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Gharbaran R. Insights into the molecular roles of FOXR2 in the pathology of primary pediatric brain tumors. Crit Rev Oncol Hematol 2023; 192:104188. [PMID: 37879492 DOI: 10.1016/j.critrevonc.2023.104188] [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: 03/13/2023] [Revised: 08/23/2023] [Accepted: 10/16/2023] [Indexed: 10/27/2023] Open
Abstract
Forkhead box gene R2 (FOXR2) belongs to the family of FOX genes which codes for highly conserved transcription factors (TFs) with critical roles in biological processes ranging from development to organogenesis to metabolic and immune regulation to cellular homeostasis. A number of FOX genes are associated with cancer development and progression and poor prognosis. A growing body of evidence suggests that FOXR2 is an oncogene. Studies suggested important roles for FOXR2 in cancer cell growth, metastasis, and drug resistance. Recent studies showed that FOXR2 is overexpressed by a subset of newly identified entities of embryonal tumors. This review discusses the role(s) FOXR2 plays in the pathology of pediatric brain cancers and its potential as a therapeutic target.
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Affiliation(s)
- Rajendra Gharbaran
- Biological Sciences Department, Bronx Community College/City University of New York, 2155 University Avenue, Bronx, NY 10453, USA.
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2
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Sharif Rahmani E, Lawarde A, Lingasamy P, Moreno SV, Salumets A, Modhukur V. MBMethPred: a computational framework for the accurate classification of childhood medulloblastoma subgroups using data integration and AI-based approaches. Front Genet 2023; 14:1233657. [PMID: 37745846 PMCID: PMC10513500 DOI: 10.3389/fgene.2023.1233657] [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: 06/02/2023] [Accepted: 08/24/2023] [Indexed: 09/26/2023] Open
Abstract
Childhood medulloblastoma is a malignant form of brain tumor that is widely classified into four subgroups based on molecular and genetic characteristics. Accurate classification of these subgroups is crucial for appropriate treatment, monitoring plans, and targeted therapies. However, misclassification between groups 3 and 4 is common. To address this issue, an AI-based R package called MBMethPred was developed based on DNA methylation and gene expression profiles of 763 medulloblastoma samples to classify subgroups using machine learning and neural network models. The developed prediction models achieved a classification accuracy of over 96% for subgroup classification by using 399 CpGs as prediction biomarkers. We also assessed the prognostic relevance of prediction biomarkers using survival analysis. Furthermore, we identified subgroup-specific drivers of medulloblastoma using functional enrichment analysis, Shapley values, and gene network analysis. In particular, the genes involved in the nervous system development process have the potential to separate medulloblastoma subgroups with 99% accuracy. Notably, our analysis identified 16 genes that were specifically significant for subgroup classification, including EP300, CXCR4, WNT4, ZIC4, MEIS1, SLC8A1, NFASC, ASCL2, KIF5C, SYNGAP1, SEMA4F, ROR1, DPYSL4, ARTN, RTN4RL1, and TLX2. Our findings contribute to enhanced survival outcomes for patients with medulloblastoma. Continued research and validation efforts are needed to further refine and expand the utility of our approach in other cancer types, advancing personalized medicine in pediatric oncology.
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Affiliation(s)
| | - Ankita Lawarde
- Competence Centre on Health Technologies, Tartu, Estonia
- Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | | | - Sergio Vela Moreno
- Competence Centre on Health Technologies, Tartu, Estonia
- Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Andres Salumets
- Competence Centre on Health Technologies, Tartu, Estonia
- Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
| | - Vijayachitra Modhukur
- Competence Centre on Health Technologies, Tartu, Estonia
- Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
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3
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Goddard J, Castle J, Southworth E, Fletcher A, Crosier S, Martin-Guerrero I, García-Ariza M, Navajas A, Masliah-Planchon J, Bourdeaut F, Dufour C, Ayrault O, Goschzik T, Pietsch T, Sill M, Pfister SM, Rutkowski S, Richardson S, Hill RM, Williamson D, Bailey S, Schwalbe EC, Clifford SC, Hicks D. Molecular characterisation defines clinically-actionable heterogeneity within Group 4 medulloblastoma and improves disease risk-stratification. Acta Neuropathol 2023; 145:651-666. [PMID: 37014508 PMCID: PMC10119222 DOI: 10.1007/s00401-023-02566-0] [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: 01/18/2023] [Revised: 03/17/2023] [Accepted: 03/17/2023] [Indexed: 04/05/2023]
Abstract
Group 4 tumours (MBGrp4) represent the majority of non-WNT/non-SHH medulloblastomas. Their clinical course is poorly predicted by current risk-factors. MBGrp4 molecular substructures have been identified (e.g. subgroups/cytogenetics/mutations), however their inter-relationships and potential to improve clinical sub-classification and risk-stratification remain undefined. We comprehensively characterised the paediatric MBGrp4 molecular landscape and determined its utility to improve clinical management. A clinically-annotated discovery cohort (n = 362 MBGrp4) was assembled from UK-CCLG institutions and SIOP-UKCCSG-PNET3, HIT-SIOP-PNET4 and PNET HR + 5 clinical trials. Molecular profiling was undertaken, integrating driver mutations, second-generation non-WNT/non-SHH subgroups (1-8) and whole-chromosome aberrations (WCAs). Survival models were derived for patients ≥ 3 years of age who received contemporary multi-modal therapies (n = 323). We first independently derived and validated a favourable-risk WCA group (WCA-FR) characterised by ≥ 2 features from chromosome 7 gain, 8 loss, and 11 loss. Remaining patients were high-risk (WCA-HR). Subgroups 6 and 7 were enriched for WCA-FR (p < 0·0001) and aneuploidy. Subgroup 8 was defined by predominantly balanced genomes with isolated isochromosome 17q (p < 0·0001). While no mutations were associated with outcome and overall mutational burden was low, WCA-HR harboured recurrent chromatin remodelling mutations (p = 0·007). Integration of methylation and WCA groups improved risk-stratification models and outperformed established prognostication schemes. Our MBGrp4 risk-stratification scheme defines: favourable-risk (non-metastatic disease and (i) subgroup 7 or (ii) WCA-FR (21% of patients, 5-year PFS 97%)), very-high-risk (metastatic disease with WCA-HR (36%, 5-year PFS 49%)) and high-risk (remaining patients; 43%, 5-year PFS 67%). These findings validated in an independent MBGrp4 cohort (n = 668). Importantly, our findings demonstrate that previously established disease-wide risk-features (i.e. LCA histology and MYC(N) amplification) have little prognostic relevance in MBGrp4 disease. Novel validated survival models, integrating clinical features, methylation and WCA groups, improve outcome prediction and re-define risk-status for ~ 80% of MBGrp4. Our MBGrp4 favourable-risk group has MBWNT-like excellent outcomes, thereby doubling the proportion of medulloblastoma patients who could benefit from therapy de-escalation approaches, aimed at reducing treatment induced late-effects while sustaining survival outcomes. Novel approaches are urgently required for the very-high-risk patients.
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Affiliation(s)
- Jack Goddard
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Jemma Castle
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Emily Southworth
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Anya Fletcher
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Stephen Crosier
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Idoia Martin-Guerrero
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, Leioa, Spain
| | - Miguel García-Ariza
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
- Department of Pediatric Hematology and Oncology, Cruces University Hospital, Barakaldo, Spain
| | - Aurora Navajas
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | | | - Franck Bourdeaut
- SIREDO Pediatric Oncology Center, Curie Institute, Paris, France
| | - Christelle Dufour
- Department of Pediatric and Adolescent Oncology, Gustave Roussy, Rue Edouard Vaillant, 94805, Villejuif, France
| | - Olivier Ayrault
- UMR 3347, INSERM U1021, Institut Curie, PSL Research University, Université Paris Sud, Université Paris-Saclay, CNRS, Paris, France
| | - Tobias Goschzik
- Department of Neuropathology, DGNN Brain Tumour Reference Center, University of Bonn Medical Center, Bonn, Germany
| | - Torsten Pietsch
- Department of Neuropathology, DGNN Brain Tumour Reference Center, University of Bonn Medical Center, Bonn, Germany
| | - Martin Sill
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Paediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Paediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Paediatric Haematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan Rutkowski
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stacey Richardson
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Rebecca M Hill
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Daniel Williamson
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Simon Bailey
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Edward C Schwalbe
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
- Department of Applied Sciences, Northumbria University, Newcastle Upon Tyne, UK
| | - Steven C Clifford
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK.
| | - Debbie Hicks
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK.
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Bailey S, Davidson A, Parkes J, Tabori U, Figaji A, Epari S, Chinnaswamy G, Dias-Coronado R, Casavilca-Zambrano S, Amayiri N, Vassal G, Bouffet E, Clifford SC. How Can Genomic Innovations in Pediatric Brain Tumors Transform Outcomes in Low- and Middle-Income Countries? JCO Glob Oncol 2022; 8:e2200156. [PMID: 36252166 PMCID: PMC9812475 DOI: 10.1200/go.22.00156] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Pragmatic ways to apply molecular innovation to childhood brain cancer diagnosis and therapy in LMICs![]()
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Affiliation(s)
- Simon Bailey
- Great North Children's Hospital and Newcastle University, Newcastle upon Tyne, United Kingdom,Simon Bailey, MBChB, PhD, Sir James Spence Institute of Child Health, Royal Victoria Infirmary, Queen Victoria Rd, Newcastle upon Tyne NE1 4LP, United Kingdom;
| | - Alan Davidson
- Haematology Oncology Service, Red Cross War Memorial Children's Hospital, Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
| | - Jeannette Parkes
- Department of Radiation Oncology, Groote Schuur Hospital and University of Cape Town, Cape Town, South Africa
| | - Uri Tabori
- Neuro-oncology Program, Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Anthony Figaji
- Department of Neurosurgery, Red Cross War Memorial Children's Hospital and University of Cape Town, Cape Town, South Africa
| | - Shridar Epari
- Department of Pathology, ACTREC and Tata Memorial Hospital, Tata Memorial Centre, Homi Bhabha National Institute, Mumbai, India
| | - Girish Chinnaswamy
- Department of Pediatric Oncology, Tata Memorial Hospital, Parel, Mumbai, India
| | - Rosaldi Dias-Coronado
- Pediatric Oncology Department—Instituto Nacional de Enfermedades Neoplásicas, Surquillo, Peru
| | - Sandro Casavilca-Zambrano
- Instituto Nacional de Enfermedades Neoplásicas, Lima, Perú and Facultad de Ciencias de la Salud de La Universidad de Huánuco, Huánuco, Peru
| | - Nisreen Amayiri
- Department of Hematology and Oncology, King Hussein Cancer Centre, Amman, Jordan
| | - Gilles Vassal
- Department of Pediatric and Adolescent Oncology, Institut Gustave-Roussy, Villejuif, France
| | - Eric Bouffet
- Neuro-oncology Program, Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Steven C. Clifford
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle upon Tyne, United Kingdom
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5
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Zhang M, Wong SW, Wright JN, Wagner MW, Toescu S, Han M, Tam LT, Zhou Q, Ahmadian SS, Shpanskaya K, Lummus S, Lai H, Eghbal A, Radmanesh A, Nemelka J, Harward S, Malinzak M, Laughlin S, Perreault S, Braun KRM, Lober RM, Cho YJ, Ertl-Wagner B, Ho CY, Mankad K, Vogel H, Cheshier SH, Jacques TS, Aquilina K, Fisher PG, Taylor M, Poussaint T, Vitanza NA, Grant GA, Pfister S, Thompson E, Jaju A, Ramaswamy V, Yeom KW. MRI Radiogenomics of Pediatric Medulloblastoma: A Multicenter Study. Radiology 2022; 304:406-416. [PMID: 35438562 PMCID: PMC9340239 DOI: 10.1148/radiol.212137] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 11/09/2021] [Accepted: 02/08/2022] [Indexed: 08/03/2023]
Abstract
Background Radiogenomics of pediatric medulloblastoma (MB) offers an opportunity for MB risk stratification, which may aid therapeutic decision making, family counseling, and selection of patient groups suitable for targeted genetic analysis. Purpose To develop machine learning strategies that identify the four clinically significant MB molecular subgroups. Materials and Methods In this retrospective study, consecutive pediatric patients with newly diagnosed MB at MRI at 12 international pediatric sites between July 1997 and May 2020 were identified. There were 1800 features extracted from T2- and contrast-enhanced T1-weighted preoperative MRI scans. A two-stage sequential classifier was designed-one that first identifies non-wingless (WNT) and non-sonic hedgehog (SHH) MB and then differentiates therapeutically relevant WNT from SHH. Further, a classifier that distinguishes high-risk group 3 from group 4 MB was developed. An independent, binary subgroup analysis was conducted to uncover radiomics features unique to infantile versus childhood SHH subgroups. The best-performing models from six candidate classifiers were selected, and performance was measured on holdout test sets. CIs were obtained by bootstrapping the test sets for 2000 random samples. Model accuracy score was compared with the no-information rate using the Wald test. Results The study cohort comprised 263 patients (mean age ± SD at diagnosis, 87 months ± 60; 166 boys). A two-stage classifier outperformed a single-stage multiclass classifier. The combined, sequential classifier achieved a microaveraged F1 score of 88% and a binary F1 score of 95% specifically for WNT. A group 3 versus group 4 classifier achieved an area under the receiver operating characteristic curve of 98%. Of the Image Biomarker Standardization Initiative features, texture and first-order intensity features were most contributory across the molecular subgroups. Conclusion An MRI-based machine learning decision path allowed identification of the four clinically relevant molecular pediatric medulloblastoma subgroups. © RSNA, 2022 Online supplemental material is available for this article. See also the editorial by Chaudhary and Bapuraj in this issue.
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6
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de Lima LG, Howe E, Singh VP, Potapova T, Li H, Xu B, Castle J, Crozier S, Harrison CJ, Clifford SC, Miga KH, Ryan SL, Gerton JL. PCR amplicons identify widespread copy number variation in human centromeric arrays and instability in cancer. CELL GENOMICS 2021; 1:100064. [PMID: 34993501 PMCID: PMC8730464 DOI: 10.1016/j.xgen.2021.100064] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 07/13/2021] [Accepted: 08/24/2021] [Indexed: 12/13/2022]
Abstract
Centromeric α-satellite repeats represent ~6% of the human genome, but their length and repetitive nature make sequencing and analysis of those regions challenging. However, centromeres are essential for the stable propagation of chromosomes, so tools are urgently needed to monitor centromere copy number and how it influences chromosome transmission and genome stability. We developed and benchmarked droplet digital PCR (ddPCR) assays that measure copy number for five human centromeric arrays. We applied them to characterize natural variation in centromeric array size, analyzing normal tissue from 37 individuals from China and 39 individuals from the US and UK. Each chromosome-specific array varies in size up to 10-fold across individuals and up to 50-fold across chromosomes, indicating a unique complement of arrays in each individual. We also used the ddPCR assays to analyze centromere copy number in 76 matched tumor-normal samples across four cancer types, representing the most-comprehensive quantitative analysis of centromeric array stability in cancer to date. In contrast to stable transmission in cultured cells, centromeric arrays show gain and loss events in each of the cancer types, suggesting centromeric α-satellite DNA represents a new category of genome instability in cancer. Our methodology for measuring human centromeric-array copy number will advance research on centromeres and genome integrity in normal and disease states.
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Affiliation(s)
| | - Edmund Howe
- The Stowers Institute for Medical Research, Kansas City, MO, USA
| | | | - Tamara Potapova
- The Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Hua Li
- The Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Baoshan Xu
- Hospital of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Institute of Stomatological Research, Sun Yat-sen University, Guangzhou, Guangdong Province, China
| | - Jemma Castle
- Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Steve Crozier
- Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | | | | | - Karen H. Miga
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Sarra L. Ryan
- Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Jennifer L. Gerton
- The Stowers Institute for Medical Research, Kansas City, MO, USA
- University of Kansas Medical Center, Kansas City, KS, USA
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7
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Papanicolau-Sengos A, Aldape K. DNA Methylation Profiling: An Emerging Paradigm for Cancer Diagnosis. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2021; 17:295-321. [PMID: 34736341 DOI: 10.1146/annurev-pathol-042220-022304] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Histomorphology has been a mainstay of cancer diagnosis in anatomic pathology for many years. DNA methylation profiling is an additional emerging tool that will serve as an adjunct to increase accuracy of pathological diagnosis. Genome-wide interrogation of DNA methylation signatures, in conjunction with machine learning methods, has allowed for the creation of clinical-grade classifiers, most prominently in central nervous system and soft tissue tumors. Tumor DNA methylation profiling has led to the identification of new entities and the consolidation of morphologically disparate cancers into biologically coherent entities, and it will progressively become mainstream in the future. In addition, DNA methylation patterns in circulating tumor DNA hold great promise for minimally invasive cancer detection and classification. Despite practical challenges that accompany any new technology, methylation profiling is here to stay and will become increasingly utilized as a cancer diagnostic tool across a range of tumor types. Expected final online publication date for the Annual Review of Pathology: Mechanisms of Disease, Volume 17 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
| | - Kenneth Aldape
- Laboratory of Pathology, National Cancer Institute, Bethesda, Maryland 20892, USA; ,
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8
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Grist JT, Withey S, Bennett C, Rose HEL, MacPherson L, Oates A, Powell S, Novak J, Abernethy L, Pizer B, Bailey S, Clifford SC, Mitra D, Arvanitis TN, Auer DP, Avula S, Grundy R, Peet AC. Combining multi-site magnetic resonance imaging with machine learning predicts survival in pediatric brain tumors. Sci Rep 2021; 11:18897. [PMID: 34556677 PMCID: PMC8460620 DOI: 10.1038/s41598-021-96189-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 07/27/2021] [Indexed: 12/02/2022] Open
Abstract
Brain tumors represent the highest cause of mortality in the pediatric oncological population. Diagnosis is commonly performed with magnetic resonance imaging. Survival biomarkers are challenging to identify due to the relatively low numbers of individual tumor types. 69 children with biopsy-confirmed brain tumors were recruited into this study. All participants had perfusion and diffusion weighted imaging performed at diagnosis. Imaging data were processed using conventional methods, and a Bayesian survival analysis performed. Unsupervised and supervised machine learning were performed with the survival features, to determine novel sub-groups related to survival. Sub-group analysis was undertaken to understand differences in imaging features. Survival analysis showed that a combination of diffusion and perfusion imaging were able to determine two novel sub-groups of brain tumors with different survival characteristics (p < 0.01), which were subsequently classified with high accuracy (98%) by a neural network. Analysis of high-grade tumors showed a marked difference in survival (p = 0.029) between the two clusters with high risk and low risk imaging features. This study has developed a novel model of survival for pediatric brain tumors. Tumor perfusion plays a key role in determining survival and should be considered as a high priority for future imaging protocols.
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Affiliation(s)
- James T Grist
- Institute of Cancer and Genomic Sciences, School of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Stephanie Withey
- Institute of Cancer and Genomic Sciences, School of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- Oncology, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
- RRPPS, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Christopher Bennett
- Institute of Cancer and Genomic Sciences, School of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Heather E L Rose
- Institute of Cancer and Genomic Sciences, School of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- Oncology, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Lesley MacPherson
- Radiology, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Adam Oates
- Radiology, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Stephen Powell
- Institute of Cancer and Genomic Sciences, School of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Jan Novak
- Oncology, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
- Psychology, College of Health and Life Sciences Aston University, Birmingham, UK
- Aston Neuroscience Institute, Aston University, Birmingham, UK
| | | | - Barry Pizer
- Oncology, Alder Hey Children's NHS Foundation Trust, Liverpool, UK
| | - Simon Bailey
- Sir James Spence Institute of Child Health, Royal Victoria Infirmary, Newcastle upon Tyne, UK
| | - Steven C Clifford
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, University of Newcastle, Newcastle upon Tyne, UK
| | - Dipayan Mitra
- Neuroradiology, Royal Victoria Infirmary, Newcastle Upon Tyne, UK
| | - Theodoros N Arvanitis
- Institute of Cancer and Genomic Sciences, School of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- Oncology, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
- Institute of Digital Healthcare, WMG, University of Warwick, Coventry, UK
| | - Dorothee P Auer
- Sir Peter Mansfield Imaging Centre, University of Nottingham Biomedical Research Centre, Nottingham, UK
- NIHR Nottingham Biomedical Research Centre, Nottingham, UK
| | - Shivaram Avula
- Radiology, Alder Hey Children's NHS Foundation Trust, Liverpool, UK
| | - Richard Grundy
- The Children's Brain Tumor Research Centre, University of Nottingham, Nottingham, UK
| | - Andrew C Peet
- Institute of Cancer and Genomic Sciences, School of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
- Oncology, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK.
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9
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Hill RM, Richardson S, Schwalbe EC, Hicks D, Lindsey JC, Crosier S, Rafiee G, Grabovska Y, Wharton SB, Jacques TS, Michalski A, Joshi A, Pizer B, Williamson D, Bailey S, Clifford SC. Time, pattern, and outcome of medulloblastoma relapse and their association with tumour biology at diagnosis and therapy: a multicentre cohort study. THE LANCET CHILD & ADOLESCENT HEALTH 2020; 4:865-874. [PMID: 33222802 PMCID: PMC7671998 DOI: 10.1016/s2352-4642(20)30246-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/20/2020] [Accepted: 07/24/2020] [Indexed: 01/08/2023]
Abstract
Background Disease relapse occurs in around 30% of children with medulloblastoma, and is almost universally fatal. We aimed to establish whether the clinical and molecular characteristics of the disease at diagnosis are associated with the nature of relapse and subsequent disease course, and whether these associations could inform clinical management. Methods In this multicentre cohort study we comprehensively surveyed the clinical features of medulloblastoma relapse (time to relapse, pattern of relapse, time from relapse to death, and overall outcome) in centrally reviewed patients who relapsed following standard upfront therapies, from 16 UK Children's Cancer and Leukaemia Group institutions and four collaborating centres. We compared these relapse-associated features with clinical and molecular features at diagnosis, including established and recently described molecular features, prognostic factors, and treatment at diagnosis and relapse. Findings 247 patients (175 [71%] boys and 72 [29%] girls) with medulloblastoma relapse (median year of diagnosis 2000 [IQR 1995–2006]) were included in this study. 17 patients were later excluded from further analyses because they did not meet the age and treatment criteria for inclusion. Patients who received upfront craniospinal irradiation (irradiated group; 178 [72%] patients) had a more prolonged time to relapse compared with patients who did not receive upfront craniospinal irradiation (non-irradiated group; 52 [21%] patients; p<0·0001). In the non-irradiated group, craniospinal irradiation at relapse (hazard ratio [HR] 0·27, 95% CI 0·11–0·68) and desmoplastic/nodular histology (0·23, 0·07–0·77) were associated with prolonged time to death after relapse, MYC amplification was associated with a reduced overall survival (23·52, 4·85–114·05), and re-resection at relapse was associated with longer overall survival (0·17, 0·05–0·57). In the irradiated group, patients with MBGroup3 tumours relapsed significantly more quickly than did patients with MBGroup4 tumours (median 1·34 [0·99–1·89] years vs 2·04 [1·39–3·42 years; p=0·0043). Distant disease was prevalent in patients with MBGroup3 (23 [92%] of 25 patients) and MBGroup4 (56 [90%] of 62 patients) tumour relapses. Patients with distantly-relapsed MBGroup3 and MBGroup4 displayed both nodular and diffuse patterns of disease whereas isolated nodular relapses were rare in distantly-relapsed MBSHH (1 [8%] of 12 distantly-relapsed MBSHH were nodular alone compared with 26 [34%] of 77 distantly-relapsed MBGroup3 and MBGroup4). In MBGroup3 and MBGroup4, nodular disease was associated with a prolonged survival after relapse (HR 0·42, 0·21–0·81). Investigation of second-generation MBGroup3 and MBGroup4 molecular subtypes refined our understanding of heterogeneous relapse characteristics. Subtype VIII had prolonged time to relapse and subtype II had a rapid time from relapse to death. Subtypes II, III, and VIII developed a significantly higher incidence of distant disease at relapse whereas subtypes V and VII did not (equivalent rates to diagnosis). Interpretation This study suggests that the nature and outcome of medulloblastoma relapse are biology and therapy-dependent, providing translational opportunities for improved disease management through biology-directed disease surveillance, post-relapse prognostication, and risk-stratified selection of second-line treatment strategies. Funding Cancer Research UK, Action Medical Research, The Tom Grahame Trust, The JGW Patterson Foundation, Star for Harris, The Institute of Child Health - Newcastle University - Institute of Child Health High-Risk Childhood Brain Tumour Network (co-funded by The Brain Tumour Charity, Great Ormond Street Children's Charity, and Children with Cancer UK).
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Affiliation(s)
- Rebecca M Hill
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Stacey Richardson
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Edward C Schwalbe
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK; Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Debbie Hicks
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Janet C Lindsey
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Stephen Crosier
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Gholamreza Rafiee
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK; School of Electronics, Electrical Engineering and Computer Science, Queen's University Belfast, Centre for Cancer Research & Cell Biology, UK
| | - Yura Grabovska
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Stephen B Wharton
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Thomas S Jacques
- Neural Development Unit, UCL Institute of Child Health, London, UK
| | - Antony Michalski
- Neural Development Unit, UCL Institute of Child Health, London, UK
| | - Abhijit Joshi
- Department of Neuropathology, Royal Victoria Infirmary, Newcastle University Teaching Hospitals, NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Barry Pizer
- Institute of Translational Research, University of Liverpool, Liverpool, UK
| | - Daniel Williamson
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Simon Bailey
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Steven C Clifford
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK.
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10
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Dietzsch S, Placzek F, Pietschmann K, von Bueren AO, Matuschek C, Glück A, Guckenberger M, Budach V, Welzel J, Pöttgen C, Schmidberger H, Heinzelmann F, Paulsen F, Escudero MP, Schwarz R, Hornung D, Martini C, Grosu AL, Stueben G, Jablonska K, Dunst J, Stranzl-Lawatsch H, Dieckmann K, Timmermann B, Pietsch T, Warmuth-Metz M, Bison B, Kwiecien R, Benesch M, Gerber NU, Grotzer MA, Pfister SM, Clifford SC, von Hoff K, Klagges S, Rutkowski S, Kortmann RD, Mynarek M. Evaluation of Prognostic Factors and Role of Participation in a Randomized Trial or a Prospective Registry in Pediatric and Adolescent Nonmetastatic Medulloblastoma - A Report From the HIT 2000 Trial. Adv Radiat Oncol 2020; 5:1158-1169. [PMID: 33305077 PMCID: PMC7718550 DOI: 10.1016/j.adro.2020.09.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 09/11/2020] [Accepted: 09/17/2020] [Indexed: 12/01/2022] Open
Abstract
Purpose We aimed to compare treatment results in and outside of a randomized trial and to confirm factors influencing outcome in a large retrospective cohort of nonmetastatic medulloblastoma treated in Austria, Switzerland and Germany. Methods and Materials Patients with nonmetastatic medulloblastoma (n = 382) aged 4 to 21 years and primary neurosurgical resection between 2001 and 2011 were assessed. Between 2001 and 2006, 176 of these patients (46.1%) were included in the randomized HIT SIOP PNET 4 trial. From 2001 to 2011 an additional 206 patients were registered to the HIT 2000 study center and underwent the identical central review program. Three different radiation therapy protocols were applied. Genetically defined tumor entity (former molecular subgroup) was available for 157 patients. Results Median follow-up time was 7.3 (range, 0.09-13.86) years. There was no difference between HIT SIOP PNET 4 trial patients and observational patients outside the randomized trial, with 7 years progression-free survival rates (PFS) of 79.5% ± 3.1% versus 78.7% ± 3.1% (P = .62). On univariate analysis, the time interval between surgery and irradiation (≤ 48 days vs ≥ 49 days) showed a strong trend to affect PFS (80.4% ± 2.2% vs 64.6% ± 9.1%; P = .052). Furthermore, histologically and genetically defined tumor entities and the extent of postoperative residual tumor influenced PFS. On multivariate analyses, a genetically defined tumor entity wingless-related integration site-activated vs non-wingless-related integration site/non-SHH, group 3 hazard ratio, 5.49; P = .014) and time interval between surgery and irradiation (hazard ratio, 2.2; P = .018) were confirmed as independent risk factors. Conclusions Using a centralized review program and risk-stratified therapy for all patients registered to the study center, outcome was identical for patients with nonmetastatic medulloblastoma treated on and off the randomized HIT SIOP PNET 4 trial. The prognostic values of prolonged time to RT and genetically defined tumor entity were confirmed.
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Affiliation(s)
- Stefan Dietzsch
- Department for Radiation Oncology, University of Leipzig Medical Center, Leipzig, Germany
| | - Felix Placzek
- Department for Radiation Oncology, University of Leipzig Medical Center, Leipzig, Germany
| | - Klaus Pietschmann
- Department for Radiation Oncology, University of Leipzig Medical Center, Leipzig, Germany
- Department of Radiation Oncology, Chemnitz Municipal Hospital, Chemnitz, Germany
| | - André O. von Bueren
- Department of Pediatrics, Obstetrics and Gynecology, Division of Pediatric Hematology and Oncology, University Hospital Geneva, CANSEARCH Research Laboratory, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Christiane Matuschek
- Department of Radiation Oncology, Medical Faculty, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany
| | - Albrecht Glück
- Radiation Oncology, Munich-Schwabing Municipal Hospital, Munich, Germany
| | - Matthias Guckenberger
- Department of Radiation Oncology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Volker Budach
- Department for Radiation Oncology, Charité School of Medicine and University Hospital Berlin, Berlin, Germany
| | - Jutta Welzel
- Department of Radiation Oncology, Pius Hospital Oldenburg, Oldenburg, Germany
| | - Christoph Pöttgen
- Department of Radiotherapy, West German Cancer Center, University of Duisburg-Essen, Essen, Germany
| | - Heinz Schmidberger
- Department for Radiation Oncology, University of Mainz Medical Center, Mainz, Germany
| | - Frank Heinzelmann
- Department for Radiation Oncology, University of Tuebingen Medical Center, Tuebingen, Germany
| | - Frank Paulsen
- Department for Radiation Oncology, University of Tuebingen Medical Center, Tuebingen, Germany
| | - Montserrat Pazos Escudero
- Department of Radiotherapy and Radiation Oncology, Ludwig Maximilian University Munich, Munich, Germany
| | - Rudolf Schwarz
- Department of Radiation Oncology, University Medical Center Eppendorf, Hamburg, Germany
| | - Dagmar Hornung
- Department of Radiation Oncology, University Medical Center Eppendorf, Hamburg, Germany
| | - Carmen Martini
- Department of Radiation Oncology, University Medical Center Freiburg, Freiburg, Germany
| | - Anca Ligia Grosu
- Department of Radiation Oncology, University Medical Center Freiburg, Freiburg, Germany
| | - Georg Stueben
- Department of Radiation Oncology, University Medical Center Augsburg, Augsburg, Germany
| | - Karolina Jablonska
- Department of Radiation Oncology, University Medical Center Cologne, Cologne, Germany
| | - Juergen Dunst
- Department of Radiation Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Heidi Stranzl-Lawatsch
- Department of Therapeutic Radiology and Oncology, Medical University of Graz, Graz, Austria
| | - Karin Dieckmann
- Department of Radiotherapy, Medical University of Vienna, Vienna, Austria
| | - Beate Timmermann
- Clinic for Particle Therapy, West German Proton Therapy Centre, University of Essen, Essen, Germany
| | - Torsten Pietsch
- Department of Neuropathology, DGNN Brain Tumor Reference Center, University of Bonn, Bonn, Germany
| | - Monika Warmuth-Metz
- Institute of Diagnostic and Interventional Neuroradiology, University Hospital of Wuerzburg, Wuerzburg, Germany
| | - Brigitte Bison
- Institute of Diagnostic and Interventional Neuroradiology, University Hospital of Wuerzburg, Wuerzburg, Germany
| | - Robert Kwiecien
- Institute of Biometry and Clinical Research, University of Muenster, Muenster, Germany
| | - Martin Benesch
- Division of Pediatric Hematology/Oncology, Department of Pediatrics and Adolescent Medicine, Medical University of Graz, Graz, Austria
| | | | | | - Stefan M. Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Steven C. Clifford
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle upon Tyne, United Kingdom
| | - Katja von Hoff
- Department of Pediatric Oncology and Hematology, Charité University Medicine Berlin, Berlin, Germany
| | - Sabine Klagges
- Department for Radiation Oncology, University of Leipzig Medical Center, Leipzig, Germany
| | - Stefan Rutkowski
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Rolf-Dieter Kortmann
- Department for Radiation Oncology, University of Leipzig Medical Center, Leipzig, Germany
- Corresponding author: Rolf-Dieter Kortmann, MD
| | - Martin Mynarek
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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11
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Pickles JC, Stone TJ, Jacques TS. Methylation-based algorithms for diagnosis: experience from neuro-oncology. J Pathol 2020; 250:510-517. [PMID: 32057098 DOI: 10.1002/path.5397] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 01/31/2020] [Accepted: 02/10/2020] [Indexed: 12/17/2022]
Abstract
Brain tumours are the most common tumour-related cause of death in young people. Survivors are at risk of significant disability, at least in part related to the effects of treatment. Therefore, there is a need for a precise diagnosis that stratifies patients for the most suitable treatment, matched to the underlying biology of their tumour. Although traditional histopathology has been accurate in predicting treatment responses in many cases, molecular profiling has revealed a remarkable, previously unappreciated, level of biological complexity in the classification of these tumours. Among different molecular technologies, DNA methylation profiling has had the most pronounced impact on brain tumour classification. Furthermore, using machine learning-based algorithms, DNA methylation profiling is changing diagnostic practice. This can be regarded as an exemplar for how molecular pathology can influence diagnostic practice and illustrates some of the unanticipated benefits and risks. © 2020 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Jessica C Pickles
- Developmental Biology and Cancer Research & Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK.,Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Thomas J Stone
- Developmental Biology and Cancer Research & Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK.,Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Thomas S Jacques
- Developmental Biology and Cancer Research & Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK.,Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
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12
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Schepke E, Tisell M, Kennedy C, Puget S, Ferroli P, Chevignard M, Doz F, Pizer B, Rutkowski S, Massimino M, Navajas A, Schwalbe E, Hicks D, Clifford SC, Pietsch T, Lannering B. Effects of the growth pattern of medulloblastoma on short-term neurological impairments after surgery: results from the prospective multicenter HIT-SIOP PNET 4 study. J Neurosurg Pediatr 2020; 25:425-433. [PMID: 31952041 DOI: 10.3171/2019.11.peds19349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 11/01/2019] [Indexed: 11/06/2022]
Abstract
OBJECTIVE Extensive resection of a tumor in the posterior fossa in children is associated with the risk of neurological deficits. The objective of this study was to prospectively evaluate the short-term neurological morbidity in children after medulloblastoma surgery and relate this to the tumor's growth pattern and to the extent of resection. METHODS In 160 patients taking part in the HIT-SIOP PNET 4 (Hyperfractionated Versus Conventionally Fractionated Radiotherapy in Standard Risk Medulloblastoma) trial, neurosurgeons prospectively responded to questions concerning the growth pattern of the tumor they had resected. The extent of resection (gross, near, or subtotal) was evaluated using MRI. The patients' neurological status before resection and around 30 days after resection was recorded. RESULTS Invasive tumor growth, defined as local invasion in the brain or meninges, cranial nerve, or major vessel, was reported in 58% of the patients. After surgery almost 70% of all patients were affected by one or several neurological impairments (e.g., impaired vision, impaired extraocular movements, and ataxia). However, this figure was very similar to the preoperative findings. Invasive tumor growth implied a significantly higher number of impairments after surgery (p = 0.03) and greater deterioration regarding extraocular movements (p = 0.012), facial weakness (p = 0.048), and ataxia in the arms (p = 0.014) and trunk (p = 0.025) compared with noninvasive tumor growth. This deterioration was not dependent on the extent of resection performed. Progression-free survival (PFS) at 5 years was 80% ± 4% and 76% ± 5% for patients with invasive and noninvasive tumor growth, respectively, with no difference in the 5-year PFS for extent of resection. CONCLUSIONS Preoperative neurological impairments and invasive tumor growth were strong predictors of deterioration in short-term neurological outcome after medulloblastoma neurosurgery, whereas the extent of resection was not. Neither tumor invasiveness nor extent of resection influenced PFS. These findings support the continuation of maximal safe resection in medulloblastoma surgery where functional risks are not taken in areas with tumor invasion.
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Affiliation(s)
- Elizabeth Schepke
- 1Sahlgrenska Cancer Center, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg
- 2Department of Pediatrics, Sahlgrenska University Hospital, Gothenburg
| | - Magnus Tisell
- 3Department of Neurosurgery, Sahlgrenska University Hospital and
- 4Institute of Neuroscience and Physiology, Department of Neuroscience, Sahlgrenska Academy, University of Gothenburg, Sweden
| | - Colin Kennedy
- 5University of Southampton Faculty of Medicine and University Hospital Southampton National Health Service Foundation Trust, Southampton, United Kingdom
| | - Stephanie Puget
- 6Département de Neurochirurgie Pédiatrique, Hôpital Necker-Enfants Malades, Université, Paris, France
| | - Paolo Ferroli
- 7Department of Neurosurgery, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Mathilde Chevignard
- 8Rehabilitation Department for Children with Acquired Neurological Injury, Saint Maurice Hospitals, Saint Maurice
- 9Laboratoire d'Imagerie Biomédicale and
- 10GRC 24 HaMCRe, Sorbonne Université, Paris
| | - François Doz
- 11SIREDO Cancer Center (Care, Innovation & Research, in Childhood, Adolescent and Young-Adult Oncology), Institut Curie Paris
- 12Department of Pediatrics, University Paris Descartes, Paris, France
| | - Barry Pizer
- 13Department of Oncology, Alder Hey Children's NHS Foundation Trust, Liverpool, United Kingdom
| | - Stefan Rutkowski
- 14Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Maura Massimino
- 15Fondazione Istituto di Ricovero e Cura a Carattere Scientifico IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | | | - Edward Schwalbe
- 17Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle-upon-Tyne
- 18Department of Applied Sciences, Northumbria University, Newcastle-upon-Tyne, United Kingdom
| | - Debbie Hicks
- 17Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle-upon-Tyne
| | - Steven C Clifford
- 17Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle-upon-Tyne
| | - Torsten Pietsch
- 19Institute of Neuropathology, DGNN Brain Tumour Reference Center, University of Bonn, Germany; and
| | - Birgitta Lannering
- 20Department of Pediatrics, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Germany
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13
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Hovestadt V, Ayrault O, Swartling FJ, Robinson GW, Pfister SM, Northcott PA. Medulloblastomics revisited: biological and clinical insights from thousands of patients. Nat Rev Cancer 2020; 20:42-56. [PMID: 31819232 PMCID: PMC9113832 DOI: 10.1038/s41568-019-0223-8] [Citation(s) in RCA: 134] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/25/2019] [Indexed: 12/16/2022]
Abstract
Medulloblastoma, a malignant brain tumour primarily diagnosed during childhood, has recently been the focus of intensive molecular profiling efforts, profoundly advancing our understanding of biologically and clinically heterogeneous disease subgroups. Genomic, epigenomic, transcriptomic and proteomic landscapes have now been mapped for an unprecedented number of bulk samples from patients with medulloblastoma and, more recently, for single medulloblastoma cells. These efforts have provided pivotal new insights into the diverse molecular mechanisms presumed to drive tumour initiation, maintenance and recurrence across individual subgroups and subtypes. Translational opportunities stemming from this knowledge are continuing to evolve, providing a framework for improved diagnostic and therapeutic interventions. In this Review, we summarize recent advances derived from this continued molecular characterization of medulloblastoma and contextualize this progress towards the deployment of more effective, molecularly informed treatments for affected patients.
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Affiliation(s)
- Volker Hovestadt
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Olivier Ayrault
- Institut Curie, PSL Research University, CNRS UMR, INSERM, Orsay, France
- Université Paris Sud, Université Paris-Saclay, CNRS UMR 3347, INSERM U1021, Orsay, France
| | - Fredrik J Swartling
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Giles W Robinson
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Paediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Paediatric Haematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Paul A Northcott
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA.
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14
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Stock A, Mynarek M, Pietsch T, Pfister SM, Clifford SC, Goschzik T, Sturm D, Schwalbe EC, Hicks D, Rutkowski S, Bison B, Pham M, Warmuth-Metz M. Imaging Characteristics of Wingless Pathway Subgroup Medulloblastomas: Results from the German HIT/SIOP-Trial Cohort. AJNR Am J Neuroradiol 2019; 40:1811-1817. [PMID: 31649159 DOI: 10.3174/ajnr.a6286] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 09/03/2019] [Indexed: 12/16/2022]
Abstract
BACKGROUND AND PURPOSE In addition to the 4 histopathologically defined entities of medulloblastoma, 4 distinct genetically defined subgroups have been included in the World Health Organization classification of 2016. The smallest subgroup is the medulloblastoma with activated wingless pathway. The goal of this study was to identify a typical MR imaging morphology in a larger number of pediatric patients with wingless pathway medulloblastoma. MATERIALS AND METHODS From January 2001 to October 2017, of 75 patients with histologically confirmed and molecularly subgrouped wingless pathway medulloblastomas recruited to the German Pediatric Brain Tumor (HIT) trials, 38 patients (median age, 12.8 ± 4.6 years at diagnosis; 24 [63.2%] female) had preoperative imaging that passed the entry criteria for this study. Images were rated by the local standardized imaging criteria of the National Reference Center of Neuroradiology. Additionally, a modified laterality score was used to determine tumor localization and extension. RESULTS Twenty-eight of 38 (73.7%) were primary midline tumors but with a lateral tendency in 39.3%. One extensively eccentric midline tumor was rated by the laterality score as in an off-midline position. Five tumors were found in the cerebellopontine angle; 3, in the deep white matter; and 2, in a cerebellar hemisphere. Leptomeningeal dissemination was rare (11.5%). In 60.5%, intratumoral blood-degradation products were found, and 26.3% showed cysts with blood contents. CONCLUSIONS According to our observations, wingless pathway medulloblastomas are not preferentially off-midline tumors as postulated in previous studies with smaller wingless pathway medulloblastoma cohorts. Dense intratumoral blood-degradation products and cysts with blood contents are frequently found and might help to differentiate wingless pathway medulloblastoma from other medulloblastoma subtypes.
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Affiliation(s)
- A Stock
- From the Department of Neuroradiology (A.S., B.B., M.P., M.W.-M.), University Hospital Wuerzburg, Wuerzburg, Germany
| | - M Mynarek
- Department of Pediatric Hematology and Oncology (M.M., S.R.), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - T Pietsch
- Institute of Neuropathology (T.P., T.G.), DGNN Brain Tumor Reference Center, University of Bonn Medical Center, Bonn, Germany
| | - S M Pfister
- Department of Pediatric Hematology and Oncology (S.M.P.), Heidelberg University Hospital, Heidelberg, Germany.,Division of Pediatric Neurooncology (S.M.P.), German Cancer Consortium, German Cancer Research Center, Heidelberg, Germany.,Hopp Children's Cancer Heidelberg (S.M.P., D.S.), Heidelberg, Germany
| | - S C Clifford
- Wolfson Childhood Cancer Research Centre (S.C.C., E.C.S., D.H.), Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - T Goschzik
- Institute of Neuropathology (T.P., T.G.), DGNN Brain Tumor Reference Center, University of Bonn Medical Center, Bonn, Germany
| | - D Sturm
- Hopp Children's Cancer Heidelberg (S.M.P., D.S.), Heidelberg, Germany
| | - E C Schwalbe
- Wolfson Childhood Cancer Research Centre (S.C.C., E.C.S., D.H.), Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK.,Department of Applied Sciences (E.C.S.), Northumbria University, Newcastle upon Tyne, UK
| | - D Hicks
- Wolfson Childhood Cancer Research Centre (S.C.C., E.C.S., D.H.), Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - S Rutkowski
- Department of Pediatric Hematology and Oncology (M.M., S.R.), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - B Bison
- From the Department of Neuroradiology (A.S., B.B., M.P., M.W.-M.), University Hospital Wuerzburg, Wuerzburg, Germany
| | - M Pham
- From the Department of Neuroradiology (A.S., B.B., M.P., M.W.-M.), University Hospital Wuerzburg, Wuerzburg, Germany
| | - M Warmuth-Metz
- From the Department of Neuroradiology (A.S., B.B., M.P., M.W.-M.), University Hospital Wuerzburg, Wuerzburg, Germany
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15
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Sharma T, Schwalbe EC, Williamson D, Sill M, Hovestadt V, Mynarek M, Rutkowski S, Robinson GW, Gajjar A, Cavalli F, Ramaswamy V, Taylor MD, Lindsey JC, Hill RM, Jäger N, Korshunov A, Hicks D, Bailey S, Kool M, Chavez L, Northcott PA, Pfister SM, Clifford SC. Second-generation molecular subgrouping of medulloblastoma: an international meta-analysis of Group 3 and Group 4 subtypes. Acta Neuropathol 2019; 138:309-326. [PMID: 31076851 PMCID: PMC6660496 DOI: 10.1007/s00401-019-02020-0] [Citation(s) in RCA: 157] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 04/23/2019] [Accepted: 04/23/2019] [Indexed: 12/18/2022]
Abstract
In 2012, an international consensus paper reported that medulloblastoma comprises four molecular subgroups (WNT, SHH, Group 3, and Group 4), each associated with distinct genomic features and clinical behavior. Independently, multiple recent reports have defined further intra-subgroup heterogeneity in the form of biologically and clinically relevant subtypes. However, owing to differences in patient cohorts and analytical methods, estimates of subtype number and definition have been inconsistent, especially within Group 3 and Group 4. Herein, we aimed to reconcile the definition of Group 3/Group 4 MB subtypes through the analysis of a series of 1501 medulloblastomas with DNA-methylation profiling data, including 852 with matched transcriptome data. Using multiple complementary bioinformatic approaches, we compared the concordance of subtype calls between published cohorts and analytical methods, including assessments of class-definition confidence and reproducibility. While the lowest complexity solutions continued to support the original consensus subgroups of Group 3 and Group 4, our analysis most strongly supported a definition comprising eight robust Group 3/Group 4 subtypes (types I–VIII). Subtype II was consistently identified across all component studies, while all others were supported by multiple class-definition methods. Regardless of analytical technique, increasing cohort size did not further increase the number of identified Group 3/Group 4 subtypes. Summarizing the molecular and clinico-pathological features of these eight subtypes indicated enrichment of specific driver gene alterations and cytogenetic events amongst subtypes, and identified highly disparate survival outcomes, further supporting their biological and clinical relevance. Collectively, this study provides continued support for consensus Groups 3 and 4 while enabling robust derivation of, and categorical accounting for, the extensive intertumoral heterogeneity within Groups 3 and 4, revealed by recent high-resolution subclassification approaches. Furthermore, these findings provide a basis for application of emerging methods (e.g., proteomics/single-cell approaches) which may additionally inform medulloblastoma subclassification. Outputs from this study will help shape definition of the next generation of medulloblastoma clinical protocols and facilitate the application of enhanced molecularly guided risk stratification to improve outcomes and quality of life for patients and their families.
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Affiliation(s)
- Tanvi Sharma
- Hopp Children’s Cancer Centre at National Centre for Tumour Diseases Heidelberg (KiTZ), Heidelberg, Germany
- Division of Paediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Edward C. Schwalbe
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Daniel Williamson
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Martin Sill
- Hopp Children’s Cancer Centre at National Centre for Tumour Diseases Heidelberg (KiTZ), Heidelberg, Germany
- Division of Paediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Volker Hovestadt
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114 USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142 USA
| | - Martin Mynarek
- Department of Pediatric Hematology and Oncology, Center for Obstetrics and Pediatrics, Universitatsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Rutkowski
- Department of Pediatric Hematology and Oncology, Center for Obstetrics and Pediatrics, Universitatsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Giles W. Robinson
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105 USA
| | - Amar Gajjar
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105 USA
| | - Florence Cavalli
- Programme in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON Canada
| | - Vijay Ramaswamy
- Programme in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON Canada
- Division of Haematology/Oncology, Department of Pediatrics, The Hospital for Sick Children, 555 University Ave, Toronto, ON M5G 1X8 Canada
| | - Michael D. Taylor
- Programme in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON Canada
| | - Janet C. Lindsey
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Rebecca M. Hill
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Natalie Jäger
- Hopp Children’s Cancer Centre at National Centre for Tumour Diseases Heidelberg (KiTZ), Heidelberg, Germany
- Division of Paediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andrey Korshunov
- Division of Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Debbie Hicks
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Simon Bailey
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Marcel Kool
- Hopp Children’s Cancer Centre at National Centre for Tumour Diseases Heidelberg (KiTZ), Heidelberg, Germany
- Division of Paediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lukas Chavez
- Department of Medicine, University of California, San Diego, USA
| | - Paul A. Northcott
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105 USA
| | - Stefan M. Pfister
- Hopp Children’s Cancer Centre at National Centre for Tumour Diseases Heidelberg (KiTZ), Heidelberg, Germany
- Division of Paediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Paediatric Haematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Steven C. Clifford
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
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Abstract
PURPOSE OF REVIEW Medulloblastoma is no more a unique disease. Clinical and biologic classification used so far are challenged by molecular classification(s). Following the consensus article that described four molecular groups of medulloblastoma in 2012, several articles in 2017 provided more relevant classifications that may impact on further clinical trial design. RECENT FINDINGS Though wingless (WNT) and sonic hedgehog (SHH) are defined by the activation of their respective pathways, the age and type of activation define various subgroups with specific features and outcome. Groups 3 and 4 remain ill defined. The whole population of medulloblastoma may be divided in 12 subgroups: WNTαβ, SHHαβγδ, group 3αβγ and group 4αβγ. The paediatric population may be divided in seven subgroups: WNT, SHH of infants and children, and low-risk and high-risk groups 3 and 4. SHH of infants may be divided as iSHH-I vs. iSHH-II that have different prognosis. Moreover, specific drivers of groups 3 and 4 were reported. SUMMARY These findings have and will have direct implications on the conception of clinical trials. Low-risk groups will benefit from less toxic therapies, and high-risk groups will benefit from targeted therapies.
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Cruzeiro GAV, Salomão KB, de Biagi Jr CAO, Baumgartner M, Sturm D, Lira RCP, de Almeida Magalhães T, Baroni Milan M, da Silva Silveira V, Saggioro FP, de Oliveira RS, dos Santos Klinger PH, Seidinger AL, Yunes JA, de Paula Queiroz RG, Oba-Shinjo SM, Scrideli CA, Nagahashi SMK, Tone LG, Valera ET. A simplified approach using Taqman low-density array for medulloblastoma subgrouping. Acta Neuropathol Commun 2019; 7:33. [PMID: 30832734 PMCID: PMC6398239 DOI: 10.1186/s40478-019-0681-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 02/18/2019] [Indexed: 12/31/2022] Open
Abstract
Next-generation sequencing platforms are routinely used for molecular assignment due to their high impact for risk stratification and prognosis in medulloblastomas. Yet, low and middle-income countries still lack an accurate cost-effective platform to perform this allocation. TaqMan Low Density array (TLDA) assay was performed using a set of 20 genes in 92 medulloblastoma samples. The same methodology was assessed in silico using microarray data for 763 medulloblastoma samples from the GSE85217 study, which performed MB classification by a robust integrative method (Transcriptional, Methylation and cytogenetic profile). Furthermore, we validated in 11 MBs samples our proposed method by Methylation Array 450 K to assess methylation profile along with 390 MB samples (GSE109381) and copy number variations. TLDA with only 20 genes accurately assigned MB samples into WNT, SHH, Group 3 and Group 4 using Pearson distance with the average-linkage algorithm and showed concordance with molecular assignment provided by Methylation Array 450 k. Similarly, we tested this simplified set of gene signatures in 763 MB samples and we were able to recapitulate molecular assignment with an accuracy of 99.1% (SHH), 94.29% (WNT), 92.36% (Group 3) and 95.40% (Group 4), against 97.31, 97.14, 88.89 and 97.24% (respectively) with the Ward.D2 algorithm. t-SNE analysis revealed a high level of concordance (k = 4) with minor overlapping features between Group 3 and Group 4. Finally, we condensed the number of genes to 6 without significantly losing accuracy in classifying samples into SHH, WNT and non-SHH/non-WNT subgroups. Additionally, we found a relatively high frequency of WNT subgroup in our cohort, which requires further epidemiological studies. TLDA is a rapid, simple and cost-effective assay for classifying MB in low/middle income countries. A simplified method using six genes and restricting the final stratification into SHH, WNT and non-SHH/non-WNT appears to be a very interesting approach for rapid clinical decision-making.
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Abstract
Medulloblastoma (MB) comprises a biologically heterogeneous group of embryonal tumours of the cerebellum. Four subgroups of MB have been described (WNT, sonic hedgehog (SHH), Group 3 and Group 4), each of which is associated with different genetic alterations, age at onset and prognosis. These subgroups have broadly been incorporated into the WHO classification of central nervous system tumours but still need to be accounted for to appropriately tailor disease risk to therapy intensity and to target therapy to disease biology. In this Primer, the epidemiology (including MB predisposition), molecular pathogenesis and integrative diagnosis taking histomorphology, molecular genetics and imaging into account are reviewed. In addition, management strategies, which encompass surgical resection of the tumour, cranio-spinal irradiation and chemotherapy, are discussed, together with the possibility of focusing more on disease biology and robust molecularly driven patient stratification in future clinical trials.
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Prognostic effect of whole chromosomal aberration signatures in standard-risk, non-WNT/non-SHH medulloblastoma: a retrospective, molecular analysis of the HIT-SIOP PNET 4 trial. Lancet Oncol 2018; 19:1602-1616. [PMID: 30392813 PMCID: PMC6262170 DOI: 10.1016/s1470-2045(18)30532-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 07/06/2018] [Accepted: 07/11/2018] [Indexed: 12/18/2022]
Abstract
Background Most children with medulloblastoma fall within the standard-risk clinical disease group defined by absence of high-risk features (metastatic disease, large-cell/anaplastic histology, and MYC amplification), which includes 50–60% of patients and has a 5-year event-free survival of 75–85%. Within standard-risk medulloblastoma, patients in the WNT subgroup are established as having a favourable prognosis; however, outcome prediction for the remaining majority of patients is imprecise. We sought to identify novel prognostic biomarkers to enable improved risk-adapted therapies. Methods The HIT-SIOP PNET 4 trial recruited 338 patients aged 4–21 years with medulloblastoma between Jan 1, 2001, and Dec 31, 2006, in 120 treatment institutions in seven European countries to investigate hyperfractionated radiotherapy versus standard radiotherapy. In this retrospective analysis, we assessed the remaining tumour samples from patients in the HIT-SIOP PNET 4 trial (n=136). We assessed the clinical behaviour of the molecularly defined WNT and SHH subgroups, and identified novel independent prognostic markers and models for standard-risk patients with non-WNT/non-SHH disease. Because of the scarcity and low quality of available genomic material, we used a mass spectrometry-minimal methylation classifier assay (MS-MIMIC) to assess methylation subgroup and a molecular inversion probe array to detect genome-wide copy number aberrations. Prognostic biomarkers and models identified were validated in an independent, demographically matched cohort (n=70) of medulloblastoma patients with non-WNT/non-SHH standard-risk disease treated with conventional therapies (maximal surgical resection followed by adjuvant craniospinal irradiation [all patients] and chemotherapy [65 of 70 patients], at UK Children's Cancer and Leukaemia Group and European Society for Paediatric Oncology (SIOPE) associated treatment centres between 1990 and 2014. These samples were analysed by Illumina 450k DNA methylation microarray. HIT-SIOP PNET 4 is registered with ClinicalTrials.gov, number NCT01351870. Findings We analysed methylation subgroup, genome-wide copy number aberrations, and mutational features in 136 assessable tumour samples from the HIT-SIOP PNET 4 cohort, representing 40% of the 338 patients in the trial cohort. This cohort of 136 samples consisted of 28 (21%) classified as WNT, 17 (13%) as SHH, and 91 (67%) as non-WNT/non-SHH (we considered Group3 and Group4 medulloblastoma together in our analysis because of their similar molecular and clinical features). Favourable outcomes for WNT tumours were confirmed in patients younger than 16 years, and all relapse events in SHH (four [24%] of 17) occurred in patients with TP53 mutation (TP53mut) or chromosome 17p loss. A novel whole chromosomal aberration signature associated with increased ploidy and multiple non-random whole chromosomal aberrations was identified in 38 (42%) of the 91 samples from patients with non-WNT/non-SHH medulloblastoma in the HIT-SIOP PNET 4 cohort. Biomarkers associated with this whole chromosomal aberration signature (at least two of chromosome 7 gain, chromosome 8 loss, and chromosome 11 loss) predicted favourable prognosis. Patients with non-WNT/non-SHH medulloblastoma could be reclassified by these markers as having favourable-risk or high-risk disease. In patients in the HIT-SIOP PNET4 cohort with non-WNT/non-SHH medulloblastoma, with a median follow-up of 6·7 years (IQR 5·8–8·2), 5-year event-free survival was 100% in the favourable-risk group and 68% (95% CI 57·5–82·7; p=0·00014) in the high-risk group. In the validation cohort, with a median follow-up of 5·6 years (IQR 3·1–8·1), 5-year event-free survival was 94·7% (95% CI 85·2–100) in the favourable-risk group and 58·6% (95% CI 45·1–76·1) in the high-risk group (hazard ratio 9·41, 95% CI 1·25–70·57; p=0·029). Our comprehensive molecular investigation identified subgroup-specific risk models which allowed 69 (51%) of 134 accessible patients from the standard-risk medulloblastoma HIT-SIOP PNET 4 cohort to be assigned to a favourable-risk group. Interpretation We define a whole chromosomal signature that allows the assignment of non-WNT/non-SHH medulloblastoma patients normally classified as standard-risk into favourable-risk and high-risk categories. In addition to patients younger than 16 years with WNT tumours, patients with non-WNT/non-SHH tumours with our defined whole chromosomal aberration signature and patients with SHH-TP53wild-type tumours should be considered for therapy de-escalation in future biomarker-driven, risk-adapted clinical trials. The remaining subgroups of patients with high-risk medulloblastoma might benefit from more intensive therapies. Funding Cancer Research UK, Swedish Childhood Cancer Foundation, French Ministry of Health/French National Cancer Institute, and the German Children's Cancer Foundation.
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Fujita K, Hashimoto M. Separation-free single-base extension assay with fluorescence resonance energy transfer for rapid and convenient determination of DNA methylation status at specific cytosine and guanine dinucleotide sites. Electrophoresis 2018; 40:281-288. [PMID: 30280389 DOI: 10.1002/elps.201800144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 09/15/2018] [Accepted: 09/29/2018] [Indexed: 11/08/2022]
Abstract
A separation-free single-base extension (SBE) assay utilizing fluorescence resonance energy transfer (FRET) was developed for rapid and convenient interrogation of DNA methylation status at specific cytosine and guanine dinucleotide sites. In this assay, the SBE was performed in a tube using an allele-specific oligonucleotide primer (i.e., extension primer) labeled with Cy3 as a FRET donor fluorophore at the 5'-end, a nucleotide terminator (dideoxynucleotide triphosphate) labeled with Cy5 as a FRET acceptor, a PCR amplicon derived from bisulfite-converted genomic DNA, and a DNA polymerase. A single base-extended primer (i.e., SBE product) that was 5'-Cy3- and 3'-Cy5-tagged was formed by incorporation of the Cy5-labeled terminator into the 3'-end of the extension primer, but only if the terminator added was complementary to the target nucleotide. The resulting SBE product brought the Cy3 donor and the Cy5 acceptor into close proximity. Illumination of the Cy3 donor resulted in successful FRET and excitation of the Cy5 acceptor, generating fluorescence emission from the acceptor. The capacity of the developed assay to discriminate as low as 10% methylation from a mixture of methylated and unmethylated DNA was demonstrated at multiple cytosine and guanine dinucleotide sites.
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Affiliation(s)
- Keisuke Fujita
- Department of Chemical Engineering and Materials Science, Faculty of Science and Engineering, Doshisha University, Kyotanabe, Kyoto, Japan
| | - Masahiko Hashimoto
- Department of Chemical Engineering and Materials Science, Faculty of Science and Engineering, Doshisha University, Kyotanabe, Kyoto, Japan
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