hohenegger M, Ambros IM, Ambros PF. Metronomic topotecan impedes tumor growth of MYCN-amplified neuroblastoma cells in vitro and in vivo by therapy induced senescence. Oncotarget 2016; 7:3571-86. [PMID: 26657295 PMCID: PMC4823128 DOI: 10.18632/oncotarget.6527] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 11/17/2015] [Indexed: 12/13/2022] Open
Abstract
Poor prognosis and frequent relapses are major challenges for patients with high-risk neuroblastoma (NB), especially when tumors show MYCN amplification. High-dose chemotherapy triggers apoptosis, necrosis and senescence, a cellular stress response leading to permanent proliferative arrest and a typical senescence-associated secretome (SASP). SASP components reinforce growth-arrest and act immune-stimulatory, while others are tumor-promoting. We evaluated whether metronomic, i.e. long-term, repetitive low-dose, drug treatment induces senescence in vitro and in vivo. And importantly, by using the secretome as a discriminator for beneficial versus adverse effects of senescence, drugs with a tumor-inhibiting SASP were identified. We demonstrate that metronomic application of chemotherapeutic drugs induces therapy-induced senescence, characterized by cell cycle arrest, p21WAF/CIP1 up-regulation and DNA double-strand breaks selectively in MYCN-amplified NB. Low-dose topotecan (TPT) was identified as an inducer of a favorable SASP while lacking NFKB1/p50 activation. In contrast, Bromo-deoxy-uridine induced senescent NB-cells secret a tumor-promoting SASP in a NFKB1/p50-dependent manner. Importantly, TPT-treated senescent tumor cells act growth-inhibitory in a dose-dependent manner on non-senescent tumor cells and MYCN expression is significantly reduced in vitro and in vivo. Furthermore, in a mouse xenotransplant-model for MYCN-amplified NB metronomic TPT leads to senescence selectively in tumor cells, complete or partial remission, prolonged survival and a favorable SASP. This new mode-of-action of metronomic TPT treatment, i.e. promoting a tumor-inhibiting type of senescence in MYCN-amplified tumors, is clinically relevant as metronomic regimens are increasingly implemented in therapy protocols of various cancer entities and are considered as a feasible maintenance treatment option with moderate adverse event profiles.
Collapse
Affiliation(s)
| | | | - Johanna Blaha
- CCRI, Chlidren's Cancer Research Institute, Vienna, Austria
| | | | - Florian Kromp
- CCRI, Chlidren's Cancer Research Institute, Vienna, Austria
| | - Nelli Frank
- CCRI, Chlidren's Cancer Research Institute, Vienna, Austria
| | | | - Tamara Weiss
- CCRI, Chlidren's Cancer Research Institute, Vienna, Austria
| | - Ruth Ladenstein
- CCRI, Chlidren's Cancer Research Institute, Vienna, Austria.,Department of Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Martin Hohenegger
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Inge M Ambros
- CCRI, Chlidren's Cancer Research Institute, Vienna, Austria
| | - Peter F Ambros
- CCRI, Chlidren's Cancer Research Institute, Vienna, Austria.,Department of Pediatrics, Medical University of Vienna, Vienna, Austria
| |
Collapse
|
29
|
Abstract
Neuroblastoma is the most common extracranial solid tumour occurring in childhood and has a diverse clinical presentation and course depending on the tumour biology. Unique features of these neuroendocrine tumours are the early age of onset, the high frequency of metastatic disease at diagnosis and the tendency for spontaneous regression of tumours in infancy. The most malignant tumours have amplification of the MYCN oncogene (encoding a transcription factor), which is usually associated with poor survival, even in localized disease. Although transgenic mouse models have shown that MYCN overexpression can be a tumour-initiating factor, many other cooperating genes and tumour suppressor genes are still under investigation and might also have a role in tumour development. Segmental chromosome alterations are frequent in neuroblastoma and are associated with worse outcome. The rare familial neuroblastomas are usually associated with germline mutations in ALK, which is mutated in 10-15% of primary tumours, and provides a potential therapeutic target. Risk-stratified therapy has facilitated the reduction of therapy for children with low-risk and intermediate-risk disease. Advances in therapy for patients with high-risk disease include intensive induction chemotherapy and myeloablative chemotherapy, followed by the treatment of minimal residual disease using differentiation therapy and immunotherapy; these have improved 5-year overall survival to 50%. Currently, new approaches targeting the noradrenaline transporter, genetic pathways and the tumour microenvironment hold promise for further improvements in survival and long-term quality of life.
Collapse
|
30
|
Rawcopy: Improved copy number analysis with Affymetrix arrays. Sci Rep 2016; 6:36158. [PMID: 27796336 PMCID: PMC5086940 DOI: 10.1038/srep36158] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 10/10/2016] [Indexed: 11/08/2022] Open
Abstract
Microarray data is subject to noise and systematic variation that negatively affects the resolution of copy number analysis. We describe Rawcopy, an R package for processing of Affymetrix CytoScan HD, CytoScan 750k and SNP 6.0 microarray raw intensities (CEL files). Noise characteristics of a large number of reference samples are used to estimate log ratio and B-allele frequency for total and allele-specific copy number analysis. Rawcopy achieves better signal-to-noise ratio and higher proportion of validated alterations than commonly used free and proprietary alternatives. In addition, Rawcopy visualizes each microarray sample for assessment of technical quality, patient identity and genome-wide absolute copy number states. Software and instructions are available at http://rawcopy.org.
Collapse
|
31
|
Brunner C, Brunner-Herglotz B, Ziegler A, Frech C, Amann G, Ladenstein R, Ambros IM, Ambros PF. Tumor Touch Imprints as Source for Whole Genome Analysis of Neuroblastoma Tumors. PLoS One 2016; 11:e0161369. [PMID: 27560999 PMCID: PMC4999140 DOI: 10.1371/journal.pone.0161369] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 08/04/2016] [Indexed: 12/26/2022] Open
Abstract
INTRODUCTION Tumor touch imprints (TTIs) are routinely used for the molecular diagnosis of neuroblastomas by interphase fluorescence in-situ hybridization (I-FISH). However, in order to facilitate a comprehensive, up-to-date molecular diagnosis of neuroblastomas and to identify new markers to refine risk and therapy stratification methods, whole genome approaches are needed. We examined the applicability of an ultra-high density SNP array platform that identifies copy number changes of varying sizes down to a few exons for the detection of genomic changes in tumor DNA extracted from TTIs. MATERIAL AND METHODS DNAs were extracted from TTIs of 46 neuroblastoma and 4 other pediatric tumors. The DNAs were analyzed on the Cytoscan HD SNP array platform to evaluate numerical and structural genomic aberrations. The quality of the data obtained from TTIs was compared to that from randomly chosen fresh or fresh frozen solid tumors (n = 212) and I-FISH validation was performed. RESULTS SNP array profiles were obtained from 48 (out of 50) TTI DNAs of which 47 showed genomic aberrations. The high marker density allowed for single gene analysis, e.g. loss of nine exons in the ATRX gene and the visualization of chromothripsis. Data quality was comparable to fresh or fresh frozen tumor SNP profiles. SNP array results were confirmed by I-FISH. CONCLUSION TTIs are an excellent source for SNP array processing with the advantage of simple handling, distribution and storage of tumor tissue on glass slides. The minimal amount of tumor tissue needed to analyze whole genomes makes TTIs an economic surrogate source in the molecular diagnostic work up of tumor samples.
Collapse
Affiliation(s)
- Clemens Brunner
- Department of Tumor Biology, CCRI, Children’s Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Bettina Brunner-Herglotz
- Department of Tumor Biology, CCRI, Children’s Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Andrea Ziegler
- Department of Tumor Biology, CCRI, Children’s Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Christian Frech
- Department of Tumor Biology, CCRI, Children’s Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Gabriele Amann
- Institute of Clinical Pathology, Medical University Vienna, Vienna, Austria
| | - Ruth Ladenstein
- S2IRP, CCRI, Children’s Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
- Department of Pediatrics, Medical University Vienna, Vienna, Austria
| | - Inge M. Ambros
- Department of Tumor Biology, CCRI, Children’s Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Peter F. Ambros
- Department of Tumor Biology, CCRI, Children’s Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
- Department of Pediatrics, Medical University Vienna, Vienna, Austria
- * E-mail:
| |
Collapse
|
32
|
Chicard M, Boyault S, Colmet Daage L, Richer W, Gentien D, Pierron G, Lapouble E, Bellini A, Clement N, Iacono I, Bréjon S, Carrere M, Reyes C, Hocking T, Bernard V, Peuchmaur M, Corradini N, Faure-Conter C, Coze C, Plantaz D, Defachelles AS, Thebaud E, Gambart M, Millot F, Valteau-Couanet D, Michon J, Puisieux A, Delattre O, Combaret V, Schleiermacher G. Genomic Copy Number Profiling Using Circulating Free Tumor DNA Highlights Heterogeneity in Neuroblastoma. Clin Cancer Res 2016; 22:5564-5573. [DOI: 10.1158/1078-0432.ccr-16-0500] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 06/04/2016] [Accepted: 06/28/2016] [Indexed: 11/16/2022]
|
33
|
Bogen D, Brunner C, Walder D, Ziegler A, Abbasi R, Ladenstein RL, Noguera R, Martinsson T, Amann G, Schilling FH, Ussowicz M, Benesch M, Ambros PF, Ambros IM. The genetic tumor background is an important determinant for heterogeneous MYCN-amplified neuroblastoma. Int J Cancer 2016; 139:153-63. [PMID: 26910568 PMCID: PMC4949549 DOI: 10.1002/ijc.30050] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 02/03/2016] [Accepted: 02/08/2016] [Indexed: 12/18/2022]
Abstract
Amplification of MYCN is the signature genetic aberration of 20-25% of neuroblastoma and a stratifying marker associated with aggressive tumor behavior. The detection of heterogeneous MYCN amplification (hetMNA) poses a diagnostic dilemma due to the uncertainty of its relevance to tumor behavior. Here, we aimed to shed light on the genomic background which permits hetMNA in neuroblastoma and tied the occurrence to other stratifying markers and disease outcome. We performed SNP analysis using Affymetrix Cytoscan HD arrays on 63 samples including constitutional DNA, tumor, bone marrow and relapse samples of 26 patients with confirmed hetMNA by MYCN-FISH. Tumors of patients ≤18m were mostly aneuploid with numeric chromosomal aberrations (NCAs), presented a prominent MNA subclone and carried none or a few segmental chromosomal aberrations (SCAs). In older patients, tumors were mostly di- or tetraploid, contained a lower number of MNA cells and displayed a multitude of SCAs including concomitant 11q deletions. These patients often suffered disease progression, tumor dissemination and relapse. Restricted to aneuploid tumors, we detected chromosomes with uniparental di- or trisomy (UPD/UPT) in almost every sample. UPD11 was exclusive to tumors of younger patients whereas older patients featured UPD14. In this study, the MNA subclone appears to be constraint by the tumor environment and thus less relevant for tumor behavior in aggressive tumors with a high genomic instability and many segmental aberrations. A more benign tumor background and lower tumor stage may favor an outgrowth of the MNA clone but tumors generally responded better to treatment.
Collapse
Affiliation(s)
- Dominik Bogen
- Department of Tumor Biology, CCRI, Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Clemens Brunner
- Department of Tumor Biology, CCRI, Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Diana Walder
- Department of Tumor Biology, CCRI, Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Andrea Ziegler
- Department of Tumor Biology, CCRI, Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Reza Abbasi
- Department of Tumor Biology, CCRI, Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Ruth L Ladenstein
- S2IRP, CCRI, Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria.,Department of Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Rosa Noguera
- Pathology Department, Medical School, University of Valencia, INCLIVA, Valencia, Spain
| | - Tommy Martinsson
- Department of Clinical Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Gabriele Amann
- Department of Clinical Pathology, Medical University of Vienna, Vienna, Austria
| | | | - Marek Ussowicz
- Department of Pediatric Oncology, Hematology and BMT, Wroclaw Medical University, Wroclaw, Poland
| | - Martin Benesch
- Division of Pediatric Hematology/Oncology, Department of Pediatrics and Adolescent Medicine, Medical University of Graz, Graz, Austria
| | - Peter F Ambros
- Department of Tumor Biology, CCRI, Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria.,Department of Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Inge M Ambros
- Department of Tumor Biology, CCRI, Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| |
Collapse
|
34
|
Rode A, Maass KK, Willmund KV, Lichter P, Ernst A. Chromothripsis in cancer cells: An update. Int J Cancer 2015; 138:2322-33. [PMID: 26455580 DOI: 10.1002/ijc.29888] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 09/28/2015] [Accepted: 09/30/2015] [Indexed: 12/27/2022]
Abstract
In 2011, a novel form of genome instability was reported by Stephens et al., characterized by tens to hundreds of locally clustered rearrangements affecting one or a few chromosome(s) in cancer cells. This phenomenon, termed chromothripsis, is likely due to a single catastrophic event leading to the simultaneous formation of multiple double-strand breaks, which are repaired by error-prone mechanisms. Since then, the occurrence of chromothripsis was detected in a wide range of tumor entities. In this review, we will discuss potential mechanisms of chromothripsis initiation in cancer and outline the prevalence of chromothripsis across entities. Furthermore, we will examine how chromothriptic events may promote cancer development and how they may affect cancer therapy.
Collapse
Affiliation(s)
- Agata Rode
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kendra Korinna Maass
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Peter Lichter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Aurélie Ernst
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| |
Collapse
|
35
|
Rifatbegovic F, Abbasi MR, Taschner-Mandl S, Kauer M, Weinhäusel A, Handgretinger R, Ambros PF. Enriched Bone Marrow Derived Disseminated Neuroblastoma Cells Can Be a Reliable Source for Gene Expression Studies-A Validation Study. PLoS One 2015; 10:e0137995. [PMID: 26360775 PMCID: PMC4567134 DOI: 10.1371/journal.pone.0137995] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 08/25/2015] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Metastases in the bone marrow (BM) in form of disseminated tumor cells (DTCs) are frequent events at diagnosis and also at relapse in high-risk neuroblastoma patients. The frequently highly diluted occurrence of DTCs requires adequate enrichment strategies to enable their detailed characterization. However, to avoid methodical artifacts we tested whether pre-analytical processing steps-including transport duration, temperature and, importantly, tumor cell enrichment techniques-are confounding factors for gene expression analysis in DTCs. METHODS LAN-1 neuroblastoma cells were spiked into tumor free BM and/or peripheral blood and: i) kept at room temperature or at 4°C for 24, 48 and 72 hours; ii) frozen down at -80°C and thawed; iii) enriched via magnetic beads. The effect on the gene expression signature of LAN-1 cells was analyzed by qPCR arrays and gene expression microarrays. RESULTS Neither storage at -80°C in DMSO and subsequent thawing nor enrichment of spiked-in neuroblastoma cells changed the expression of the analyzed genes significantly. Whereas storage at 4°C altered the expression of analyzed genes (14.3%) only at the 72h-timepoint in comparison to the 0h-timepoint, storage at room temperature had a much more profound effect on gene expression by affecting 20% at 24h, 26% at 48h and 43% at 72h of the analyzed genes. CONCLUSION Using neuroblastoma as a model, we show that tumor cell enrichment by magnetic bead separation has virtually no effect on gene expression in DTCs. However, transport time and temperature can influence the expression profile remarkably. Thus, the expression profile of routinely collected BM samples can be analyzed without concern as long as the transport conditions are monitored.
Collapse
Affiliation(s)
- Fikret Rifatbegovic
- CCRI, Children’s Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
- * E-mail: (FR); (PFA)
| | - M. Reza Abbasi
- CCRI, Children’s Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Sabine Taschner-Mandl
- CCRI, Children’s Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Maximilian Kauer
- CCRI, Children’s Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Andreas Weinhäusel
- Molecular Diagnostics, Health & Environment Department, AIT Austrian Institute of Technology GmbH, Vienna, Austria
| | | | - Peter F. Ambros
- CCRI, Children’s Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
- Department of Pediatrics, Medical University of Vienna, Vienna, Austria
- * E-mail: (FR); (PFA)
| |
Collapse
|
36
|
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
|
37
|
Zahir FR, Marra MA. Use of Affymetrix Arrays in the Diagnosis of Gene Copy-Number Variation. ACTA ACUST UNITED AC 2015; 85:8.13.1-8.13.13. [PMID: 25827348 DOI: 10.1002/0471142905.hg0813s85] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Diagnosing constitutional pathogenic copy number variants (CNVs) requires detecting submicroscopic segmental chromosomal imbalances. The Affymetrix GeneChip mapping array was one of the initial microarray platforms used to measure duplication and deletion of genetic material in DNA samples. Unlike oligonucleotide microarrays from NimbleGen and Agilent, developed around the same time to infer copy number status for the DNA sequence covered by the probe, the Affymetrix GeneChip system used 25-mer oligonucleotide probes designed to interrogate SNPs. Thus, it was possible to use the Affymetrix 'SNP chips' to both identify SNPs and to identify copy number status. Affymetrix now offers the CytoScan microarray platforms, which are optimized for copy-number analyses, and provides accompanying software. They also offer several other microarray platforms suitable for copy-number analyses. Here we discuss the application of the CytoScan high-density (HD) platform for the detection of genomic imbalance. We provide an overview of the sequence of computational analyses involved in identifying pathogenic CNVs and highlight important parameters for consideration in assessing the pathogenicity of a detected CNV.
Collapse
Affiliation(s)
- Farah R Zahir
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada.,University of British Columbia, Department of Medical Genetics, Vancouver, British Columbia, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada.,University of British Columbia, Department of Medical Genetics, Vancouver, British Columbia, Canada
| |
Collapse
|
38
|
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
|