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Stathakis S, Pissakas G, Alexiou A, Bertrand B, Bondiau P, Claude L, Cuthbert T, Damatopoulou A, Dejean C, Doukakis C, Güngör G, Hardy L, Maani E, Martel-Lafay I, Mavroidis P, Paragios N, Peppa V, Remonde D, Shumway J, Ugurluer G, Ozyar E. Evaluation of AI vs. Clinical Experts SBRT-Thorax Computed Tomography OARs Delineation. Int J Radiat Oncol Biol Phys 2022. [DOI: 10.1016/j.ijrobp.2022.07.897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Burgenske DM, Yang J, Decker PA, Kollmeyer TM, Kosel ML, Mladek AC, Caron AA, Vaubel RA, Gupta SK, Kitange GJ, Sicotte H, Youland RS, Remonde D, Voss JS, Fritcher EGB, Kolsky KL, Ida CM, Meyer FB, Lachance DH, Parney IJ, Kipp BR, Giannini C, Sulman EP, Jenkins RB, Eckel-Passow JE, Sarkaria JN. Molecular profiling of long-term IDH-wildtype glioblastoma survivors. Neuro Oncol 2020; 21:1458-1469. [PMID: 31346613 DOI: 10.1093/neuonc/noz129] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Glioblastoma (GBM) represents an aggressive cancer type with a median survival of only 14 months. With fewer than 5% of patients surviving 5 years, comprehensive profiling of these rare patients could elucidate prognostic biomarkers that may confer better patient outcomes. We utilized multiple molecular approaches to characterize the largest patient cohort of isocitrate dehydrogenase (IDH)-wildtype GBM long-term survivors (LTS) to date. METHODS Retrospective analysis was performed on 49 archived formalin-fixed paraffin embedded tumor specimens from patients diagnosed with GBM at the Mayo Clinic between December 1995 and September 2013. These patient samples were subdivided into 2 groups based on survival (12 LTS, 37 short-term survivors [STS]) and subsequently examined by mutation sequencing, copy number analysis, methylation profiling, and gene expression. RESULTS Of the 49 patients analyzed in this study, LTS were younger at diagnosis (P = 0.016), more likely to be female (P = 0.048), and MGMT promoter methylated (UniD, P = 0.01). IDH-wildtype STS and LTS demonstrated classic GBM mutations and copy number changes. Pathway analysis of differentially expressed genes showed LTS enrichment for sphingomyelin metabolism, which has been linked to decreased GBM growth, invasion, and angiogenesis. STS were enriched for DNA repair and cell cycle control networks. CONCLUSIONS While our findings largely report remarkable similarity between these LTS and more typical STS, unique attributes were observed in regard to altered gene expression and pathway enrichment. These attributes may be valuable prognostic markers and are worth further examination. Importantly, this study also underscores the limitations of existing biomarkers and classification methods in predicting patient prognosis.
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Affiliation(s)
| | - Jie Yang
- Department of Radiation Oncology, NYU Langone School of Medicine, New York, New York
| | - Paul A Decker
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Thomas M Kollmeyer
- Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Matthew L Kosel
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Ann C Mladek
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | - Alissa A Caron
- Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Rachael A Vaubel
- Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Shiv K Gupta
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | - Gaspar J Kitange
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | - Hugues Sicotte
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Ryan S Youland
- Department of Radiation Oncology, Gundersen Health System, La Crosse, Wisconsin
| | - Dioval Remonde
- Department of Radiation Oncology, Mays Cancer Center, University of Texas Health San Antonio, San Antonio, Texas
| | - Jesse S Voss
- Molecular Anatomic Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Emily G Barr Fritcher
- Molecular Anatomic Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Kathryn L Kolsky
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | - Cristiane M Ida
- Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Fredric B Meyer
- Department of Neurosurgery, Mayo Clinic, Rochester, Minnesota
| | | | - Ian J Parney
- Department of Neurosurgery, Mayo Clinic, Rochester, Minnesota
| | - Benjamin R Kipp
- Molecular Anatomic Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Caterina Giannini
- Anatomic Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Erik P Sulman
- Department of Radiation Oncology, NYU Langone School of Medicine, New York, New York
| | - Robert B Jenkins
- Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | | | - Jann N Sarkaria
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
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Vaubel RA, Tian S, Remonde D, Schroeder MA, Mladek AC, Kitange GJ, Caron A, Kollmeyer TM, Grove R, Peng S, Carlson BL, Ma DJ, Sarkar G, Evers L, Decker PA, Yan H, Dhruv HD, Berens ME, Wang Q, Marin BM, Klee EW, Califano A, LaChance DH, Eckel-Passow JE, Verhaak RG, Sulman EP, Burns TC, Meyer FB, O'Neill BP, Tran NL, Giannini C, Jenkins RB, Parney IF, Sarkaria JN. Genomic and Phenotypic Characterization of a Broad Panel of Patient-Derived Xenografts Reflects the Diversity of Glioblastoma. Clin Cancer Res 2020; 26:1094-1104. [PMID: 31852831 PMCID: PMC7056576 DOI: 10.1158/1078-0432.ccr-19-0909] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 05/25/2019] [Accepted: 12/12/2019] [Indexed: 11/16/2022]
Abstract
PURPOSE Glioblastoma is the most frequent and lethal primary brain tumor. Development of novel therapies relies on the availability of relevant preclinical models. We have established a panel of 96 glioblastoma patient-derived xenografts (PDX) and undertaken its genomic and phenotypic characterization. EXPERIMENTAL DESIGN PDXs were established from glioblastoma, IDH-wildtype (n = 93), glioblastoma, IDH-mutant (n = 2), diffuse midline glioma, H3 K27M-mutant (n = 1), and both primary (n = 60) and recurrent (n = 34) tumors. Tumor growth rates, histopathology, and treatment response were characterized. Integrated molecular profiling was performed by whole-exome sequencing (WES, n = 83), RNA-sequencing (n = 68), and genome-wide methylation profiling (n = 76). WES data from 24 patient tumors was compared with derivative models. RESULTS PDXs recapitulate many key phenotypic and molecular features of patient tumors. Orthotopic PDXs show characteristic tumor morphology and invasion patterns, but largely lack microvascular proliferation and necrosis. PDXs capture common and rare molecular drivers, including alterations of TERT, EGFR, PTEN, TP53, BRAF, and IDH1, most at frequencies comparable with human glioblastoma. However, PDGFRA amplification was absent. RNA-sequencing and genome-wide methylation profiling demonstrated broad representation of glioblastoma molecular subtypes. MGMT promoter methylation correlated with increased survival in response to temozolomide. WES of 24 matched patient tumors showed preservation of most genetic driver alterations, including EGFR amplification. However, in four patient-PDX pairs, driver alterations were gained or lost on engraftment, consistent with clonal selection. CONCLUSIONS Our PDX panel captures the molecular heterogeneity of glioblastoma and recapitulates many salient genetic and phenotypic features. All models and genomic data are openly available to investigators.
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Affiliation(s)
| | | | - Dioval Remonde
- Brody School of Medicine at East Carolina University, Greenville, North Carolina
| | | | | | | | | | | | | | - Sen Peng
- Translational Genomics Research Institute, Phoenix, Arizona
| | | | | | | | - Lisa Evers
- Translational Genomics Research Institute, Phoenix, Arizona
| | | | | | | | | | | | | | | | | | | | | | - Roel G Verhaak
- Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - Erik P Sulman
- New York University Langone Health, New York, New York
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Vaubel R, Tian S, Remonde D, Schroeder M, Kollmeyer T, Peng S, Mladek A, Carlson B, Ma D, Kitange G, Evers L, Decker P, Kosel M, Berens M, Klee E, Califano A, James CD, Lachance D, Eckel-Passow J, Verhaak R, Sulman E, Tran N, Giannini C, Jenkins R, Parney I, Sarkaria J. TMOD-18. THE PATIENT DERIVED XENOGRAFT NATIONAL RESOURCE: A COMPREHENSIVE COLLECTION OF HIGH-GRADE GLIOMA MODELS FOR PRE-CLINICAL AND TRANSLATIONAL STUDIES. Neuro Oncol 2018. [DOI: 10.1093/neuonc/noy148.1130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
| | | | - Dioval Remonde
- Brody School of Medicine at East Carolina University, Greenville, NC, USA
| | | | | | - Sen Peng
- Cancer and Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | | | | | | | | | - Lisa Evers
- TGen, Translational Genomics Research Institute, Phoenix, AZ, USA
| | | | | | - Michael Berens
- TGen, Translational Genomics Research Institute, Phoenix, AZ, USA
| | | | | | - C David James
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | | | - Jeanette Eckel-Passow
- Division of Biomedical Statistics and Informatics, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Roel Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Erik Sulman
- University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Nhan Tran
- Departments of Cancer Biology and Neurosurgery, Mayo Clinic Arizona, Scottsdale, AZ, USA
| | | | | | | | - Jann Sarkaria
- Translational Neuro-Oncology Laboratory, Mayo Clinic, Rochester, MN, USA
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Burgenske D, Eckel-Passow J, Decker P, Kosel M, Youland R, Remonde D, Kollmeyer T, Sicotte H, Caron A, Giannini C, Lachance D, Jenkins R, Sarkaria J. GENE-28. CLINICAL AND MOLECULAR ANALYSES OF LONG-TERM SURVIVORS OF GLIOBLASTOMA. Neuro Oncol 2017. [DOI: 10.1093/neuonc/nox168.402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Sarkaria J, Decker P, Remonde D, Kosel M, Carlson B, Schroeder M, Bakken K, Sulman E, Eckel Passow J. Experimental design recommendations for PDX pre-clinical trials: Reanalysis of radiation and temozolomide orthotopic survival data in GBM models. Eur J Cancer 2016. [DOI: 10.1016/s0959-8049(16)32761-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Allison R, Remonde D, Salenius S, Hnatov A, Ballenger C, Mantz C, Fernandez E, Dosoretz D, Finkelstein S. EP-1114: Clinical outcomes in modern management of infratentorial ependymoma. Radiother Oncol 2016. [DOI: 10.1016/s0167-8140(16)32364-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Youland R, Remonde D, Caron A, Mladek A, Decker P, Sicotte H, Lachance D, Kipp B, Eckel-Passow J, Huse J, Giannini C, Jenkins R, Sarkaria J. GENO-37MOLECULAR PROFILING OF LONG-TERM SURVIVORS OF GLIOBLASTOMA. Neuro Oncol 2015. [DOI: 10.1093/neuonc/nov215.37] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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