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Hu X, Zhou Y, Hill C, Chen K, Cheng C, Liu X, Duan P, Gu Y, Wu Y, Ewing RM, Li Z, Wu Z, Wang Y. Identification of MYCN non-amplified neuroblastoma subgroups points towards molecular signatures for precision prognosis and therapy stratification. Br J Cancer 2024; 130:1841-1854. [PMID: 38553589 PMCID: PMC7616008 DOI: 10.1038/s41416-024-02666-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 03/13/2024] [Accepted: 03/19/2024] [Indexed: 04/07/2024] Open
Abstract
BACKGROUND Despite the extensive study of MYCN-amplified neuroblastomas, there is a significant unmet clinical need in MYCN non-amplified cases. In particular, the extent of heterogeneity within the MYCN non-amplified population is unknown. METHODS A total of 1566 samples from 16 datasets were identified in Gene Expression Omnibus (GEO) and ArrayExpress. Characterisation of the subtypes was analysed by ConsensusClusterPlus. Independent predictors for subgrouping were constructed from the single sample predictor based on the multiclassPairs package. Findings were verified using immunohistochemistry and CIBERSORTx analysis. RESULTS We demonstrate that MYCN non-amplified neuroblastomas are heterogeneous and can be classified into 3 subgroups based on their transcriptional signatures. Within these groups, subgroup_2 has the worst prognosis and this group shows a 'MYCN' signature that is potentially induced by the overexpression of Aurora Kinase A (AURKA); whilst subgroup_3 is characterised by an 'inflamed' gene signature. The clinical implications of this subtype classification are significant, as each subtype demonstrates a unique prognosis and vulnerability to investigational therapies. A total of 420 genes were identified as independent subgroup predictors with average balanced accuracy of 0.93 and 0.84 for train and test datasets, respectively. CONCLUSION We propose that transcriptional subtyping may enhance precision prognosis and therapy stratification for patients with MYCN non-amplified neuroblastomas.
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Affiliation(s)
- Xiaoxiao Hu
- Department of Paediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, 200092, China
- Department of Paediatric Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325000, China
- Division of Paediatric Oncology, Shanghai Institute of Paediatric Research, Shanghai, 200092, China
| | - Yilu Zhou
- Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
- Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Charlotte Hill
- Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Kai Chen
- Department of Paediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, 200092, China
- Division of Paediatric Oncology, Shanghai Institute of Paediatric Research, Shanghai, 200092, China
| | - Cheng Cheng
- Department of Paediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, 200092, China
- Division of Paediatric Oncology, Shanghai Institute of Paediatric Research, Shanghai, 200092, China
| | - Xiaowei Liu
- Department of Paediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, 200092, China
- Division of Paediatric Oncology, Shanghai Institute of Paediatric Research, Shanghai, 200092, China
| | - Peiwen Duan
- Department of Paediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, 200092, China
- Division of Paediatric Oncology, Shanghai Institute of Paediatric Research, Shanghai, 200092, China
| | - Yaoyao Gu
- Department of Paediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, 200092, China
- Division of Paediatric Oncology, Shanghai Institute of Paediatric Research, Shanghai, 200092, China
| | - Yeming Wu
- Department of Paediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, 200092, China
- Division of Paediatric Oncology, Shanghai Institute of Paediatric Research, Shanghai, 200092, China
- Department of Paediatric Surgery, Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Rob M Ewing
- Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
- Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Zhongrong Li
- Department of Paediatric Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Zhixiang Wu
- Department of Paediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, 200092, China.
- Division of Paediatric Oncology, Shanghai Institute of Paediatric Research, Shanghai, 200092, China.
- Department of Paediatric Surgery, Children's Hospital of Soochow University, Suzhou, 215003, China.
| | - Yihua Wang
- Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
- Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
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Amano H, Uchida H, Harada K, Narita A, Fumino S, Yamada Y, Kumano S, Abe M, Ishigaki T, Sakairi M, Shirota C, Tainaka T, Sumida W, Yokota K, Makita S, Karakawa S, Mitani Y, Matsumoto S, Tomioka Y, Muramatsu H, Nishio N, Osawa T, Taguri M, Koh K, Tajiri T, Kato M, Matsumoto K, Takahashi Y, Hinoki A. Scoring system for diagnosis and pretreatment risk assessment of neuroblastoma using urinary biomarker combinations. Cancer Sci 2024; 115:1634-1645. [PMID: 38411285 DOI: 10.1111/cas.16116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/25/2024] [Accepted: 02/05/2024] [Indexed: 02/28/2024] Open
Abstract
The urinary catecholamine metabolites, homovanillic acid (HVA) and vanillylmandelic acid (VMA), are used for the adjunctive diagnosis of neuroblastomas. We aimed to develop a scoring system for the diagnosis and pretreatment risk assessment of neuroblastoma, incorporating age and other urinary catecholamine metabolite combinations. Urine samples from 227 controls (227 samples) and 68 patients with neuroblastoma (228 samples) were evaluated. First, the catecholamine metabolites vanillactic acid (VLA) and 3-methoxytyramine sulfate (MTS) were identified as urinary marker candidates through comprehensive analysis using liquid chromatography-mass spectrometry. The concentrations of these marker candidates and conventional markers were then compared among controls, patients, and numerous risk groups to develop a scoring system. Participants were classified into four groups: control, low risk, intermediate risk, and high risk, and the proportional odds model was fitted using the L2-penalized maximum likelihood method, incorporating age on a monthly scale for adjustment. This scoring model using the novel urine catecholamine metabolite combinations, VLA and MTS, had greater area under the curve values than the model using HVA and VMA for diagnosis (0.978 vs. 0.964), pretreatment risk assessment (low and intermediate risk vs. high risk: 0.866 vs. 0.724; low risk vs. intermediate and high risk: 0.871 vs. 0.680), and prognostic factors (MYCN status: 0.741 vs. 0.369, histology: 0.932 vs. 0.747). The new system also had greater accuracy in detecting missing high-risk neuroblastomas, and in predicting the pretreatment risk at the time of screening. The new scoring system employing VLA and MTS has the potential to replace the conventional adjunctive diagnostic method using HVA and VMA.
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Affiliation(s)
- Hizuru Amano
- Department of Rare/Intractable Cancer Analysis Research, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Department of Pediatric Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hiroo Uchida
- Department of Pediatric Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kazuharu Harada
- Department of Health Data Science, Tokyo Medical University, Tokyo, Japan
| | - Atsushi Narita
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shigehisa Fumino
- Department of Pediatric Surgery, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yuji Yamada
- Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Shun Kumano
- Department of Rare/Intractable Cancer Analysis Research, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Research & Development Group, Hitachi, Ltd., Tokyo, Japan
| | - Mayumi Abe
- Department of Rare/Intractable Cancer Analysis Research, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Research & Development Group, Hitachi, Ltd., Tokyo, Japan
| | - Takashi Ishigaki
- Department of Rare/Intractable Cancer Analysis Research, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Research & Development Group, Hitachi, Ltd., Tokyo, Japan
| | - Minoru Sakairi
- Department of Rare/Intractable Cancer Analysis Research, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Chiyoe Shirota
- Department of Pediatric Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takahisa Tainaka
- Department of Pediatric Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Wataru Sumida
- Department of Pediatric Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kazuki Yokota
- Department of Pediatric Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Satoshi Makita
- Department of Pediatric Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shuhei Karakawa
- Department of Pediatrics, Hiroshima University, Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Yuichi Mitani
- Department of Hematology/Oncology, Saitama Children's Medical Center, Saitama, Japan
| | - Shojiro Matsumoto
- Department of Complex Systems Science, Graduate School of Information Science, Nagoya University, Nagoya, Japan
| | - Yutaka Tomioka
- Department for the Promotion of Medical Device Innovation, National Cancer Center Hospital East, Chiba, Japan
| | - Hideki Muramatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Nobuhiro Nishio
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tsuyoshi Osawa
- Division of Integrative Nutriomics and Oncology, RCAST, The University of Tokyo, Tokyo, Japan
| | - Masataka Taguri
- Department of Health Data Science, Tokyo Medical University, Tokyo, Japan
| | - Katsuyoshi Koh
- Department of Hematology/Oncology, Saitama Children's Medical Center, Saitama, Japan
| | - Tatsuro Tajiri
- Department of Pediatric Surgery, Kyoto Prefectural University of Medicine, Kyoto, Japan
- Department of Pediatric Surgery, Reproductive and Developmental Medicine, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Motohiro Kato
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kimikazu Matsumoto
- Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Yoshiyuki Takahashi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Akinari Hinoki
- Department of Rare/Intractable Cancer Analysis Research, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Department of Pediatric Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
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Bei Y, Bramé L, Kirchner M, Fritsche-Guenther R, Kunz S, Bhattacharya A, Rusu MC, Gürgen D, Dubios FPB, Köppke JKC, Proba J, Wittstruck N, Sidorova OA, Chamorro González R, Dorado Garcia H, Brückner L, Xu R, Giurgiu M, Rodriguez-Fos E, Yu Q, Spanjaard B, Koche RP, Schmitt CA, Schulte JH, Eggert A, Haase K, Kirwan J, Hagemann AIH, Mertins P, Dörr JR, Henssen AG. Passenger Gene Coamplifications Create Collateral Therapeutic Vulnerabilities in Cancer. Cancer Discov 2024; 14:492-507. [PMID: 38197697 PMCID: PMC10911929 DOI: 10.1158/2159-8290.cd-23-1189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/30/2023] [Accepted: 12/19/2023] [Indexed: 01/11/2024]
Abstract
DNA amplifications in cancer do not only harbor oncogenes. We sought to determine whether passenger coamplifications could create collateral therapeutic vulnerabilities. Through an analysis of >3,000 cancer genomes followed by the interrogation of CRISPR-Cas9 loss-of-function screens across >700 cancer cell lines, we determined that passenger coamplifications are accompanied by distinct dependency profiles. In a proof-of-principle study, we demonstrate that the coamplification of the bona fide passenger gene DEAD-Box Helicase 1 (DDX1) creates an increased dependency on the mTOR pathway. Interaction proteomics identified tricarboxylic acid (TCA) cycle components as previously unrecognized DDX1 interaction partners. Live-cell metabolomics highlighted that this interaction could impair TCA activity, which in turn resulted in enhanced mTORC1 activity. Consequently, genetic and pharmacologic disruption of mTORC1 resulted in pronounced cell death in vitro and in vivo. Thus, structurally linked coamplification of a passenger gene and an oncogene can result in collateral vulnerabilities. SIGNIFICANCE We demonstrate that coamplification of passenger genes, which were largely neglected in cancer biology in the past, can create distinct cancer dependencies. Because passenger coamplifications are frequent in cancer, this principle has the potential to expand target discovery in oncology. This article is featured in Selected Articles from This Issue, p. 384.
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Affiliation(s)
- Yi Bei
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Luca Bramé
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marieluise Kirchner
- Core Unit Proteomics, Berlin Institute of Health at Charité-Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Raphaela Fritsche-Guenther
- Core Unit Metabolomics, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Severine Kunz
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Technology Platform Electron Microscopy, Berlin, Germany
| | - Animesh Bhattacharya
- Department of Hematology, Oncology and Tumor Immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Mara-Camelia Rusu
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Technology Platform Electron Microscopy, Berlin, Germany
| | - Dennis Gürgen
- Experimental Pharmacology and Oncology (EPO), Berlin, Germany
| | - Frank P B Dubios
- Institute of pathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Julia K C Köppke
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Jutta Proba
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Nadine Wittstruck
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Olga Alexandra Sidorova
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Rocío Chamorro González
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Heathcliff Dorado Garcia
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Lotte Brückner
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Technology Platform Electron Microscopy, Berlin, Germany
| | - Robin Xu
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Mădălina Giurgiu
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Elias Rodriguez-Fos
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Qinghao Yu
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Bastiaan Spanjaard
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Richard P Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Clemens A Schmitt
- Department of Hematology, Oncology and Tumor Immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Johannes H Schulte
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Angelika Eggert
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kerstin Haase
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jennifer Kirwan
- Core Unit Metabolomics, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Anja I H Hagemann
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Philipp Mertins
- Core Unit Proteomics, Berlin Institute of Health at Charité-Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Jan R Dörr
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Berlin Institute of Health, Berlin, Germany
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
| | - Anton G Henssen
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Technology Platform Electron Microscopy, Berlin, Germany
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
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Jahangiri L. Predicting Neuroblastoma Patient Risk Groups, Outcomes, and Treatment Response Using Machine Learning Methods: A Review. Med Sci (Basel) 2024; 12:5. [PMID: 38249081 PMCID: PMC10801560 DOI: 10.3390/medsci12010005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 12/28/2023] [Accepted: 01/03/2024] [Indexed: 01/23/2024] Open
Abstract
Neuroblastoma, a paediatric malignancy with high rates of cancer-related morbidity and mortality, is of significant interest to the field of paediatric cancers. High-risk NB tumours are usually metastatic and result in survival rates of less than 50%. Machine learning approaches have been applied to various neuroblastoma patient data to retrieve relevant clinical and biological information and develop predictive models. Given this background, this study will catalogue and summarise the literature that has used machine learning and statistical methods to analyse data such as multi-omics, histological sections, and medical images to make clinical predictions. Furthermore, the question will be turned on its head, and the use of machine learning to accurately stratify NB patients by risk groups and to predict outcomes, including survival and treatment response, will be summarised. Overall, this study aims to catalogue and summarise the important work conducted to date on the subject of expression-based predictor models and machine learning in neuroblastoma for risk stratification and patient outcomes including survival, and treatment response which may assist and direct future diagnostic and therapeutic efforts.
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Affiliation(s)
- Leila Jahangiri
- School of Science and Technology, Nottingham Trent University, Clifton Site, Nottingham NG11 8NS, UK;
- Division of Cellular and Molecular Pathology, Addenbrookes Hospital, University of Cambridge, Cambridge CB2 0QQ, UK
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Wang H, Wang X, Xu L. Chromosome 1p36 candidate gene ZNF436 predicts the prognosis of neuroblastoma: a bioinformatic analysis. Ital J Pediatr 2023; 49:145. [PMID: 37904225 PMCID: PMC10617224 DOI: 10.1186/s13052-023-01549-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 10/16/2023] [Indexed: 11/01/2023] Open
Abstract
BACKGROUND Genetic 1p deletion is reported in 30% of all neuroblastoma and is associated with the unfavorable prognosis of neuroblastoma. The expressions and prognosis of 1p candidate genes in neuroblastoma are unclear. METHODS Public neuroblastoma cohorts were obtained for secondary analysis. The prognosis of 1p candidate genes in neuroblastoma was determined using Kaplan-Meier and cox regression analysis. The prediction of the nomogram model was determined using timeROC. RESULTS First, we confirmed the bad prognosis of 1p deletion in neuroblastoma. Moreover, zinc finger protein 436 (ZNF436) located at 1p36 region was down-regulated in 1p deleted neuroblastoma and higher ZNF436 expression was associated with the longer event free survival and overall survival of neuroblastoma. The expression levels of ZNF436 were lower in neuroblastoma patients with MYCN amplification or age at diagnosis ≥ 18months, or with stage 4 neuroblastoma. ZNF436 had robust predictive values of MYCN amplification and overall survival of neuroblastoma. Furthermore, the prognostic significance of ZNF436 in neuroblastoma was independent of MYCN amplification and age of diagnosis. Combinations of ZNF436 with MYCN amplification or age of diagnosis achieved better prognosis. At last, we constructed a nomogram risk model based on age, MYCN amplification and ZNF436. The nomogram model could predict the overall survival of neuroblastoma with high specificity and sensitivity. CONCLUSIONS Chromosome 1p36 candidate gene ZNF436 was a prognostic maker of neuroblastoma.
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Affiliation(s)
- Haiwei Wang
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China.
| | - Xinrui Wang
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Liangpu Xu
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
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Ognibene M, De Marco P, Amoroso L, Cangelosi D, Zara F, Parodi S, Pezzolo A. Multiple Genes with Potential Tumor Suppressive Activity Are Present on Chromosome 10q Loss in Neuroblastoma and Are Associated with Poor Prognosis. Cancers (Basel) 2023; 15:cancers15072035. [PMID: 37046696 PMCID: PMC10093755 DOI: 10.3390/cancers15072035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
Neuroblastoma (NB) is a tumor affecting the peripheral sympathetic nervous system that substantially contributes to childhood cancer mortality. Despite recent advances in understanding the complexity of NB, the mechanisms determining its progression are still largely unknown. Some recurrent segmental chromosome aberrations (SCA) have been associated with poor survival. However, the prognostic role of most SCA has not yet been investigated. We examined a cohort of 260 NB primary tumors at disease onset for the loss of chromosome 10q, by array-comparative genomic hybridization (a-CGH) and Single Nucleotide Polymorphism (SNP) array and we found that 26 showed 10q loss, while the others 234 displayed different SCA. We observed a lower event-free survival for NB patients displaying 10q loss compared to patients with tumors carrying other SCA. Furthermore, analyzing the region of 10q loss, we identified a cluster of 75 deleted genes associated with poorer outcome. Low expression of six of these genes, above all CCSER2, was significantly correlated to worse survival using in silico data from 786 NB patients. These potential tumor suppressor genes can be partly responsible for the poor prognosis of NB patients with 10q loss.
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Nectin2 influences cell apoptosis by regulating ANXA2 expression in neuroblastoma. Acta Biochim Biophys Sin (Shanghai) 2023; 55:356-366. [PMID: 36916296 PMCID: PMC10160223 DOI: 10.3724/abbs.2023020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023] Open
Abstract
Neuroblastoma (NB) is a pediatric cancer of the peripheral sympathetic nervous system and represents the most frequent solid malignancy in infants. Nectin2 belongs to the immunoglobulin superfamily and has been shown to play a role in tumorigenesis. In the current study, we demonstrate that serum Nectin2 level is increased in NB patients compared with that in healthy controls and Nectin2 level is correlated with neuroblastoma international neuroblastoma staging system (INSS) classification. There is a positive correlation between Nectin2 level and shorter overall survival in NB patients. Knockdown of Nectin2 reduces the migration of SH-SY5Y and SK-N-BE2 cells and induces their apoptosis and cell cycle arrest. RNA-seq analysis demonstrates that Nectin2 knockdown affects the expressions of 258 genes, including 240 that are upregulated and 18 that are downregulated compared with negative controls. qRT-PCR and western blot analysis confirm that ANXA2 expression is decreased in Nectin2-knockdown SH-SY5Y cells, consistent with the RNA-seq results. ANXA2 overexpression rescues the percentage of apoptotic NB cells induced by Nectin2 knockdown and compensates for the impact of Nectin2 knockdown on cleaved caspase3 and bax expressions. In addition, western blot analysis results show that ANXA2 overexpression rescues the effect of Nectin2 knockdown on MMP2 and MMP9 expressions. The current data highlight the importance of Nectin2 in NB progression and the potential of Nectin2 as a novel candidate target for gene therapy.
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Zhang Y, Yang Y, Ning G, Wu X, Yang G, Li Y. Contrast computed tomography-based radiomics is correlation with COG risk stratification of neuroblastoma. Abdom Radiol (NY) 2023; 48:2111-2121. [PMID: 36951989 DOI: 10.1007/s00261-023-03875-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/23/2023] [Accepted: 02/23/2023] [Indexed: 03/24/2023]
Abstract
PURPOSE Although a risk stratification strategy for neuroblastoma (NB) has been proposed, precise and convenient clinical risk estimation remains challenging. This study aimed to investigate the correlation of contrast computed tomography (CT)-based radiomics with NB risk stratification. METHODS Patients with NB (n = 289) from two centers (244 and 45 patients in the training/testing and external validation cohorts, respectively) were divided into nonhigh- and high-risk groups. A total of 1648 radiomics features were extracted from the arterial phase, and the radiomics signature was constructed using rad scores, whereas the clinical model was established based on clinical factors. Further, a combined nomogram was developed based on the clinical factors and radiomics signatures. Finally, receiver operating characteristic curve and decision curve analyses (DCA) were used to assess the performance of the established models. RESULTS Seventeen radiomics features were used to construct the radiomics signature. A significant difference was observed in the rad score between the two groups in the training (0.540 vs. 0.704, P < 0.001) and testing (0.563 vs. 0.969, P < 0.001) cohorts. The nomogram showed a higher area under the curve (AUC) in the training (AUC = 0.87), testing (AUC = 0.83), and external validation (AUC = 0.84) cohorts than other models. The Hosmer-Lemeshow test and calibration curves indicated that the nomogram fit perfectly. DCA demonstrated that the clinical-radiomics nomogram was more beneficial. CONCLUSIONS Contrast CT-based radiomics shows correlation with COG risk stratification of NB. Radiomics features combined with clinical factors showed the best performance, which may improve the management of patients with NB.
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Affiliation(s)
- Yimao Zhang
- Department of Pediatric Surgery, West China Hospital, Sichuan University, No. 37 Guo Xue Xiang, Chengdu, Sichuan, China
| | - Yuhan Yang
- Department of Pediatric Surgery, West China Hospital, Sichuan University, No. 37 Guo Xue Xiang, Chengdu, Sichuan, China
| | - Gang Ning
- Department of Radiology, West China Second Hospital, Sichuan University, No. 20, Section 3, Renmin South Road, Chengdu, Sichuan, China
| | - Xin Wu
- Department of Radiology, West China Hospital, Sichuan University, No. 37 Guo Xue Xiang, Chengdu, Sichuan, China
| | - Gang Yang
- Department of Pediatric Surgery, West China Hospital, Sichuan University, No. 37 Guo Xue Xiang, Chengdu, Sichuan, China
| | - Yuan Li
- Department of Pediatric Surgery, West China Hospital, Sichuan University, No. 37 Guo Xue Xiang, Chengdu, Sichuan, China.
- Laboratory of Digestive Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
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Wieczorek A, Szewczyk K, Klekawka T, Stefanowicz J, Ussowicz M, Drabik G, Pawinska-Wasikowska K, Balwierz W. Segmental chromosomal aberrations as the poor prognostic factor in children over 18 months with stage 3 neuroblastoma without MYCN amplification. Front Oncol 2023; 13:1134772. [PMID: 36865795 PMCID: PMC9972431 DOI: 10.3389/fonc.2023.1134772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 01/30/2023] [Indexed: 02/16/2023] Open
Abstract
Introduction Patients with stage 3 neuroblastoma (NBL) according to International Neuroblastoma Staging System (INSS) without MYCN amplification represent a heterogenous group with respect to disease presentation and prognosis. Methods Retrospective analysis of 40 stage 3 patients with NBL without MYCN amplification was performed. The prognostic value of age at diagnosis (under 18 vs over 18 months), International Neuroblastoma Pathology Classification (INPC) diagnostic category and presence of segmental or numerical chromosomes aberrations were evaluated, as well as biochemical markers. Array comparative genomic hybridization (aCGH) for analyzing copy number variations and Sanger sequencing for ALK point mutations were done. Results In 12 patients (two patients under 18 months), segmental chromosomal aberrations (SCA) were found and numerical chromosomal aberrations (NCA) were found in 16 patients (14 patients under 18 months). In children over 18 months SCA were more common (p=0.0001). Unfavorable pathology was significantly correlated with SCA genomic profile (p=0.04) and age over 18 months (p=0.008). No therapy failures occurred in children with NCA profile over or under 18 months or in children under 18 months, irrespective of pathology and CGH results. Three treatment failures occurred in the SCA group, in one patient CGH profile was not available. For the whole group at 3, 5 and 10-year OS and DFS were 0.95 (95% CI 0.81-0.99), 0.91 (95% CI 0.77-0.97) and 0.91 (95% CI 0.77-0.97), and 0.95 (95% CI 0.90-0.99), 0.92 (95% CI 0.85-0.98) and 0.86 (95% CI 0.78-0.97), respectively. DFS was significantly lower in the SCA group than in the NCA group (3-years, 5-years, and 10-years DFS 0.92 (95% CI 0.53-0.95), 0.80 (95% CI 0.40-0.95) and 0.60 (95% CI 0.16-0.87) vs 1.0, 1.0 and 1.0, respectively, p=0.005). Conclusions The risk of treatment failure was higher in patients with SCA profile, but only in patients over 18 months. All relapses occurred in children having obtained the complete remission, with no previous radiotherapy. In patients over 18 months, SCA profile should be taken into consideration for therapy stratification as it increases the risk of relapse and this group may require more intensive treatment.
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Affiliation(s)
- Aleksandra Wieczorek
- Department of Pediatric Oncology and Hematology, Medical College, Jagiellonian University, Krakow, Poland,Department of Pediatric Oncology and Hematology, University Children’s Hospital of Krakow, Krakow, Poland,*Correspondence: Aleksandra Wieczorek, ; Katarzyna Pawinska-Wasikowska,
| | - Katarzyna Szewczyk
- Department of Medical Genetics, Institute of Pediatrics, Medical College, Jagiellonian University, Krakow, Poland
| | - Tomasz Klekawka
- Department of Pediatric Oncology and Hematology, University Children’s Hospital of Krakow, Krakow, Poland
| | - Joanna Stefanowicz
- Department of Pediatrics, Pediatric Hematology and Oncology, Medical University of Gdansk, Gdansk, Poland
| | - Marek Ussowicz
- Department of Pediatric Bone Marrow Transplantation, Oncology, and Hematology, Wroclaw Medical University, Wroclaw, Poland
| | - Grazyna Drabik
- Department of Pathology, University Children’s Hospital of Krakow, Krakow, Poland
| | - Katarzyna Pawinska-Wasikowska
- Department of Pediatric Oncology and Hematology, Medical College, Jagiellonian University, Krakow, Poland,Department of Pediatric Oncology and Hematology, University Children’s Hospital of Krakow, Krakow, Poland,*Correspondence: Aleksandra Wieczorek, ; Katarzyna Pawinska-Wasikowska,
| | - Walentyna Balwierz
- Department of Pediatric Oncology and Hematology, Medical College, Jagiellonian University, Krakow, Poland,Department of Pediatric Oncology and Hematology, University Children’s Hospital of Krakow, Krakow, Poland
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10
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Sugino RP, Ohira M, Mansai SP, Kamijo T. Comparative epigenomics by machine learning approach for neuroblastoma. BMC Genomics 2022; 23:852. [PMID: 36572864 PMCID: PMC9793522 DOI: 10.1186/s12864-022-09061-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 12/02/2022] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Neuroblastoma (NB) is the second most common pediatric solid tumor. Because the number of genetic mutations found in tumors are small, even in some patients with unfavorable NB, epigenetic variation is expected to play an important role in NB progression. DNA methylation is a major epigenetic mechanism, and its relationship with NB prognosis has been a concern. One limitation with the analysis of variation in DNA methylation is the lack of a suitable analytical model. Therefore, in this study, we performed a random forest (RF) analysis of the DNA methylome data of NB from multiple databases. RESULTS RF is a popular machine learning model owing to its simplicity, intuitiveness, and computational cost. RF analysis identified novel intermediate-risk patient groups with characteristic DNA methylation patterns within the low-risk group. Feature selection analysis based on probe annotation revealed that enhancer-annotated regions had strong predictive power, particularly for MYCN-amplified NBs. We developed a gene-based analytical model to identify candidate genes related to disease progression, such as PRDM8 and FAM13A-AS1. RF analysis revealed sufficient predictive power compared to other machine learning models. CONCLUSIONS RF is a useful tool for DNA methylome analysis in cancer epigenetic studies, and has potential to identify a novel cancer-related genes.
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Affiliation(s)
- Ryuichi P. Sugino
- grid.416695.90000 0000 8855 274XResearch Institute for Clinical Oncology, Saitama Cancer Center, Ina, Saitama, 362-0806 Japan
| | - Miki Ohira
- grid.416695.90000 0000 8855 274XResearch Institute for Clinical Oncology, Saitama Cancer Center, Ina, Saitama, 362-0806 Japan
| | - Sayaka P. Mansai
- grid.416695.90000 0000 8855 274XResearch Institute for Clinical Oncology, Saitama Cancer Center, Ina, Saitama, 362-0806 Japan
| | - Takehiko Kamijo
- grid.416695.90000 0000 8855 274XResearch Institute for Clinical Oncology, Saitama Cancer Center, Ina, Saitama, 362-0806 Japan ,grid.263023.60000 0001 0703 3735Laboratory of Tumor Molecular Biology, Department of Graduate School of Science and Engineering, Saitama University, Kita-Urawa, Saitama, Japan
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11
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Ognibene M, Cangelosi D, Sorrentino S, Zanardi S, Zara F, Pezzolo A, Parodi S. E2F3 gene expression is a potential negative prognostic marker for localised and MYCN not-amplified neuroblastoma: Results of in silico analysis of 786 samples. Pediatr Blood Cancer 2022; 69:e29800. [PMID: 35652628 DOI: 10.1002/pbc.29800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 04/13/2022] [Accepted: 05/09/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND Neuroblastoma (NB) is an enigmatic childhood malignancy characterised by a wide range of clinical behaviour. Many potential oncogenes for NB have recently been identified. Among them, E2 transcription factor 3 (E2F3) expression was associated with a poor survival in 134 stage 4S patients, but evidence for other stage groups remains poorly investigated. METHODS We have analysed the expression of E2F3 gene from a database of 786 NB samples. Overall and event-free survivals (EFS) were assessed by the Kaplan-Meier method, splitting the data on the median and tertile expression values. The Cox model was applied to control for the confounding by stage, age and MYCN amplification. Validation was performed by an in silico analysis of an independent cohort of 283 NB patients. Furthermore, an immunofluorescence analysis on 48 formalin-fixed, paraffin-embedded NB specimens was also performed. RESULTS E2F3 overexpression was associated with a poor survival (EFS = 84%, 95% CI: 79%-95%, for low expression levels; EFS = 62%, 95% CI: 56%-68% for middle levels; EFS = 30%, 95% CI: 24%-36%, for high levels, p < .001). This association was confirmed in multivariable analysis and was more evident in patients with MYCN not-amplified and localised stages. Immunofluorescence results and the validation on an independent cohort of NB primary samples confirmed these findings. CONCLUSIONS E2F3 is a new potential prognostic marker in NB with favourable characteristics at diagnosis. Further studies are needed to elucidate the potential role of E2F3 in NB oncogenesis and progression, in order to identify new targets for therapeutic interventions.
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Affiliation(s)
- Marzia Ognibene
- U.O.C. Genetica Medica, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Davide Cangelosi
- Unità di Bioinformatica Clinica, Direzione Scientifica, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Stefania Sorrentino
- U.O.C. Divisione di Oncologia, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Sabrina Zanardi
- U.O.S.I.D. Epidemiologia e Biostatistica, Direzione Scientifica, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Federico Zara
- U.O.C. Genetica Medica, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | | | - Stefano Parodi
- Direzione Scientifica, IRCCS Istituto Giannina Gaslini, Genova, Italy
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12
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Lin L, Miao L, Lin H, Cheng J, Li M, Zhuo Z, He J. Targeting RAS in neuroblastoma: Is it possible? Pharmacol Ther 2022; 236:108054. [PMID: 34915055 DOI: 10.1016/j.pharmthera.2021.108054] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 12/06/2021] [Accepted: 12/08/2021] [Indexed: 02/07/2023]
Abstract
Neuroblastoma is a common solid tumor in children and a leading cause of cancer death in children. Neuroblastoma exhibits genetic, morphological, and clinical heterogeneity that limits the efficacy of current monotherapies. With further research on neuroblastoma, the pathogenesis of neuroblastoma is found to be complex, and more and more treatment therapies are needed. The importance of personalized therapy is growing. Currently, various molecular features, including RAS mutations, are being used as targets for the development of new therapies for patients with neuroblastoma. A recent study found that RAS mutations are frequently present in recurrent neuroblastoma. RAS mutations have been shown to activate the MAPK pathway and play an important role in neuroblastoma. Treating RAS mutated neuroblastoma is a difficult challenge, but many preclinical studies have yielded effective results. At the same time, many of the therapies used to treat RAS mutated tumors also have good reference values for treating RAS mutated neuroblastoma. The success of KRAS-G12C inhibitors has greatly stimulated confidence in the direct suppression of RAS. This review describes the biological role of RAS and the frequency of RAS mutations in neuroblastoma. This paper focuses on the strategies, preclinical, and clinical progress of targeting carcinogenic RAS in neuroblastoma, and proposes possible prospects and challenges in the future.
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Affiliation(s)
- Lei Lin
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China
| | - Lei Miao
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China
| | - Huiran Lin
- Faculty of Medicine, Macau University of Science and Technology, Macau 999078, China
| | - Jiwen Cheng
- Department of Pediatric Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710004, Shaanxi, China
| | - Meng Li
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China
| | - Zhenjian Zhuo
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China; Laboratory Animal Center, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China.
| | - Jing He
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China.
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13
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Wang H, Wang X, Xu L, Zhang J. TP53 and TP53-associated genes are correlated with the prognosis of paediatric neuroblastoma. BMC Genom Data 2022; 23:41. [PMID: 35655142 PMCID: PMC9164562 DOI: 10.1186/s12863-022-01059-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 05/27/2022] [Indexed: 11/18/2022] Open
Abstract
Background TP53 is rarely mutated in paediatric neuroblastoma. The prognosis of TP53 and TP53-associated genes in paediatric neuroblastoma is unclear. The objectives of the study were to analyse datasets of 2477 paediatric neuroblastoma patients from eight independent cohorts to reveal the prognosis of TP53 and TP53-associated genes. Results High TP53 mRNA expression was associated with shortened event-free survival and overall survival in paediatric neuroblastoma. Moreover, a higher enrichment score of the TP53 signalling pathway was associated with worse clinical outcomes of paediatric neuroblastoma. Among the genes associated with TP53, CCNE1, CDK2 and CHEK2 were correlated with unfavourable clinical outcomes, while SESN1 was correlated with favourable clinical outcomes of paediatric neuroblastoma in the eight independent neuroblastoma cohorts. TP53, CCNE1, CDK2 and CHEK2 were overexpressed in neuroblastoma patients with MYCN amplification, while SESN1 was downregulated in neuroblastoma patients with MYCN amplification. CCNE1, SESN1, MYCN amplification and age at diagnosis were independent prognostic markers of neuroblastoma. CCNE1 was also highly expressed in paediatric neuroblastoma patients with an age at diagnosis ≥ 18 months, while SESN1 was downregulated in paediatric neuroblastoma patients with an age at diagnosis ≥ 18 months. Combinations of CCNE1 with age at diagnosis or combinations of SESN1 with age at diagnosis achieved superior prognostic effects in paediatric neuroblastoma. Finally, we constructed a nomogram risk model of paediatric neuroblastoma based on age and TP53, CCNE1, CDK2, CHEK2 and SESN1 expression. The nomogram model could predict the overall survival of paediatric neuroblastoma and MYCN nonamplified paediatric neuroblastoma with high specificity and sensitivity. Conclusions TP53 and TP53-associated genes CCNE1, CDK2, CHEK2 and SESN1 were significantly associated with the clinical outcomes of paediatric neuroblastoma. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-022-01059-5.
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Affiliation(s)
- Haiwei Wang
- Medical Research Center, Fujian Maternity and Child Health Hospital, Fuzhou, Fujian, China.
| | - Xinrui Wang
- Medical Research Center, Fujian Maternity and Child Health Hospital, Fuzhou, Fujian, China
| | - Liangpu Xu
- Medical Research Center, Fujian Maternity and Child Health Hospital, Fuzhou, Fujian, China
| | - Ji Zhang
- State Key Laboratory for Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital Affiliated to School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
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14
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Druy AE, Tsaur GA, Shorikov EV, Tytgat GAM, Fechina LG. Suppressed miR-128-3p combined with TERT overexpression predicts dismal outcomes for neuroblastoma. Cancer Biomark 2022; 34:661-671. [PMID: 35634846 DOI: 10.3233/cbm-210414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
BACKGROUND Molecular and clinical diversity of neuroblastomas is notorious. The activating TERT rearrangements have been associated with dismal prognosis. Suppression of miR-128-3p may complement and enhance the adverse effects of TERT overexpression. OBJECTIVE The study aimed at evaluation of prognostic significance of the miR-128-3p/TERT expression in patients with primary neuroblastoma. METHODS RNA samples isolated from fresh-frozen tumor specimens (n= 103) were reverse transcribed for evaluation of miR-128-3p and TERT expression by qPCR. The normalized expression levels were tested for correlations with the event-free survival (EFS). ROC-analysis was used to establish threshold expression levels (TLs) for the possible best prediction of the outcomes. The median follow-up was 57 months. RESULTS Both TERT overexpression and miR-128-3p downregulation were independently associated with superior rates of adverse events (p= 0.027, TL =-2.32 log10 and p= 0.080, TL =-1.33 log10, respectively). The MYCN single-copy patients were stratified into groups based on the character of alterations in expression of the studied transcripts. Five-year EFS in the groups of patients with elevated TERT/normal miR-128-3p expression and normal TERT/reduced miR-128-3p expression were 0.74 ± 0.08 and 0.60 ± 0.16, respectively. The patients with elevated TERT/reduced miR-128-3p expression had the worst outcomes, with 5-year EFS of 0.40 ± 0.16 compared with 0.91 ± 0.06 for the patients with unaltered levels of both transcripts (p< 0.001). Cumulative incidence of relapse/progression for the groups constituted 0.23 ± 0.08, 0.40 ± 0.16, 0.60 ± 0.16 and 0.09 ± 0.06, respectively. Moreover, the loss of miR-128-3p was qualified as independent adverse predictor which outperformed the conventional clinical and genetic risk factors in the multivariate Cox regression model of EFS. CONCLUSIONS Combined expression levels of miR-128-3p and TERT represent a novel prognostic biomarker for neuroblastoma.
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Affiliation(s)
- A E Druy
- Laboratory of Molecular Oncology, Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation.,Laboratory of the Cellular Therapy of Oncohematological Disorders, Research Institute of Medical Cell Technologies, Yekaterinburg, Russian Federation
| | - G A Tsaur
- Laboratory of the Cellular Therapy of Oncohematological Disorders, Research Institute of Medical Cell Technologies, Yekaterinburg, Russian Federation.,Pediatric Oncology and Hematology Center, Regional Children's Hospital, Yekaterinburg, Russian Federation.,Chair of Laboratory Medicine, Ural State Medical University, Yekaterinburg, Russian Federation
| | - E V Shorikov
- PET-Technology Center of Nuclear Medicine, Yekaterinburg, Russian Federation
| | - G A M Tytgat
- Princess Máxima Centre for Pediatric Oncology (PMC), Utrecht, The Netherlands
| | - L G Fechina
- Laboratory of the Cellular Therapy of Oncohematological Disorders, Research Institute of Medical Cell Technologies, Yekaterinburg, Russian Federation.,Pediatric Oncology and Hematology Center, Regional Children's Hospital, Yekaterinburg, Russian Federation
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15
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Verly IRN, Matser YAH, Leen R, Meinsma R, Fiocco M, Koster J, Volckmann R, Savci-Heijink D, Cangemi G, Barco S, Valentijn LJ, Tytgat GAM, van Kuilenburg ABP. Urinary 3-Methoxytyramine Is a Biomarker for MYC Activity in Patients With Neuroblastoma. JCO Precis Oncol 2022; 6:e2000447. [PMID: 35085004 PMCID: PMC8830522 DOI: 10.1200/po.20.00447] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Elevated urinary 3-methoxytyramine (3MT) level at diagnosis was recently put forward as independent risk factor for poor prognosis in neuroblastoma. Here, we investigated the biologic basis underlying the putative association between elevated 3MT levels and poor prognosis. Elevated urinary 3-methoxytyramine (3MT) at diagnosis is an independent risk factor for poor event-free survival and poor overall survival in neuroblastoma. Our analysis including gene-expression data and urinary 3MT showed that increased urinary 3MT corresponds with tumor MYC activity.![]()
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Affiliation(s)
- Iedan R N Verly
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Department of Clinical Chemistry, Cancer Center Amsterdam, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Center, University of Amsterdam, the Netherlands
| | - Yvette A H Matser
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Department of Clinical Chemistry, Cancer Center Amsterdam, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Center, University of Amsterdam, the Netherlands
| | - René Leen
- Department of Clinical Chemistry, Cancer Center Amsterdam, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Center, University of Amsterdam, the Netherlands
| | - Rutger Meinsma
- Department of Clinical Chemistry, Cancer Center Amsterdam, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Center, University of Amsterdam, the Netherlands
| | - Marta Fiocco
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, the Netherlands.,Mathematical Institute, Leiden University, Leiden, the Netherlands
| | - Jan Koster
- Department of Oncogenomics, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Richard Volckmann
- Department of Oncogenomics, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Dilara Savci-Heijink
- Department of Pathology, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Giuliana Cangemi
- Central Laboratory of Analyses, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Sebastiano Barco
- Central Laboratory of Analyses, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Linda J Valentijn
- Department of Oncogenomics, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | | | - André B P van Kuilenburg
- Department of Clinical Chemistry, Cancer Center Amsterdam, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Center, University of Amsterdam, the Netherlands
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16
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Li L, Chen S, Li J, Rong G, Yang J, Li Y. Characterization of m6A-related lncRNA signature in neuroblastoma. Front Pediatr 2022; 10:927885. [PMID: 36324814 PMCID: PMC9618704 DOI: 10.3389/fped.2022.927885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 09/20/2022] [Indexed: 11/28/2022] Open
Abstract
N6-methyladenosine (m6A) constitutes one of the most common modifications in mRNA, rRNA, tRNA, microRNA, and long-chain noncoding RNA. The influence of modifications of m6A on the stability of RNA depends upon the expression of methyltransferase ("writer") and demethylase ("eraser") and m6A binding protein ("reader"). In this study, we identified a set of m6A-related lncRNA expression profiles in neuroblastoma (NBL) based on the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) program. Thereupon, we identified two subgroups of neuroblastoma (high-risk group and low-risk group) by applying consensus clustering to m6A RNA methylation regulators ("Readers,", "Writer," and "Erase"). Relative to the low-risk group, the high-risk group correlates with a poorer prognosis. Moreover, the present study also revealed that the high-risk group proves to be significantly positively enriched in the tumor-related signaling pathways, including the P53 signaling pathway, cell cycle, and DNA repair. This finding indicates that these molecular prognostic markers may also be potentially valuable in early diagnosis, which provides a new research direction for the study of molecular mechanisms underlying the development of NBL. In conclusion, this study constructed a new model of NBL prognosis based on m6a-associated lncRNAs. Ultimately, this model is helpful for stratification of prognosis and development of treatment strategies.
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Affiliation(s)
- Liming Li
- Department of Pediatric Surgery, GuiPing People's Hospital, Guangxi, China
| | - Sisi Chen
- Department of Pediatric Surgery, GuiPing People's Hospital, Guangxi, China
| | - Jianhong Li
- Department of Pediatric Surgery, GuiPing People's Hospital, Guangxi, China
| | - Guochou Rong
- Department of Pediatric Surgery, GuiPing People's Hospital, Guangxi, China
| | - Juchao Yang
- Department of Pediatric Surgery, GuiPing People's Hospital, Guangxi, China
| | - Yunquan Li
- Department of Pediatric Surgery, GuiPing People's Hospital, Guangxi, China
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17
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Retrospective Analysis of INRG Clinical and Genomic Factors for 605 Neuroblastomas in Japan: A Report from the Japan Children’s Cancer Group Neuroblastoma Committee (JCCG-JNBSG). Biomolecules 2021; 12:biom12010018. [PMID: 35053166 PMCID: PMC8774029 DOI: 10.3390/biom12010018] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/17/2021] [Accepted: 12/21/2021] [Indexed: 12/31/2022] Open
Abstract
Neuroblastomas (NBs) exhibit broad and divergent clinical behaviors and tumor risk classification at diagnosis is crucial for the selection of an appropriate therapeutic strategy for each patient. The present study aimed to validate the clinical relevance of International Neuroblastoma Risk Group (INRG) prognostic and genomic markers in a Japanese NB cohort using a retrospective analysis. Follow-up data based on 30 common INRG queries in 605 NB cases diagnosed in Japan between 1990 and 2014 were collected and the genome signature of each tumor sample was integrated. As previously indicated, age, tumor stage, MYCN, DNA ploidy, the adrenals as the primary tumor site, serum ferritin and lactate dehydrogenase (LDH) levels, segmental chromosome aberrations, and the number of chromosome breakpoints (BP) correlated with lower survival rates, while the thorax as the primary tumor site and numerical chromosome aberrations correlated with a favorable prognosis. In the patient group with stage 4, MYCN non-amplified tumors (n = 225), one of the challenging subsets for risk stratification, age ≥ 18 months, LDH ≥ 1400 U/L, and BP ≥ 7 correlated with lower overall and event-free survival rates (p < 0.05). The genome subgroup GG-P2s (partial chromosome gain/loss type with 1p/11q losses and 17q gain, n = 30) was strongly associated with a lower overall survival rate (5-year survival rate: 34%, p < 0.05). Therefore, the combination of the tumor genomic pattern (GG-P2s and BP ≥ 7) with age at diagnosis and LDH will be a promising predictor for MYCN-non-amplified high-risk NBs in patient subsets, in accordance with previous findings from the INRG project.
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18
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High Grade of Amplification of Six Regions on Chromosome 2p in a Neuroblastoma Patient with Very Poor Outcome: The Putative New Oncogene TSSC1. Cancers (Basel) 2021; 13:cancers13225792. [PMID: 34830942 PMCID: PMC8616235 DOI: 10.3390/cancers13225792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/14/2021] [Accepted: 11/16/2021] [Indexed: 12/02/2022] Open
Abstract
Simple Summary Here, a case of neuroblastoma (NB) carrying a high-grade amplification of six loci besides MYCN is described. Since the patient had a very poor outcome, we postulated that these DNA co-amplifications might have a synergistic effect in increasing NB cell proliferation. In order to verify this hypothesis, we analyzed in silico the impact of high expression of the genes located within the amplifications on the NB patients’ outcome using a large dataset integrating three different platforms. These analyses disclosed that high expression of the TSSC1 gene was the most significantly associated with reduced overall survival of NB patients, suggesting that it may have a potential prognostic role in NB in both MYCN amplified and MYCN not amplified tumors. Further studies on TSSC1 interactions and functioning could lead to possible focused therapies for high-risk NB patients. Abstract We observed a case of high-risk neuroblastoma (NB) carried by a 28-month-old girl, displaying metastatic disease and a rapid decline of clinical conditions. By array-CGH analysis of the tumor tissue and of the metastatic bone marrow aspirate cells, we found a high-grade amplification of six regions besides MYCN on bands 2p25.3–p24.3. The genes involved in these amplifications were MYT1L, TSSC1, CMPK2, RSAD2, RNF144A, GREB1, NTSR2, LPIN1, NBAS, and the two intergenic non-protein coding RNAs LOC730811 and LOC339788. We investigated if these DNA co-amplifications may have an effect on enhancing tumor aggressiveness. We evaluated the association between the high expression of the amplified genes and NB patient’s outcome using the integration of gene expression data of 786 NB samples profiled with different public platforms from patients with at least five-year follow-up. NB patients with high expression of the TSSC1 gene were associated with a reduced survival rate. Immunofluorescence staining on primary tumor tissues confirmed that the TSSC1 protein expression was high in the relapsed or dead stage 4 cases, but it was generally low in NB patients in complete remission. TSSC1 appears as a putative new oncogene in NB.
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Berthold F, Rosswog C, Christiansen H, Frühwald M, Hemstedt N, Klingebiel T, Fröhlich B, Schilling FH, Schmid I, Simon T, Hero B, Fischer M, Ernst A. Clinical and molecular characterization of patients with stage 4(M) neuroblastoma aged less than 18 months without MYCN amplification. Pediatr Blood Cancer 2021; 68:e29038. [PMID: 33826231 DOI: 10.1002/pbc.29038] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/23/2021] [Accepted: 03/13/2021] [Indexed: 11/06/2022]
Abstract
INTRODUCTION The survival of children with stage 4(M) neuroblastoma without MYCN amplification and below the age of 18 months is considered better than the still dismal outcome of older high-risk neuroblastoma patients. This study analyzes the impact of clinical and molecular characteristics on the long-term outcome. PATIENTS AND METHODS Clinical presentation, survival, and recurrence patterns of patients enrolled onto trials NB90, NB97, and NB2004 were retrospectively analyzed. Gene expression signatures based on RNA microarrays (TH10) were investigated if tumor material was available. RESULTS Between 1990 and 2015, 177 patients with stage 4(M) MYCN nonamplified neuroblastoma aged less than 18 months at diagnosis were eligible. After a median follow-up of 9.7 years (IQR 5.0, 13.4), the proportions of 10-year event-free survival (EFS) and overall survival (OS) were 73% (95% confidence interval [CI] 67-79%) and 86% (95% CI 80-92%), respectively. Of the 27 neuroblastoma recurrences, 44% occurred in more than one site. Four additional patients presented histologically mature ganglioneuroma at recurrence. Six patients developed a secondary malignancy. The secondary 5-year EFS and OS of the 27 patients with neuroblastoma recurrence were 44% and 59%, respectively. TH10 gene expression signature was not prognostically predictive in the investigated subcohort. CONCLUSION The outcome of patients with stage 4(M) neuroblastoma aged less than 18 months is favorable when treated with high-risk or otherwise intensive therapy. The development of secondary malignancies and the potential of maturation to ganglioneuroma call for a controlled stepwise reduction of treatment intensity.
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Affiliation(s)
- Frank Berthold
- Department of Pediatric Oncology and Hematology, University of Cologne, Cologne, Germany
| | - Carolina Rosswog
- Department of Experimental Pediatric Oncology, University of Cologne, Cologne, Germany.,Center for Molecular Medicine, Medical Faculty, University of Cologne, Cologne, Germany
| | - Holger Christiansen
- Department of Pediatric Oncology and Hematology, University of Leipzig, Leipzig, Germany
| | - Michael Frühwald
- Swabian Children's Cancer Center, Children's Hospital, University Hospital Augsburg, Augsburg, Germany
| | - Nadine Hemstedt
- Department of Experimental Pediatric Oncology, University of Cologne, Cologne, Germany.,Center for Molecular Medicine, Medical Faculty, University of Cologne, Cologne, Germany
| | - Thomas Klingebiel
- Department of Children and Adolescents, University Hospital, Goethe University Frankfurt (Main), Frankfurt, Germany
| | - Birgit Fröhlich
- Department of Pediatric Oncology and Hematology, University of Munster, Munster, Germany
| | - Freimut H Schilling
- Department of Pediatric Oncology and Hematology, Olgahospital Stuttgart, Stuttgart, Germany
| | - Irene Schmid
- Department of Pediatric Hematology and Oncology and Hematology, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Thorsten Simon
- Department of Pediatric Oncology and Hematology, University of Cologne, Cologne, Germany
| | - Barbara Hero
- Department of Pediatric Oncology and Hematology, University of Cologne, Cologne, Germany
| | - Matthias Fischer
- Department of Experimental Pediatric Oncology, University of Cologne, Cologne, Germany.,Center for Molecular Medicine, Medical Faculty, University of Cologne, Cologne, Germany
| | - Angela Ernst
- Institute of Medical Statistics and Computational Biology, University of Cologne, Cologne, Germany
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Discovery of Spatial Peptide Signatures for Neuroblastoma Risk Assessment by MALDI Mass Spectrometry Imaging. Cancers (Basel) 2021; 13:cancers13133184. [PMID: 34202325 PMCID: PMC8269054 DOI: 10.3390/cancers13133184] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/16/2021] [Accepted: 06/22/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary The childhood tumor, neuroblastoma, has a broad clinical presentation. Risk assessment at diagnosis is particularly difficult in molecularly heterogeneous high-risk cases. Here we investigate the potential of imaging mass spectrometry to directly detect intratumor heterogeneity on the protein level in tissue sections. We show that this approach can produce discriminatory peptide signatures separating high- from low- and intermediate-risk tumors, identify 8 proteins aassociated with these signatures and validate two marker proteins using tissue immunostaining that have promise for further basic and translational research in neuroblastoma. We provide proof-of-concept that mass spectrometry-based technology could assist early risk assessment in neuroblastoma and provide insights into peptide signature-based detection of intratumor heterogeneity. Abstract Risk classification plays a crucial role in clinical management and therapy decisions in children with neuroblastoma. Risk assessment is currently based on patient criteria and molecular factors in single tumor biopsies at diagnosis. Growing evidence of extensive neuroblastoma intratumor heterogeneity drives the need for novel diagnostics to assess molecular profiles more comprehensively in spatial resolution to better predict risk for tumor progression and therapy resistance. We present a pilot study investigating the feasibility and potential of matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) to identify spatial peptide heterogeneity in neuroblastoma tissues of divergent current risk classification: high versus low/intermediate risk. Univariate (receiver operating characteristic analysis) and multivariate (segmentation, principal component analysis) statistical strategies identified spatially discriminative risk-associated MALDI-based peptide signatures. The AHNAK nucleoprotein and collapsin response mediator protein 1 (CRMP1) were identified as proteins associated with these peptide signatures, and their differential expression in the neuroblastomas of divergent risk was immunohistochemically validated. This proof-of-concept study demonstrates that MALDI-MSI combined with univariate and multivariate analysis strategies can identify spatially discriminative risk-associated peptide signatures in neuroblastoma tissues. These results suggest a promising new analytical strategy improving risk classification and providing new biological insights into neuroblastoma intratumor heterogeneity.
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Guo YF, Duan JJ, Wang J, Li L, Wang D, Liu XZ, Yang J, Zhang HR, Lv J, Yang YJ, Yang ZY, Cai J, Liao XM, Tang T, Huang TT, Wu F, Yang XY, Wen Q, Bian XW, Yu SC. Inhibition of the ALDH18A1-MYCN positive feedback loop attenuates MYCN-amplified neuroblastoma growth. Sci Transl Med 2021; 12:12/531/eaax8694. [PMID: 32075946 DOI: 10.1126/scitranslmed.aax8694] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 01/28/2020] [Indexed: 12/14/2022]
Abstract
MYCN-amplified neuroblastoma (NB) is characterized by poor prognosis, and directly targeting MYCN has proven challenging. Here, we showed that aldehyde dehydrogenase family 18 member A1 (ALDH18A1) exerts profound impacts on the proliferation, self-renewal, and tumorigenicity of NB cells and is a potential risk factor in patients with NB, especially those with MYCN amplification. Mechanistic studies revealed that ALDH18A1 could both transcriptionally and posttranscriptionally regulate MYCN expression, with MYCN reciprocally transactivating ALDH18A1 and thus forming a positive feedback loop. Using molecular docking and screening, we identified an ALDH18A1-specific inhibitor, YG1702, and demonstrated that pharmacological inhibition of ALDH18A1 was sufficient to induce a less proliferative phenotype and confer tumor regression and prolonged survival in NB xenograft models, providing therapeutic insights into the disruption of this reciprocal regulatory loop in MYCN-amplified NB.
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Affiliation(s)
- Yu-Feng Guo
- Department of Stem Cell and Regenerative Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.,Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.,Key Laboratory of Tumor Immunopathology of the Ministry of Education, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Jiang-Jie Duan
- Department of Stem Cell and Regenerative Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.,Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.,Key Laboratory of Tumor Immunopathology of the Ministry of Education, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Jun Wang
- Department of Stem Cell and Regenerative Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.,Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.,Key Laboratory of Tumor Immunopathology of the Ministry of Education, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Lin Li
- Department of Stem Cell and Regenerative Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.,Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.,Key Laboratory of Tumor Immunopathology of the Ministry of Education, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Di Wang
- Department of Stem Cell and Regenerative Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.,Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.,Key Laboratory of Tumor Immunopathology of the Ministry of Education, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Xun-Zhou Liu
- Department of Stem Cell and Regenerative Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.,Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Jing Yang
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.,Key Laboratory of Tumor Immunopathology of the Ministry of Education, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Hua-Rong Zhang
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.,Key Laboratory of Tumor Immunopathology of the Ministry of Education, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Jing Lv
- Department of Stem Cell and Regenerative Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.,Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.,Key Laboratory of Tumor Immunopathology of the Ministry of Education, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Yong-Jun Yang
- Department of Stem Cell and Regenerative Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.,Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.,Key Laboratory of Tumor Immunopathology of the Ministry of Education, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Ze-Yu Yang
- Department of Stem Cell and Regenerative Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.,Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.,Key Laboratory of Tumor Immunopathology of the Ministry of Education, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Jiao Cai
- Department of Stem Cell and Regenerative Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.,Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.,Key Laboratory of Tumor Immunopathology of the Ministry of Education, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Xue-Mei Liao
- Department of Stem Cell and Regenerative Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.,Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.,Key Laboratory of Tumor Immunopathology of the Ministry of Education, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Tao Tang
- Department of Stem Cell and Regenerative Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.,Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.,Key Laboratory of Tumor Immunopathology of the Ministry of Education, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Ting-Ting Huang
- Department of Stem Cell and Regenerative Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.,Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.,Key Laboratory of Tumor Immunopathology of the Ministry of Education, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Feng Wu
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.,Key Laboratory of Tumor Immunopathology of the Ministry of Education, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Xian-Yan Yang
- Department of Stem Cell and Regenerative Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.,Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.,Key Laboratory of Tumor Immunopathology of the Ministry of Education, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Qian Wen
- Department of Stem Cell and Regenerative Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.,Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.,Key Laboratory of Tumor Immunopathology of the Ministry of Education, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Xiu-Wu Bian
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China. .,Key Laboratory of Tumor Immunopathology of the Ministry of Education, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Shi-Cang Yu
- Department of Stem Cell and Regenerative Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China. .,Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.,Key Laboratory of Tumor Immunopathology of the Ministry of Education, Third Military Medical University (Army Medical University), Chongqing 400038, China
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22
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Körber F, Schäfer JF. [Radiological imaging of neuroblastoma]. Radiologe 2021; 61:639-648. [PMID: 34156482 DOI: 10.1007/s00117-021-00875-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/09/2021] [Indexed: 10/21/2022]
Abstract
BACKGROUND Neuroblastomas are tumors of the sympathetic nervous system that arise from the sympathetic trunk and adrenal glands. Tissue compositions, molecular genetics, and overall prognosis are heterogeneous. With an incidence of 1:6000, neuroblastomas account for 5.5% of childhood tumors. They usually occur in children up to preschool age with the mean age of 14 months. Adults are very rarely affected. Imaging, especially magnetic resonance imaging (MRI), plays an essential role in diagnosis, risk stratification, and therapy control. MATERIALS AND METHODS Based on a selective literature search in the PubMed database, the national and international societies' guidelines and study protocols, the imaging standards and the latest developments are presented. CONCLUSION Imaging plays a key role in neuroblastomas due to the heterogeneous prognosis and the resulting very different therapy. A high degree of standardization in implementation and interpretation is important in every phase of the disease process. Sonography, MRI with diffusion weighting, and 123I‑mIBG-SPECT are essential modalities. The extent of the diffusion restriction for assessing the degree of maturity and assessing the therapeutic response is becoming increasingly important in clinical routine. Up to now, PET imaging has mostly been complementary. Newly developed PET tracers promise comprehensive diagnostics and may also play a major role in theranostics.
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Affiliation(s)
- Friederike Körber
- Institut für Diagnostische und Interventionelle Radiologie, Schwerpunkt Kinder- und Jugendradiologie, Uniklinik Köln, Kerpener Str. 62, 50937, Köln, Deutschland.
| | - Jürgen Frank Schäfer
- Bereich pädiatrische Radiologie, Abteilung für Diagnostische und Interventionelle Radiologie, Universitätsklinikum Tübingen, Hoppe-Seyler-Straße 3, 72076, Tübingen, Deutschland
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23
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Association of RASSF1A, DCR2, and CASP8 Methylation with Survival in Neuroblastoma: A Pooled Analysis Using Reconstructed Individual Patient Data. BIOMED RESEARCH INTERNATIONAL 2020; 2020:7390473. [PMID: 33381579 PMCID: PMC7755470 DOI: 10.1155/2020/7390473] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 10/09/2020] [Accepted: 10/17/2020] [Indexed: 12/15/2022]
Abstract
Neuroblastoma (NB) is a heterogeneous tumor affecting children. It shows a wide spectrum of clinical outcomes; therefore, development of risk stratification is critical to provide optimum treatment. Since epigenetic alterations such as DNA methylation have emerged as an important feature of both development and progression in NB, in this study, we aimed to quantify the effect of methylation of three distinct genes (RASSF1A, DCR2, and CASP8) on overall survival in NB patients. We performed a systematic review using PubMed, Embase, and Cochrane libraries. Individual patient data was retrieved from extracted Kaplan–Meier curves. Data from studies was then merged, and analysis was done on the full data set. Seven studies met the inclusion criteria. Methylation of the three genes had worse overall survival than the unmethylated arms. Five-year survival for the methylated arm of RASSF1A, DCR2, and CASP8 was 63.19% (95% CI 56.55-70.60), 57.78% (95% CI 47.63-70.08), and 56.39% (95% CI 49.53-64.19), respectively, while for the unmethylated arm, it was 93.10% (95% CI 87.40–99.1), 84.84% (95% CI 80.04-89.92), and 83.68% (95% CI 80.28-87.22), respectively. In conclusion, our results indicate that in NB patients, RASSF1A, DCR2, and CASP8 methylation is associated with poor prognosis. Large prospective studies will be necessary to confirm definitive correlation between methylation of these genes and survival taking into account all other known risk factors. (PROSPERO registration number CRD42017082264).
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Cai Y, Chen K, Cheng C, Xu Y, Cheng Q, Xu G, Wu Y, Wu Z. Prp19 Is an Independent Prognostic Marker and Promotes Neuroblastoma Metastasis by Regulating the Hippo-YAP Signaling Pathway. Front Oncol 2020; 10:575366. [PMID: 33224878 PMCID: PMC7667276 DOI: 10.3389/fonc.2020.575366] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 08/19/2020] [Indexed: 01/06/2023] Open
Abstract
Pre-mRNA processing factor 19 (Prp19) was previously reported to be involved in tumor progression. However, Prp19 expression and its functions remain elusive in neuroblastoma. Here, we aim to identify the functions and mechanisms of Prp19 in neuroblastoma. Neuroblastic tumor tissue microarrays and two independent validation data sets indicate that Prp19 is associated with high-risk markers and bone marrow metastasis and serves as a prognostic marker for worse clinical outcomes with neuroblastoma. Gain- and loss-of-expression assays reveal that Prp19 promotes invasion, migration, and epithelial-mesenchymal transition (EMT) of neuroblastoma cells in vitro. Bioinformatics analysis of RNA-seq data shows that the expressions of YAP and its downstream genes are significantly inhibited after downregulation of Prp19. Prp19 and YAP expression in metastatic lymph nodes is higher than in situ neuroblastoma tissue. Further experiments show that Prp19 regulates YAP expression and consequently affects cell invasion, migration, and EMT in neuroblastoma by pre-mRNA splicing of YAP. In conclusion, our findings provide the first evidence that Prp19 is a potential therapeutic target and prognostic biomarker for patients with neuroblastoma.
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Affiliation(s)
- Yuanxia Cai
- Department of Pediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China.,Division of Pediatric Oncology, Shanghai Institute of Pediatric Research, Shanghai, China
| | - Kai Chen
- Department of Pediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China.,Division of Pediatric Oncology, Shanghai Institute of Pediatric Research, Shanghai, China
| | - Cheng Cheng
- Department of Pediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China.,Division of Pediatric Oncology, Shanghai Institute of Pediatric Research, Shanghai, China
| | - Yonghu Xu
- Department of Pediatric Urology, Xinhua Hospital, National Key Clinical Specialty, Shanghai Top-Priority Clinical Center, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Qianqian Cheng
- Department of Pediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China.,Division of Pediatric Oncology, Shanghai Institute of Pediatric Research, Shanghai, China
| | - Guofeng Xu
- Department of Pediatric Urology, Xinhua Hospital, National Key Clinical Specialty, Shanghai Top-Priority Clinical Center, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Yeming Wu
- Department of Pediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China.,Division of Pediatric Oncology, Shanghai Institute of Pediatric Research, Shanghai, China.,Department of Pediatric Surgery, Children's Hospital of Soochow University, Suzhou, China
| | - Zhixiang Wu
- Department of Pediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China.,Division of Pediatric Oncology, Shanghai Institute of Pediatric Research, Shanghai, China.,Department of Pediatric Surgery, Children's Hospital of Soochow University, Suzhou, China
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25
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Liang WH, Federico SM, London WB, Naranjo A, Irwin MS, Volchenboum SL, Cohn SL. Tailoring Therapy for Children With Neuroblastoma on the Basis of Risk Group Classification: Past, Present, and Future. JCO Clin Cancer Inform 2020; 4:895-905. [PMID: 33058692 PMCID: PMC7608590 DOI: 10.1200/cci.20.00074] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/01/2020] [Indexed: 12/12/2022] Open
Abstract
For children with neuroblastoma, the likelihood of cure varies widely according to age at diagnosis, disease stage, and tumor biology. Treatments are tailored for children with this clinically heterogeneous malignancy on the basis of a combination of markers that are predictive of risk of relapse and death. Sequential risk-based, cooperative-group clinical trials conducted during the past 4 decades have led to improved outcome for children with neuroblastoma. Increasingly accurate risk classification and refinements in treatment stratification strategies have been achieved with the more recent discovery of robust genomic and molecular biomarkers. In this review, we discuss the history of neuroblastoma risk classification in North America and Europe and highlight efforts by the International Neuroblastoma Risk Group (INRG) Task Force to develop a consensus approach for pretreatment stratification using seven risk criteria including an image-based staging system-the INRG Staging System. We also update readers on the current Children's Oncology Group risk classifier and outline plans for the development of a revised 2021 Children's Oncology Group classifier that will incorporate INRG Staging System criteria to facilitate harmonization of risk-based frontline treatment strategies conducted around the globe. In addition, we discuss new approaches to establish increasingly robust, future risk classification algorithms that will further refine treatment stratification using machine learning tools and expanded data from electronic health records and the INRG Data Commons.
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Affiliation(s)
- Wayne H. Liang
- Department of Pediatrics and Informatics Institute, University of Alabama at Birmingham, Birmingham, AL
| | - Sara M. Federico
- Department of Oncology, St Jude Children’s Research Hospital, Memphis, TN
| | - Wendy B. London
- Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA
| | - Arlene Naranjo
- Department of Biostatistics, Children’s Oncology Group Statistics and Data Center, University of Florida, Gainesville, FL
| | - Meredith S. Irwin
- Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Samuel L. Volchenboum
- Department of Pediatrics and Comer Children’s Hospital, University of Chicago, Chicago, IL
| | - Susan L. Cohn
- Department of Pediatrics and Comer Children’s Hospital, University of Chicago, Chicago, IL
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Cangelosi D, Morini M, Zanardi N, Sementa AR, Muselli M, Conte M, Garaventa A, Pfeffer U, Bosco MC, Varesio L, Eva A. Hypoxia Predicts Poor Prognosis in Neuroblastoma Patients and Associates with Biological Mechanisms Involved in Telomerase Activation and Tumor Microenvironment Reprogramming. Cancers (Basel) 2020; 12:E2343. [PMID: 32825087 PMCID: PMC7563184 DOI: 10.3390/cancers12092343] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/09/2020] [Accepted: 08/17/2020] [Indexed: 12/23/2022] Open
Abstract
The biological and clinical heterogeneity of neuroblastoma (NB) demands novel biomarkers and therapeutic targets in order to drive the most appropriate treatment for each patient. Hypoxia is a condition of low-oxygen tension occurring in poorly vascularized tumor tissues. In this study, we aimed to assess the role of hypoxia in the pathogenesis of NB and at developing a new clinically relevant hypoxia-based predictor of outcome. We analyzed the gene expression profiles of 1882 untreated NB primary tumors collected at diagnosis and belonging to four existing data sets. Analyses took advantage of machine learning methods. We identified NB-hop, a seven-gene hypoxia biomarker, as a predictor of NB patient prognosis, which is able to discriminate between two populations of patients with unfavorable or favorable outcome on a molecular basis. NB-hop retained its prognostic value in a multivariate model adjusted for established risk factors and was able to additionally stratify clinically relevant groups of patients. Tumors with an unfavorable NB-hop expression showed a significant association with telomerase activation and a hypoxic, immunosuppressive, poorly differentiated, and apoptosis-resistant tumor microenvironment. NB-hop defines a new population of NB patients with hypoxic tumors and unfavorable prognosis and it represents a critical factor for the stratification and treatment of NB patients.
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Affiliation(s)
- Davide Cangelosi
- Laboratory of Molecular Biology, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy; (M.M.); (N.Z.); (L.V.); (A.E.)
| | - Martina Morini
- Laboratory of Molecular Biology, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy; (M.M.); (N.Z.); (L.V.); (A.E.)
| | - Nicolò Zanardi
- Laboratory of Molecular Biology, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy; (M.M.); (N.Z.); (L.V.); (A.E.)
| | - Angela Rita Sementa
- Laboratory of Pathology, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy;
| | - Marco Muselli
- Institute of Electronics, Computer and Telecommunication Engineering, Italian National Research Council, 16149 Genova, Italy;
| | - Massimo Conte
- Pediatric Oncology Unit, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy; (M.C.); (A.G.)
| | - Alberto Garaventa
- Pediatric Oncology Unit, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy; (M.C.); (A.G.)
| | - Ulrich Pfeffer
- Integrated Oncology Therapies Department, Molecular Pathology, IRCCS Ospedale Policlinico San Martino, 16132 Genova, Italy;
| | - Maria Carla Bosco
- Laboratory of Molecular Biology, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy; (M.M.); (N.Z.); (L.V.); (A.E.)
| | - Luigi Varesio
- Laboratory of Molecular Biology, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy; (M.M.); (N.Z.); (L.V.); (A.E.)
| | - Alessandra Eva
- Laboratory of Molecular Biology, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy; (M.M.); (N.Z.); (L.V.); (A.E.)
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He X, Qin C, Zhao Y, Zou L, Zhao H, Cheng C. Gene signatures associated with genomic aberrations predict prognosis in neuroblastoma. Cancer Commun (Lond) 2020; 40:105-118. [PMID: 32237073 PMCID: PMC7163660 DOI: 10.1002/cac2.12016] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 02/13/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Neuroblastoma (NB) is a heterogeneous disease with respect to genomic abnormalities and clinical behaviors. Despite recent advances in our understanding of the association between the genetic aberrations and clinical features, it remains one of the major challenges to predict prognosis and stratify patients for determining personalized therapy in this disease. The aim of this study was to develop an effective prognosis prediction model for NB patients. METHODS We integrated diverse computational analyses to define gene signatures that reflect MYCN activity and chromosomal aberrations including deletion of chromosome 1p (Chr1p_del) and chromosome 11q (Chr11q_del) as well as chromosome 11q whole loss (Chr11q_wls). We evaluated the prognostic and predictive values of these signatures in seven NB gene expression datasets (the number of samples ranges from 94 to 498, with a total of 2120) generated from both RNA sequencing and microarray platforms. RESULTS MYCN signature was a more effective prognostic marker than MYCN amplification status and MYCN expression. Similarly, the Chr1p_del score was more prognostic than Chr1p status. The activity scores of MYCN, Chr1p_del and Chr11q_del were associated with poor prognosis, while the Chr11q_wls score was linked to good outcome. We integrated the activity scores of MYCN, Chr1p_del, Chr11q_del, and Chr11q_wls and clinical variables into an integrative prognostic model, which displayed significant performance over the clinical variables or each genomic aberration alone. CONCLUSIONS Our integrative gene signature model shows a significantly improved forecast performance with prognostic and predictive information, and thereby can be served as a biomarker to stratify NB patients for prognosis evaluation and surveillance programs.
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Affiliation(s)
- Xiaoyan He
- Center for Clinical Molecular Medicine, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Key Laboratory of PediatricsChildren's Hospital of Chongqing Medical UniversityChongqing400014P. R. China
- Department of Biomedical Data ScienceGeisel School of Medicine at DartmouthLebanonNH03766USA
| | - Chao Qin
- Beijing Key Lab of Traffic Data Analysis and MiningSchool of Computer and Information TechnologyBeijing Jiaotong UniversityBeijing100044P. R. China
- Department of Biomedical Data ScienceGeisel School of Medicine at DartmouthLebanonNH03766USA
| | - Yanding Zhao
- Department of Biomedical Data ScienceGeisel School of Medicine at DartmouthLebanonNH03766USA
| | - Lin Zou
- Center for Clinical Molecular Medicine, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Key Laboratory of PediatricsChildren's Hospital of Chongqing Medical UniversityChongqing400014P. R. China
| | - Hui Zhao
- School of Biomedical SciencesFaculty of MedicineThe Chinese University of Hong KongHong Kong999077P. R. China
| | - Chao Cheng
- Department of Biomedical Data ScienceGeisel School of Medicine at DartmouthLebanonNH03766USA
- Department of MedicineBaylor College of MedicineHoustonTX77030USA
- Institute for Clinical and Translational ResearchBaylor College of MedicineHoustonTX77030USA
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28
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Ghilu S, Li Q, Fontaine SD, Santi DV, Kurmasheva RT, Zheng S, Houghton PJ. Prospective use of the single-mouse experimental design for the evaluation of PLX038A. Cancer Chemother Pharmacol 2020; 85:251-263. [PMID: 31927611 PMCID: PMC7039322 DOI: 10.1007/s00280-019-04017-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 12/17/2019] [Indexed: 12/12/2022]
Abstract
PURPOSE Defining robust criteria for drug activity in preclinical studies allows for fewer animals per treatment group, and potentially allows for inclusion of additional cancer models that more accurately represent genetic diversity and, potentially, allows for tumor sensitivity biomarker identification. METHODS Using a single-mouse design, 32 pediatric xenograft tumor models representing diverse pediatric cancer types [Ewing sarcoma (9), brain (4), rhabdomyosarcoma (10), Wilms tumor (4), and non-CNS rhabdoid tumors (5)] were evaluated for response to a single administration of pegylated-SN38 (PLX038A), a controlled-release PEGylated formulation of SN-38. Endpoints measured were percent tumor regression, and event-free survival (EFS). The correlation between response to PLX038A was compared to that for ten models treated with irinotecan (2.5 mg/kg × 5 days × 2 cycles), using a traditional design (10 mice/group). Correlations between tumor sensitivity, genetic mutations and gene expression were sought. Models showing no disease at week 20 were categorized as 'extreme responders' to PLX038A, whereas those with EFS less than 5 weeks were categorized as 'resistant'. RESULTS The activity of PLX038A was evaluable in 31/32 models. PLX038A induced > 50% volume regressions in 25 models (78%). Initial tumor volume regression correlated only modestly with EFS (r2 = 0.238), but sensitivity to PLX038A was better correlated with response to irinotecan when one tumor hypersensitive to PLX038A was omitted (r2 = 0.6844). Mutations in 53BP1 were observed in three of six sensitive tumor models compared to none in resistant models (n = 6). CONCLUSIONS This study demonstrates the feasibility of using a single-mouse design for assessing the antitumor activity of an agent, while encompassing greater genetic diversity representative of childhood cancers. PLX038A was highly active in most xenograft models, and tumor sensitivity to PLX038A was correlated with sensitivity to irinotecan, validating the single-mouse design in identifying agents with the same mechanism of action. Biomarkers that correlated with model sensitivity included wild-type TP53, or mutant TP53 but with a mutation in 53BP1, thus a defect in DNA damage response. These results support the value of the single-mouse experimental design.
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Affiliation(s)
- Samson Ghilu
- Greehey Children's Cancer Research Institute, UT Health San Antonio, 8403 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Qilin Li
- Greehey Children's Cancer Research Institute, UT Health San Antonio, 8403 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Shaun D Fontaine
- ProLynx LLC, 455 Mission Bay Blvd, South San Francisco, CA, 94158, USA
| | - Daniel V Santi
- ProLynx LLC, 455 Mission Bay Blvd, South San Francisco, CA, 94158, USA
| | - Raushan T Kurmasheva
- Greehey Children's Cancer Research Institute, UT Health San Antonio, 8403 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Siyuan Zheng
- Greehey Children's Cancer Research Institute, UT Health San Antonio, 8403 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Peter J Houghton
- Greehey Children's Cancer Research Institute, UT Health San Antonio, 8403 Floyd Curl Drive, San Antonio, TX, 78229, USA.
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29
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Roderwieser A, Sand F, Walter E, Fischer J, Gecht J, Bartenhagen C, Ackermann S, Otte F, Welte A, Kahlert Y, Lieberz D, Hertwig F, Reinhardt HC, Simon T, Peifer M, Ortmann M, Büttner R, Hero B, O'Sullivan RJ, Berthold F, Fischer M. Telomerase Is a Prognostic Marker of Poor Outcome and a Therapeutic Target in Neuroblastoma. JCO Precis Oncol 2019; 3:1-20. [PMID: 35100718 DOI: 10.1200/po.19.00072] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
PURPOSE Telomere maintenance is a hallmark of high-risk neuroblastoma; however, the contribution of telomerase and alternative lengthening of telomeres (ALT) to clinical phenotypes has remained unclear. We aimed to determine the clinical relevance of telomerase activation versus ALT as biomarkers in pretreatment neuroblastoma and to assess the potential value of telomerase as a therapeutic target. MATERIALS AND METHODS The genomic status of TERT and MYCN was assessed in 457 pretreatment neuroblastomas by fluorescence in situ hybridization. ALT was examined in 273 of 457 tumors by detection of ALT-associated promyelocytic leukemia nuclear bodies, and TERT expression was determined by microarrays in 223 of these. Cytotoxic effects of telomerase-interacting compounds were analyzed in neuroblastoma cell lines in vitro and in vivo. RESULTS We detected TERT rearrangements in 46 of 457 cases (10.1%), MYCN amplification in 93 of 457 cases (20.4%), and elevated TERT expression in tumors lacking TERT or MYCN alterations in 10 of 223 cases (4.5%). ALT activation was found in 49 of 273 cases (17.9%). All these alterations occurred almost mutually exclusively and were associated with unfavorable prognostic variables and adverse outcome. The presence of activated telomerase (ie, TERT rearrangements, MYCN amplification, or high TERT expression without these alterations) was associated with poorest overall survival and was an independent prognostic marker in multivariable analyses. We also found that the telomerase-interacting compound 6-thio-2'-deoxyguanosine effectively inhibited viability and proliferation of neuroblastoma cells bearing activated telomerase. Similarly, tumor growth was strongly impaired upon 6-thio-2'-deoxyguanosine treatment in telomerase-positive neuroblastoma xenografts in mice. CONCLUSION Our data suggest telomerase activation and ALT define distinct neuroblastoma subgroups with adverse outcome and that telomerase may represent a promising therapeutic target in many high-risk neuroblastomas.
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Affiliation(s)
- Andrea Roderwieser
- University Children's Hospital of Cologne, Cologne, Germany.,University of Cologne, Cologne, Germany
| | - Frederik Sand
- University Children's Hospital of Cologne, Cologne, Germany
| | - Esther Walter
- University Children's Hospital of Cologne, Cologne, Germany
| | - Janina Fischer
- University Children's Hospital of Cologne, Cologne, Germany
| | - Judith Gecht
- University Children's Hospital of Cologne, Cologne, Germany
| | - Christoph Bartenhagen
- University Children's Hospital of Cologne, Cologne, Germany.,University of Cologne, Cologne, Germany
| | - Sandra Ackermann
- University Children's Hospital of Cologne, Cologne, Germany.,University of Cologne, Cologne, Germany
| | - Felix Otte
- University Children's Hospital of Cologne, Cologne, Germany
| | - Anne Welte
- University Children's Hospital of Cologne, Cologne, Germany.,University of Cologne, Cologne, Germany
| | - Yvonne Kahlert
- University Children's Hospital of Cologne, Cologne, Germany.,University of Cologne, Cologne, Germany
| | | | - Falk Hertwig
- Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - H Christian Reinhardt
- University of Cologne, Cologne, Germany.,University Hospital of Cologne, Cologne, Germany
| | - Thorsten Simon
- University Children's Hospital of Cologne, Cologne, Germany
| | | | | | | | - Barbara Hero
- University Children's Hospital of Cologne, Cologne, Germany
| | | | - Frank Berthold
- University Children's Hospital of Cologne, Cologne, Germany
| | - Matthias Fischer
- University Children's Hospital of Cologne, Cologne, Germany.,University of Cologne, Cologne, Germany
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30
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Mühling J, Eberherr C, Müller Höcker J, Grote V, von Schweinitz D, Kappler R, Fröba-Pohl A. Vessel adherent growth represents a major challenge in the surgical resection of neuroblastoma and Is associated with adverse outcome. J Pediatr Surg 2019; 54:2336-2342. [PMID: 31402147 DOI: 10.1016/j.jpedsurg.2019.07.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 07/17/2019] [Accepted: 07/19/2019] [Indexed: 01/02/2023]
Abstract
PURPOSE Neuroblastoma (NB) is the most common extracranial, solid tumor in childhood, with a peak incidence in children under 6 years of age. Due to its variable course of disease, which ranges from spontaneous regression to metastatic spread, NB still represents a significant therapeutic challenge. Strikingly, a certain number of NBs intraoperatively show vessel adhesion and/or infiltrative growth, which is often not visible in pre-operative imaging. We proposed the term unexpected vessel infiltration of NB (UVIN) to denote this phenomenon. UVIN represents a major surgical challenge. METHODS In this study, we determined frequency and clinical relevance of UVIN in a cohort of 100 NB-patients with subsequent correlation to several unfavorable characteristics of disease. RNA expression levels of MYCN and its co-regulated antisense transcript MYCNOS to identify markers was measured by PCR. RESULTS We found UVIN to be present in 34% of cases and significantly correlated with incomplete resection, MYCN amplification, complications, neoadjuvant therapy, tumor grade and MYCNOS expression levels. MYCN expression levels showed no significant results with UVIN. CONCLUSION Collectively, our data show that UVIN represents a frequent surgical problem associated with a poor outcome in NB patients. MYCN and MYCNOS seem to be no appropriate markers for UVIN. TYPE OF STUDY Prognosis study. LEVEL OF EVIDENCE Level III.
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Affiliation(s)
- Jakob Mühling
- Department of Pediatric Surgery, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Germany.
| | - Corinna Eberherr
- Department of Pediatric Surgery, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Germany
| | | | - Veit Grote
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Germany
| | - Dietrich von Schweinitz
- Department of Pediatric Surgery, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Germany
| | - Roland Kappler
- Department of Pediatric Surgery, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Germany
| | - Alexandra Fröba-Pohl
- Department of Pediatric Surgery, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Germany
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31
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Identification of 15 T Cell Restricted Genes Evaluates T Cell Infiltration of Human Healthy Tissues and Cancers and Shows Prognostic and Predictive Potential. Int J Mol Sci 2019; 20:ijms20205242. [PMID: 31652661 PMCID: PMC6829269 DOI: 10.3390/ijms20205242] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 10/17/2019] [Accepted: 10/21/2019] [Indexed: 01/05/2023] Open
Abstract
T cell gene signatures are used to evaluate T cell infiltration of non-lymphoid tissues and cancers in both experimental and clinical settings. However, some genes included in the available T cell signatures are not T cell-restricted. Herein, we propose a new human T cell signature that has been developed via a six-step procedure and comprises 15 T cell restricted genes. We demonstrate the new T cell signature, named signature-H, that differs from other gene signatures since it shows higher sensitivity and better predictivity in the evaluation of T cell infiltration in healthy tissues as well as 32 cancers. Further, results from signature-H are highly concordant with the immunohistochemistry methods currently used for assessing the prognosis of neuroblastoma, as demonstrated by the Kaplan–Meier curves of patients ranked by tumor T cell infiltration. Moreover, T cell infiltration levels calculated using signature-H correlate with the risk groups determined by the staging of the neuroblastoma. Finally, multiparametric analysis of tumor-infiltrating T cells based on signature-H let us favorably predict the response of melanoma to the anti-PD-1 antibody nivolumab. These findings suggest that signature-H evaluates T cell infiltration levels of tissues and may be used as a prognostic tool in the precision medicine perspective after appropriate clinical validation.
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32
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Montemurro L, Raieli S, Angelucci S, Bartolucci D, Amadesi C, Lampis S, Scardovi AL, Venturelli L, Nieddu G, Cerisoli L, Fischer M, Teti G, Falconi M, Pession A, Hrelia P, Tonelli R. A Novel MYCN-Specific Antigene Oligonucleotide Deregulates Mitochondria and Inhibits Tumor Growth in MYCN-Amplified Neuroblastoma. Cancer Res 2019; 79:6166-6177. [PMID: 31615807 DOI: 10.1158/0008-5472.can-19-0008] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 07/10/2019] [Accepted: 10/07/2019] [Indexed: 11/16/2022]
Abstract
Approximately half of high-risk neuroblastoma is characterized by MYCN amplification. N-Myc promotes tumor progression by inducing cell growth and inhibiting differentiation. MYCN has also been shown to play an active role in mitochondrial metabolism, but this relationship is not well understood. Although N-Myc is a known driver of the disease, it remains a target for which no therapeutic drug exists. Here, we evaluated a novel MYCN-specific antigene PNA oligonucleotide (BGA002) in MYCN-amplified (MNA) or MYCN-expressing neuroblastoma and investigated the mechanism of its antitumor activity. MYCN mRNA and cell viability were reduced in a broad set of neuroblastoma cell lines following BGA002 treatment. Furthermore, BGA002 decreased N-Myc protein levels and apoptosis in MNA neuroblastoma. Analysis of gene expression data from patients with neuroblastoma revealed that MYCN was associated with increased reactive oxygen species (ROS), downregulated mitophagy, and poor prognosis. Inhibition of MYCN caused profound mitochondrial damage in MNA neuroblastoma cells through downregulation of the mitochondrial molecular chaperone TRAP1, which subsequently increased ROS. Correspondingly, inhibition of MYCN reactivated mitophagy. Systemic administration of BGA002 downregulated N-Myc and TRAP1, with a concomitant decrease in MNA neuroblastoma xenograft tumor weight. In conclusion, this study highlights the role of N-Myc in blocking mitophagy in neuroblastoma and in conferring protection to ROS in mitochondria through upregulation of TRAP1. BGA002 is a potently improved MYCN-specific antigene oligonucleotide that reverts N-Myc-dysregulated mitochondrial pathways, leading to loss of the protective effect of N-Myc against mitochondrial ROS. SIGNIFICANCE: A second generation antigene peptide oligonucleotide targeting MYCN induces mitochondrial damage and inhibits growth of MYCN-amplified neuroblastoma cells.
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Affiliation(s)
- Luca Montemurro
- Interdepartmental Center for Cancer Research, University of Bologna, Bologna, Italy
| | | | - Silvia Angelucci
- Interdepartmental Center for Cancer Research, University of Bologna, Bologna, Italy
| | - Damiano Bartolucci
- Interdepartmental Center for Cancer Research, University of Bologna, Bologna, Italy
| | | | | | | | | | | | | | - Matthias Fischer
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Gabriella Teti
- Department of Biomedical and Neuromotor Sciences-DBNS, University of Bologna, Bologna, Italy
| | - Mirella Falconi
- Department of Biomedical and Neuromotor Sciences-DBNS, University of Bologna, Bologna, Italy
| | - Andrea Pession
- Interdepartmental Center for Cancer Research, University of Bologna, Bologna, Italy
| | - Patrizia Hrelia
- Department of Pharmacy and Biotechnologies, University of Bologna, Bologna, Italy
| | - Roberto Tonelli
- Department of Pharmacy and Biotechnologies, University of Bologna, Bologna, Italy.
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33
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Pozzoli G, Petrucci G, Navarra P, Marei HE, Cenciarelli C. Aspirin inhibits proliferation and promotes differentiation of neuroblastoma cells via p21 Waf1 protein up-regulation and Rb1 pathway modulation. J Cell Mol Med 2019; 23:7078-7087. [PMID: 31429199 PMCID: PMC6787451 DOI: 10.1111/jcmm.14610] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 08/06/2019] [Accepted: 08/07/2019] [Indexed: 02/06/2023] Open
Abstract
Several clinical and experimental studies have demonstrated that regular use of aspirin (acetylsalicylic acid, ASA) correlates with a reduced risk of cancer and that the drug exerts direct anti‐tumour effects. We have previously reported that ASA inhibits proliferation of human glioblastoma multiforme‐derived cancer stem cells. In the present study, we analysed the effects of ASA on nervous system‐derived cancer cells, using the SK‐N‐SH (N) human neuroblastoma cell line as an experimental model. ASA treatment of SK‐N‐SH (N) dramatically reduced cell proliferation and motility, and induced neuronal‐like differentiation, indicated by the appearance of the neuronal differentiation marker tyrosine hydroxylase (TH) after 5 days. ASA did not affect cell viability, but caused a time‐dependent accumulation of cells in the G0/G1 phase of the cell cycle, with a concomitant decrease in the percentage of cells in the G2 phase. These effects appear to be mediated by a COX‐independent mechanism involving an increase in p21Waf1 and underphosphorylated retinoblastoma (hypo‐pRb1) protein levels. These findings may support a potential role of ASA as adjunctive therapeutic agent in the clinical management of neuroblastoma.
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Affiliation(s)
- Giacomo Pozzoli
- Institute of Pharmacology, Università Cattolica del Sacro Cuore, Rome, Italy.,Pharmacology Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Giovanna Petrucci
- Institute of Pharmacology, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Pierluigi Navarra
- Institute of Pharmacology, Università Cattolica del Sacro Cuore, Rome, Italy.,Pharmacology Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Hany E Marei
- Department of Cytology and Histology, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
| | - Carlo Cenciarelli
- Institute of Translational Pharmacology (IFT), National Research Council (CNR), Rome, Italy
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34
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Twist CJ, Schmidt ML, Naranjo A, London WB, Tenney SC, Marachelian A, Shimada H, Collins MH, Esiashvili N, Adkins ES, Mattei P, Handler M, Katzenstein H, Attiyeh E, Hogarty MD, Gastier-Foster J, Wagner E, Matthay KK, Park JR, Maris JM, Cohn SL. Maintaining Outstanding Outcomes Using Response- and Biology-Based Therapy for Intermediate-Risk Neuroblastoma: A Report From the Children's Oncology Group Study ANBL0531. J Clin Oncol 2019; 37:3243-3255. [PMID: 31386611 DOI: 10.1200/jco.19.00919] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
PURPOSE The primary objective of the Children's Oncology Group study ANBL0531 (ClinicalTrials.gov identifier: NCT00499616) was to reduce therapy for subsets of patients with intermediate-risk neuroblastoma using a biology- and response-based algorithm to assign treatment duration while maintaining a 3-year overall survival (OS) of 95% or more for the entire cohort. PATIENTS AND METHODS Children younger than age 12 years with intermediate-risk stage 2A/2B or stage 3 tumors with favorable histology; infants younger than age 365 days with stage 3, 4 or 4S disease; and toddlers from 365 to younger than 547 days with favorable histology, hyperdiploid stage 4, or unfavorable histology stage 3 tumors were eligible. Patients with MYCN-amplified tumors were excluded. Patients were assigned to initially receive two (group 2), four (group 3), or eight (group 4) cycles of chemotherapy with or without surgery on the basis of prognostic markers, including allelic status of chromosomes 1p and 11q; ultimate duration of therapy was determined by overall response. RESULTS Between 2007 and 2011, 404 evaluable patients were enrolled. Compared with legacy Children's Oncology Group studies, subsets of patients had a reduction in treatment. The 3-year event-free survival and OS rates were 83.2% (95% CI, 79.4% to 87.0%) and 94.9% (95% CI, 92.7% to 97.2%), respectively. Infants with stage 4 tumors with favorable biology (n = 61) had superior 3-year event-free survival compared with patients with one or more unfavorable biologic features (n = 47; 86.9% [95% CI, 78.3% to 95.4%] v 66.8% [95% CI, 53.1% to 80.6%]; P = .02), with a trend toward OS advantage (95.0% [95% CI, 89.5% to 100%] v 86.7% [95% CI, 76.6% to 96.7%], respectively; P = .08). OS for patients with localized disease was 100%. CONCLUSION Excellent survival was achieved with this treatment algorithm, with reduction of therapy for subsets of patients. More-effective treatment strategies still are needed for infants with unfavorable biology stage 4 disease.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Peter Mattei
- Children's Hospital of Philadelphia, Philadelphia, PA
| | | | | | - Edward Attiyeh
- Children's Hospital of Philadelphia, Philadelphia, PA.,Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Michael D Hogarty
- Children's Hospital of Philadelphia, Philadelphia, PA.,Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Julie Gastier-Foster
- Nationwide Children's Hospital, Columbus, OH.,The Ohio State University College of Medicine, Columbus, OH
| | | | - Katherine K Matthay
- University of California, San Francisco, School of Medicine, and UCSF Benioff Children's Hospital, San Francisco, CA
| | | | - John M Maris
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
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35
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Applebaum MA, Barr EK, Karpus J, Nie J, Zhang Z, Armstrong AE, Uppal S, Sukhanova M, Zhang W, Chlenski A, Salwen HR, Wilkinson E, Dobratic M, Grossman R, Godley LA, Stranger BE, He C, Cohn SL. 5-Hydroxymethylcytosine Profiles Are Prognostic of Outcome in Neuroblastoma and Reveal Transcriptional Networks That Correlate With Tumor Phenotype. JCO Precis Oncol 2019; 3. [PMID: 31179414 PMCID: PMC6553657 DOI: 10.1200/po.18.00402] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
PURPOSE Whole-genome profiles of the epigenetic modification 5-hydroxymethylcytosine (5-hmC) are robust diagnostic biomarkers in adult patients with cancer. We investigated if 5-hmC profiles would serve as novel prognostic markers in neuroblastoma, a clinically heterogeneous pediatric cancer. Because this DNA modification facilitates active gene expression, we hypothesized that 5-hmC profiles would identify transcriptomic networks driving the clinical behavior of neuroblastoma. PATIENTS AND METHODS Nano-hmC-Seal sequencing was performed on DNA from Discovery (n = 51), Validation (n = 38), and Children’s Oncology Group (n = 20) cohorts of neuroblastoma tumors. RNA was isolated from 48 tumors for RNA sequencing. Genes with differential 5-hmC or expression between clusters were identified using DESeq2. A 5-hmC model predicting outcome in high-risk patients was established using linear discriminant analysis. RESULTS Comparison of low- versus high-risk tumors in the Discovery cohort revealed 577 genes with differential 5-hmC. Hierarchical clustering of tumors from the Discovery and Validation cohorts using these genes identified two main clusters highly associated with established prognostic markers, clinical risk group, and outcome. Genes with increased 5-hmC and expression in the favorable cluster were enriched for pathways of neuronal differentiation and KRAS activation, whereas genes involved in inflammation and the PRC2 complex were identified in the unfavorable cluster. The linear discriminant analysis model trained on high-risk Discovery cohort tumors was prognostic of outcome when applied to high-risk tumors from the Validation and Children’s Oncology Group cohorts (hazard ratio, 3.8). CONCLUSION 5-hmC profiles may be optimal DNA-based biomarkers in neuroblastoma. Analysis of transcriptional networks regulated by these epigenomic modifications may lead to a deeper understanding of drivers of neuroblastoma phenotype.
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Affiliation(s)
| | - Erin K Barr
- Texas Tech University Health Sciences, Lubbock, TX
| | | | - Ji Nie
- University of Chicago, Chicago, IL
| | | | | | | | | | - Wei Zhang
- Northwestern University, Chicago, IL
| | | | | | | | | | | | | | | | - Chuan He
- University of Chicago, Chicago, IL.,Howard Hughes Medical Institute, Chevy Chase, MD
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Radhakrishnan V, Raja A, Dhanushkodi M, Ganesan TS, Selvaluxmy G, Sagar TG. Real World Experience of Treating Neuroblastoma: Experience from a Tertiary Cancer Centre in India. Indian J Pediatr 2019; 86:417-426. [PMID: 30778950 DOI: 10.1007/s12098-018-2834-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 12/03/2018] [Indexed: 12/13/2022]
Abstract
OBJECTIVES Management of neuroblastoma, especially high-risk (HR) disease is difficult in a resource-limited setting. There is a paucity of literature on outcomes of patients treated in India. The present study was conducted to analyse the clinical profile, treatment, and outcomes of patients with neuroblastoma treated at authors' centre. METHODS The study was a retrospective analysis of newly diagnosed patients with neuroblastoma treated at authors' centre between 2000 to 2017. The International Neuroblastoma Staging System and risk grouping were used to classify patients as low-risk (LR), intermediate-risk (IR) and high-risk (HR). Treatment was individualised and risk-adapted. Kaplan-Meier method was used to calculate the event-free survival (EFS) and overall survival (OS). RESULTS The study included 85 patients with a median age of 4 y and 67% were males. Malnutrition was observed in 55% of patients. Adrenal gland was the most common site in 75% patients followed by mediastinum in 12%. LR was observed in 7/85 (8%) patients, IR 20/85 (24%) and HR in 58/85 (68%) patients. The CCG-3891 protocol was used to treat 80% of the patients. Autologous stem cell transplantation (ASCT) was performed in 32% of HR patients. The median follow-up was 16.6 mo. The median EFS and OS for all patients were 19.2 mo and 26.9 mo respectively and the 3 y EFS and OS was 36% and 47% respectively. The 3y EFS for LR, IR and HR patients was 100%, 54%, and 18.9% respectively (P < 0.001) and for OS was 100%, 77%, and 34% respectively (P = 0.002). On multivariate analysis, a hemoglobin less than 10 g% predicted inferior EFS (P = 0.002) and OS (p = 0.005) for all patients. For patients with high-risk disease, on multivariate analysis, hemoglobin (P = 0.002) and 13-Cis Retinoic acid maintenance (P = 0.002) predicted EFS and only radiotherapy to the primary (P = 0.01) predicted OS. Only 4/19 (21%) are alive and in remission post ASCT. CONCLUSIONS Majority of patients with neuroblastoma presented to authors' centre with advanced disease. Survival outcomes of patients with LR disease are excellent. However, patients with HR disease have poor outcomes despite multimodality management. Non-availability of N-MYC testing in few patients could have falsely down-staged them to IR from HR. A low hemoglobin at diagnosis is a poor predictor of outcome.
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Affiliation(s)
| | - Anand Raja
- Department of Surgical Oncology, Cancer Institute (WIA), Adyar, Chennai, Tamilnadu, India
| | - Manikandan Dhanushkodi
- Department of Medical Oncology, Cancer Institute (WIA), Adyar, Chennai, Tamilnadu, India
| | - T S Ganesan
- Department of Medical Oncology, Cancer Institute (WIA), Adyar, Chennai, Tamilnadu, India
| | - G Selvaluxmy
- Department of Radiotherapy, Cancer Institute (WIA), Adyar, Chennai, Tamilnadu, India
| | - T G Sagar
- Department of Medical Oncology, Cancer Institute (WIA), Adyar, Chennai, Tamilnadu, India
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Ackermann S, Cartolano M, Hero B, Welte A, Kahlert Y, Roderwieser A, Bartenhagen C, Walter E, Gecht J, Kerschke L, Volland R, Menon R, Heuckmann JM, Gartlgruber M, Hartlieb S, Henrich KO, Okonechnikov K, Altmüller J, Nürnberg P, Lefever S, de Wilde B, Sand F, Ikram F, Rosswog C, Fischer J, Theissen J, Hertwig F, Singhi AD, Simon T, Vogel W, Perner S, Krug B, Schmidt M, Rahmann S, Achter V, Lang U, Vokuhl C, Ortmann M, Büttner R, Eggert A, Speleman F, O'Sullivan RJ, Thomas RK, Berthold F, Vandesompele J, Schramm A, Westermann F, Schulte JH, Peifer M, Fischer M. A mechanistic classification of clinical phenotypes in neuroblastoma. Science 2019; 362:1165-1170. [PMID: 30523111 DOI: 10.1126/science.aat6768] [Citation(s) in RCA: 173] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 07/26/2018] [Accepted: 10/31/2018] [Indexed: 12/20/2022]
Abstract
Neuroblastoma is a pediatric tumor of the sympathetic nervous system. Its clinical course ranges from spontaneous tumor regression to fatal progression. To investigate the molecular features of the divergent tumor subtypes, we performed genome sequencing on 416 pretreatment neuroblastomas and assessed telomere maintenance mechanisms in 208 of these tumors. We found that patients whose tumors lacked telomere maintenance mechanisms had an excellent prognosis, whereas the prognosis of patients whose tumors harbored telomere maintenance mechanisms was substantially worse. Survival rates were lowest for neuroblastoma patients whose tumors harbored telomere maintenance mechanisms in combination with RAS and/or p53 pathway mutations. Spontaneous tumor regression occurred both in the presence and absence of these mutations in patients with telomere maintenance-negative tumors. On the basis of these data, we propose a mechanistic classification of neuroblastoma that may benefit the clinical management of patients.
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Affiliation(s)
- Sandra Ackermann
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Maria Cartolano
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, Cologne, Germany
| | - Barbara Hero
- Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany
| | - Anne Welte
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Yvonne Kahlert
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Andrea Roderwieser
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Christoph Bartenhagen
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Esther Walter
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Judith Gecht
- Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany
| | - Laura Kerschke
- Institute of Biostatistics and Clinical Research, University of Münster, Münster, Germany
| | - Ruth Volland
- Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany
| | | | | | - Moritz Gartlgruber
- Division of Neuroblastoma Genomics (B087), German Cancer Research Center, and Hopp Children's Cancer Center at NCT Heidelberg (KiTZ), Heidelberg, Germany
| | - Sabine Hartlieb
- Division of Neuroblastoma Genomics (B087), German Cancer Research Center, and Hopp Children's Cancer Center at NCT Heidelberg (KiTZ), Heidelberg, Germany
| | - Kai-Oliver Henrich
- Division of Neuroblastoma Genomics (B087), German Cancer Research Center, and Hopp Children's Cancer Center at NCT Heidelberg (KiTZ), Heidelberg, Germany
| | - Konstantin Okonechnikov
- Division of Pediatric Neurooncology, German Cancer Research Center, and Hopp Children's Cancer Center at NCT Heidelberg (KiTZ), Heidelberg, Germany
| | - Janine Altmüller
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Peter Nürnberg
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,Cologne Center for Genomics, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Steve Lefever
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Bram de Wilde
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Frederik Sand
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Fakhera Ikram
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,Interdisciplinary Research Centre in Biomedical Materials (IRCBM), COMSATS University Islamabad, Lahore Campus, Lahore, Pakistan
| | - Carolina Rosswog
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Janina Fischer
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Jessica Theissen
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany.,Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany
| | - Falk Hertwig
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, Berlin, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,Berlin Institute of Health, Berlin, Germany
| | - Aatur D Singhi
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Thorsten Simon
- Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany
| | - Wenzel Vogel
- Pathology of the University Medical Center Schleswig-Holstein, Campus Luebeck, Luebeck, Germany.,Research Center Borstel, Leibniz Center for Medicine and Biosciences, Borstel, Germany
| | - Sven Perner
- Pathology of the University Medical Center Schleswig-Holstein, Campus Luebeck, Luebeck, Germany.,Research Center Borstel, Leibniz Center for Medicine and Biosciences, Borstel, Germany
| | - Barbara Krug
- Department of Diagnostic and Interventional Radiology, University Hospital of Cologne, Cologne, Germany
| | - Matthias Schmidt
- Department of Nuclear Medicine, University of Cologne, Cologne, Germany
| | - Sven Rahmann
- Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Computer Science, TU Dortmund, Dortmund, Germany
| | - Viktor Achter
- Computing Center, University of Cologne, Cologne, Germany
| | - Ulrich Lang
- Computing Center, University of Cologne, Cologne, Germany.,Department of Informatics, University of Cologne, Cologne, Germany
| | - Christian Vokuhl
- Kiel Pediatric Tumor Registry, Department of Pediatric Pathology, University of Kiel, Kiel, Germany
| | - Monika Ortmann
- Department of Pathology, University of Cologne, Cologne, Germany
| | - Reinhard Büttner
- Department of Pathology, University of Cologne, Cologne, Germany
| | - Angelika Eggert
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, Berlin, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,Berlin Institute of Health, Berlin, Germany
| | - Frank Speleman
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Roderick J O'Sullivan
- Department of Pharmacology and Chemical Biology, University of Pittsburgh Cancer Institute (UPCI), Hillman Cancer Center, Pittsburgh, PA, USA
| | - Roman K Thomas
- Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, Cologne, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,Department of Pathology, University of Cologne, Cologne, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Frank Berthold
- Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany
| | - Jo Vandesompele
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Alexander Schramm
- Department of Medical Oncology, West German Cancer Center Essen, University of Duisburg-Essen, Essen, Germany
| | - Frank Westermann
- Division of Neuroblastoma Genomics (B087), German Cancer Research Center, and Hopp Children's Cancer Center at NCT Heidelberg (KiTZ), Heidelberg, Germany
| | - Johannes H Schulte
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, Berlin, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,Berlin Institute of Health, Berlin, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Peifer
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, Cologne, Germany
| | - Matthias Fischer
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany. .,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
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Abstract
PURPOSE OF REVIEW Our understanding of the biologic basis of neuroblastoma, the genetic heterogeneity of this malignancy and the role of host factors has expanded significantly in recent years. In this review, we highlight current and future risk-based treatment approaches and discuss the opportunities and challenges of selecting optimal therapies for specific patient subsets. RECENT FINDINGS Significant progress has been made in understanding neuroblastoma predisposition and new approaches have been taken to treatment of this disease. Although survival remains poor for patients with high-risk neuroblastoma, current-era therapy has improved outcomes. Integration of new prognostic markers into neuroblastoma classification systems will allow more precise risk classification and refined treatment assignment. Promising treatments that include targeted therapies as well as immunotherapeutics are being evaluated in clinical trials, and new predictive biomarkers are being developed. SUMMARY As our understanding of neuroblastoma biology deepens, our approaches to therapy for this disease continue to evolve. Improved risk stratification and the use of predictive biomarkers will aid in treatment selection for patients with neuroblastoma, and it is expected that future treatments will be associated with greater efficacy and less toxicity.
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Chlenski A, Park C, Dobratic M, Salwen HR, Budke B, Park JH, Miller R, Applebaum MA, Wilkinson E, Nakamura Y, Connell PP, Cohn SL. Maternal Embryonic Leucine Zipper Kinase (MELK), a Potential Therapeutic Target for Neuroblastoma. Mol Cancer Ther 2019; 18:507-516. [PMID: 30674566 DOI: 10.1158/1535-7163.mct-18-0819] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 12/07/2018] [Accepted: 01/15/2019] [Indexed: 01/10/2023]
Abstract
Maternal embryonic leucine zipper kinase (MELK) activates pathways that mediate aggressive tumor growth and therapy resistance in many types of adult cancers. Pharmacologic and genomic inhibition of MELK impairs tumor growth and increases sensitivity to radiation and chemotherapy. On the basis of these promising preclinical studies, early-phase adult clinical trials testing the MELK inhibitor OTS167 are ongoing. To investigate whether MELK is also a therapeutic target in neuroblastoma, we analyzed MELK expression in primary tumors and cell lines, and examined the effects of OTS167 on neuroblastoma growth. In primary tumors, high levels of MELK were associated with advanced stage disease and inferior survival. Higher levels of MELK were also detected in tumorigenic versus nontumorigenic neuroblastoma cell lines, and cells with higher levels of MELK expression were more sensitive to OTS167 than low-MELK expressing cells. OTS167 suppressed the growth of neuroblastoma xenografts, and in a preclinical model of minimal residual disease, survival was prolonged with MELK inhibition. OTS167 treatment downregulated MELK and its target enhancer of zeste homolog 2 (EZH2), a component of the polycomb repressive complex 2 (PRC2) that is known to modulate the DNA damage response. We also show that OTS167 reduced the formation of collapsed replication forks induced by camptothecin or radiation. Taken together, our results indicate that MELK indirectly mediates efficient processing of replication-associated DNA lesions in neuroblastoma, and that OTS167 sensitizes cells to DNA-damaging agents by abrogating this process. Further studies evaluating the activity of combination treatment regimens with OTS167 in neuroblastoma are warranted.
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Affiliation(s)
| | - Chanyoung Park
- Department of Radiation and Cellular Oncology, University of Chicago, Chicago, Illinois
| | - Marija Dobratic
- Department of Pediatrics, University of Chicago, Chicago, Illinois
| | - Helen R Salwen
- Department of Pediatrics, University of Chicago, Chicago, Illinois
| | - Brian Budke
- Department of Radiation and Cellular Oncology, University of Chicago, Chicago, Illinois
| | - Jae-Hyun Park
- Department of Medicine, University of Chicago, Chicago, Illinois
| | - Ryan Miller
- Department of Pediatrics, University of Chicago, Chicago, Illinois
| | - Mark A Applebaum
- Department of Pediatrics, University of Chicago, Chicago, Illinois
| | - Emma Wilkinson
- Department of Pediatrics, University of Chicago, Chicago, Illinois
| | - Yusuke Nakamura
- Department of Medicine, University of Chicago, Chicago, Illinois
- Department of Surgery, University of Chicago, Chicago, Illinois
| | - Philip P Connell
- Department of Radiation and Cellular Oncology, University of Chicago, Chicago, Illinois
| | - Susan L Cohn
- Department of Pediatrics, University of Chicago, Chicago, Illinois.
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Meany HJ. Non-High-Risk Neuroblastoma: Classification and Achievements in Therapy. CHILDREN (BASEL, SWITZERLAND) 2019; 6:E5. [PMID: 30626019 PMCID: PMC6352142 DOI: 10.3390/children6010005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 12/23/2018] [Accepted: 12/28/2018] [Indexed: 12/12/2022]
Abstract
Neuroblastoma, a tumor of the sympathetic nervous system, is the most common extra-cranial neoplasm of childhood. Variables with prognostic significance in patients with neuroblastoma, including age at diagnosis, disease stage, tumor histology, MYCN gene amplification, tumor cell ploidy, and the presence of segmental chromosomal aberrations are utilized to classify patients based on risk of disease recurrence. Patients with non-high-risk neuroblastoma, low- and intermediate-risk categories, represent nearly half of all newly diagnosed cases. This group has an excellent event-free and overall survival with current therapy. Over time, the objective in treatment of non-high-risk neuroblastoma has been reduction of therapy intensity to minimize short- and long-term adverse events all the while maintaining excellent outcomes.
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Affiliation(s)
- Holly J Meany
- Center for Cancer and Blood Disorders, Children's National Health System, The George Washington University School of Medicine and Health Sciences, Washington, DC 20010, USA.
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41
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Maggio V, Chierici M, Jurman G, Furlanello C. Distillation of the clinical algorithm improves prognosis by multi-task deep learning in high-risk Neuroblastoma. PLoS One 2018; 13:e0208924. [PMID: 30532223 PMCID: PMC6285384 DOI: 10.1371/journal.pone.0208924] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 11/26/2018] [Indexed: 02/07/2023] Open
Abstract
We introduce the CDRP (Concatenated Diagnostic-Relapse Prognostic) architecture for multi-task deep learning that incorporates a clinical algorithm, e.g., a risk stratification schema to improve prognostic profiling. We present the first application to survival prediction in High-Risk (HR) Neuroblastoma from transcriptomics data, a task that studies from the MAQC consortium have shown to remain the hardest among multiple diagnostic and prognostic endpoints predictable from the same dataset. To obtain a more accurate risk stratification needed for appropriate treatment strategies, CDRP combines a first component (CDRP-A) synthesizing a diagnostic task and a second component (CDRP-N) dedicated to one or more prognostic tasks. The approach leverages the advent of semi-supervised deep learning structures that can flexibly integrate multimodal data or internally create multiple processing paths. CDRP-A is an autoencoder trained on gene expression on the HR/non-HR risk stratification by the Children’s Oncology Group, obtaining a 64-node representation in the bottleneck layer. CDRP-N is a multi-task classifier for two prognostic endpoints, i.e., Event-Free Survival (EFS) and Overall Survival (OS). CDRP-A provides the HR embedding input to the CDRP-N shared layer, from which two branches depart to model EFS and OS, respectively. To control for selection bias, CDRP is trained and evaluated using a Data Analysis Protocol (DAP) developed within the MAQC initiative. CDRP was applied on Illumina RNA-Seq of 498 Neuroblastoma patients (HR: 176) from the SEQC study (12,464 Entrez genes) and on Affymetrix Human Exon Array expression profiles (17,450 genes) of 247 primary diagnostic Neuroblastoma of the TARGET NBL cohort. On the SEQC HR patients, CDRP achieves Matthews Correlation Coefficient (MCC) 0.38 for EFS and MCC = 0.19 for OS in external validation, improving over published SEQC models. We show that a CDRP-N embedding is indeed parametrically associated to increasing severity and the embedding can be used to better stratify patients’ survival.
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LDHA in Neuroblastoma Is Associated with Poor Outcome and Its Depletion Decreases Neuroblastoma Growth Independent of Aerobic Glycolysis. Clin Cancer Res 2018; 24:5772-5783. [DOI: 10.1158/1078-0432.ccr-17-2578] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 04/20/2018] [Accepted: 06/12/2018] [Indexed: 11/16/2022]
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Chikaraishi K, Takenobu H, Sugino RP, Mukae K, Akter J, Haruta M, Kurosumi M, Endo TA, Koseki H, Shimojo N, Ohira M, Kamijo T. CFC1 is a cancer stemness-regulating factor in neuroblastoma. Oncotarget 2018; 8:45046-45059. [PMID: 28620148 PMCID: PMC5542166 DOI: 10.18632/oncotarget.18464] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 05/28/2017] [Indexed: 01/06/2023] Open
Abstract
Background Despite the use of aggressive therapy, survival rates among high-risk neuroblastoma (NB) patients remain poor. Cancer stem cells (CSCs) are considered to be critically involved in the recurrence and metastasis of NB and are isolated as NB spheres. Methods The gene expression profiling of adherent (control) and sphere-forming primary NB cells was conducted using a gene expression microarray. CFC1, which functions in the development of embryos and decides the left-right axis, was strongly expressed in sphere-forming cells only and was related to the unfavorable prognosis of NB patients. The knockdown and overexpression of CFC1 were performed using a lentiviral system in NB cell lines. Sphere formation, cell proliferation, colony formation in soft agar, and xenograft tumor formation were analyzed. Results The overexpression of CFC1 increased sphere formation, cell growth, and colony formation. These phenotypes, particularly sphere formation, and xenograft tumor formation were significantly suppressed by the knockdown of CFC1. CFC1 inhibited Activin A-induced NB cell differentiation and Smad2 phosphorylation in NB cell lines, indicating its involvement in tumorigenesis related to EGF-CFC co-receptor family molecule pathways. Collectively, these results indicate that CFC1 is a candidate molecule for the development of CSC-targeted therapy for NB.
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Affiliation(s)
- Koji Chikaraishi
- Research Institute for Clinical Oncology, Saitama Cancer Center, Saitama, Japan.,Department of Pediatrics, Chiba University, Chiba, Japan
| | - Hisanori Takenobu
- Research Institute for Clinical Oncology, Saitama Cancer Center, Saitama, Japan.,Laboratory of Tumor Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Ryuichi P Sugino
- Research Institute for Clinical Oncology, Saitama Cancer Center, Saitama, Japan
| | - Kyosuke Mukae
- Research Institute for Clinical Oncology, Saitama Cancer Center, Saitama, Japan.,Laboratory of Tumor Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Jesmin Akter
- Research Institute for Clinical Oncology, Saitama Cancer Center, Saitama, Japan
| | - Masayuki Haruta
- Research Institute for Clinical Oncology, Saitama Cancer Center, Saitama, Japan.,Laboratory of Tumor Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | | | - Takaho A Endo
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Naoki Shimojo
- Department of Pediatrics, Chiba University, Chiba, Japan
| | - Miki Ohira
- Research Institute for Clinical Oncology, Saitama Cancer Center, Saitama, Japan.,Laboratory of Tumor Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Takehiko Kamijo
- Research Institute for Clinical Oncology, Saitama Cancer Center, Saitama, Japan.,Laboratory of Tumor Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
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Nakagawara A, Li Y, Izumi H, Muramori K, Inada H, Nishi M. Neuroblastoma. Jpn J Clin Oncol 2018; 48:214-241. [PMID: 29378002 DOI: 10.1093/jjco/hyx176] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Indexed: 02/07/2023] Open
Abstract
Neuroblastoma is one of the most common solid tumors in children and has a diverse clinical behavior that largely depends on the tumor biology. Neuroblastoma exhibits unique features, such as early age of onset, high frequency of metastatic disease at diagnosis in patients over 1 year of age and the tendency for spontaneous regression of tumors in infants. The high-risk tumors frequently have amplification of the MYCN oncogene as well as segmental chromosome alterations with poor survival. Recent advanced genomic sequencing technology has revealed that mutation of ALK, which is present in ~10% of primary tumors, often causes familial neuroblastoma with germline mutation. However, the frequency of gene mutations is relatively small and other aberrations, such as epigenetic abnormalities, have also been proposed. The risk-stratified therapy was introduced by the Japan Neuroblastoma Study Group (JNBSG), which is now moving to the Neuroblastoma Committee of Japan Children's Cancer Group (JCCG). Several clinical studies have facilitated the reduction of therapy for children with low-risk neuroblastoma disease and the significant improvement of cure rates for patients with intermediate-risk as well as high-risk disease. Therapy for patients with high-risk disease includes intensive induction chemotherapy and myeloablative chemotherapy, followed by the treatment of minimal residual disease using differentiation therapy and immunotherapy. The JCCG aims for better cures and long-term quality of life for children with cancer by facilitating new approaches targeting novel driver proteins, genetic pathways and the tumor microenvironment.
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Affiliation(s)
| | - Yuanyuan Li
- Laboratory of Molecular Biology, Life Science Research Institute, Saga Medical Center Koseikan
| | - Hideki Izumi
- Laboratory of Molecular Biology, Life Science Research Institute, Saga Medical Center Koseikan
| | | | - Hiroko Inada
- Department of Pediatrics, Saga Medical Center Koseikan
| | - Masanori Nishi
- Department of Pediatrics, Saga University, Saga 849-8501, Japan
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45
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Applebaum MA, Jha AR, Kao C, Hernandez KM, DeWane G, Salwen HR, Chlenski A, Dobratic M, Mariani CJ, Godley LA, Prabhakar N, White K, Stranger BE, Cohn SL. Integrative genomics reveals hypoxia inducible genes that are associated with a poor prognosis in neuroblastoma patients. Oncotarget 2018; 7:76816-76826. [PMID: 27765905 PMCID: PMC5340231 DOI: 10.18632/oncotarget.12713] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 10/12/2016] [Indexed: 11/30/2022] Open
Abstract
Neuroblastoma is notable for its broad spectrum of clinical behavior ranging from spontaneous regression to rapidly progressive disease. Hypoxia is well known to confer a more aggressive phenotype in neuroblastoma. We analyzed transcriptome data from diagnostic neuroblastoma tumors and hypoxic neuroblastoma cell lines to identify genes whose expression levels correlate with poor patient outcome and are involved in the hypoxia response. By integrating a diverse set of transcriptome datasets, including those from neuroblastoma patients and neuroblastoma derived cell lines, we identified nine genes (SLCO4A1, ENO1, HK2, PGK1, MTFP1, HILPDA, VKORC1, TPI1, and HIST1H1C) that are up-regulated in hypoxia and whose expression levels are correlated with poor patient outcome in three independent neuroblastoma cohorts. Analysis of 5-hydroxymethylcytosine and ENCODE data indicate that at least five of these nine genes have an increase in 5-hydroxymethylcytosine and a more open chromatin structure in hypoxia versus normoxia and are putative targets of hypoxia inducible factor (HIF) as they contain HIF binding sites in their regulatory regions. Four of these genes are key components of the glycolytic pathway and another three are directly involved in cellular metabolism. We experimentally validated our computational findings demonstrating that seven of the nine genes are significantly up-regulated in response to hypoxia in the four neuroblastoma cell lines tested. This compact and robustly validated group of genes, is associated with the hypoxia response in aggressive neuroblastoma and may represent a novel target for biomarker and therapeutic development.
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Affiliation(s)
- Mark A Applebaum
- Departments of Pediatrics, University of Chicago, Chicago, Illinois, 60637, United States of America.,Committee on Clinical Pharmacology and Pharmacogenomics, University of Chicago, Chicago, Illinois, 60637, United States of America
| | - Aashish R Jha
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, Illinois, 60637, United States of America.,Department of Human Genetics, University of Chicago, Chicago, Illinois, 60637, United States of America
| | - Clara Kao
- Department of Human Genetics, University of Chicago, Chicago, Illinois, 60637, United States of America
| | - Kyle M Hernandez
- Center for Research Informatics, University of Chicago, Chicago, Illinois, 60637, United States of America
| | - Gillian DeWane
- Departments of Pediatrics, University of Chicago, Chicago, Illinois, 60637, United States of America
| | - Helen R Salwen
- Departments of Pediatrics, University of Chicago, Chicago, Illinois, 60637, United States of America
| | - Alexandre Chlenski
- Departments of Pediatrics, University of Chicago, Chicago, Illinois, 60637, United States of America
| | - Marija Dobratic
- Departments of Pediatrics, University of Chicago, Chicago, Illinois, 60637, United States of America
| | - Christopher J Mariani
- Department of Medicine, University of Chicago, Chicago, Illinois, 60637, United States of America
| | - Lucy A Godley
- Department of Medicine, University of Chicago, Chicago, Illinois, 60637, United States of America
| | - Nanduri Prabhakar
- Department of Medicine, University of Chicago, Chicago, Illinois, 60637, United States of America
| | - Kevin White
- Department of Human Genetics, University of Chicago, Chicago, Illinois, 60637, United States of America
| | - Barbara E Stranger
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, Illinois, 60637, United States of America.,Department of Medicine, University of Chicago, Chicago, Illinois, 60637, United States of America.,Center for Data Intensive Science, University of Chicago, Chicago, Illinois, 60637, United States of America
| | - Susan L Cohn
- Departments of Pediatrics, University of Chicago, Chicago, Illinois, 60637, United States of America.,Committee on Clinical Pharmacology and Pharmacogenomics, University of Chicago, Chicago, Illinois, 60637, United States of America
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46
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Verly IRN, van Kuilenburg ABP, Abeling NGGM, Goorden SMI, Fiocco M, Vaz FM, van Noesel MM, Zwaan CM, Kaspers GJL, Merks JHM, Caron HN, Tytgat GAM. 3-Methoxytyramine: An independent prognostic biomarker that associates with high-risk disease and poor clinical outcome in neuroblastoma patients. Eur J Cancer 2017; 90:102-110. [PMID: 29274926 DOI: 10.1016/j.ejca.2017.11.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 11/15/2017] [Accepted: 11/23/2017] [Indexed: 01/23/2023]
Abstract
INTRODUCTION Prognosis of neuroblastoma patients is very diverse, indicating the need for more accurate prognostic parameters. The excretion of catecholamine metabolites by most neuroblastomas is used for diagnostic purposes, but their correlation with prognosis has hardly been investigated. Therefore, we performed an in-depth analysis of a panel of elevated urinary catecholamine metabolites at diagnosis and their correlation with prognosis. PATIENTS AND METHODS Retrospective study of eight urinary catecholamine metabolites in a test (n = 96) and validation (n = 205) cohort of patients with neuroblastoma (all stages) at diagnosis. RESULTS Multivariate analyses, including risk factors such as stage and MYCN amplification, revealed that 3-methoxytyramine (3MT) was an independent risk factor for event-free survival (EFS) and overall survival (OS). Furthermore, only 3MT appeared to be an independent risk factor for both EFS and OS in high-risk patients, which was independent of modern high-risk therapy and immunotherapy. Among high-risk patients, those with elevated 3MT and older than 18 months had an extremely poor prognosis compared to patients with non-elevated 3MT and younger than 18 months (5-year EFS of 14.3% ± 4% and 66.7% ± 18%, respectively, p = 0.001; 5-year OS of 21.8% ± 5% and 87.5% ± 12%, respectively, p < 0.001). CONCLUSIONS Elevated 3MT at diagnosis was associated with high-risk disease and poor prognosis. For high-risk patients, elevated 3MT at diagnosis was the only significant risk factor for EFS and OS. 3MT was also able to identify subgroups of high-risk patients with favourable and extremely poor prognosis.
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Affiliation(s)
- I R N Verly
- Department of Pediatric Oncology/Hematology, Emma Children's Hospital/Academic Medical Center, Amsterdam, The Netherlands; Laboratory Genetic Metabolic Diseases, Emma Children's Hospital/Academic Medical Center, Amsterdam, The Netherlands; Princess Máxima Center for Pediatric Oncology/Hematology, Utrecht, The Netherlands
| | - A B P van Kuilenburg
- Laboratory Genetic Metabolic Diseases, Emma Children's Hospital/Academic Medical Center, Amsterdam, The Netherlands
| | - N G G M Abeling
- Laboratory Genetic Metabolic Diseases, Emma Children's Hospital/Academic Medical Center, Amsterdam, The Netherlands
| | - S M I Goorden
- Laboratory Genetic Metabolic Diseases, Emma Children's Hospital/Academic Medical Center, Amsterdam, The Netherlands
| | - M Fiocco
- Mathematical Institute, Leiden University, Leiden, The Netherlands; Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands
| | - F M Vaz
- Laboratory Genetic Metabolic Diseases, Emma Children's Hospital/Academic Medical Center, Amsterdam, The Netherlands
| | - M M van Noesel
- Princess Máxima Center for Pediatric Oncology/Hematology, Utrecht, The Netherlands; University Medical Center Utrecht, Utrecht, The Netherlands
| | - C M Zwaan
- Department of Pediatric Oncology/Hematology, Sophia Children's Hospital/Erasmus Medical Center, Rotterdam, The Netherlands
| | - G J L Kaspers
- Princess Máxima Center for Pediatric Oncology/Hematology, Utrecht, The Netherlands; Department of Pediatric Oncology/Hematology, VU University Medical Center, Amsterdam, The Netherlands
| | - J H M Merks
- Department of Pediatric Oncology/Hematology, Emma Children's Hospital/Academic Medical Center, Amsterdam, The Netherlands; Princess Máxima Center for Pediatric Oncology/Hematology, Utrecht, The Netherlands
| | - H N Caron
- Department of Pediatric Oncology/Hematology, Emma Children's Hospital/Academic Medical Center, Amsterdam, The Netherlands
| | - G A M Tytgat
- Department of Pediatric Oncology/Hematology, Emma Children's Hospital/Academic Medical Center, Amsterdam, The Netherlands; Princess Máxima Center for Pediatric Oncology/Hematology, Utrecht, The Netherlands.
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47
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Ognibene M, Cangelosi D, Morini M, Segalerba D, Bosco MC, Sementa AR, Eva A, Varesio L. Immunohistochemical analysis of PDK1, PHD3 and HIF-1α expression defines the hypoxic status of neuroblastoma tumors. PLoS One 2017; 12:e0187206. [PMID: 29117193 PMCID: PMC5678880 DOI: 10.1371/journal.pone.0187206] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 10/16/2017] [Indexed: 01/31/2023] Open
Abstract
Neuroblastoma (NB) is the most common solid tumor during infancy and the first cause of death among the preschool age diseases. The availability of several NB genomic profiles improves the prognostic ability, but the outcome prediction for this pathology remains imperfect. We previously produced a novel prognostic gene signature based on the response of NB cells to hypoxia, a condition of tumor microenvironment strictly connected with cancer aggressiveness. Here we attempted to further define the expression of hypoxia-modulated specific genes, looking at their protein level in NB specimens, considering in particular the hypoxia inducible factor-1α (HIF-1α), the mitochondrial pyruvate dehydrogenase kinase 1 (PDK1), and the HIF-prolyl hydroxylase domain 3 (PHD3). The evaluation of expression was performed by Western blot and immunocytochemistry on NB cell lines and by immunohistochemistry on tumor specimens. Stimulation of both HIF-1α and PDK1 and inhibition of PHD3 expression were observed in NB cell lines cultured under prolonged hypoxic conditions as well as in most of the tumors with poor outcome. Our results indicate that the immunohistochemistry analysis of the protein expression of PDK1, PHD3, and HIF-1α defines the hypoxic status of NB tumors and can be used as a simple and relevant tool to stratify high-risk patients.
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Affiliation(s)
- Marzia Ognibene
- Laboratory of Molecular Biology, Giannina Gaslini Institute, Genova, Italy
- * E-mail: (AE); (MO)
| | - Davide Cangelosi
- Laboratory of Molecular Biology, Giannina Gaslini Institute, Genova, Italy
| | - Martina Morini
- Laboratory of Molecular Biology, Giannina Gaslini Institute, Genova, Italy
| | - Daniela Segalerba
- Laboratory of Molecular Biology, Giannina Gaslini Institute, Genova, Italy
| | - Maria Carla Bosco
- Laboratory of Molecular Biology, Giannina Gaslini Institute, Genova, Italy
| | | | - Alessandra Eva
- Laboratory of Molecular Biology, Giannina Gaslini Institute, Genova, Italy
- * E-mail: (AE); (MO)
| | - Luigi Varesio
- Laboratory of Molecular Biology, Giannina Gaslini Institute, Genova, Italy
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48
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Rosswog C, Schmidt R, Oberthuer A, Juraeva D, Brors B, Engesser A, Kahlert Y, Volland R, Bartenhagen C, Simon T, Berthold F, Hero B, Faldum A, Fischer M. Molecular Classification Substitutes for the Prognostic Variables Stage, Age, and MYCN Status in Neuroblastoma Risk Assessment. Neoplasia 2017; 19:982-990. [PMID: 29091799 PMCID: PMC5678736 DOI: 10.1016/j.neo.2017.09.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 09/29/2017] [Accepted: 09/29/2017] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND: Current risk stratification systems for neuroblastoma patients consider clinical, histopathological, and genetic variables, and additional prognostic markers have been proposed in recent years. We here sought to select highly informative covariates in a multistep strategy based on consecutive Cox regression models, resulting in a risk score that integrates hazard ratios of prognostic variables. METHODS: A cohort of 695 neuroblastoma patients was divided into a discovery set (n = 75) for multigene predictor generation, a training set (n = 411) for risk score development, and a validation set (n = 209). Relevant prognostic variables were identified by stepwise multivariable L1-penalized least absolute shrinkage and selection operator (LASSO) Cox regression, followed by backward selection in multivariable Cox regression, and then integrated into a novel risk score. RESULTS: The variables stage, age, MYCN status, and two multigene predictors, NB-th24 and NB-th44, were selected as independent prognostic markers by LASSO Cox regression analysis. Following backward selection, only the multigene predictors were retained in the final model. Integration of these classifiers in a risk scoring system distinguished three patient subgroups that differed substantially in their outcome. The scoring system discriminated patients with diverging outcome in the validation cohort (5-year event-free survival, 84.9 ± 3.4 vs 63.6 ± 14.5 vs 31.0 ± 5.4; P < .001), and its prognostic value was validated by multivariable analysis. CONCLUSION: We here propose a translational strategy for developing risk assessment systems based on hazard ratios of relevant prognostic variables. Our final neuroblastoma risk score comprised two multigene predictors only, supporting the notion that molecular properties of the tumor cells strongly impact clinical courses of neuroblastoma patients.
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Affiliation(s)
- Carolina Rosswog
- Department of Experimental Pediatric Oncology, Children's Hospital, University of Cologne, Kerpener Strasse 62, 50937 Cologne, Germany
| | - Rene Schmidt
- Institute of Biostatistics and Clinical Research, University of Muenster, Schmeddingstrasse 56, 48149 Münster, Germany
| | - André Oberthuer
- Department of Experimental Pediatric Oncology, Children's Hospital, University of Cologne, Kerpener Strasse 62, 50937 Cologne, Germany
| | - Dilafruz Juraeva
- Department of Applied Bioinformatics, German Cancer Research Center, Berliner Strasse 41, 69120 Heidelberg, Germany
| | - Benedikt Brors
- Department of Applied Bioinformatics, German Cancer Research Center, Berliner Strasse 41, 69120 Heidelberg, Germany
| | - Anne Engesser
- Department of Experimental Pediatric Oncology, Children's Hospital, University of Cologne, Kerpener Strasse 62, 50937 Cologne, Germany
| | - Yvonne Kahlert
- Department of Experimental Pediatric Oncology, Children's Hospital, University of Cologne, Kerpener Strasse 62, 50937 Cologne, Germany
| | - Ruth Volland
- Department of Pediatric Oncology and Hematology, Children's Hospital, University of Cologne, Kerpener Strasse 62, 50937 Cologne, Germany
| | - Christoph Bartenhagen
- Department of Experimental Pediatric Oncology, Children's Hospital, University of Cologne, Kerpener Strasse 62, 50937 Cologne, Germany
| | - Thorsten Simon
- Department of Pediatric Oncology and Hematology, Children's Hospital, University of Cologne, Kerpener Strasse 62, 50937 Cologne, Germany
| | - Frank Berthold
- Department of Pediatric Oncology and Hematology, Children's Hospital, University of Cologne, Kerpener Strasse 62, 50937 Cologne, Germany
| | - Barbara Hero
- Department of Pediatric Oncology and Hematology, Children's Hospital, University of Cologne, Kerpener Strasse 62, 50937 Cologne, Germany
| | - Andreas Faldum
- Institute of Biostatistics and Clinical Research, University of Muenster, Schmeddingstrasse 56, 48149 Münster, Germany
| | - Matthias Fischer
- Department of Experimental Pediatric Oncology, Children's Hospital, University of Cologne, Kerpener Strasse 62, 50937 Cologne, Germany; Department of Pediatric Oncology and Hematology, Children's Hospital, University of Cologne, Kerpener Strasse 62, 50937 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), Medical Faculty, University of Cologne, Robert-Koch-Strasse 21, 50931 Cologne, Germany.
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49
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Zanon C, Tonini GP. Transcription instability in high-risk neuroblastoma is associated with a global perturbation of chromatin domains. Mol Oncol 2017; 11:1646-1658. [PMID: 28941026 PMCID: PMC5664000 DOI: 10.1002/1878-0261.12139] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 09/07/2017] [Accepted: 09/13/2017] [Indexed: 12/16/2022] Open
Abstract
Chromosome instability has a pivotal role among the hallmarks of cancer, but its transcriptional counterpart is rarely considered a relevant factor in cell destabilization. To examine transcription instability (TIN), we first devised a metric we named TIN index and used it to evaluate TIN on a dataset containing more than 500 neuroblastoma samples. We found that metastatic tumors from high-risk (HR) patients are characterized by significantly different TIN index values compared to low/intermediate-risk patients. Our results indicate that the TIN index is a good predictor of neuroblastoma patient's outcome, and a related TIN index gene signature (TIN-signature) is also able to predict the neuroblastoma patient's outcome with high confidence. Interestingly, we find that TIN-signature genes have a strong positional association with superenhancers in neuroblastoma tumors. Finally, we show that TIN is linked to chromatin structural domains and interferes with their integrity in HR neuroblastoma patients. This novel approach to gene expression analysis broadens the perspective of genome instability investigations to include functional aspects.
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Affiliation(s)
- Carlo Zanon
- Neuroblastoma Laboratory, Pediatric Research Institute, Citta' della Speranza, Padua, Italy
| | - Gian Paolo Tonini
- Neuroblastoma Laboratory, Pediatric Research Institute, Citta' della Speranza, Padua, Italy
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50
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Ryl T, Kuchen EE, Bell E, Shao C, Flórez AF, Mönke G, Gogolin S, Friedrich M, Lamprecht F, Westermann F, Höfer T. Cell-Cycle Position of Single MYC-Driven Cancer Cells Dictates Their Susceptibility to a Chemotherapeutic Drug. Cell Syst 2017; 5:237-250.e8. [PMID: 28843484 DOI: 10.1016/j.cels.2017.07.005] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 04/25/2017] [Accepted: 07/24/2017] [Indexed: 12/26/2022]
Abstract
While many tumors initially respond to chemotherapy, regrowth of surviving cells compromises treatment efficacy in the long term. The cell-biological basis of this regrowth is not understood. Here, we characterize the response of individual, patient-derived neuroblastoma cells driven by the prominent oncogene MYC to the first-line chemotherapy, doxorubicin. Combining live-cell imaging, cell-cycle-resolved transcriptomics, and mathematical modeling, we demonstrate that a cell's treatment response is dictated by its expression level of MYC and its cell-cycle position prior to treatment. All low-MYC cells enter therapy-induced senescence. High-MYC cells, by contrast, disable their cell-cycle checkpoints, forcing renewed proliferation despite treatment-induced DNA damage. After treatment, the viability of high-MYC cells depends on their cell-cycle position during treatment: newborn cells promptly halt in G1 phase, repair DNA damage, and form re-growing clones; all other cells show protracted DNA repair and ultimately die. These findings demonstrate that fast-proliferating tumor cells may resist cytotoxic treatment non-genetically, by arresting within a favorable window of the cell cycle.
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Affiliation(s)
- Tatsiana Ryl
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Bioquant Center, University of Heidelberg, 69120 Heidelberg, Germany
| | - Erika E Kuchen
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Bioquant Center, University of Heidelberg, 69120 Heidelberg, Germany
| | - Emma Bell
- Neuroblastoma Genomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Chunxuan Shao
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Bioquant Center, University of Heidelberg, 69120 Heidelberg, Germany
| | - Andrés F Flórez
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Bioquant Center, University of Heidelberg, 69120 Heidelberg, Germany
| | - Gregor Mönke
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Bioquant Center, University of Heidelberg, 69120 Heidelberg, Germany
| | - Sina Gogolin
- Neuroblastoma Genomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Mona Friedrich
- Neuroblastoma Genomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Florian Lamprecht
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Bioquant Center, University of Heidelberg, 69120 Heidelberg, Germany
| | - Frank Westermann
- Neuroblastoma Genomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
| | - Thomas Höfer
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Bioquant Center, University of Heidelberg, 69120 Heidelberg, Germany.
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