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Keller KM, Eleveld TF, Schild L, van den Handel K, van den Boogaard M, Amo-Addae V, Eising S, Ober K, Koopmans B, Looijenga L, Tytgat GA, Ylstra B, Molenaar JJ, Dolman MEM, van Hooff SR. Chromosome 11q loss and MYCN amplification demonstrate synthetic lethality with checkpoint kinase 1 inhibition in neuroblastoma. Front Oncol 2022; 12:929123. [PMID: 36237330 PMCID: PMC9552537 DOI: 10.3389/fonc.2022.929123] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 08/26/2022] [Indexed: 11/13/2022] Open
Abstract
Neuroblastoma is the most common extracranial solid tumor found in children and despite intense multi-modal therapeutic approaches, low overall survival rates of high-risk patients persist. Tumors with heterozygous loss of chromosome 11q and MYCN amplification are two genetically distinct subsets of neuroblastoma that are associated with poor patient outcome. Using an isogenic 11q deleted model system and high-throughput drug screening, we identify checkpoint kinase 1 (CHK1) as a potential therapeutic target for 11q deleted neuroblastoma. Further investigation reveals MYCN amplification as a possible additional biomarker for CHK1 inhibition, independent of 11q loss. Overall, our study highlights the potential power of studying chromosomal aberrations to guide preclinical development of novel drug targets and combinations. Additionally, our study builds on the growing evidence that DNA damage repair and replication stress response pathways offer therapeutic vulnerabilities for the treatment of neuroblastoma.
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Affiliation(s)
- Kaylee M. Keller
- Department of Research, Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Thomas F. Eleveld
- Department of Research, Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Linda Schild
- Department of Research, Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Kim van den Handel
- Department of Research, Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | | | - Vicky Amo-Addae
- Department of Research, Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Selma Eising
- Department of Research, Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Kimberley Ober
- Department of Research, Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Bianca Koopmans
- Department of Research, Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Leendert Looijenga
- Department of Research, Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Godelieve A.M. Tytgat
- Department of Research, Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Bauke Ylstra
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit, Amsterdam, Netherlands
| | - Jan J. Molenaar
- Department of Research, Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Department of Pharmaceutical Sciences, University Utrecht, Utrecht, Netherlands
- *Correspondence: Jan J. Molenaar,
| | - M. Emmy M. Dolman
- Department of Research, Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Children’s Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
- School of Women’s and Children’s Health, Faculty of Medicine, UNSW Sydney, Kensington, NSW, Australia
| | - Sander R. van Hooff
- Department of Research, Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
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2
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Decaesteker B, Durinck K, Van Roy N, De Wilde B, Van Neste C, Van Haver S, Roberts S, De Preter K, Vermeirssen V, Speleman F. From DNA Copy Number Gains and Tumor Dependencies to Novel Therapeutic Targets for High-Risk Neuroblastoma. J Pers Med 2021; 11:1286. [PMID: 34945759 PMCID: PMC8707517 DOI: 10.3390/jpm11121286] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/19/2021] [Accepted: 11/20/2021] [Indexed: 12/15/2022] Open
Abstract
Neuroblastoma is a pediatric tumor arising from the sympatho-adrenal lineage and a worldwide leading cause of childhood cancer-related deaths. About half of high-risk patients die from the disease while survivors suffer from multiple therapy-related side-effects. While neuroblastomas present with a low mutational burden, focal and large segmental DNA copy number aberrations are highly recurrent and associated with poor survival. It can be assumed that the affected chromosomal regions contain critical genes implicated in neuroblastoma biology and behavior. More specifically, evidence has emerged that several of these genes are implicated in tumor dependencies thus potentially providing novel therapeutic entry points. In this review, we briefly review the current status of recurrent DNA copy number aberrations in neuroblastoma and provide an overview of the genes affected by these genomic variants for which a direct role in neuroblastoma has been established. Several of these genes are implicated in networks that positively regulate MYCN expression or stability as well as cell cycle control and apoptosis. Finally, we summarize alternative approaches to identify and prioritize candidate copy-number driven dependency genes for neuroblastoma offering novel therapeutic opportunities.
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Grants
- P30 CA008748 NCI NIH HHS
- G087221N, G.0507.12, G049720N,12U4718N, 11C3921N, 11J8313N, 12B5313N, 1514215N, 1197617N,1238420N, 12Q8322N, 3F018519, 12N6917N Fund for Scientific Research Flanders
- 2018-087, 2018-125, 2020-112 Belgian Foundation against Cancer
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Affiliation(s)
- Bieke Decaesteker
- Department for Biomolecular Medicine, Ghent University, Medical Research Building (MRB1), Corneel Heymanslaan 10, B-9000 Ghent, Belgium; (B.D.); (K.D.); (N.V.R.); (B.D.W.); (C.V.N.); (S.V.H.); (K.D.P.); (V.V.)
| | - Kaat Durinck
- Department for Biomolecular Medicine, Ghent University, Medical Research Building (MRB1), Corneel Heymanslaan 10, B-9000 Ghent, Belgium; (B.D.); (K.D.); (N.V.R.); (B.D.W.); (C.V.N.); (S.V.H.); (K.D.P.); (V.V.)
| | - Nadine Van Roy
- Department for Biomolecular Medicine, Ghent University, Medical Research Building (MRB1), Corneel Heymanslaan 10, B-9000 Ghent, Belgium; (B.D.); (K.D.); (N.V.R.); (B.D.W.); (C.V.N.); (S.V.H.); (K.D.P.); (V.V.)
| | - Bram De Wilde
- Department for Biomolecular Medicine, Ghent University, Medical Research Building (MRB1), Corneel Heymanslaan 10, B-9000 Ghent, Belgium; (B.D.); (K.D.); (N.V.R.); (B.D.W.); (C.V.N.); (S.V.H.); (K.D.P.); (V.V.)
- Department of Internal Medicine and Pediatrics, Ghent University Hospital, Corneel Heymanslaan 10, B-9000 Ghent, Belgium
| | - Christophe Van Neste
- Department for Biomolecular Medicine, Ghent University, Medical Research Building (MRB1), Corneel Heymanslaan 10, B-9000 Ghent, Belgium; (B.D.); (K.D.); (N.V.R.); (B.D.W.); (C.V.N.); (S.V.H.); (K.D.P.); (V.V.)
| | - Stéphane Van Haver
- Department for Biomolecular Medicine, Ghent University, Medical Research Building (MRB1), Corneel Heymanslaan 10, B-9000 Ghent, Belgium; (B.D.); (K.D.); (N.V.R.); (B.D.W.); (C.V.N.); (S.V.H.); (K.D.P.); (V.V.)
| | - Stephen Roberts
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA;
| | - Katleen De Preter
- Department for Biomolecular Medicine, Ghent University, Medical Research Building (MRB1), Corneel Heymanslaan 10, B-9000 Ghent, Belgium; (B.D.); (K.D.); (N.V.R.); (B.D.W.); (C.V.N.); (S.V.H.); (K.D.P.); (V.V.)
| | - Vanessa Vermeirssen
- Department for Biomolecular Medicine, Ghent University, Medical Research Building (MRB1), Corneel Heymanslaan 10, B-9000 Ghent, Belgium; (B.D.); (K.D.); (N.V.R.); (B.D.W.); (C.V.N.); (S.V.H.); (K.D.P.); (V.V.)
- Department of Biomedical Molecular Biology, Ghent University, Technologiepark 71, B-9052 Zwijnaarde, Belgium
| | - Frank Speleman
- Department for Biomolecular Medicine, Ghent University, Medical Research Building (MRB1), Corneel Heymanslaan 10, B-9000 Ghent, Belgium; (B.D.); (K.D.); (N.V.R.); (B.D.W.); (C.V.N.); (S.V.H.); (K.D.P.); (V.V.)
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3
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Borenäs M, Umapathy G, Lai WY, Lind DE, Witek B, Guan J, Mendoza-Garcia P, Masudi T, Claeys A, Chuang TP, El Wakil A, Arefin B, Fransson S, Koster J, Johansson M, Gaarder J, Van den Eynden J, Hallberg B, Palmer RH. ALK ligand ALKAL2 potentiates MYCN-driven neuroblastoma in the absence of ALK mutation. EMBO J 2021; 40:e105784. [PMID: 33411331 PMCID: PMC7849294 DOI: 10.15252/embj.2020105784] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 10/19/2020] [Accepted: 10/23/2020] [Indexed: 12/18/2022] Open
Abstract
High‐risk neuroblastoma (NB) is responsible for a disproportionate number of childhood deaths due to cancer. One indicator of high‐risk NB is amplification of the neural MYC (MYCN) oncogene, which is currently therapeutically intractable. Identification of anaplastic lymphoma kinase (ALK) as an NB oncogene raised the possibility of using ALK tyrosine kinase inhibitors (TKIs) in treatment of patients with activating ALK mutations. 8–10% of primary NB patients are ALK‐positive, a figure that increases in the relapsed population. ALK is activated by the ALKAL2 ligand located on chromosome 2p, along with ALK and MYCN, in the “2p‐gain” region associated with NB. Dysregulation of ALK ligand in NB has not been addressed, although one of the first oncogenes described was v‐sis that shares > 90% homology with PDGF. Therefore, we tested whether ALKAL2 ligand could potentiate NB progression in the absence of ALK mutation. We show that ALKAL2 overexpression in mice drives ALK TKI‐sensitive NB in the absence of ALK mutation, suggesting that additional NB patients, such as those exhibiting 2p‐gain, may benefit from ALK TKI‐based therapeutic intervention.
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Affiliation(s)
- Marcus Borenäs
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Ganesh Umapathy
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Wei-Yun Lai
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Dan E Lind
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Barbara Witek
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Jikui Guan
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Patricia Mendoza-Garcia
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Tafheem Masudi
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Arne Claeys
- Department of Human Structure and Repair, Anatomy and Embryology Unit, Ghent University, Ghent, Belgium
| | - Tzu-Po Chuang
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Abeer El Wakil
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Badrul Arefin
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Susanne Fransson
- Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Jan Koster
- Department of Oncogenomics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Mathias Johansson
- Clinical Genomics, Science for life laboratory, University of Gothenburg, Gothenburg, Sweden
| | - Jennie Gaarder
- Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Jimmy Van den Eynden
- Department of Human Structure and Repair, Anatomy and Embryology Unit, Ghent University, Ghent, Belgium
| | - Bengt Hallberg
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Ruth H Palmer
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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4
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Lopez G, Conkrite KL, Doepner M, Rathi KS, Modi A, Vaksman Z, Farra LM, Hyson E, Noureddine M, Wei JS, Smith MA, Asgharzadeh S, Seeger RC, Khan J, Auvil JG, Gerhard DS, Maris JM, Diskin SJ. Somatic structural variation targets neurodevelopmental genes and identifies SHANK2 as a tumor suppressor in neuroblastoma. Genome Res 2020; 30:1228-1242. [PMID: 32796005 PMCID: PMC7545140 DOI: 10.1101/gr.252106.119] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 08/07/2020] [Indexed: 12/18/2022]
Abstract
Neuroblastoma is a malignancy of the developing sympathetic nervous system that accounts for 12% of childhood cancer deaths. Like many childhood cancers, neuroblastoma shows a relative paucity of somatic single-nucleotide variants (SNVs) and small insertions and deletions (indels) compared to adult cancers. Here, we assessed the contribution of somatic structural variation (SV) in neuroblastoma using a combination of whole-genome sequencing (WGS) of tumor-normal pairs (n = 135) and single-nucleotide polymorphism (SNP) genotyping of primary tumors (n = 914). Our study design allowed for orthogonal validation and replication across platforms. SV frequency, type, and localization varied significantly among high-risk tumors. MYCN nonamplified high-risk tumors harbored an increased SV burden overall, including a significant excess of tandem duplication events across the genome. Genes disrupted by SV breakpoints were enriched in neuronal lineages and associated with phenotypes such as autism spectrum disorder (ASD). The postsynaptic adapter protein-coding gene, SHANK2, located on Chromosome 11q13, was disrupted by SVs in 14% of MYCN nonamplified high-risk tumors based on WGS and 10% in the SNP array cohort. Expression of SHANK2 was low across human-derived neuroblastoma cell lines and high-risk neuroblastoma tumors. Forced expression of SHANK2 in neuroblastoma cells resulted in significant growth inhibition (P = 2.6 × 10-2 to 3.4 × 10-5) and accelerated neuronal differentiation following treatment with all-trans retinoic acid (P = 3.1 × 10-13 to 2.4 × 10-30). These data further define the complex landscape of somatic structural variation in neuroblastoma and suggest that events leading to deregulation of neurodevelopmental processes, such as inactivation of SHANK2, are key mediators of tumorigenesis in this childhood cancer.
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Affiliation(s)
- Gonzalo Lopez
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Karina L Conkrite
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Miriam Doepner
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Komal S Rathi
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Apexa Modi
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Genomics and Computational Biology, Biomedical Graduate Studies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Zalman Vaksman
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Lance M Farra
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Eric Hyson
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Moataz Noureddine
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Jun S Wei
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Malcolm A Smith
- Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Shahab Asgharzadeh
- Division of Hematology, Oncology and Blood and Marrow Transplantation, Keck School of Medicine of the University of Southern California, Los Angeles, California 90033, USA
- The Saban Research Institute, Children's Hospital of Los Angeles, Los Angeles, California 90027, USA
| | - Robert C Seeger
- Division of Hematology, Oncology and Blood and Marrow Transplantation, Keck School of Medicine of the University of Southern California, Los Angeles, California 90033, USA
- The Saban Research Institute, Children's Hospital of Los Angeles, Los Angeles, California 90027, USA
| | - Javed Khan
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Jaime Guidry Auvil
- Office of Cancer Genomics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Daniela S Gerhard
- Office of Cancer Genomics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - John M Maris
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Sharon J Diskin
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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5
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Iehara T, Yagyu S, Gotoh T, Ouchi K, Yoshida H, Miyachi M, Kikuchi K, Sugimoto T, Hosoi H. A prospective evaluation of liquid biopsy for detecting MYCN amplification in neuroblastoma patients. Jpn J Clin Oncol 2019; 49:743-748. [DOI: 10.1093/jjco/hyz063] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 02/25/2019] [Indexed: 02/06/2023] Open
Abstract
Abstract
Background
Our previous study reported a method for determining MYCN gene amplification (MNA) status using cell-free DNA in serum. We prospectively analyzed the serum MNA status using sera obtained before the initial diagnosis from patients with neuroblastoma and evaluated the utility of this method.
Methods
Eighty patients were enrolled in the study. The serum MYCN/NAGK ratio was assessed for all cases.
Results
Fifteen cases showed serum MNA, while 65 did not. Of the 80 total patients, tumor samples for a genetic analysis were not obtained from 27 due to the patients’ condition or other reasons. For the 43 of 80 cases that had both serum and tumor samples analyzed, the serum-based MNA status matched to tumor-based MNA status (P < 0.001). The sensitivity and the specificity were 100%, respectively. Seven of 15 cases who diagnosed as MNA by serum-based MNA status were <18 months of age, and tumor samples were not obtained from 4 of these cases. Based on the serum MNA status, these cases were able to start treatment immediately. The 4-year event-free survival rates of cases with and without MNA in sera were 37.5% and 84.8%, respectively (P < 0.001).
Conclusion
The serum-based MNA status was useful for precisely predicting the MNA status in tumor and it has clinical benefits for predicting risk stratification in patients for whom obtaining tumor samples is difficult.
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Affiliation(s)
- Tomoko Iehara
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Graduate School of Medical Science, Kawaramachi-Hirokoji Kamigyo-ku, Kyoto 602-8566, Japan
| | - Shigeki Yagyu
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Graduate School of Medical Science, Kawaramachi-Hirokoji Kamigyo-ku, Kyoto 602-8566, Japan
| | - Takahiro Gotoh
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Graduate School of Medical Science, Kawaramachi-Hirokoji Kamigyo-ku, Kyoto 602-8566, Japan
| | - Kazutaka Ouchi
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Graduate School of Medical Science, Kawaramachi-Hirokoji Kamigyo-ku, Kyoto 602-8566, Japan
| | - Hideki Yoshida
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Graduate School of Medical Science, Kawaramachi-Hirokoji Kamigyo-ku, Kyoto 602-8566, Japan
| | - Mitsuru Miyachi
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Graduate School of Medical Science, Kawaramachi-Hirokoji Kamigyo-ku, Kyoto 602-8566, Japan
| | - Ken Kikuchi
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Graduate School of Medical Science, Kawaramachi-Hirokoji Kamigyo-ku, Kyoto 602-8566, Japan
| | - Tohru Sugimoto
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Graduate School of Medical Science, Kawaramachi-Hirokoji Kamigyo-ku, Kyoto 602-8566, Japan
| | - Hajime Hosoi
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Graduate School of Medical Science, Kawaramachi-Hirokoji Kamigyo-ku, Kyoto 602-8566, Japan
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6
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Umapathy G, Mendoza-Garcia P, Hallberg B, Palmer RH. Targeting anaplastic lymphoma kinase in neuroblastoma. APMIS 2019; 127:288-302. [PMID: 30803032 PMCID: PMC6850425 DOI: 10.1111/apm.12940] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 02/18/2019] [Indexed: 12/15/2022]
Abstract
Over the last decade, anaplastic lymphoma kinase (ALK), a receptor tyrosine kinase (RTK), has been identified as a fusion partner in a diverse variety of translocation events resulting in oncogenic signaling in many different cancer types. In tumors where the full‐length ALK RTK itself is mutated, such as neuroblastoma, the picture regarding the role of ALK as an oncogenic driver is less clear. Neuroblastoma is a complex and heterogeneous tumor that arises from the neural crest derived peripheral nervous system. Although high‐risk neuroblastoma is rare, it often relapses and becomes refractory to treatment. Thus, neuroblastoma accounts for 10–15% of all childhood cancer deaths. Since most cases are in children under the age of 2, understanding the role and regulation of ALK during neural crest development is an important goal in addressing neuroblastoma tumorigenesis. An impressive array of tyrosine kinase inhibitors (TKIs) that act to inhibit ALK have been FDA approved for use in ALK‐driven cancers. ALK TKIs bind differently within the ATP‐binding pocket of the ALK kinase domain and have been associated with different resistance mutations within ALK itself that arise in response to therapeutic use, particularly in ALK‐fusion positive non‐small cell lung cancer (NSCLC). This patient population has highlighted the importance of considering the relevant ALK TKI to be used for a given ALK mutant variant. In this review, we discuss ALK in neuroblastoma, as well as the use of ALK TKIs and other strategies to inhibit tumor growth. Current efforts combining novel approaches and increasing our understanding of the oncogenic role of ALK in neuroblastoma are aimed at improving the efficacy of ALK TKIs as precision medicine options in the clinic.
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Affiliation(s)
- Ganesh Umapathy
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Patricia Mendoza-Garcia
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Bengt Hallberg
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Ruth H Palmer
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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7
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Qu X, Li H, Braziel RM, Passerini V, Rimsza LM, Hsi ED, Leonard JP, Smith SM, Kridel R, Press O, Weigert O, LeBlanc M, Friedberg JW, Fang M. Genomic alterations important for the prognosis in patients with follicular lymphoma treated in SWOG study S0016. Blood 2019; 133:81-93. [PMID: 30446494 PMCID: PMC6318431 DOI: 10.1182/blood-2018-07-865428] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 11/06/2018] [Indexed: 02/08/2023] Open
Abstract
Although recent advances in molecular genetics have enabled improved risk classification of follicular lymphoma (FL) using, for example, the m7-FLIPI score, the impact on treatment has been limited. We aimed to assess the prognostic significance of copy-number aberrations (CNAs) and copy-neutral loss of heterozygosity (cnLOH) identified by chromosome genomic-array testing (CGAT) at FL diagnosis using prospectively collected clinical trial specimens from 255 patients enrolled in the SWOG study S0016. The impact of genomic aberrations was assessed for early progression (progressed or died within 2 years after registration), progression-free survival (PFS), and overall survival (OS). We showed that increased genomic complexity (ie, the total number of aberration calls) was associated with poor outcome in FL. Certain chromosome arms were critical for clinical outcome. Prognostic CNAs/cnLOH were identified: whereas early progression was correlated with 2p gain (P = .007; odds ratio [OR] = 2.55 [1.29, 5.03]) and 2p cnLOH (P = .005; OR = 10.9 [2.08, 57.2]), 2p gain specifically encompassing VRK2 and FANCL predicted PFS (P = .01; hazard ratio = 1.80 [1.14, 2.68]) as well as OS (P = .005; 2.40 [1.30, 4.40]); CDKN2A/B (9p) deletion correlated with worse PFS (P = .004, 3.50 [1.51, 8.28]); whereas CREBBP (16p) (P < .001; 6.70 [2.52, 17.58]) and TP53 (17p) (P < .001; 3.90 [1.85, 8.31]) deletion predicted worse OS. An independent cohort from the m7-FLIPI study was explored, and the prognostic significance of aberration count, and TP53 and CDKN2A/B deletion were further validated. In conclusion, assessing genomic aberrations at FL diagnosis with CGAT improves risk stratification independent of known clinical parameters, and provides a framework for development of future rational targeted therapies.
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Affiliation(s)
- Xiaoyu Qu
- Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Hongli Li
- SWOG Statistical Center, Seattle, WA
| | - Rita M Braziel
- Department of Pathology, Oregon Health & Science University, Portland, OR
| | - Verena Passerini
- Department of Medicine III, University Hospital, Ludwig Maximilians University Munich, Munich, Germany
- German Cancer Consortium, German Cancer Research Center, Heidelberg, Germany
| | | | | | - John P Leonard
- Weill Cornell Medicine/New York Presbyterian Hospital, New York, NY
| | - Sonali M Smith
- Department of Medicine, University of Chicago, Chicago, IL
| | - Robert Kridel
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, ON, Canada; and
| | - Oliver Press
- Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Oliver Weigert
- Department of Medicine III, University Hospital, Ludwig Maximilians University Munich, Munich, Germany
- German Cancer Consortium, German Cancer Research Center, Heidelberg, Germany
| | | | | | - Min Fang
- Fred Hutchinson Cancer Research Center, Seattle, WA
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8
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Rajbhandari P, Lopez G, Capdevila C, Salvatori B, Yu J, Rodriguez-Barrueco R, Martinez D, Yarmarkovich M, Weichert-Leahey N, Abraham BJ, Alvarez MJ, Iyer A, Harenza JL, Oldridge D, De Preter K, Koster J, Asgharzadeh S, Seeger RC, Wei JS, Khan J, Vandesompele J, Mestdagh P, Versteeg R, Look AT, Young RA, Iavarone A, Lasorella A, Silva JM, Maris JM, Califano A. Cross-Cohort Analysis Identifies a TEAD4-MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma. Cancer Discov 2018; 8:582-599. [PMID: 29510988 PMCID: PMC5967627 DOI: 10.1158/2159-8290.cd-16-0861] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 11/06/2017] [Accepted: 02/23/2018] [Indexed: 01/21/2023]
Abstract
High-risk neuroblastomas show a paucity of recurrent somatic mutations at diagnosis. As a result, the molecular basis for this aggressive phenotype remains elusive. Recent progress in regulatory network analysis helped us elucidate disease-driving mechanisms downstream of genomic alterations, including recurrent chromosomal alterations. Our analysis identified three molecular subtypes of high-risk neuroblastomas, consistent with chromosomal alterations, and identified subtype-specific master regulator proteins that were conserved across independent cohorts. A 10-protein transcriptional module-centered around a TEAD4-MYCN positive feedback loop-emerged as the regulatory driver of the high-risk subtype associated with MYCN amplification. Silencing of either gene collapsed MYCN-amplified (MYCNAmp) neuroblastoma transcriptional hallmarks and abrogated viability in vitro and in vivo Consistently, TEAD4 emerged as a robust prognostic marker of poor survival, with activity independent of the canonical Hippo pathway transcriptional coactivators YAP and TAZ. These results suggest novel therapeutic strategies for the large subset of MYCN-deregulated neuroblastomas.Significance: Despite progress in understanding of neuroblastoma genetics, little progress has been made toward personalized treatment. Here, we present a framework to determine the downstream effectors of the genetic alterations sustaining neuroblastoma subtypes, which can be easily extended to other tumor types. We show the critical effect of disrupting a 10-protein module centered around a YAP/TAZ-independent TEAD4-MYCN positive feedback loop in MYCNAmp neuroblastomas, nominating TEAD4 as a novel candidate for therapeutic intervention. Cancer Discov; 8(5); 582-99. ©2018 AACR.This article is highlighted in the In This Issue feature, p. 517.
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Affiliation(s)
- Presha Rajbhandari
- Department of Systems Biology, Columbia University, New York, New York
- Department of Biological Sciences, Columbia University, New York, New York
| | - Gonzalo Lopez
- Department of Systems Biology, Columbia University, New York, New York
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Claudia Capdevila
- Department of Systems Biology, Columbia University, New York, New York
| | | | - Jiyang Yu
- Department of Systems Biology, Columbia University, New York, New York
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Ruth Rodriguez-Barrueco
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York
- Departament de Patologia i Terapèutica Experimental, Facultat de Medicina i Ciències de la Salut, IDIBELL, Universitat de Barcelona, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Daniel Martinez
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Mark Yarmarkovich
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Nina Weichert-Leahey
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Brian J Abraham
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts
| | - Mariano J Alvarez
- Department of Systems Biology, Columbia University, New York, New York
| | - Archana Iyer
- Department of Systems Biology, Columbia University, New York, New York
| | - Jo Lynne Harenza
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Derek Oldridge
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Katleen De Preter
- Center for Medical Genetics & Cancer Research Institute Ghent (CRIG), Ghent University, Gent, Belgium
| | - Jan Koster
- Department of Oncogenomics, Academic Medical Center, Amsterdam, the Netherlands
| | - Shahab Asgharzadeh
- Division of Hematology/Oncology, Saban Research Institute, The Children's Hospital Los Angeles, Los Angeles, California
- Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Robert C Seeger
- Division of Hematology/Oncology, Saban Research Institute, The Children's Hospital Los Angeles, Los Angeles, California
- Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Jun S Wei
- Genetics Branch, Oncogenomics Section, Center for Cancer Research, NIH, Bethesda, Maryland
| | - Javed Khan
- Genetics Branch, Oncogenomics Section, Center for Cancer Research, NIH, Bethesda, Maryland
| | - Jo Vandesompele
- Center for Medical Genetics & Cancer Research Institute Ghent (CRIG), Ghent University, Gent, Belgium
| | - Pieter Mestdagh
- Center for Medical Genetics & Cancer Research Institute Ghent (CRIG), Ghent University, Gent, Belgium
| | - Rogier Versteeg
- Department of Oncogenomics, Academic Medical Center, Amsterdam, the Netherlands
| | - A Thomas Look
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Antonio Iavarone
- Department of Neurology and Pathology and Cell Biology, Institute for Cancer Genetics, Columbia University, New York, New York
| | - Anna Lasorella
- Department of Pediatrics and Pathology and Cell Biology, Institute for Cancer Genetics, Columbia University, New York, New York
| | - Jose M Silva
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - John M Maris
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Abramson Family Cancer Research Institute, Philadelphia, Pennsylvania
| | - Andrea Califano
- Department of Systems Biology, Columbia University, New York, New York.
- Department of Biomedical Informatics, Columbia University, New York, New York
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York
- Herbert Irving Comprehensive Cancer Center and J.P. Sulzberger Columbia Genome Center, Columbia University, New York, New York
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9
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Costa RA, Seuánez HN. Investigation of major genetic alterations in neuroblastoma. Mol Biol Rep 2018; 45:287-295. [PMID: 29455316 DOI: 10.1007/s11033-018-4161-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 02/08/2018] [Indexed: 12/11/2022]
Abstract
Neuroblastoma (NB) is the most common extracranial solid tumor in childhood. This malignancy shows a wide spectrum of clinical outcome and its prognosis is conditioned by manifold biological and genetic factors. We investigated the tumor genetic profile and clinical data of 29 patients with NB by multiplex ligation-dependent probe amplification (MLPA) to assess therapeutic risk. In 18 of these tumors, MYCN status was assessed by fluorescence in situ hybridization (FISH). Copy number variation was also determined for confirming MLPA findings in two 6p loci. We found 2p, 7q and 17q gains, and 1p and 11q losses as the most frequent chromosome alterations in this cohort. FISH confirmed all cases of MYCN amplification detected by MLPA. In view of unexpected 6p imbalance, copy number variation of two 6p loci was assessed for validating MLPA findings. Based on clinical data and genetic profiles, patients were stratified in pretreatment risk groups according to international consensus. MLPA proved to be effective for detecting multiple genetic alterations in all chromosome regions as requested by the International Neuroblastoma Risk Group (INRG) for therapeutic stratification. Moreover, this technique proved to be cost effective, reliable, only requiring standard PCR equipment, and attractive for routine analysis. However, the observed 6p imbalances made PKHD1 and DCDC2 inadequate for control loci. This must be considered when designing commercial MLPA kits for NB. Finally, four patients showed a normal MLPA profile, suggesting that NB might have a more complex genetic pattern than the one assessed by presently available MLPA kits.
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Affiliation(s)
- Régis Afonso Costa
- Genetics Program, Instituto Nacional de Câncer, Rua André Cavalcanti 37, Rio de Janeiro, RJ, 20231-050, Brazil.,Department of Genetics, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Héctor N Seuánez
- Genetics Program, Instituto Nacional de Câncer, Rua André Cavalcanti 37, Rio de Janeiro, RJ, 20231-050, Brazil. .,Department of Genetics, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
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10
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Novel Mechanisms of ALK Activation Revealed by Analysis of the Y1278S Neuroblastoma Mutation. Cancers (Basel) 2017; 9:cancers9110149. [PMID: 29084134 PMCID: PMC5704167 DOI: 10.3390/cancers9110149] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 10/09/2017] [Accepted: 10/23/2017] [Indexed: 12/20/2022] Open
Abstract
Numerous mutations have been observed in the Anaplastic Lymphoma Kinase (ALK) receptor tyrosine kinase (RTK) in both germline and sporadic neuroblastoma. Here, we have investigated the Y1278S mutation, observed in four patient cases, and its potential importance in the activation of the full length ALK receptor. Y1278S is located in the 1278-YRASYY-1283 motif of the ALK activation loop, which has previously been reported to be important in the activation of the ALK kinase domain. In this study, we have characterized activation loop mutations within the context of the full length ALK employing cell culture and Drosophila melanogaster model systems. Our results show that the Y1278S mutant observed in patients with neuroblastoma harbors gain-of-function activity. Secondly, we show that the suggested interaction between Y1278 and other amino acids might be of less importance in the activation process of the ALK kinase than previously proposed. Thirdly, of the three individual tyrosines in the 1278-YRASYY-1283 activation loop, we find that Y1283 is the critical tyrosine in the activation process. Taken together, our observations employing different model systems reveal new mechanistic insights on how the full length ALK receptor is activated and highlight differences with earlier described activation mechanisms observed in the NPM-ALK fusion protein, supporting a mechanism of activation more in line with those observed for the Insulin Receptor (InR).
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11
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Mlakar V, Jurkovic Mlakar S, Lopez G, Maris JM, Ansari M, Gumy-Pause F. 11q deletion in neuroblastoma: a review of biological and clinical implications. Mol Cancer 2017; 16:114. [PMID: 28662712 PMCID: PMC5492892 DOI: 10.1186/s12943-017-0686-8] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 06/25/2017] [Indexed: 12/12/2022] Open
Abstract
Deletion of the long arm of chromosome 11 (11q deletion) is one of the most frequent events that occur during the development of aggressive neuroblastoma. Clinically, 11q deletion is associated with higher disease stage and decreased survival probability. During the last 25 years, extensive efforts have been invested to identify the precise frequency of 11q aberrations in neuroblastoma, the recurrently involved genes, and to understand the molecular mechanisms of 11q deletion, but definitive answers are still unclear. In this review, it is our intent to compile and review the evidence acquired to date on 11q deletion in neuroblastoma.
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Affiliation(s)
- Vid Mlakar
- CANSEARCH Research Laboratory, Geneva University Medical School, Avenue de la Roseraie 64, 1205, Geneva, Switzerland
| | - Simona Jurkovic Mlakar
- CANSEARCH Research Laboratory, Geneva University Medical School, Avenue de la Roseraie 64, 1205, Geneva, Switzerland
| | - Gonzalo Lopez
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - John M Maris
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Marc Ansari
- CANSEARCH Research Laboratory, Geneva University Medical School, Avenue de la Roseraie 64, 1205, Geneva, Switzerland.,Department of Pediatrics, Onco-Hematology Unit, Geneva University Hospitals, Rue Willy-Donzé 6, 1205, Geneva, Switzerland
| | - Fabienne Gumy-Pause
- CANSEARCH Research Laboratory, Geneva University Medical School, Avenue de la Roseraie 64, 1205, Geneva, Switzerland. .,Department of Pediatrics, Onco-Hematology Unit, Geneva University Hospitals, Rue Willy-Donzé 6, 1205, Geneva, Switzerland.
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12
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Salazar BM, Balczewski EA, Ung CY, Zhu S. Neuroblastoma, a Paradigm for Big Data Science in Pediatric Oncology. Int J Mol Sci 2016; 18:E37. [PMID: 28035989 PMCID: PMC5297672 DOI: 10.3390/ijms18010037] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 12/14/2016] [Accepted: 12/17/2016] [Indexed: 12/13/2022] Open
Abstract
Pediatric cancers rarely exhibit recurrent mutational events when compared to most adult cancers. This poses a challenge in understanding how cancers initiate, progress, and metastasize in early childhood. Also, due to limited detected driver mutations, it is difficult to benchmark key genes for drug development. In this review, we use neuroblastoma, a pediatric solid tumor of neural crest origin, as a paradigm for exploring "big data" applications in pediatric oncology. Computational strategies derived from big data science-network- and machine learning-based modeling and drug repositioning-hold the promise of shedding new light on the molecular mechanisms driving neuroblastoma pathogenesis and identifying potential therapeutics to combat this devastating disease. These strategies integrate robust data input, from genomic and transcriptomic studies, clinical data, and in vivo and in vitro experimental models specific to neuroblastoma and other types of cancers that closely mimic its biological characteristics. We discuss contexts in which "big data" and computational approaches, especially network-based modeling, may advance neuroblastoma research, describe currently available data and resources, and propose future models of strategic data collection and analyses for neuroblastoma and other related diseases.
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Affiliation(s)
- Brittany M Salazar
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55902, USA.
| | - Emily A Balczewski
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.
| | - Choong Yong Ung
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.
| | - Shizhen Zhu
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55902, USA.
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.
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13
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Mazzocco K, Defferrari R, Sementa AR, Garaventa A, Longo L, De Mariano M, Esposito MR, Negri F, Ircolò D, Viscardi E, Luksch R, D'Angelo P, Prete A, Castellano A, Massirio P, Erminio G, Gigliotti AR, Tonini GP, Conte M. Genetic abnormalities in adolescents and young adults with neuroblastoma: A report from the Italian Neuroblastoma group. Pediatr Blood Cancer 2015; 62:1725-32. [PMID: 25925003 DOI: 10.1002/pbc.25552] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 03/19/2015] [Indexed: 02/06/2023]
Abstract
BACKGROUND Less than 5% of neuroblastomas (NB) occur in adolescents and young adults (AYA), in whom the disease has an indolent and fatal course. PROCEDURE We studied the genomic profile and histological characteristics of 34 NBs from AYA patients enrolled in the Italian Neuroblastoma Registry (INBR) between 1979 and 2009. RESULTS Disease was disseminated in 20 patients and localized in 14; 30/34 tumors were classified as NB and 4/34 as nodular ganglioneuroblastoma (nGNB). Segmental Chromosome Aberrations (SCAs) were observed in 29 tumors (85%) namely 1p imbalance (58%), 17q gain (52%), 9p loss (32%), 11q loss (30%), 1q gain (17%), 7q gain (17%), 2p gain (14%), 3p loss (14%), and 4p loss (7%). MYCN amplification and MYCN gain were detected in 3 (10%) and 2 cases (7%) respectively. An anaplastic lymphoma receptor tyrosine kinase (ALK) gene mutation study on the available cases from this cohort revealed 4/25 (16%) mutated cases. In parallel, alpha thalassaemia/mental retardation syndrome X linked (ATRX) gene mutations were also sought, a novel mutation being detected in 1/21 (4,7%) cases. CONCLUSION This study confirmed the low incidence of MYCN amplification in AYA and recorded a high frequency of 17q gain and 9p and 11q loss independently from the stage of the disease. The presence of 1q gain, which identifies patients with particularly aggressive disease, relapse and poor survival, was also detected. Furthermore, the frequency of ALK mutations suggests that a target-based therapy with ALK inhibitors might be effective in this subset of patients.
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Affiliation(s)
- Katia Mazzocco
- Department of Pathology, Istituto Giannina Gaslini, Genova, Italy
| | | | | | - Alberto Garaventa
- Department of Hematology-Oncology, Istituto Giannina Gaslini, Genova, Italy
| | - Luca Longo
- U.O.C. Bioterapie IRCSS A.O.U. San Martino-IST, Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy
| | - Marilena De Mariano
- U.O.C. Bioterapie IRCSS A.O.U. San Martino-IST, Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy
| | - Maria Rosaria Esposito
- Neuroblastoma Laboratory, Onco/Hematology Laboratory, SDB Department, University of Padova, Pediatric Research Institute, Fondazione Città della Speranza, Padova, Italy
| | - Francesca Negri
- Department of Pathology, Istituto Giannina Gaslini, Genova, Italy
| | - Davide Ircolò
- Department of Pathology, Istituto Giannina Gaslini, Genova, Italy
| | | | - Roberto Luksch
- Department of Pediatric Oncology, National Cancer Institute, Milano, Italy
| | - Paolo D'Angelo
- Department of Pediatric Hematology and Oncology, ARNAS Civico Di Cristina Benfratelli Hospital, Palermo, Italy
| | - Arcangelo Prete
- Pediatric Oncology and Hematology Unit "Lalla Seràgnoli", University of Bologna Sant'Orsola-Malpighi Hospital, Bologna, Italy
| | - Aurora Castellano
- Department of Pediatric Hematology-Oncology, IRCCS, Ospedale Bambino Gesù, Rome, Italy
| | - Paolo Massirio
- Department of Hematology-Oncology, Istituto Giannina Gaslini, Genova, Italy
| | - Giovanni Erminio
- Department of Epidemiology and Biostatistics, Istituto Giannina Gaslini, Genova, Italy
| | | | - Gian Paolo Tonini
- Neuroblastoma Laboratory, Onco/Hematology Laboratory, SDB Department, University of Padova, Pediatric Research Institute, Fondazione Città della Speranza, Padova, Italy
| | - Massimo Conte
- Department of Hematology-Oncology, Istituto Giannina Gaslini, Genova, Italy
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14
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Berbegall AP, Villamón E, Tadeo I, Martinsson T, Cañete A, Castel V, Navarro S, Noguera R. Neuroblastoma after childhood: prognostic relevance of segmental chromosome aberrations, ATRX protein status, and immune cell infiltration. Neoplasia 2015; 16:471-80. [PMID: 25077701 PMCID: PMC4198743 DOI: 10.1016/j.neo.2014.05.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 05/09/2014] [Accepted: 05/16/2014] [Indexed: 01/08/2023] Open
Abstract
Neuroblastoma (NB) is a common malignancy in children but rarely occurs during adolescence or adulthood. This subgroup is characterized by an indolent disease course, almost uniformly fatal, yet little is known about the biologic characteristics. The aim of this study was to identify differential features regarding DNA copy number alterations, α-thalassemia/mental retardation syndrome X-linked (ATRX) protein expression, and the presence of tumor-associated inflammatory cells. Thirty-one NB patients older than 10 years who were included in the Spanish NB Registry were considered for the current study; seven young and middle-aged adult patients (range 18-60 years) formed part of the cohort. We performed single nucleotide polymorphism arrays, immunohistochemistry for immune markers (CD4, CD8, CD20, CD11b, CD11c, and CD68), and ATRX protein expression. Assorted genetic profiles were found with a predominant presence of a segmental chromosome aberration (SCA) profile. Preadolescent and adolescent NB tumors showed a higher number of SCA, including 17q gain and 11q deletion. There was also a marked infiltration of immune cells, mainly high and heterogeneous, in young and middle-aged adult tumors. ATRX negative expression was present in the tumors. The characteristics of preadolescent, adolescent, young adult, and middle-aged adult NB tumors are different, not only from childhood NB tumors but also from each other. Similar examinations of a larger number of such tumor tissues from cooperative groups should lead to a better older age–dependent tumor pattern and to innovative, individual risk-adapted therapeutic approaches for these patients.
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Affiliation(s)
- Ana P Berbegall
- Pathology Department, Medical School, University of Valencia, INCLIVA, Valencia, Spain; Medical Research Foundation INCLIVA, Hospital Clínico, INCLIVA, Valencia, Spain
| | - Eva Villamón
- Pathology Department, Medical School, University of Valencia, INCLIVA, Valencia, Spain
| | - Irene Tadeo
- Pathology Department, Medical School, University of Valencia, INCLIVA, Valencia, Spain; Medical Research Foundation INCLIVA, Hospital Clínico, INCLIVA, Valencia, Spain
| | - Tommy Martinsson
- Department of Clinical Genetics, Göteborg University, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Adela Cañete
- Pediatric Oncology Unit, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Victoria Castel
- Pediatric Oncology Unit, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Samuel Navarro
- Pathology Department, Medical School, University of Valencia, INCLIVA, Valencia, Spain
| | - Rosa Noguera
- Pathology Department, Medical School, University of Valencia, INCLIVA, Valencia, Spain.
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15
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Marquez SB, Thompson KW, Lu L, Reisman D. Beyond Mutations: Additional Mechanisms and Implications of SWI/SNF Complex Inactivation. Front Oncol 2015; 4:372. [PMID: 25774356 PMCID: PMC4343012 DOI: 10.3389/fonc.2014.00372] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 12/11/2014] [Indexed: 01/14/2023] Open
Abstract
UNLABELLED SWI/SNF is a major regulator of gene expression. Its role is to facilitate the shifting and exposure of DNA segments within the promoter and other key domains to transcription factors and other essential cellular proteins. This complex interacts with a wide range of proteins and does not function within a single, specific pathway; thus, it is involved in a multitude of cellular processes, including DNA repair, differentiation, development, cell adhesion, and growth control. Given SWI/SNF's prominent role in these processes, many of which are important for blocking cancer development, it is not surprising that the SWI/SNF complex is targeted during cancer initiation and progression both by mutations and by non-mutational mechanisms. Currently, the understanding of the types of alterations, their frequency, and their impact on the SWI/SNF subunits is an area of intense research that has been bolstered by a recent cadre of NextGen sequencing studies. These studies have revealed mutations in SWI/SNF subunits, indicating that this complex is thus important for cancer development. The purpose of this review is to put into perspective the role of mutations versus other mechanisms in the silencing of SWI/SNF subunits, in particular, BRG1 and BRM. In addition, this review explores the recent development of synthetic lethality and how it applies to this complex, as well as how BRM polymorphisms are becoming recognized as potential clinical biomarkers for cancer risk. SIGNIFICANCE Recent reviews have detailed the occurrence of mutations in nearly all SWI/SNF subunits, which indicates that this complex is an important target for cancer. However, when the frequency of mutations in a given tumor type is compared to the frequency of subunit loss, it becomes clear that other non-mutational mechanisms must play a role in the inactivation of SWI/SNF subunits. Such data indicate that epigenetic mechanisms that are known to regulate BRM may also be involved in the loss of expression of other SWI/SNF subunits. This is important since epigenetically silenced genes are inducible, and thus, the reversal of the silencing of these non-mutationally suppressed subunits may be a viable mode of targeted therapy.
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Affiliation(s)
- Stefanie B Marquez
- Department of Medicine, Division of Hematology/Oncology, University of Florida , Gainesville, FL , USA
| | - Kenneth W Thompson
- Department of Medicine, Division of Hematology/Oncology, University of Florida , Gainesville, FL , USA
| | - Li Lu
- Department of Pathology, University of Florida , Gainesville, FL , USA
| | - David Reisman
- Department of Medicine, Division of Hematology/Oncology, University of Florida , Gainesville, FL , USA
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16
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Defferrari R, Mazzocco K, Ambros IM, Ambros PF, Bedwell C, Beiske K, Bénard J, Berbegall AP, Bown N, Combaret V, Couturier J, Erminio G, Gambini C, Garaventa A, Gross N, Haupt R, Kohler J, Jeison M, Lunec J, Marques B, Martinsson T, Noguera R, Parodi S, Schleiermacher G, Tweddle DA, Valent A, Van Roy N, Vicha A, Villamon E, Tonini GP. Influence of segmental chromosome abnormalities on survival in children over the age of 12 months with unresectable localised peripheral neuroblastic tumours without MYCN amplification. Br J Cancer 2014; 112:290-5. [PMID: 25356804 PMCID: PMC4453444 DOI: 10.1038/bjc.2014.557] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 09/22/2014] [Accepted: 10/04/2014] [Indexed: 01/06/2023] Open
Abstract
Background: The prognostic impact of segmental chromosome alterations (SCAs) in children older than 1 year, diagnosed with localised unresectable neuroblastoma (NB) without MYCN amplification enrolled in the European Unresectable Neuroblastoma (EUNB) protocol is still to be clarified, while, for other group of patients, the presence of SCAs is associated with poor prognosis. Methods: To understand the role of SCAs we performed multilocus/pangenomic analysis of 98 tumour samples from patients enrolled in the EUNB protocol. Results: Age at diagnosis was categorised into two groups using 18 months as the age cutoff. Significant difference in the presence of SCAs was seen in tumours of patients between 12 and 18 months and over 18 months of age at diagnosis, respectively (P=0.04). A significant correlation (P=0.03) was observed between number of SCAs per tumour and age. Event-free (EFS) and overall survival (OS) were calculated in both age groups, according to both the presence and number of SCAs. In older patients, a poorer survival was associated with the presence of SCAs (EFS=46% vs 75%, P=0.023; OS=66.8% vs 100%, P=0.003). Moreover, OS of older patients inversely correlated with number of SCAs (P=0.002). Finally, SCAs provided additional prognostic information beyond histoprognosis, as their presence was associated with poorer OS in patients over 18 months with unfavourable International Neuroblastoma Pathology Classification (INPC) histopathology (P=0.018). Conclusions: The presence of SCAs is a negative prognostic marker that impairs outcome of patients over the age of 18 months with localised unresectable NB without MYCN amplification, especially when more than one SCA is present. Moreover, in older patients with unfavourable INPC tumour histoprognosis, the presence of SCAs significantly affects OS.
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Affiliation(s)
- R Defferrari
- Department of Pathology, Istituto Giannina Gaslini, Genova 16148, Italy
| | - K Mazzocco
- Department of Pathology, Istituto Giannina Gaslini, Genova 16148, Italy
| | - I M Ambros
- Children's Cancer Research Institute, St Anna Kinderkrebsforschung, Vienna 1090, Austria
| | - P F Ambros
- Children's Cancer Research Institute, St Anna Kinderkrebsforschung, Vienna 1090, Austria
| | - C Bedwell
- Northern Genetics Service, Newcastle upon Tyne NEI 3 BZ, UK
| | - K Beiske
- Department of Pathology, Oslo University Hospital Rikshopitalet, Oslo 0424, Norway
| | - J Bénard
- Département de Biologie et de Pathologie Médicales, Gustave Roussy Cancer Campus, Villejuif 94800, France
| | - A P Berbegall
- Department of Pathology, Medical School of Valencia, University of Valencia, Valencia 46010, Spain
| | - N Bown
- Northern Genetics Service, Newcastle upon Tyne NEI 3 BZ, UK
| | - V Combaret
- Laboratoire de Recherche Translationnelle, Centre Léon-Bérard, Lyon 69008, France
| | - J Couturier
- Unité de Génétique Somatique et Cytogénétique, Institut Curie, Paris Cedex 05 75248, France
| | - G Erminio
- Epidemiology, Biostatistics and Committees Unit, Istituto Giannina Gaslini, Genova 16148, Italy
| | - C Gambini
- Department of Pathology, Istituto Giannina Gaslini, Genova 16148, Italy
| | - A Garaventa
- Department of Haematology-Oncology, Istituto Giannina Gaslini, Genova 16148, Italy
| | - N Gross
- Pediatric Oncology Research Unit, Lausanne University Hospital (CHUV), Lausanne 1011, Switzerland
| | - R Haupt
- Epidemiology, Biostatistics and Committees Unit, Istituto Giannina Gaslini, Genova 16148, Italy
| | - J Kohler
- Department of Paediatric Oncology, Southampton General Hospital, Southampton S016 6YD, UK
| | - M Jeison
- Cancer Cytogenetique and Molecular Cytogenetique Laboratory, Schneider Children's Medical Center of Israel, Petah Tikva, Israel
| | - J Lunec
- Northern Institute for Cancer Research, Newcastle University, Newcastle NE2 4HH, UK
| | - B Marques
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, Lisbon 1649-016, Portugal
| | - T Martinsson
- Department of Clinical Genetics, Göteborg University, Sahlgrenska University Hospital, Göteborg 413 45, Sweden
| | - R Noguera
- Department of Pathology, Medical School of Valencia, University of Valencia, Valencia 46010, Spain
| | - S Parodi
- Institute of Electronics, Computer and Telecommunication Engineering, National Research Council, Genova 16149, Italy
| | - G Schleiermacher
- 1] INSERM U830, Laboratoire de Génétique et Biologie des Cancers, Paris Cedex 05 75248, France [2] Département d'Oncologie Pédiatrique, Institut Curie, Paris Cedex 05 75248, France
| | - D A Tweddle
- Northern Institute for Cancer Research, Newcastle University, Newcastle NE2 4HH, UK
| | - A Valent
- Département de Biologie et de Pathologie Médicales, Gustave Roussy Cancer Campus, Villejuif 94800, France
| | - N Van Roy
- Center for Medical Genetics, Ghent University Hospital, Ghent 9000, Belgium
| | - A Vicha
- Department of Paediatric Haematology and Oncology, Charles University and University Hospital Motol, Prague 15008, Czech Republic
| | - E Villamon
- Department of Hematology, Hospital Universitari i Politècnic La Fe, Valencia 46009, Spain
| | - G P Tonini
- Laboratory of Neuroblastoma, Onco/Haematology Laboratory, University of Padua, Pediatric Research Institute (IRP)-Città della Speranza, Corso Stati Uniti 4, Padova 35127, Italy
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17
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Umapathy G, El Wakil A, Witek B, Chesler L, Danielson L, Deng X, Gray NS, Johansson M, Kvarnbrink S, Ruuth K, Schönherr C, Palmer RH, Hallberg B. The kinase ALK stimulates the kinase ERK5 to promote the expression of the oncogene MYCN in neuroblastoma. Sci Signal 2014; 7:ra102. [PMID: 25351247 DOI: 10.1126/scisignal.2005470] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Anaplastic lymphoma kinase (ALK) is an important molecular target in neuroblastoma. Although tyrosine kinase inhibitors abrogating ALK activity are currently in clinical use for the treatment of ALK-positive (ALK(+)) disease, monotherapy with ALK tyrosine kinase inhibitors may not be an adequate solution for ALK(+) neuroblastoma patients. Increased expression of the gene encoding the transcription factor MYCN is common in neuroblastomas and correlates with poor prognosis. We found that the kinase ERK5 [also known as big mitogen-activated protein kinase (MAPK) 1 (BMK1)] is activated by ALK through a pathway mediated by phosphoinositide 3-kinase (PI3K), AKT, MAPK kinase kinase 3 (MEKK3), and MAPK kinase 5 (MEK5). ALK-induced transcription of MYCN and stimulation of cell proliferation required ERK5. Pharmacological or RNA interference-mediated inhibition of ERK5 suppressed the proliferation of neuroblastoma cells in culture and enhanced the antitumor efficacy of the ALK inhibitor crizotinib in both cells and xenograft models. Together, our results indicate that ERK5 mediates ALK-induced transcription of MYCN and proliferation of neuroblastoma, suggesting that targeting both ERK5 and ALK may be beneficial in neuroblastoma patients.
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Affiliation(s)
- Ganesh Umapathy
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-405 30 Göteborg, Sweden
| | - Abeer El Wakil
- Department of Molecular Biology, Building 6L, Umeå University, 901 87 Umeå, Sweden
| | - Barbara Witek
- Department of Molecular Biology, Building 6L, Umeå University, 901 87 Umeå, Sweden
| | - Louis Chesler
- The Institute of Cancer Research, The Royal Marsden NHS Foundation Trust, Sutton, Surrey SM2 5NG, UK
| | - Laura Danielson
- The Institute of Cancer Research, The Royal Marsden NHS Foundation Trust, Sutton, Surrey SM2 5NG, UK
| | - Xianming Deng
- School of Life Sciences, Xiamen University, Xiamen, Fujian 361005, China. Dana-Farber Cancer Institute, Harvard Medical School, Seeley G. Mudd Building, 628A, 250 Longwood Avenue, Boston, MA 02115, USA
| | - Nathanael S Gray
- Dana-Farber Cancer Institute, Harvard Medical School, Seeley G. Mudd Building, 628A, 250 Longwood Avenue, Boston, MA 02115, USA
| | - Mikael Johansson
- Department of Radiation Sciences, Oncology, Umeå University, 901 87 Umea, Sweden
| | - Samuel Kvarnbrink
- Department of Radiation Sciences, Oncology, Umeå University, 901 87 Umea, Sweden
| | - Kristina Ruuth
- Department of Molecular Biology, Building 6L, Umeå University, 901 87 Umeå, Sweden
| | - Christina Schönherr
- Department of Molecular Biology, Building 6L, Umeå University, 901 87 Umeå, Sweden
| | - Ruth H Palmer
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-405 30 Göteborg, Sweden. Department of Molecular Biology, Building 6L, Umeå University, 901 87 Umeå, Sweden
| | - Bengt Hallberg
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-405 30 Göteborg, Sweden.
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18
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Ambros IM, Brunner C, Abbasi R, Frech C, Ambros PF. Ultra-High Density SNParray in Neuroblastoma Molecular Diagnostics. Front Oncol 2014; 4:202. [PMID: 25161957 PMCID: PMC4129917 DOI: 10.3389/fonc.2014.00202] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 07/15/2014] [Indexed: 12/27/2022] Open
Abstract
Neuroblastoma serves as a paradigm for applying tumor genomic data for determining patient prognosis and thus for treatment allocation. MYCN status, i.e., amplified vs. non-amplified, was one of the very first biomarkers in oncology to discriminate aggressive from less aggressive or even favorable clinical courses of neuroblastoma. However, MYCN amplification is by far not the only genetic change associated with unfavorable clinical courses. So called “segmental chromosomal aberrations,” (SCAs) i.e., gains or losses of chromosomal fragments, can also indicate tumor aggressiveness. The clinical use of these genomic aberrations has, however, been hampered for many years by methodical and interpretational problems. Only after reaching worldwide consensus on markers, methodology, and data interpretation, information on SCAs has recently been implemented in clinical studies. Now, a number of collaborative studies within COG, GPOH, and SIOPEN use genomic information to stratify therapy for patients with localized and metastatic disease. Recently, new types of DNA based aberrations influencing the clinical behavior of neuroblastomas have been described. Deletions or mutations of genes like ATRX and a phenomenon referred to as “chromothripsis” are all assumed to correlate with an unfavorable clinical behavior. However, these genomic aberrations need to be scrutinized in larger studies applying the most appropriate techniques. Single nucleotide polymorphism arrays have proven successful in deciphering genomic aberrations of cancer cells; these techniques, however, are usually not applied in the daily routine. Here, we present an ultra-high density (UHD) SNParray technique which is, because of its high specificity and sensitivity and the combined copy number and allele information, highly appropriate for the genomic diagnosis of neuroblastoma and other malignancies.
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Affiliation(s)
- Inge M Ambros
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung , Vienna , Austria
| | - Clemens Brunner
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung , Vienna , Austria
| | - Reza Abbasi
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung , Vienna , Austria
| | - Christian Frech
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung , Vienna , Austria
| | - Peter F Ambros
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung , Vienna , Austria ; Department of Pediatrics, Medical University of Vienna , Vienna , Austria
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19
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Gustafson WC, Matthay KK. Progress towards personalized therapeutics: biologic- and risk-directed therapy for neuroblastoma. Expert Rev Neurother 2014; 11:1411-23. [DOI: 10.1586/ern.11.103] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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20
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Romania P, Castellano A, Surace C, Citti A, De Ioris MA, Sirleto P, De Mariano M, Longo L, Boldrini R, Angioni A, Locatelli F, Fruci D. High-resolution array CGH profiling identifies Na/K transporting ATPase interacting 2 (NKAIN2) as a predisposing candidate gene in neuroblastoma. PLoS One 2013; 8:e78481. [PMID: 24205241 PMCID: PMC3808344 DOI: 10.1371/journal.pone.0078481] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 09/13/2013] [Indexed: 02/06/2023] Open
Abstract
Neuroblastoma (NB), the most common solid cancer in early childhood, usually occurs sporadically but also its familial occurance is known in 1-2% of NB patients. Germline mutations in the ALK and PHOX2B genes have been found in a subset of familial NBs. However, because some individuals harbouring mutations in these genes do not develop this tumor, additional genetic alterations appear to be required for NB pathogenesis. Herein, we studied an Italian family with three NB patients, two siblings and a first cousin, carrying an ALK germline-activating mutation R1192P, that was inherited from their unaffected mothers and with no mutations in the PHOX2B gene. A comparison between somatic and germline DNA copy number changes in the two affected siblings by a high resolution array-based Comparative Genomic Hybridization (CGH) analysis revealed a germline gain at NKAIN2 (Na/K transporting ATPase interacting 2) locus in one of the sibling, that was inherited from the parent who does not carry the ALK mutation. Surprisingly, NKAIN2 was expressed at high levels also in the affected sibling that lacks the genomic gain at this locus, clearly suggesting the existance of other regulatory mechanisms. High levels of NKAIN2 were detected in the MYCN-amplified NB cell lines and in the most aggressive NB lesions as well as in the peripheral blood of a large cohort of NB patients. Consistent with a role of NKAIN2 in NB development, NKAIN2 was down-regulated during all-trans retinoic acid differentiation in two NB cell lines. Taken together, these data indicate a potential role of NKAIN2 gene in NB growth and differentiation.
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Affiliation(s)
- Paolo Romania
- Paediatric Haematology/Oncology Department, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Aurora Castellano
- Paediatric Haematology/Oncology Department, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Cecilia Surace
- Cytogenetics and Molecular Genetics Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Arianna Citti
- Pathology Department, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | | | - Pietro Sirleto
- Cytogenetics and Molecular Genetics Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Marilena De Mariano
- Immunological Therapy, IRCCS A.O.U. San Martino-IST, Istituto Nazionale per la Ricerca sul Cancro, Genoa, Italy
| | - Luca Longo
- Immunological Therapy, IRCCS A.O.U. San Martino-IST, Istituto Nazionale per la Ricerca sul Cancro, Genoa, Italy
| | - Renata Boldrini
- Pathology Department, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Adriano Angioni
- Cytogenetics and Molecular Genetics Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Franco Locatelli
- Paediatric Haematology/Oncology Department, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
- Pediatrics Department, University of Pavia, Pavia, Italy
| | - Doriana Fruci
- Paediatric Haematology/Oncology Department, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
- * E-mail:
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21
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Abstract
The burgeoning field of anaplastic lymphoma kinase (ALK) in cancer encompasses many cancer types, from very rare cancers to the more prevalent non-small-cell lung cancer (NSCLC). The common activation of ALK has led to the use of the ALK tyrosine kinase inhibitor (TKI) crizotinib in a range of patient populations and to the rapid development of second-generation drugs targeting ALK. In this Review, we discuss our current understanding of ALK function in human cancer and the implications for tumour treatment.
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MESH Headings
- Anaplastic Lymphoma Kinase
- Animals
- Antineoplastic Agents/therapeutic use
- Caenorhabditis elegans Proteins/physiology
- Cell Transformation, Neoplastic/genetics
- Clinical Trials as Topic
- Crizotinib
- Drosophila Proteins/physiology
- Drug Resistance, Neoplasm
- Enzyme Induction
- Gene Expression Regulation, Developmental
- Gene Expression Regulation, Neoplastic
- Humans
- Lymphoma, Large-Cell, Anaplastic/enzymology
- Lymphoma, Large-Cell, Anaplastic/genetics
- Mice
- Models, Biological
- Models, Molecular
- Mutation
- Neoplasm Proteins/biosynthesis
- Neoplasm Proteins/chemistry
- Neoplasm Proteins/genetics
- Neoplasm Proteins/physiology
- Neoplasms/drug therapy
- Neoplasms/enzymology
- Neoplasms/genetics
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/physiology
- Protein Conformation
- Protein-Tyrosine Kinases/physiology
- Pyrazoles/therapeutic use
- Pyridines/therapeutic use
- Receptor Protein-Tyrosine Kinases/biosynthesis
- Receptor Protein-Tyrosine Kinases/chemistry
- Receptor Protein-Tyrosine Kinases/genetics
- Receptor Protein-Tyrosine Kinases/physiology
- Signal Transduction
- Translocation, Genetic
- Zebrafish Proteins/physiology
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Affiliation(s)
- Bengt Hallberg
- Department of Molecular Biology, Building 6L, Umeå University, Umeå S-90187, Sweden
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22
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Wilzén A, Krona C, Sveinbjörnsson B, Kristiansson E, Dalevi D, Øra I, De Preter K, Stallings RL, Maris J, Versteeg R, Nilsson S, Kogner P, Abel F. ERBB3 is a marker of a ganglioneuroblastoma/ganglioneuroma-like expression profile in neuroblastic tumours. Mol Cancer 2013; 12:70. [PMID: 23835063 PMCID: PMC3766266 DOI: 10.1186/1476-4598-12-70] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 06/25/2013] [Indexed: 12/21/2022] Open
Abstract
Background Neuroblastoma (NB) tumours are commonly divided into three cytogenetic subgroups. However, by unsupervised principal components analysis of gene expression profiles we recently identified four distinct subgroups, r1-r4. In the current study we characterized these different subgroups in more detail, with a specific focus on the fourth divergent tumour subgroup (r4). Methods Expression microarray data from four international studies corresponding to 148 neuroblastic tumour cases were subject to division into four expression subgroups using a previously described 6-gene signature. Differentially expressed genes between groups were identified using Significance Analysis of Microarray (SAM). Next, gene expression network modelling was performed to map signalling pathways and cellular processes representing each subgroup. Findings were validated at the protein level by immunohistochemistry and immunoblot analyses. Results We identified several significantly up-regulated genes in the r4 subgroup of which the tyrosine kinase receptor ERBB3 was most prominent (fold change: 132–240). By gene set enrichment analysis (GSEA) the constructed gene network of ERBB3 (n = 38 network partners) was significantly enriched in the r4 subgroup in all four independent data sets. ERBB3 was also positively correlated to the ErbB family members EGFR and ERBB2 in all data sets, and a concurrent overexpression was seen in the r4 subgroup. Further studies of histopathology categories using a fifth data set of 110 neuroblastic tumours, showed a striking similarity between the expression profile of r4 to ganglioneuroblastoma (GNB) and ganglioneuroma (GN) tumours. In contrast, the NB histopathological subtype was dominated by mitotic regulating genes, characterizing unfavourable NB subgroups in particular. The high ErbB3 expression in GN tumour types was verified at the protein level, and showed mainly expression in the mature ganglion cells. Conclusions Conclusively, this study demonstrates the importance of performing unsupervised clustering and subtype discovery of data sets prior to analyses to avoid a mixture of tumour subtypes, which may otherwise give distorted results and lead to incorrect conclusions. The current study identifies ERBB3 as a clear-cut marker of a GNB/GN-like expression profile, and we suggest a 7-gene expression signature (including ERBB3) as a complement to histopathology analysis of neuroblastic tumours. Further studies of ErbB3 and other ErbB family members and their role in neuroblastic differentiation and pathogenesis are warranted.
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Affiliation(s)
- Annica Wilzén
- Department of Clinical Genetics, Institution of Biomedicine, Box 413, S- 405 30, Gothenburg University, Gothenburg, Sweden.
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23
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Cetinkaya C, Martinsson T, Sandgren J, Träger C, Kogner P, Dumanski J, Díaz de Ståhl T, Hedborg F. Age dependence of tumor genetics in unfavorable neuroblastoma: arrayCGH profiles of 34 consecutive cases, using a Swedish 25-year neuroblastoma cohort for validation. BMC Cancer 2013; 13:231. [PMID: 23656755 PMCID: PMC3664071 DOI: 10.1186/1471-2407-13-231] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 04/23/2013] [Indexed: 12/18/2022] Open
Abstract
Background Aggressive neuroblastoma remains a significant cause of childhood cancer death despite current intensive multimodal treatment protocols. The purpose of the present work was to characterize the genetic and clinical diversity of such tumors by high resolution arrayCGH profiling. Methods Based on a 32K BAC whole-genome tiling path array and using 50-250K Affymetrix SNP array platforms for verification, DNA copy number profiles were generated for 34 consecutive high-risk or lethal outcome neuroblastomas. In addition, age and MYCN amplification (MNA) status were retrieved for 112 unfavorable neuroblastomas of the Swedish Childhood Cancer Registry, representing a 25-year neuroblastoma cohort of Sweden, here used for validation of the findings. Statistical tests used were: Fisher’s exact test, Bayes moderated t-test, independent samples t-test, and correlation analysis. Results MNA or segmental 11q loss (11q-) was found in 28/34 tumors. With two exceptions, these aberrations were mutually exclusive. Children with MNA tumors were diagnosed at significantly younger ages than those with 11q- tumors (mean: 27.4 vs. 69.5 months; p=0.008; n=14/12), and MNA tumors had significantly fewer segmental chromosomal aberrations (mean: 5.5 vs. 12.0; p<0.001). Furthermore, in the 11q- tumor group a positive correlation was seen between the number of segmental aberrations and the age at diagnosis (Pearson Correlation 0.606; p=0.037). Among nonMNA/non11q- tumors (n=6), one tumor displayed amplicons on 11q and 12q and three others bore evidence of progression from low-risk tumors due to retrospective evidence of disease six years before diagnosis, or due to tumor profiles with high proportions of numerical chromosomal aberrations. An early age at diagnosis of MNA neuroblastomas was verified by registry data, with an average of 29.2 months for 43 cases that were not included in the present study. Conclusion MNA and segmental 11q loss define two major genetic variants of unfavorable neuroblastoma with apparent differences in their pace of tumor evolution and in genomic integrity. Other possible, but less common, routes in the development of aggressive tumors are progression of low-risk infant-type lesions, and gene amplifications other than MYCN. Knowledge on such nosological diversity of aggressive neuroblastoma might influence future strategies for therapy.
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Affiliation(s)
- Cihan Cetinkaya
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala SE-751 85, Sweden
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24
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Domingo-Fernandez R, Watters K, Piskareva O, Stallings RL, Bray I. The role of genetic and epigenetic alterations in neuroblastoma disease pathogenesis. Pediatr Surg Int 2013; 29:101-19. [PMID: 23274701 PMCID: PMC3557462 DOI: 10.1007/s00383-012-3239-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/12/2012] [Indexed: 12/11/2022]
Abstract
Neuroblastoma is a highly heterogeneous tumor accounting for 15 % of all pediatric cancer deaths. Clinical behavior ranges from the spontaneous regression of localized, asymptomatic tumors, as well as metastasized tumors in infants, to rapid progression and resistance to therapy. Genomic amplification of the MYCN oncogene has been used to predict outcome in neuroblastoma for over 30 years, however, recent methodological advances including miRNA and mRNA profiling, comparative genomic hybridization (array-CGH), and whole-genome sequencing have enabled the detailed analysis of the neuroblastoma genome, leading to the identification of new prognostic markers and better patient stratification. In this review, we will describe the main genetic factors responsible for these diverse clinical phenotypes in neuroblastoma, the chronology of their discovery, and the impact on patient prognosis.
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Affiliation(s)
- Raquel Domingo-Fernandez
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland,Children’s Research Centre, Our Lady’s Children’s Hospital, Crumlin, Dublin, Ireland
| | - Karen Watters
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland,Children’s Research Centre, Our Lady’s Children’s Hospital, Crumlin, Dublin, Ireland
| | - Olga Piskareva
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland,Children’s Research Centre, Our Lady’s Children’s Hospital, Crumlin, Dublin, Ireland
| | - Raymond L. Stallings
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland,Children’s Research Centre, Our Lady’s Children’s Hospital, Crumlin, Dublin, Ireland
| | - Isabella Bray
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland,Children’s Research Centre, Our Lady’s Children’s Hospital, Crumlin, Dublin, Ireland
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25
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Kumps C, Fieuw A, Mestdagh P, Menten B, Lefever S, Pattyn F, De Brouwer S, Sante T, Schulte JH, Schramm A, Van Roy N, Van Maerken T, Noguera R, Combaret V, Devalck C, Westermann F, Laureys G, Eggert A, Vandesompele J, De Preter K, Speleman F. Focal DNA copy number changes in neuroblastoma target MYCN regulated genes. PLoS One 2013; 8:e52321. [PMID: 23308108 PMCID: PMC3537730 DOI: 10.1371/journal.pone.0052321] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Accepted: 11/16/2012] [Indexed: 02/07/2023] Open
Abstract
Neuroblastoma is an embryonic tumor arising from immature sympathetic nervous system cells. Recurrent genomic alterations include MYCN and ALK amplification as well as recurrent patterns of gains and losses of whole or large partial chromosome segments. A recent whole genome sequencing effort yielded no frequently recurring mutations in genes other than those affecting ALK. However, the study further stresses the importance of DNA copy number alterations in this disease, in particular for genes implicated in neuritogenesis. Here we provide additional evidence for the importance of focal DNA copy number gains and losses, which are predominantly observed in MYCN amplified tumors. A focal 5 kb gain encompassing the MYCN regulated miR-17∼92 cluster as sole gene was detected in a neuroblastoma cell line and further analyses of the array CGH data set demonstrated enrichment for other MYCN target genes in focal gains and amplifications. Next we applied an integrated genomics analysis to prioritize MYCN down regulated genes mediated by MYCN driven miRNAs within regions of focal heterozygous or homozygous deletion. We identified RGS5, a negative regulator of G-protein signaling implicated in vascular normalization, invasion and metastasis, targeted by a focal homozygous deletion, as a new MYCN target gene, down regulated through MYCN activated miRNAs. In addition, we expand the miR-17∼92 regulatory network controlling TGFß signaling in neuroblastoma with the ring finger protein 11 encoding gene RNF11, which was previously shown to be targeted by the miR-17∼92 member miR-19b. Taken together, our data indicate that focal DNA copy number imbalances in neuroblastoma (1) target genes that are implicated in MYCN signaling, possibly selected to reinforce MYCN oncogene addiction and (2) serve as a resource for identifying new molecular targets for treatment.
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Affiliation(s)
- Candy Kumps
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Annelies Fieuw
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Pieter Mestdagh
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Björn Menten
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Steve Lefever
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Filip Pattyn
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Sara De Brouwer
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Tom Sante
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Johannes Hubertus Schulte
- Department of Pediatric Oncology and Haematology, University Children's Hospital Essen, Essen, Germany
| | - Alexander Schramm
- Department of Pediatric Oncology and Haematology, University Children's Hospital Essen, Essen, Germany
| | - Nadine Van Roy
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Tom Van Maerken
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Rosa Noguera
- Department of Pathology, Medical School, University of Valencia, Valencia, Spain
| | - Valérie Combaret
- Centre Léon Bérard, FNCLCC, Laboratoire de Recherche Translationnelle, Lyon, France
| | - Christine Devalck
- Children's University Hospital, Hematology-Oncology, Brussels, Belgium
| | - Frank Westermann
- Department of Tumor Genetics, German Cancer Research Center, Heidelberg, Germany
| | - Geneviève Laureys
- Department of Pediatric Hematology-Oncology, Ghent University Hospital, Ghent, Belgium
| | - Angelika Eggert
- Department of Pediatric Oncology and Haematology, University Children's Hospital Essen, Essen, Germany
| | - Jo Vandesompele
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Katleen De Preter
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Frank Speleman
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- * E-mail:
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Wilkerson PM, Reis-Filho JS. the 11q13-q14 amplicon: Clinicopathological correlations and potential drivers. Genes Chromosomes Cancer 2012; 52:333-55. [DOI: 10.1002/gcc.22037] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2012] [Accepted: 11/01/2012] [Indexed: 01/04/2023] Open
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Krüppel-like factor 4 (KLF4) suppresses neuroblastoma cell growth and determines non-tumorigenic lineage differentiation. Oncogene 2012; 32:4086-99. [PMID: 23045286 DOI: 10.1038/onc.2012.437] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2011] [Revised: 06/27/2012] [Accepted: 07/25/2012] [Indexed: 02/07/2023]
Abstract
Neuroblastoma (NB) is an embryonal tumor and possesses a unique propensity to exhibit either a spontaneous regression or an unrestrained growth. However, the underlying mechanism for this paradoxical clinical outcome remains largely unclear. Quantitative RT-PCR analysis on 102 primary NB tumors revealed that lower Krüppel-like factor 4 (KLF4) expression is frequently found in the unfavorable NB (Mann-Whitney test, P=0.027). In particular with the high-risk factors such as age of patient >1 year, MYCN amplification and low TRKA expression, the decreased expression of KLF4 was significantly associated with an unfavorable NB outcome. Despite knockdown of KLF4 alone is not sufficient to increase tumorigenicity of NB cells in vivo, stable expression of KLF4 short hairpin RNA in Be(2)-C cells significantly promoted growth of NB cells and inhibited cell differentiation toward fibromuscular lineage. In concordant with these observations, overexpression of KLF4 in SH-SY-5Y cells profoundly suppressed cell proliferation by direct upregulation of cell-cycle inhibitor protein p21(WAF1/CIP1), and knocking down p21(WAF1/CIP1) could partially rescue the suppressive effect of KLF4. Importantly, KLF4 overexpressing cells have lost their neuroblastic phenotypes, they were epithelial-like, strongly substrate-adherent, expressing smooth muscle marker and became non-tumorigenic, suggesting that KLF4 expression is crucial for lineage determination of NB cells, probably, favoring spontaneous tumor regression. Subsequent global gene expression profiling further revealed that transforming growth factor beta (TGFβ) and cell-cycle pathways are highly dysregulated upon KLF4 overexpression, and myogenic modulators, MEF2A and MYOD1 were found significantly upregulated. Taken together, we have demonstrated that KLF4 contributes to the favorable disease outcome by directly mediating the growth and lineage determination of NB cells.
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Ooi WF, Re A, Sidarovich V, Canella V, Arseni N, Adami V, Guarguaglini G, Giubettini M, Scaruffi P, Stigliani S, Lavia P, Tonini GP, Quattrone A. Segmental chromosome aberrations converge on overexpression of mitotic spindle regulatory genes in high-risk neuroblastoma. Genes Chromosomes Cancer 2012; 51:545-56. [PMID: 22337647 DOI: 10.1002/gcc.21940] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2011] [Revised: 01/06/2012] [Accepted: 01/07/2012] [Indexed: 12/21/2022] Open
Abstract
Integration of genome-wide profiles of DNA copy number alterations (CNAs) and gene expression variations (GEVs) could provide combined power to the identification of driver genes and gene networks in tumors. Here we merge matched genome and transcriptome microarray analyses from neuroblastoma samples to derive correlation patterns of CNAs and GEVs, irrespective of their genomic location. Neuroblastoma correlation patterns are strongly asymmetrical, being on average 10 CNAs linked to 1 GEV, and show the widespread prevalence of long range covariance. Functional enrichment and network analysis of the genes covarying with CNAs consistently point to a major cell function, the regulation of mitotic spindle assembly. Moreover, elevated expression of 14 key genes promoting this function is strongly associated to high-risk neuroblastomas with 1p loss and MYCN amplification in a set of 410 tumor samples (P < 0.00001). Independent CNA/GEV profiling on neuroblastoma cell lines shows that increased levels of expression of these genes are linked to 1p loss. By this approach, we reveal a convergence of clustered neuroblastoma CNAs toward increased expression of a group of prognostic and functionally cooperating genes. We therefore propose gain of function of the spindle assembly machinery as a lesion potentially offering new targets for therapy of high-risk neuroblastoma.
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Affiliation(s)
- Wen Fong Ooi
- Laboratory of Translational Genomics, Centre for Integrative Biology and Department of Information Engineering and Computer Science, University of Trento, 38122 Trento, Italy
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Anaplastic Lymphoma Kinase (ALK) regulates initiation of transcription of MYCN in neuroblastoma cells. Oncogene 2012; 31:5193-200. [PMID: 22286764 DOI: 10.1038/onc.2012.12] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Neuroblastoma is a neural crest-derived embryonal tumour of the postganglionic sympathetic nervous system and a disease with several different chromosomal gains and losses, which include MYCN-amplified neuroblastoma on chromosome 2, deletions of parts of the chromosomes 1p and 11q, gain of parts of 17q and triploidy. Recently, activating mutations of the ALK (Anaplastic Lymphoma Kinase) RTK (Receptor Tyrosine Kinase) gene have been described in neuroblastoma. A meta-analysis of neuroblastoma cases revealed that ALK mutations (49 of 709 cases) in relation to genomic subtype were most frequently observed in MYCN amplified tumours (8.9%), correlating with a poor clinical outcome. MYCN proteins target proliferation and apoptotic pathways, and have an important role in the progression of neuroblastoma. Here, we show that both wild-type and gain-of-function mutants in ALK are able to stimulate transcription at the MYCN promoter and initiate mRNA transcription of the MYCN gene in both neuronal and neuroblastoma cell lines. Further, this stimulation of MYCN gene transcription and de novo MYCN protein expression is abrogated by specific ALK inhibitors, such as crizotinib (PF-2341066), NVP-TAE684, and by small interfering RNA to ALK resulting in a decrease in proliferation rate. Finally, co-transfection of ALK gain-of-function mutations together with MYCN leads to an increase in transformation potential. Taken together, our results indicate that ALK signalling regulates initiation of transcription of the MYCN gene providing a possible explanation for the poor clinical outcome observed when MYCN is amplified together with activated ALK.
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Jeison M, Yaniv I, Ash S. Genetic stratification of neuroblastoma for treatment tailoring. Future Oncol 2012; 7:1087-99. [PMID: 21919696 DOI: 10.2217/fon.11.87] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Neuroblastoma is the most common extracranial tumor of childhood. The clinical behavior is variable, ranging from spontaneous regression to fatal progression despite aggressive therapy. The most highly statistically significant and clinically relevant factors that are currently used for classification include stage, age, histopathologic category, MYCN oncogene status, chromosome 11q status and DNA ploidy. These genetic markers were analyzed separately by classical methods until recently: mainly fluorescence in situ hybridization or loss of heterozygosity. The development of genome-wide techniques such as comparative genomic hybridization, array comparative genomic hybridization and single nucleotide polymorphism allows the analysis of copy number variations through the whole genome in one step. This enabled the investigators to refine different genetic subtypes for the better comprehension of neuroblastoma tumor behavior and reach the conclusion that these data together with a genomic profile based on gene expression should be included in future treatment stratification.
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Affiliation(s)
- Marta Jeison
- Department of Pediatric Hematology-Oncology, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
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High anaplastic lymphoma kinase immunohistochemical staining in neuroblastoma and ganglioneuroblastoma is an independent predictor of poor outcome. THE AMERICAN JOURNAL OF PATHOLOGY 2011; 180:1223-1231. [PMID: 22203052 DOI: 10.1016/j.ajpath.2011.12.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Revised: 11/22/2011] [Accepted: 12/02/2011] [Indexed: 11/22/2022]
Abstract
Anaplastic lymphoma kinase (ALK) mutations occur in 3% to 11% of neuroblastoma (NBL) cases and are associated with high ALK levels. However, high ALK levels appear to be a mutation-independent hallmark of NBL. Evidence about the prognostic relevance of ALK mutations and ALK tumor positivity in patients with NBL has been inconclusive. In this study, we investigated the prognostic relevance of ALK positivity by IHC and ALK mutation status by PCR sequencing in 71 NBL, 12 ganglioneuroblastoma (GNBL), and 20 ganglioneuroma samples in a multivariate model. ALK mutations were present in 2 of 72 NBL and 2 of 12 GNBL samples, which all contained many ALK-positive cells (>50%). In addition, half of all NBL samples showed ALK positivity in most (>50%) of tumor cells, whereas half of the GNBL showed staining in <20% of the tumor cells. In most ganglioneuroma samples, a low percentage of tumor cells stained positive for ALK, which mainly involved ganglion cells. Higher percentages of ALK-positive cells in NBL and GNBL patient samples correlated with inferior survival in univariate and multivariate analyses with established prognostic factors, such as stage, age, and MYCN status. In conclusion, ALK positivity by IHC is an independent, poor prognostic factor in patients with GNBL and NBL. ALK IHC is an easy test suitable for future risk stratification in patients with NBL and GNBL.
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Molenaar JJ, Koster J, Ebus ME, van Sluis P, Westerhout EM, de Preter K, Gisselsson D, Øra I, Speleman F, Caron HN, Versteeg R. Copy number defects of G1-cell cycle genes in neuroblastoma are frequent and correlate with high expression of E2F target genes and a poor prognosis. Genes Chromosomes Cancer 2011; 51:10-9. [PMID: 22034077 DOI: 10.1002/gcc.20926] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Accepted: 08/08/2011] [Indexed: 01/19/2023] Open
Abstract
The tightly controlled network of cell cycle genes consists of a core of cyclin dependent kinases (CDKs) that are activated by periodically expressed cyclins. The activity of the cyclin-CDK complexes is regulated by cyclin dependent kinase inhibitors (CDKIs) and multiple signal transduction routes that converge on the cell cycle. Neuroblastoma are pediatric tumors that belong to the group of small round blue cell tumors, characterized by a fast proliferation. Here, we present high throughput analyses of cell cycle regulating genes in neuroblastoma. We analyzed a series of 82 neuroblastomas by comparative genomic hybridization arrays, single nucleotide polymorphism arrays, and Affymetrix expression arrays and analyzed the datasets in parallel with the R2 bioinformatic tool (http://r2.amc.nl). About 30% of the tumors had genomic amplifications, gains, or losses with shortest regions of overlap that suggested implication of a series of G1 cell cycle regulating genes. CCND1 (cyclin D1) and CDK4 were amplified or gained and the chromosomal regions containing the CDKN2 (INK4) group of CDKIs were frequently deleted. Cluster analysis showed that tumors with genomic aberrations in G1 regulating genes over-expressed E2F target genes, which regulate S and G2/M phase progression. These tumors have a poor prognosis. Our findings suggest that pharmacological inhibition of cell cycle genes might bear therapeutic promises for patients with high risk neuroblastoma.
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Affiliation(s)
- Jan J Molenaar
- Department of Oncogenomics, AMC, University of Amsterdam, Amsterdam, The Netherlands.
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Comprehensive SNP array study of frequently used neuroblastoma cell lines; copy neutral loss of heterozygosity is common in the cell lines but uncommon in primary tumors. BMC Genomics 2011; 12:443. [PMID: 21899760 PMCID: PMC3178547 DOI: 10.1186/1471-2164-12-443] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Accepted: 09/07/2011] [Indexed: 01/19/2023] Open
Abstract
Background Copy neutral loss of heterozygosity (CN-LOH) refers to a special case of LOH occurring without any resulting loss in copy number. These alterations is sometimes seen in tumors as a way to inactivate a tumor suppressor gene and have been found to be important in several types of cancer. Results We have used high density single nucleotide polymorphism arrays in order to investigate the frequency and distribution of CN-LOH and other allelic imbalances in neuroblastoma (NB) tumors and cell lines. Our results show that the frequency of these near-CN-LOH events is significantly higher in the cell lines compared to the primary tumors and that the types of CN-LOH differ between the groups. We also show that the low-risk neuroblastomas that are generally considered to have a "triploid karyotype" often present with a complex numerical karyotype (no segmental changes) with 2-5 copies of each chromosome. Furthermore a comparison has been made between the three related cell lines SK-N-SH, SH-EP and SH-SY5Y with respect to overall genetic aberrations, and several aberrations unique to each of the cell lines has been found. Conclusions We have shown that the NB tumors analyzed contain several interesting allelic imbalances that would either go unnoticed or be misinterpreted using other genome-wide techniques. These findings indicate that the genetics underlying NB might be even more complex than previously known and that SNP arrays are important analysis tools. We have also showed that these near-CN-LOH events are more frequently seen in NB cell lines compared to NB tumors and that a set of highly related cell lines have continued to evolve secondary to the subcloning event. Taken together our analysis highlights that cell lines in many cases differ substantially from the primary tumors they are thought to represent, and that caution should be taken when drawing conclusions from cell line-based studies.
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Fieuw A, Kumps C, Schramm A, Pattyn F, Menten B, Antonacci F, Sudmant P, Schulte JH, Van Roy N, Vergult S, Buckley PG, De Paepe A, Noguera R, Versteeg R, Stallings R, Eggert A, Vandesompele J, De Preter K, Speleman F. Identification of a novel recurrent 1q42.2-1qter deletion in high risk MYCN single copy 11q deleted neuroblastomas. Int J Cancer 2011; 130:2599-606. [PMID: 21796619 DOI: 10.1002/ijc.26317] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Accepted: 07/12/2011] [Indexed: 01/04/2023]
Abstract
Neuroblastoma is an aggressive embryonal tumor that accounts for ∼15% of childhood cancer deaths. Hitherto, despite the availability of comprehensive genomic data on DNA copy number changes in neuroblastoma, relatively little is known about the genes driving neuroblastoma tumorigenesis. In this study, high resolution array comparative genome hybridization (CGH) was performed on 188 primary neuroblastoma tumors and 33 neuroblastoma cell lines to search for previously undetected recurrent DNA copy number gains and losses. A new recurrent distal chromosome 1q deletion (del(1)(q42.2qter)) was detected in seven cases. Further analysis of available array CGH datasets revealed 13 additional similar distal 1q deletions. The majority of all detected 1q deletions was found in high risk 11q deleted tumors without MYCN amplification (Fisher exact test p = 5.61 × 10(-5) ). Using ultra-high resolution (∼115 bp resolution) custom arrays covering the breakpoints on 1q for 11 samples, clustering of nine breakpoints was observed within a 12.5-kb region, of which eight were found in a 7-kb copy number variable region, whereas the remaining two breakpoints were colocated 1.4-Mb proximal. The commonly deleted region contains one miRNA (hsa-mir-1537), four transcribed ultra conserved region elements (uc.43-uc.46) and 130 protein coding genes including at least two bona fide tumor suppressor genes, EGLN1 (or PHD2) and FH. This finding further contributes to the delineation of the genomic profile of aggressive neuroblastoma, offers perspectives for the identification of genes contributing to the disease phenotype and may be relevant in the light of assessment of response to new molecular treatments.
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Affiliation(s)
- Annelies Fieuw
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
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Øra I, Eggert A. Progress in treatment and risk stratification of neuroblastoma: impact on future clinical and basic research. Semin Cancer Biol 2011; 21:217-28. [PMID: 21798350 DOI: 10.1016/j.semcancer.2011.07.002] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Accepted: 07/11/2011] [Indexed: 01/10/2023]
Abstract
Close international collaboration between pediatric oncologists has led to marked improvements in the cure of patients, seen as a long-term overall survival rate of about 80%. Despite this progress, neuroblastoma remains a challenging disease for both clinicians and researchers. Major clinical problems include lack of acceptable cure rates in high-risk neuroblastoma and potential overtreatment of subsets of patients at low and intermediate risk of the disease. Many years of intensive international cooperation have recently led to a promising joint effort to further improve risk classification for treatment stratification, the new International Neuroblastoma Risk Group Classification System. This approach will facilitate comparison of the results of clinical trials performed by different international collaborative groups. This, in turn, should accelerate refinement of risk stratification and thereby aid selection of appropriate therapies for individual patients. To be able to identify new therapeutic modalities, it will be necessary to elucidate the pathogenesis of the different subtypes of neuroblastoma. Basic and translational research have provided new tools for molecular characterization of blood and tumor samples including high-throughput technologies for analysis of DNA, mRNAs, microRNAs and other non-coding RNAs, as well as proteins and epigenetic markers. Most of these studies are array-based in design. In neuroblastoma research they aim to refine risk group stratification through incorporation of molecular tumor fingerprints and also to enable personalized treatment modalities by describing the underlying pathogenesis and aberrant signaling pathways in individual tumors. To make optimal use of these new technologies for the benefit of the patient, it is crucial to have a systematic and detailed documentation of both clinical and molecular data from diagnosis through treatment to follow-up. Close collaboration between clinicians and basic scientists will provide access to combined clinical and molecular data sets and will create more efficient steps in response to the remaining treatment challenges. This review describes the current efforts and trends in neuroblastoma research from a clinical perspective in order to highlight the urgent clinical problems we must address together with basic researchers.
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Affiliation(s)
- Ingrid Øra
- Department of Pediatric Oncology and Hematology, Skåne University Hospital, Lund University, Lund, Sweden.
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Abel F, Dalevi D, Nethander M, Jörnsten R, De Preter K, Vermeulen J, Stallings R, Kogner P, Maris J, Nilsson S. A 6-gene signature identifies four molecular subgroups of neuroblastoma. Cancer Cell Int 2011; 11:9. [PMID: 21492432 PMCID: PMC3095533 DOI: 10.1186/1475-2867-11-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2010] [Accepted: 04/14/2011] [Indexed: 12/03/2022] Open
Abstract
Background There are currently three postulated genomic subtypes of the childhood tumour neuroblastoma (NB); Type 1, Type 2A, and Type 2B. The most aggressive forms of NB are characterized by amplification of the oncogene MYCN (MNA) and low expression of the favourable marker NTRK1. Recently, mutations or high expression of the familial predisposition gene Anaplastic Lymphoma Kinase (ALK) was associated to unfavourable biology of sporadic NB. Also, various other genes have been linked to NB pathogenesis. Results The present study explores subgroup discrimination by gene expression profiling using three published microarray studies on NB (47 samples). Four distinct clusters were identified by Principal Components Analysis (PCA) in two separate data sets, which could be verified by an unsupervised hierarchical clustering in a third independent data set (101 NB samples) using a set of 74 discriminative genes. The expression signature of six NB-associated genes ALK, BIRC5, CCND1, MYCN, NTRK1, and PHOX2B, significantly discriminated the four clusters (p < 0.05, one-way ANOVA test). PCA clusters p1, p2, and p3 were found to correspond well to the postulated subtypes 1, 2A, and 2B, respectively. Remarkably, a fourth novel cluster was detected in all three independent data sets. This cluster comprised mainly 11q-deleted MNA-negative tumours with low expression of ALK, BIRC5, and PHOX2B, and was significantly associated with higher tumour stage, poor outcome and poor survival compared to the Type 1-corresponding favourable group (INSS stage 4 and/or dead of disease, p < 0.05, Fisher's exact test). Conclusions Based on expression profiling we have identified four molecular subgroups of neuroblastoma, which can be distinguished by a 6-gene signature. The fourth subgroup has not been described elsewhere, and efforts are currently made to further investigate this group's specific characteristics.
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Affiliation(s)
- Frida Abel
- Department of Clinical Genetics, Gothenburg University, Gothenburg, Sweden.
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Ambros IM, Brunner B, Aigner G, Bedwell C, Beiske K, Bénard J, Bown N, Combaret V, Couturier J, Defferrari R, Gross N, Jeison M, Lunec J, Marques B, Martinsson T, Mazzocco K, Noguera R, Schleiermacher G, Speleman F, Stallings R, Tonini GP, Tweddle DA, Valent A, Vicha A, Roy NV, Villamon E, Ziegler A, Preuner S, Drobics M, Ladenstein R, Amann G, Schuit RJ, Pötschger U, Ambros PF. A Multilocus Technique for Risk Evaluation of Patients with Neuroblastoma. Clin Cancer Res 2011; 17:792-804. [DOI: 10.1158/1078-0432.ccr-10-0830] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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De Brouwer S, De Preter K, Kumps C, Zabrocki P, Porcu M, Westerhout EM, Lakeman A, Vandesompele J, Hoebeeck J, Van Maerken T, De Paepe A, Laureys G, Schulte JH, Schramm A, Van Den Broecke C, Vermeulen J, Van Roy N, Beiske K, Renard M, Noguera R, Delattre O, Janoueix-Lerosey I, Kogner P, Martinsson T, Nakagawara A, Ohira M, Caron H, Eggert A, Cools J, Versteeg R, Speleman F. Meta-analysis of neuroblastomas reveals a skewed ALK mutation spectrum in tumors with MYCN amplification. Clin Cancer Res 2010; 16:4353-62. [PMID: 20719933 DOI: 10.1158/1078-0432.ccr-09-2660] [Citation(s) in RCA: 201] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
PURPOSE Activating mutations of the anaplastic lymphoma kinase (ALK) were recently described in neuroblastoma. We carried out a meta-analysis of 709 neuroblastoma tumors to determine their frequency and mutation spectrum in relation to genomic and clinical parameters, and studied the prognostic significance of ALK copy number and expression. EXPERIMENTAL DESIGN The frequency and type of ALK mutations, copy number gain, and expression were analyzed in a new series of 254 neuroblastoma tumors. Data from 455 published cases were used for further in-depth analysis. RESULTS ALK mutations were present in 6.9% of 709 investigated tumors, and mutations were found in similar frequencies in favorable [International Neuroblastoma Staging System (INSS) 1, 2, and 4S; 5.7%] and unfavorable (INSS 3 and 4; 7.5%) neuroblastomas (P = 0.087). Two hotspot mutations, at positions R1275 and F1174, were observed (49% and 34.7% of the mutated cases, respectively). Interestingly, the F1174 mutations occurred in a high proportion of MYCN-amplified cases (P = 0.001), and this combined occurrence was associated with a particular poor outcome, suggesting a positive cooperative effect between both aberrations. Furthermore, the F1174L mutant was characterized by a higher degree of autophosphorylation and a more potent transforming capacity as compared with the R1275Q mutant. Chromosome 2p gains, including the ALK locus (91.8%), were associated with a significantly increased ALK expression, which was also correlated with poor survival. CONCLUSIONS ALK mutations occur in equal frequencies across all genomic subtypes, but F1174L mutants are observed in a higher frequency of MYCN-amplified tumors and show increased transforming capacity as compared with the R1275Q mutants.
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Affiliation(s)
- Sara De Brouwer
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
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Rapaport F, Leslie C. Determining frequent patterns of copy number alterations in cancer. PLoS One 2010; 5:e12028. [PMID: 20711339 PMCID: PMC2920822 DOI: 10.1371/journal.pone.0012028] [Citation(s) in RCA: 7] [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: 04/27/2010] [Accepted: 07/02/2010] [Indexed: 01/18/2023] Open
Abstract
Cancer progression is often driven by an accumulation of genetic changes but also accompanied by increasing genomic instability. These processes lead to a complicated landscape of copy number alterations (CNAs) within individual tumors and great diversity across tumor samples. High resolution array-based comparative genomic hybridization (aCGH) is being used to profile CNAs of ever larger tumor collections, and better computational methods for processing these data sets and identifying potential driver CNAs are needed. Typical studies of aCGH data sets take a pipeline approach, starting with segmentation of profiles, calls of gains and losses, and finally determination of frequent CNAs across samples. A drawback of pipelines is that choices at each step may produce different results, and biases are propagated forward. We present a mathematically robust new method that exploits probe-level correlations in aCGH data to discover subsets of samples that display common CNAs. Our algorithm is related to recent work on maximum-margin clustering. It does not require pre-segmentation of the data and also provides grouping of recurrent CNAs into clusters. We tested our approach on a large cohort of glioblastoma aCGH samples from The Cancer Genome Atlas and recovered almost all CNAs reported in the initial study. We also found additional significant CNAs missed by the original analysis but supported by earlier studies, and we identified significant correlations between CNAs.
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Affiliation(s)
| | - Christina Leslie
- Computational Biology Program, Sloan-Kettering Institute, New York, New York, United States of America
- * E-mail:
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Schleiermacher G, Janoueix-Lerosey I, Ribeiro A, Klijanienko J, Couturier J, Pierron G, Mosseri V, Valent A, Auger N, Plantaz D, Rubie H, Valteau-Couanet D, Bourdeaut F, Combaret V, Bergeron C, Michon J, Delattre O. Accumulation of segmental alterations determines progression in neuroblastoma. J Clin Oncol 2010; 28:3122-30. [PMID: 20516441 DOI: 10.1200/jco.2009.26.7955] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
PURPOSE Neuroblastoma is characterized by two distinct types of genetic profiles, consisting of either numerical or segmental chromosome alterations. The latter are associated with a higher risk of relapse, even when occurring together with numerical alterations. We explored the role of segmental alterations in tumor progression and the possibility of evolution from indolent to aggressive genomic types. PATIENTS AND METHODS Array-based comparative genomic hybridization data of 394 neuroblastoma samples were analyzed and linked to clinical data. RESULTS Integration of ploidy and genomic data indicated that pseudotriploid tumors with mixed numerical and segmental profiles may be derived from pseudotriploid tumors with numerical alterations only. This was confirmed by the analysis of paired samples, at diagnosis and at relapse, as in tumors with a purely numerical profile at diagnosis additional segmental alterations at relapse were frequently observed. New segmental alterations at relapse were also seen in patients with segmental alterations at diagnosis. This was not linked to secondary effects of cytotoxic treatments since it occurred even in patients treated with surgery alone. A higher number of chromosome breakpoints were correlated with advanced age at diagnosis, advanced stage of disease, with a higher risk of relapse, and a poorer outcome. CONCLUSION These data provide further evidence of the role of segmental alterations, suggesting that tumor progression is linked to the accumulation of segmental alterations in neuroblastoma. This possibility of genomic evolution should be taken into account in treatment strategies of low- and intermediate-risk neuroblastoma and should warrant biologic reinvestigation at the time of relapse.
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Affiliation(s)
- Gudrun Schleiermacher
- L'Institut National de la Santé et de la Recherche Médicale U830, Institut Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, France
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Kumps C, Van Roy N, Heyrman L, Goossens D, Del-Favero J, Noguera R, Vandesompele J, Speleman F, De Preter K. Multiplex Amplicon Quantification (MAQ), a fast and efficient method for the simultaneous detection of copy number alterations in neuroblastoma. BMC Genomics 2010; 11:298. [PMID: 20459859 PMCID: PMC2879279 DOI: 10.1186/1471-2164-11-298] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2009] [Accepted: 05/12/2010] [Indexed: 11/10/2022] Open
Abstract
Background Cancer genomes display characteristic patterns of chromosomal imbalances, often with diagnostic and prognostic relevance. Therefore assays for genome-wide copy number screening and simultaneous detection of copy number alterations in specific chromosomal regions are of increasing importance in the diagnostic work-up of tumors. Results We tested the performance of Multiplex Amplicon Quantification, a newly developed low-cost, closed-tube and high-throughput PCR-based technique for detection of copy number alterations in regions with prognostic relevance for neuroblastoma. Comparison with array CGH and the established Multiplex Ligation-dependent Probe Amplification method on 52 neuroblastoma tumors showed that Multiplex Amplicon Quantification can reliably detect the important genomic aberrations. Conclusion Multiplex Amplicon Quantification is a low-cost and high-throughput PCR-based technique that can reliably detect copy number alterations in regions with prognostic relevance for neuroblastoma.
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Affiliation(s)
- Candy Kumps
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
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Buckley PG, Alcock L, Bryan K, Bray I, Schulte JH, Schramm A, Eggert A, Mestdagh P, De Preter K, Vandesompele J, Speleman F, Stallings RL. Chromosomal and microRNA expression patterns reveal biologically distinct subgroups of 11q- neuroblastoma. Clin Cancer Res 2010; 16:2971-8. [PMID: 20406844 DOI: 10.1158/1078-0432.ccr-09-3215] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE The purpose of this study was to further define the biology of the 11q- neuroblastoma tumor subgroup by the integration of array-based comparative genomic hybridization with microRNA (miRNA) expression profiling data to determine if improved patient stratification is possible. EXPERIMENTAL DESIGN A set of primary neuroblastoma (n = 160), which was broadly representative of all genetic subtypes, was analyzed by array-based comparative genomic hybridization and for the expression of 430 miRNAs. A 15-miRNA expression signature previously shown to be predictive of clinical outcome was used to analyze an independent cohort of 11q- tumors (n = 37). RESULTS Loss of 4p and gain of 7q occurred at a significantly higher frequency in the 11q- tumors, further defining the genetic characteristics of this subtype. The 11q- tumors could be split into two subgroups using a miRNA expression survival signature that differed significantly in clinical outcome and the overall frequency of large-scale genomic imbalances, with the poor survival subgroup having significantly more imbalances. miRNAs from the expression signature, which were upregulated in unfavorable tumors, were predicted to target downregulated genes from a published mRNA expression classifier of clinical outcome at a higher-than-expected frequency, indicating the miRNAs might contribute to the regulation of genes within the signature. CONCLUSION We show that two distinct biological subtypes of neuroblastoma with loss of 11q occur, which differ in their miRNA expression profiles, frequency of segmental imbalances, and clinical outcome. A miRNA expression signature, combined with an analysis of segmental imbalances, provides greater prediction of event-free survival and overall survival outcomes than 11q status by itself, improving patient stratification.
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Affiliation(s)
- Patrick G Buckley
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland
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Abstract
Almost all neuroblastoma tumors express excess levels of Cyclin D1 (CCND1) compared to normal tissues and other tumor types. Only a small percentage of these neuroblastoma tumors have high-level amplification of the Cyclin D1 gene. The other neuroblastoma tumors have equally high Cyclin D1 expression without amplification. Silencing of Cyclin D1 expression was previously found to trigger differentiation of neuroblastoma cells. Overexpression of Cyclin D1 is therefore one of the most frequent mechanisms with a postulated function in neuroblastoma pathogenesis. The cause for the Cyclin D1 overexpression is unknown. Here we show that Cyclin D1 overexpression results from transcriptional upregulation. To identify upstream regulators, we searched in mRNA profiles of neuroblastoma tumor series for transcription factors with expression patterns correlating to Cyclin D1. GATA3 most consistently correlated to Cyclin D1 in four independent data sets. We identified a highly conserved GATA3 binding site 27 bp upstream of the Cyclin D1 transcriptional start. Chromatin immune precipitation confirmed binding of GATA3 to the Cyclin D1 promoter. Overexpression of GATA3 induced Cyclin D1 promoter activity, which decreased after site-directed mutagenesis of the GATA3 binding site in the Cyclin D1 promoter. Silencing of GATA3 resulted in reduced Cyclin D1 promoter activity and reduced Cyclin D1 mRNA and protein levels. Moreover, GATA3 silencing caused differentiation that was similar to that caused by Cyclin D1 inhibition. These finding implicate GATA3 in Cyclin D1 overexpression in neuroblastoma.
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High-risk neuroblastoma tumors with 11q-deletion display a poor prognostic, chromosome instability phenotype with later onset. Proc Natl Acad Sci U S A 2010; 107:4323-8. [PMID: 20145112 DOI: 10.1073/pnas.0910684107] [Citation(s) in RCA: 165] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Analysis of chromosomal aberrations is used to determine the prognosis of neuroblastomas (NBs) and to aid treatment decisions. MYCN amplification (MNA) alone is an incomplete poor prognostic factor, and chromosome 11q status has recently been included in risk classification. We analyzed 165 NB tumors using high-density SNP microarrays and specifically compared the high-risk groups defined by MNA (n = 37) and 11q-deletion (n = 21). Median patient age at diagnosis was 21 months for MNA tumors and 42 months for 11q-deletion tumors, and median survival time after diagnosis was 16 months for MNA and 40 months for 11q deletion. Overall survival (at 8 years) was approximately 35% in both groups. MNA and 11q deletion were almost mutually exclusive; only one case harbored both aberrations. The numbers of segmental aberrations differed significantly; the MNA group had a median of four aberrations, whereas the 11q-deletion group had 12. The high frequency of chromosomal breaks in the 11q-deletion group is suggestive of a chromosomal instability phenotype gene located in 11q; one such gene, H2AFX, is located in 11q23.3 (within the 11q-deletion region). Furthermore, in the groups with segmental aberrations without MNA or 11q deletion, the tumors with 17q gain have worse prognosis than those with segmental aberrations without 17q gain, which have a favorable outcome. This study has implications for therapy in different risk groups and stresses that genome-wide microarray analyses should be included in clinical management to fully evaluate risk, aid diagnosis, and guide treatment.
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Janoueix-Lerosey I, Schleiermacher G, Delattre O. Molecular pathogenesis of peripheral neuroblastic tumors. Oncogene 2010; 29:1566-79. [PMID: 20101209 DOI: 10.1038/onc.2009.518] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Neuroblastoma (NB) is an embryonal cancer of the sympathetic nervous system observed in early childhood, characterized by a broad spectrum of clinical behaviors, ranging from spontaneous regression to fatal outcome despite aggressive therapies. NB accounts for 8-10% of pediatric cancers and 15% of the deaths attributable to malignant conditions in children. Interestingly, NB may occur in various contexts, being mostly sporadic but also familial or syndromic. This review focuses on recent advances in the identification of the genes and mechanisms implicated in NB pathogenesis. Although the extensive characterization of the genomic aberrations recurrently observed in sporadic NBs provides important insights into the understanding of the clinical heterogeneity of this neoplasm, analysis of familial and syndromic cases also unravels essential clues on the genetic bases of NB. Recently, the ALK gene emerged as an important NB gene, being implicated both in sporadic and familial cases. The identification of gene expression signatures associated with patient's outcome points out the potential of using gene expression profiling to improve clinical management of patients suffering from NB. Finally, based on recent observations integrating genomic analyses, biological data and clinical information, we discuss possible evolution/progression schemes in NB.
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Affiliation(s)
- I Janoueix-Lerosey
- INSERM U830, Laboratoire de Génétique et Biologie des Cancers, Institut Curie, Paris Cedex 05, France.
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Van Roy N, De Preter K, Hoebeeck J, Van Maerken T, Pattyn F, Mestdagh P, Vermeulen J, Vandesompele J, Speleman F. The emerging molecular pathogenesis of neuroblastoma: implications for improved risk assessment and targeted therapy. Genome Med 2009; 1:74. [PMID: 19638189 PMCID: PMC2717400 DOI: 10.1186/gm74] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Neuroblastoma is one of the most common solid tumors of childhood, arising from immature sympathetic nervous system cells. The clinical course of patients with neuroblastoma is highly variable, ranging from spontaneous regression to widespread metastatic disease. Although the outcome for children with cancer has improved considerably during the past decades, the prognosis of children with aggressive neuroblastoma remains dismal. The clinical heterogeneity of neuroblastoma mirrors the biological and genetic heterogeneity of these tumors. Ploidy and MYCN amplification have been used as genetic markers for risk stratification and therapeutic decision making, and, more recently, gene expression profiling and genome-wide DNA copy number analysis have come into the picture as sensitive and specific tools for assessing prognosis. The applica tion of new genetic tools also led to the discovery of an important familial neuroblastoma cancer gene, ALK, which is mutated in approximately 8% of sporadic tumors, and genome-wide association studies have unveiled loci with risk alleles for neuroblastoma development. For some of the genomic regions that are deleted in some neuroblastomas, on 1p, 3p and 11q, candidate tumor suppressor genes have been identified. In addition, evidence has emerged for the contribution of epigenetic disturbances in neuroblastoma oncogenesis. As in other cancer entities, altered microRNA expression is also being recognized as an important player in neuroblastoma. The recent successes in unraveling the genetic basis of neuroblastoma are now opening opportunities for development of targeted therapies.
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Affiliation(s)
- Nadine Van Roy
- Center for Medical Genetics, Ghent University Hospital, De Pintelaan 185, B-9000 Ghent, Belgium
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Shah SP, Cheung KJ, Johnson NA, Alain G, Gascoyne RD, Horsman DE, Ng RT, Murphy KP. Model-based clustering of array CGH data. ACTA ACUST UNITED AC 2009; 25:i30-8. [PMID: 19478003 PMCID: PMC2687959 DOI: 10.1093/bioinformatics/btp205] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Motivation: Analysis of array comparative genomic hybridization (aCGH) data for recurrent DNA copy number alterations from a cohort of patients can yield distinct sets of molecular signatures or profiles. This can be due to the presence of heterogeneous cancer subtypes within a supposedly homogeneous population. Results: We propose a novel statistical method for automatically detecting such subtypes or clusters. Our approach is model based: each cluster is defined in terms of a sparse profile, which contains the locations of unusually frequent alterations. The profile is represented as a hidden Markov model. Samples are assigned to clusters based on their similarity to the cluster's profile. We simultaneously infer the cluster assignments and the cluster profiles using an expectation maximization-like algorithm. We show, using a realistic simulation study, that our method is significantly more accurate than standard clustering techniques. We then apply our method to two clinical datasets. In particular, we examine previously reported aCGH data from a cohort of 106 follicular lymphoma patients, and discover clusters that are known to correspond to clinically relevant subgroups. In addition, we examine a cohort of 92 diffuse large B-cell lymphoma patients, and discover previously unreported clusters of biological interest which have inspired followup clinical research on an independent cohort. Availability: Software and synthetic datasets are available at http://www.cs.ubc.ca/∼sshah/acgh as part of the CNA-HMMer package. Contact:sshah@bccrc.ca Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Sohrab P Shah
- Department of Computer Science, University of British Columbia, Vancouver, BC, Canada.
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International consensus for neuroblastoma molecular diagnostics: report from the International Neuroblastoma Risk Group (INRG) Biology Committee. Br J Cancer 2009; 100:1471-82. [PMID: 19401703 PMCID: PMC2694415 DOI: 10.1038/sj.bjc.6605014] [Citation(s) in RCA: 255] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Neuroblastoma serves as a paradigm for utilising tumour genomic data for determining patient prognosis and treatment allocation. However, before the establishment of the International Neuroblastoma Risk Group (INRG) Task Force in 2004, international consensus on markers, methodology, and data interpretation did not exist, compromising the reliability of decisive genetic markers and inhibiting translational research efforts. The objectives of the INRG Biology Committee were to identify highly prognostic genetic aberrations to be included in the new INRG risk classification schema and to develop precise definitions, decisive biomarkers, and technique standardisation. The review of the INRG database (n=8800 patients) by the INRG Task Force finally enabled the identification of the most significant neuroblastoma biomarkers. In addition, the Biology Committee compared the standard operating procedures of different cooperative groups to arrive at international consensus for methodology, nomenclature, and future directions. Consensus was reached to include MYCN status, 11q23 allelic status, and ploidy in the INRG classification system on the basis of an evidence-based review of the INRG database. Standardised operating procedures for analysing these genetic factors were adopted, and criteria for proper nomenclature were developed. Neuroblastoma treatment planning is highly dependant on tumour cell genomic features, and it is likely that a comprehensive panel of DNA-based biomarkers will be used in future risk assignment algorithms applying genome-wide techniques. Consensus on methodology and interpretation is essential for uniform INRG classification and will greatly facilitate international and cooperative clinical and translational research studies.
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De Preter K, De Brouwer S, Van Maerken T, Pattyn F, Schramm A, Eggert A, Vandesompele J, Speleman F. Meta-mining of Neuroblastoma and Neuroblast Gene Expression Profiles Reveals Candidate Therapeutic Compounds. Clin Cancer Res 2009; 15:3690-6. [DOI: 10.1158/1078-0432.ccr-08-2699] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Volchenboum SL, Li C, Li S, Attiyeh EF, Reynolds CP, Maris JM, Look AT, George RE. Comparison of primary neuroblastoma tumors and derivative early-passage cell lines using genome-wide single nucleotide polymorphism array analysis. Cancer Res 2009; 69:4143-9. [PMID: 19435921 DOI: 10.1158/0008-5472.can-08-3112] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Stromal contamination is one of the major confounding factors in the analysis of solid tumor samples by single nucleotide polymorphism (SNP) arrays. As we propose to use genome-wide SNP microarray analysis as a diagnostic platform for neuroblastoma, the sensitivity, specificity, and accuracy of these studies must be optimized. To investigate the effects of stromal contamination, we derived early-passage cell lines from nine primary tumors and compared their genomic signature with that of the primary tumors using 100K SNP arrays. The average concordance between tumor and cell line for raw loss of heterozygosity (LOH) calls was 96% (range, 91-99%) and for raw copy number alterations, 71% (range, 43-87%). In general, there were a larger number of LOH events identified in the cell lines compared with the matched tumor samples (mean increase, 3.2% +/- 1.9%). We have developed an algorithm that shows that the presence of stroma contributes to under-reporting of LOH and copy number loss. Notable findings in this sample set were uniparental disomy of chromosome arms 11p, 1q, 14q, and 15q and a novel area of amplification on chromosome band 11p15. Our analysis shows that LOH was identified significantly more often in derived cell lines compared with the original tumor samples. Although these may in part be due to clonal selection during adaptation to tissue culture, our study indicates that stromal contamination may be a major contributing factor in underestimation of LOH and copy number loss events.
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Affiliation(s)
- Samuel L Volchenboum
- Department of Pediatrics and the Computation Institute, The University of Chicago, Chicago, IL 60637, USA.
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