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Tobochnik S, Dorotan MKC, Ghosh HS, Lapinskas E, Vogelzang J, Reardon DA, Ligon KL, Bi WL, Smirnakis SM, Lee JW. Glioma genetic profiles associated with electrophysiologic hyperexcitability. Neuro Oncol 2024; 26:323-334. [PMID: 37713468 PMCID: PMC10836775 DOI: 10.1093/neuonc/noad176] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 06/16/2023] [Indexed: 09/17/2023] Open
Abstract
BACKGROUND Distinct genetic alterations determine glioma aggressiveness, however, the diversity of somatic mutations contributing to peritumoral hyperexcitability and seizures over the course of the disease is uncertain. This study aimed to identify tumor somatic mutation profiles associated with clinically significant hyperexcitability. METHODS A single center cohort of adults with WHO grades 1-4 glioma and targeted exome sequencing (n = 1716) was analyzed and cross-referenced with a validated EEG database to identify the subset of individuals who underwent continuous EEG monitoring (n = 206). Hyperexcitability was defined by the presence of lateralized periodic discharges and/or electrographic seizures. Cross-validated discriminant analysis models trained exclusively on recurrent somatic mutations were used to identify variants associated with hyperexcitability. RESULTS The distribution of WHO grades and tumor mutational burdens were similar between patients with and without hyperexcitability. Discriminant analysis models classified the presence or absence of EEG hyperexcitability with an overall accuracy of 70.9%, regardless of IDH1 R132H inclusion. Predictive variants included nonsense mutations in ATRX and TP53, indel mutations in RBBP8 and CREBBP, and nonsynonymous missense mutations with predicted damaging consequences in EGFR, KRAS, PIK3CA, TP53, and USP28. This profile improved estimates of hyperexcitability in a multivariate analysis controlling for age, sex, tumor location, integrated pathologic diagnosis, recurrence status, and preoperative epilepsy. Predicted somatic mutation variants were over-represented in patients with hyperexcitability compared to individuals without hyperexcitability and those who did not undergo continuous EEG. CONCLUSION These findings implicate diverse glioma somatic mutations in cancer genes associated with peritumoral hyperexcitability. Tumor genetic profiling may facilitate glioma-related epilepsy prognostication and management.
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Affiliation(s)
- Steven Tobochnik
- Department of Neurology, VA Boston Healthcare System, Boston, Massachusetts, USA
- Department of Neurology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | | | - Hia S Ghosh
- Department of Neurosurgery, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Emily Lapinskas
- Department of Neurology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Jayne Vogelzang
- Department of Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - David A Reardon
- Department of Medical Oncology, Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Keith L Ligon
- Department of Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Wenya Linda Bi
- Department of Neurosurgery, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Stelios M Smirnakis
- Department of Neurology, VA Boston Healthcare System, Boston, Massachusetts, USA
- Department of Neurology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Jong Woo Lee
- Department of Neurology, Brigham and Women's Hospital, Boston, Massachusetts, USA
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2
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Hofman DA, Ruiz-Orera J, Yannuzzi I, Murugesan R, Brown A, Clauser KR, Condurat AL, van Dinter JT, Engels SAG, Goodale A, van der Lugt J, Abid T, Wang L, Zhou KN, Vogelzang J, Ligon KL, Phoenix TN, Roth JA, Root DE, Hubner N, Golub TR, Bandopadhayay P, van Heesch S, Prensner JR. Translation of non-canonical open reading frames as a cancer cell survival mechanism in childhood medulloblastoma. Mol Cell 2024; 84:261-276.e18. [PMID: 38176414 PMCID: PMC10872554 DOI: 10.1016/j.molcel.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 05/16/2023] [Revised: 08/30/2023] [Accepted: 12/01/2023] [Indexed: 01/06/2024]
Abstract
A hallmark of high-risk childhood medulloblastoma is the dysregulation of RNA translation. Currently, it is unknown whether medulloblastoma dysregulates the translation of putatively oncogenic non-canonical open reading frames (ORFs). To address this question, we performed ribosome profiling of 32 medulloblastoma tissues and cell lines and observed widespread non-canonical ORF translation. We then developed a stepwise approach using multiple CRISPR-Cas9 screens to elucidate non-canonical ORFs and putative microproteins implicated in medulloblastoma cell survival. We determined that multiple lncRNA-ORFs and upstream ORFs (uORFs) exhibited selective functionality independent of main coding sequences. A microprotein encoded by one of these ORFs, ASNSD1-uORF or ASDURF, was upregulated, associated with MYC-family oncogenes, and promoted medulloblastoma cell survival through engagement with the prefoldin-like chaperone complex. Our findings underscore the fundamental importance of non-canonical ORF translation in medulloblastoma and provide a rationale to include these ORFs in future studies seeking to define new cancer targets.
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Affiliation(s)
- Damon A Hofman
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - Jorge Ruiz-Orera
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Ian Yannuzzi
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Adam Brown
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Karl R Clauser
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alexandra L Condurat
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jip T van Dinter
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - Sem A G Engels
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - Amy Goodale
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jasper van der Lugt
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - Tanaz Abid
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Li Wang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kevin N Zhou
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jayne Vogelzang
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02215, USA
| | - Keith L Ligon
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02215, USA; Department of Pathology, Boston Children's Hospital, Boston MA 02115, USA
| | - Timothy N Phoenix
- Division of Pharmaceutical Sciences, James L. Winkle College of Pharmacy, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Jennifer A Roth
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - David E Root
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Norbert Hubner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; Charité-Universitätsmedizin, 10117 Berlin, Germany; German Centre for Cardiovascular Research, Partner Site Berlin, 13347 Berlin, Germany
| | - Todd R Golub
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Pratiti Bandopadhayay
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Sebastiaan van Heesch
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands.
| | - John R Prensner
- Department of Pediatrics, Division of Pediatric Hematology/Oncology and Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
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3
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Blandin AF, Giglio R, Graham MS, Garcia G, Malinowski S, Woods JK, Ramkissoon S, Ramkissoon L, Dubois F, Schoolcraft K, Tsai J, Wang D, Jones R, Vogelzang J, Pelton K, Becker S, Watkinson F, Sinai C, Cohen EF, Booker MA, Tolstorukov MY, Haemels V, Goumnerova L, Wright K, Kieran M, Fehnel K, Reardon D, Tauziede-Espariat A, Lulla R, Carcamo B, Chaleff S, Charest A, DeSmet F, Ligon AH, Dubuc A, Pages M, Varlet P, Wen PY, Alexander BM, Chi S, Alexandrescu S, Kittler R, Bachoo R, Bandopadhayay P, Beroukhim R, Ligon KL. ALK Amplification and Rearrangements Are Recurrent Targetable Events in Congenital and Adult Glioblastoma. Clin Cancer Res 2023; 29:2651-2667. [PMID: 36780194 PMCID: PMC10363218 DOI: 10.1158/1078-0432.ccr-21-3521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/31/2022] [Accepted: 02/07/2023] [Indexed: 02/14/2023]
Abstract
PURPOSE Anaplastic lymphoma kinase (ALK) aberrations have been identified in pediatric-type infant gliomas, but their occurrence across age groups, functional effects, and treatment response has not been broadly established. EXPERIMENTAL DESIGN We performed a comprehensive analysis of ALK expression and genomic aberrations in both newly generated and retrospective data from 371 glioblastomas (156 adult, 205 infant/pediatric, and 10 congenital) with in vitro and in vivo validation of aberrations. RESULTS ALK aberrations at the protein or genomic level were detected in 12% of gliomas (45/371) in a wide age range (0-80 years). Recurrent as well as novel ALK fusions (LRRFIP1-ALK, DCTN1-ALK, PRKD3-ALK) were present in 50% (5/10) of congenital/infant, 1.4% (3/205) of pediatric, and 1.9% (3/156) of adult GBMs. ALK fusions were present as the only candidate driver in congenital/infant GBMs and were sometimes focally amplified. In contrast, adult ALK fusions co-occurred with other oncogenic drivers. No activating ALK mutations were identified in any age group. Novel and recurrent ALK rearrangements promoted STAT3 and ERK1/2 pathways and transformation in vitro and in vivo. ALK-fused GBM cellular and mouse models were responsive to ALK inhibitors, including in patient cells derived from a congenital GBM. Relevant to the treatment of infant gliomas, we showed that ALK protein appears minimally expressed in the forebrain at perinatal stages, and no gross effects on perinatal brain development were seen in pregnant mice treated with the ALK inhibitor ceritinib. CONCLUSIONS These findings support use of brain-penetrant ALK inhibitors in clinical trials across infant, pediatric, and adult GBMs. See related commentary by Mack and Bertrand, p. 2567.
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Affiliation(s)
- Anne-Florence Blandin
- Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad institute of Harvard and MIT, Cambridge, MA, USA
| | - Ross Giglio
- Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | | | - Jared K. Woods
- Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad institute of Harvard and MIT, Cambridge, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | | | | | - Frank Dubois
- Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Jessica Tsai
- Dana-Farber Cancer Institute, Boston, MA, USA
- Boston Children's Cancer and Blood Disorder Center, Boston, MA, USA
| | - Dayle Wang
- Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | | | | | | | | | - Elizabeth F Cohen
- Department of Informatics and Analytics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Matthew A Booker
- Department of Informatics and Analytics, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Veerle Haemels
- Laboratory for Precision Cancer Medicine, Translational Cell and Tissue Research Unit, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | | | - Karen Wright
- Dana-Farber Cancer Institute, Boston, MA, USA
- Boston Children's Cancer and Blood Disorder Center, Boston, MA, USA
| | - Mark Kieran
- Day One Biopharmaceuticals, Brisbane, CA 94005
| | - Katie Fehnel
- Boston Children's Cancer and Blood Disorder Center, Boston, MA, USA
| | | | | | - Rishi Lulla
- Hasbro Children's Hospital, Providence, RI, USA
| | - Benjamin Carcamo
- Texas Tech University, Health Science Center, Paul L. Foster School of Medicine, El Paso, TX, USA
- El Paso Children's Hospital, El Paso, TX, USA
| | | | - Alain Charest
- Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Frederik DeSmet
- Laboratory for Precision Cancer Medicine, Translational Cell and Tissue Research Unit, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Azra H. Ligon
- Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
- Boston Children's Cancer and Blood Disorder Center, Boston, MA, USA
| | - Adrian Dubuc
- Dana-Farber Cancer Institute, Boston, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | - Melanie Pages
- Department of Genetics, Institute Curie, Paris, France. INSERM U830, Laboratory of Translational Research in Pediatric Oncology, SIREDO Pediatric Oncology Center, Institute Curie, Paris, France
| | | | - Patrick Y. Wen
- Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Brian M. Alexander
- Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | - Susan Chi
- Dana-Farber Cancer Institute, Boston, MA, USA
- Boston Children's Cancer and Blood Disorder Center, Boston, MA, USA
| | - Sanda Alexandrescu
- Dana-Farber Cancer Institute, Boston, MA, USA
- Boston Children's Cancer and Blood Disorder Center, Boston, MA, USA
| | - Ralf Kittler
- University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Robert Bachoo
- University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Pratiti Bandopadhayay
- Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad institute of Harvard and MIT, Cambridge, MA, USA
- Boston Children's Cancer and Blood Disorder Center, Boston, MA, USA
| | - Rameen Beroukhim
- Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad institute of Harvard and MIT, Cambridge, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | - Keith L. Ligon
- Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad institute of Harvard and MIT, Cambridge, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
- Boston Children's Cancer and Blood Disorder Center, Boston, MA, USA
- Dana-Farber Cancer Institute, Center for Patient Derived Models (CPDM), Boston, MA, USA
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4
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Hofman DA, Ruiz-Orera J, Yannuzzi I, Murugesan R, Brown A, Clauser KR, Condurat AL, van Dinter JT, Engels SA, Goodale A, van der Lugt J, Abid T, Wang L, Zhou KN, Vogelzang J, Ligon KL, Phoenix TN, Roth JA, Root DE, Hubner N, Golub TR, Bandopadhayay P, van Heesch S, Prensner JR. Translation of non-canonical open reading frames as a cancer cell survival mechanism in childhood medulloblastoma. bioRxiv 2023:2023.05.04.539399. [PMID: 37205492 PMCID: PMC10187264 DOI: 10.1101/2023.05.04.539399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
A hallmark of high-risk childhood medulloblastoma is the dysregulation of RNA translation. Currently, it is unknown whether medulloblastoma dysregulates the translation of putatively oncogenic non-canonical open reading frames. To address this question, we performed ribosome profiling of 32 medulloblastoma tissues and cell lines and observed widespread non-canonical ORF translation. We then developed a step-wise approach to employ multiple CRISPR-Cas9 screens to elucidate functional non-canonical ORFs implicated in medulloblastoma cell survival. We determined that multiple lncRNA-ORFs and upstream open reading frames (uORFs) exhibited selective functionality independent of the main coding sequence. One of these, ASNSD1-uORF or ASDURF, was upregulated, associated with the MYC family oncogenes, and was required for medulloblastoma cell survival through engagement with the prefoldin-like chaperone complex. Our findings underscore the fundamental importance of non-canonical ORF translation in medulloblastoma and provide a rationale to include these ORFs in future cancer genomics studies seeking to define new cancer targets.
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Affiliation(s)
- Damon A. Hofman
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, the Netherlands
- These authors contributed equally
| | - Jorge Ruiz-Orera
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
- These authors contributed equally
| | - Ian Yannuzzi
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | | | - Adam Brown
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Current address: Arbor Biotechnologies, Cambridge, MA, 02140, USA
| | - Karl R. Clauser
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Alexandra L. Condurat
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jip T. van Dinter
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, the Netherlands
| | - Sem A.G. Engels
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, the Netherlands
| | - Amy Goodale
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Jasper van der Lugt
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, the Netherlands
| | - Tanaz Abid
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Li Wang
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Kevin N. Zhou
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Current address: Kaiser Permanente Bernard J. Tyson School of Medicine, Pasadena, CA, 91101, USA
| | - Jayne Vogelzang
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, 02215, USA
| | - Keith L. Ligon
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, 02215, USA
- Department of Pathology, Boston Children’s Hospital, Boston MA 02115
| | - Timothy N. Phoenix
- Division of Pharmaceutical Sciences, James L. Winkle College of Pharmacy, University of Cincinnati, Cincinnati, OH, 45229, USA
| | | | - David E. Root
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Norbert Hubner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
- Charité-Universitätsmedizin, 10117 Berlin, Germany
- German Centre for Cardiovascular Research, Partner Site Berlin, 13347 Berlin, Germany
| | - Todd R. Golub
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Division of Pediatric Hematology/Oncology, Boston Children’s Hospital, Boston, MA, 02115, USA
| | - Pratiti Bandopadhayay
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Division of Pediatric Hematology/Oncology, Boston Children’s Hospital, Boston, MA, 02115, USA
| | - Sebastiaan van Heesch
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, the Netherlands
| | - John R. Prensner
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Division of Pediatric Hematology/Oncology, Boston Children’s Hospital, Boston, MA, 02115, USA
- Current address: Department of Pediatrics, Division of Pediatric Hematology/Oncology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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5
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Tsai JW, Cejas P, Coppola M, Wang DK, Patel S, Wu DW, Arounleut P, Wei X, Zhou N, Syamala S, Dubois FP, Pelton K, Vogelzang J, Sousa C, Baguette A, Chen X, Condurat AL, Dixon-Clarke SE, Charles A, Zhou KN, Lu SD, Gonzalez EM, Chacon MS, Digiacomo JJ, Kumbhani R, Novikov D, Tsoli M, Ziegler DS, Dirksen U, Jager N, Balasubramanian GP, Kramm CM, Nathrath M, Bielack S, Baker SJ, Zhang J, McFarland JM, Getz G, Aguet F, Jabado N, Witt O, Pfister SM, Ligon KL, Hovestadt V, Kleinman C, Long H, Jones DT, Bandopadhayay P, Phoenix TN. Abstract 3562: Dissecting mechanisms underlying FOXR2-mediated gliomagenesis in diffuse midline gliomas. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-3562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Background: Diffuse midline gliomas (DMGs) are a universally fatal brain tumor of childhood. While histone mutations are a critical tumor initiating event, they are insufficient to drive gliomagenesis. Histone mutations co-occur with somatic alterations in other pathways including TP53, MAPK, and MYC signaling. However, the mechanisms through which these pathways are activated have not been fully elucidated.
Methods: We applied an integrative approach using transcriptomics, epigenetics, proteomics, in vitro cancer models, and in vivo mouse models to systematically evaluate how FOXR2 mediates gliomagenesis.
Results: We have recently found that a subset of DMGs aberrantly express FOXR2, a forkhead transcription factor. FOXR2 is both sufficient to enhance tumor formation, and necessary for FOXR2-expressing DMGs. While FOXR2 indeed enhances MYC protein stability, FOXR2 exerts oncogenesis through MYC-independent functions and specifically hijacks E26-transformation specific (ETS) transcriptional circuits and FOXR2 DNA-binding is highly enriched at ETS motifs. We have performed proteomic and phospho-proteomic analysis of FOXR2-expressing human neural stem cells to identify proteins and phospho-sites that are highly enriched in FOXR2-expressing cells.
Conclusion: Taken together, this study elucidates how FOXR2 interacts with ETS transcription factors to mediate oncogenesis, and further highlights a role for FOXR2 in activating ETS and MAPK signaling.
Citation Format: Jessica W. Tsai, Paloma Cejas, Marissa Coppola, Dayle K. Wang, Smruti Patel, David W. Wu, Phonepasong Arounleut, Xin Wei, Ningxuan Zhou, Sudeepa Syamala, Frank P. Dubois, Kristine Pelton, Jayne Vogelzang, Cecilia Sousa, Audrey Baguette, Xiaolong Chen, Alexandra L. Condurat, Sarah E. Dixon-Clarke, Annarah Charles, Kevin N. Zhou, Sophie D. Lu, Elizabeth M. Gonzalez, Madison S. Chacon, Jeromy J. Digiacomo, Rushil Kumbhani, Dana Novikov, Maria Tsoli, David S. Ziegler, Uta Dirksen, Natalie Jager, Gnana Prakash Balasubramanian, Christof M. Kramm, Michaela Nathrath, Stefan Bielack, Suzanne J. Baker, Jinghui Zhang, James M. McFarland, Gad Getz, Francois Aguet, Nada Jabado, Olaf Witt, Stefan M. Pfister, Keith L. Ligon, Volker Hovestadt, Claudia Kleinman, Henry Long, David T. Jones, Pratiti Bandopadhayay, Timothy N. Phoenix. Dissecting mechanisms underlying FOXR2-mediated gliomagenesis in diffuse midline gliomas. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3562.
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Affiliation(s)
| | | | | | | | | | - David W. Wu
- 3Broad Institute of MIT and Harvard, Cambridge, MA
| | | | - Xin Wei
- 4University of Cincinnati, Cincinnati, OH
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Maria Tsoli
- 6Lowy Cancer Research Centre, Sydney, Australia
| | | | | | | | | | | | | | | | | | | | | | - Gad Getz
- 3Broad Institute of MIT and Harvard, Cambridge, MA
| | | | - Nada Jabado
- 12McGill University, Montreal, Quebec, Canada
| | - Olaf Witt
- 8German Cancer Research Center, Heidelberg, Germany
| | | | | | | | | | - Henry Long
- 1Dana-Farber Cancer Institute, Boston, MA
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6
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Blandin AF, Giglio R, Graham MS, Garcia G, Malinowski S, Woods JK, Ramkissoon S, Ramkissoon L, Dubois F, Schoolcraft K, Tsai JW, Wang DK, Jones R, Vogelzang J, Pelton K, Becker S, Watkinson F, Sinai C, Cohen E, Booker M, Tolstorukov M, Haemels V, Goumnerova L, Wright K, Kieran M, Fehnel K, Reardon D, Tauziede-Espariat A, Lulla R, Carcamo B, Chaleff S, Charest A, De Smet F, Ligon AH, Dubuc A, Pagès M, Varlet P, Wen P, Alexander B, Chi S, Alexandrescu S, Kittler R, Bachoo R, Beroukhim R, Bandopadhayay P, Ligon KL. Abstract 1201: ALK amplification and rearrangements are recurrent targetable events in congenital and adult glioblastoma. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-1201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Purpose: Anaplastic Lymphoma Kinase (ALK) aberrations have been identified in pediatric type infant gliomas, but their occurrence across age groups, functional effects, and treatment response have not been broadly established.
Experimental Design: We performed a comprehensive analysis of ALK expression and genomic aberrations in both newly-generated and retrospective data from 371 glioblastomas (156 adult, 205 infant/pediatric and 10 congenital) with in vitro and in vivo validation of aberrations.
Results: ALK aberrations at the protein or genomic level were detected in 12% of gliomas (45/371) in a wide age range (0-80 years). Recurrent as well as novel ALK fusions (LRRFIP1-ALK, DCTN1-ALK, PRKD3-ALK) were present in 50% (5/10) of congenital/infant, 1.4% (3/205) of pediatric, and 1.9% (3/156) of adult GBMs. ALK fusions were present as the only candidate driver in congenital/infant GBMs, and were sometimes focally amplified. In contrast, adult ALK fusions co-occurred with other oncogenic drivers. No activating ALK mutations were identified in any age group. Novel and recurrent ALK rearrangements promoted STAT3 and ERK1/2 pathways and transformation in vitro and in vivo. ALK-fused GBM cellular and mouse models were responsive to ALK inhibitors, including in patient cells derived from a congenital GBM. Relevant to treatment of infant gliomas, we showed that ALK protein appears minimally expressed in the forebrain at perinatal stages and no gross effects on perinatal brain development was seen in pregnant mice treated with the ALK inhibitor ceritinib.
Conclusions: These findings support expanded evaluation of brain-penetrant ALK inhibitors in clinical trials across infant, pediatric, and adult GBMs.
Citation Format: Anne-Florence Blandin, Ross Giglio, Maya Srikanth Graham, Guadalupe Garcia, Seth Malinowski, Jared K. Woods, Shakti Ramkissoon, Lori Ramkissoon, Frank Dubois, Kate Schoolcraft, Jessica W. Tsai, Dayle K. Wang, Robert Jones, Jayne Vogelzang, Kristine Pelton, Sarah Becker, Fiona Watkinson, Claire Sinai, Elizabeth Cohen, Matthew Booker, Michael Tolstorukov, Veerle Haemels, Liliana Goumnerova, Karen Wright, Mark Kieran, Katie Fehnel, David Reardon, Arnault Tauziede-Espariat, Rishi Lulla, Benjamin Carcamo, Stanley Chaleff, Alain Charest, Frederik De Smet, Azra H. Ligon, Adrian Dubuc, Melanie Pagès, Pascale Varlet, Patrick Wen, Brian Alexander, Susan Chi, Sanda Alexandrescu, Ralf Kittler, Robert Bachoo, Rameen Beroukhim, Pratiti Bandopadhayay, Keith L. Ligon. ALK amplification and rearrangements are recurrent targetable events in congenital and adult glioblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1201.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Veerle Haemels
- 3Laboratory for Precision Cancer Medicine, Leuven, Belgium
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Susan Chi
- 1Dana-Farber Cancer Institute, Boston, MA
| | | | - Ralf Kittler
- 12University of Texas Southwestern Medical Center, Dallas, TX
| | - Robert Bachoo
- 12University of Texas Southwestern Medical Center, Dallas, TX
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7
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Tobochnik S, Dorotan MKC, Ghosh HS, Lapinskas E, Vogelzang J, Reardon DA, Ligon KL, Bi WL, Smirnakis SM, Lee JW. Glioma genetic profiles associated with electrophysiologic hyperexcitability. medRxiv 2023:2023.02.22.23285841. [PMID: 36865325 PMCID: PMC9980233 DOI: 10.1101/2023.02.22.23285841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Distinct genetic alterations determine glioma aggressiveness, however the diversity of somatic mutations contributing to peritumoral hyperexcitability and seizures is uncertain. In a large cohort of patients with sequenced gliomas (n=1716), we used discriminant analysis models to identify somatic mutation variants associated with electrographic hyperexcitability in a subset with continuous EEG recording (n=206). Overall tumor mutational burdens were similar between patients with and without hyperexcitability. A cross-validated model trained exclusively on somatic mutations classified the presence or absence of hyperexcitability with an overall accuracy of 70.9%, and improved estimates of hyperexcitability and anti-seizure medication failure in multivariate analysis incorporating traditional demographic factors and tumor molecular classifications. Somatic mutation variants of interest were also over-represented in patients with hyperexcitability compared to internal and external reference cohorts. These findings implicate diverse mutations in cancer genes associated with the development of hyperexcitability and response to treatment.
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Affiliation(s)
- Steven Tobochnik
- Department of Neurology, VA Boston Healthcare System, Boston, MA
- Department of Neurology, Brigham and Women’s Hospital, Boston, MA
| | | | - Hia S. Ghosh
- Department of Neurosurgery, Brigham and Women’s Hospital, Boston, MA
| | - Emily Lapinskas
- Department of Neurology, Brigham and Women’s Hospital, Boston, MA
| | - Jayne Vogelzang
- Department of Pathology, Dana-Farber Cancer Institute, Boston, MA
| | - David A. Reardon
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Keith L. Ligon
- Department of Pathology, Dana-Farber Cancer Institute, Boston, MA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA
| | - Wenya Linda Bi
- Department of Neurosurgery, Brigham and Women’s Hospital, Boston, MA
| | - Stelios M. Smirnakis
- Department of Neurology, VA Boston Healthcare System, Boston, MA
- Department of Neurology, Brigham and Women’s Hospital, Boston, MA
| | - Jong Woo Lee
- Department of Neurology, Brigham and Women’s Hospital, Boston, MA
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8
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Tsai JW, Choi JJ, Ouaalam H, Murillo EA, Yeo KK, Vogelzang J, Sousa C, Woods JK, Ligon KL, Warfield SK, Bandopadhayay P, Cooney TM. Integrated response analysis of pediatric low-grade gliomas during and after targeted therapy treatment. Neurooncol Adv 2023; 5:vdac182. [PMID: 36926246 PMCID: PMC10011805 DOI: 10.1093/noajnl/vdac182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Background Pediatric low-grade gliomas (pLGGs) are the most common central nervous system tumor in children, characterized by RAS/MAPK pathway driver alterations. Genomic advances have facilitated the use of molecular targeted therapies, however, their long-term impact on tumor behavior remains critically unanswered. Methods We performed an IRB-approved, retrospective chart and imaging review of pLGGs treated with off-label targeted therapy at Dana-Farber/Boston Children's from 2010 to 2020. Response analysis was performed for BRAFV600E and BRAF fusion/duplication-driven pLGG subsets. Results Fifty-five patients were identified (dabrafenib n = 15, everolimus n = 26, trametinib n = 11, and vemurafenib n = 3). Median duration of targeted therapy was 9.48 months (0.12-58.44). The 1-year, 3-year, and 5-year EFS from targeted therapy initiation were 62.1%, 38.2%, and 31.8%, respectively. Mean volumetric change for BRAFV600E mutated pLGG on BRAF inhibitors was -54.11%; median time to best volumetric response was 8.28 months with 9 of 12 (75%) objective RAPNO responses. Median time to largest volume post-treatment was 2.86 months (+13.49%); mean volume by the last follow-up was -14.02%. Mean volumetric change for BRAF fusion/duplication pLGG on trametinib was +7.34%; median time to best volumetric response was 6.71 months with 3 of 7 (43%) objective RAPNO responses. Median time to largest volume post-treatment was 2.38 months (+71.86%); mean volume by the last follow-up was +39.41%. Conclusions Our integrated analysis suggests variability in response by pLGG molecular subgroup and targeted therapy, as well as the transience of some tumor growth following targeted therapy cessation.
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Affiliation(s)
- Jessica W Tsai
- Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Boston, Massachusetts, USA
| | - Jungwhan John Choi
- Department of Radiology, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Hakim Ouaalam
- Department of Radiology, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Efrain Aguilar Murillo
- Department of Radiology, Division of Neuroradiology and Neurointervention, Boston, Massachusetts, USA
| | - Kee Kiat Yeo
- Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Boston, Massachusetts, USA
| | - Jayne Vogelzang
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Cecilia Sousa
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Jared K Woods
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Keith L Ligon
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
- Department of Pathology, Boston Children’s Hospital, Boston Massachusetts, USA
- Department of Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Simon K Warfield
- Department of Radiology, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Pratiti Bandopadhayay
- Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Boston, Massachusetts, USA
| | - Tabitha M Cooney
- Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Boston, Massachusetts, USA
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9
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Liu I, Jiang L, Samuelsson ER, Marco Salas S, Beck A, Hack OA, Jeong D, Shaw ML, Englinger B, LaBelle J, Mire HM, Madlener S, Mayr L, Quezada MA, Trissal M, Panditharatna E, Ernst KJ, Vogelzang J, Gatesman TA, Halbert ME, Palova H, Pokorna P, Sterba J, Slaby O, Geyeregger R, Diaz A, Findlay IJ, Dun MD, Resnick A, Suvà ML, Jones DTW, Agnihotri S, Svedlund J, Koschmann C, Haberler C, Czech T, Slavc I, Cotter JA, Ligon KL, Alexandrescu S, Yung WKA, Arrillaga-Romany I, Gojo J, Monje M, Nilsson M, Filbin MG. The landscape of tumor cell states and spatial organization in H3-K27M mutant diffuse midline glioma across age and location. Nat Genet 2022; 54:1881-1894. [PMID: 36471067 PMCID: PMC9729116 DOI: 10.1038/s41588-022-01236-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 10/20/2022] [Indexed: 12/12/2022]
Abstract
Histone 3 lysine27-to-methionine (H3-K27M) mutations most frequently occur in diffuse midline gliomas (DMGs) of the childhood pons but are also increasingly recognized in adults. Their potential heterogeneity at different ages and midline locations is vastly understudied. Here, through dissecting the single-cell transcriptomic, epigenomic and spatial architectures of a comprehensive cohort of patient H3-K27M DMGs, we delineate how age and anatomical location shape glioma cell-intrinsic and -extrinsic features in light of the shared driver mutation. We show that stem-like oligodendroglial precursor-like cells, present across all clinico-anatomical groups, display varying levels of maturation dependent on location. We reveal a previously underappreciated relationship between mesenchymal cancer cell states and age, linked to age-dependent differences in the immune microenvironment. Further, we resolve the spatial organization of H3-K27M DMG cell populations and identify a mitotic oligodendroglial-lineage niche. Collectively, our study provides a powerful framework for rational modeling and therapeutic interventions.
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Affiliation(s)
- Ilon Liu
- grid.511177.4Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA USA ,grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Li Jiang
- grid.511177.4Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA USA ,grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Erik R. Samuelsson
- grid.10548.380000 0004 1936 9377Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Sergio Marco Salas
- grid.10548.380000 0004 1936 9377Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Alexander Beck
- grid.5252.00000 0004 1936 973XCenter for Neuropathology, Ludwig-Maximilians-University, Munich, Germany
| | - Olivia A. Hack
- grid.511177.4Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA USA ,grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Daeun Jeong
- grid.511177.4Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA USA ,grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - McKenzie L. Shaw
- grid.511177.4Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA USA ,grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Bernhard Englinger
- grid.511177.4Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA USA ,grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.22937.3d0000 0000 9259 8492Department of Urology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Jenna LaBelle
- grid.511177.4Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA USA ,grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Hafsa M. Mire
- grid.511177.4Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA USA ,grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Sibylle Madlener
- grid.22937.3d0000 0000 9259 8492Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Lisa Mayr
- grid.22937.3d0000 0000 9259 8492Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Michael A. Quezada
- grid.168010.e0000000419368956Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA USA
| | - Maria Trissal
- grid.511177.4Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA USA ,grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Eshini Panditharatna
- grid.511177.4Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA USA ,grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Kati J. Ernst
- grid.7497.d0000 0004 0492 0584Hopp Children’s Cancer Center Heidelberg (KiTZ), Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jayne Vogelzang
- grid.65499.370000 0001 2106 9910Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA USA
| | - Taylor A. Gatesman
- grid.21925.3d0000 0004 1936 9000Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA USA ,grid.239553.b0000 0000 9753 0008John G. Rangos Sr. Research Center, Children’s Hospital of Pittsburgh, Pittsburgh, PA USA
| | - Matthew E. Halbert
- grid.21925.3d0000 0004 1936 9000Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA USA ,grid.239553.b0000 0000 9753 0008John G. Rangos Sr. Research Center, Children’s Hospital of Pittsburgh, Pittsburgh, PA USA
| | - Hana Palova
- grid.10267.320000 0001 2194 0956Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Petra Pokorna
- grid.10267.320000 0001 2194 0956Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Jaroslav Sterba
- Pediatric Oncology Department, University Hospital Brno, Faculty of Medicine, Masaryk University, ICRC, Brno, Czech Republic
| | - Ondrej Slaby
- grid.10267.320000 0001 2194 0956Central European Institute of Technology, Masaryk University, Brno, Czech Republic ,grid.10267.320000 0001 2194 0956Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Rene Geyeregger
- grid.22937.3d0000 0000 9259 8492Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria ,grid.416346.2Department of Clinical Cell Biology and FACS Core Unit, St. Anna Children’s Cancer Research Institute (CCRI), Vienna, Austria
| | - Aaron Diaz
- grid.266102.10000 0001 2297 6811Department of Neurological Surgery, University of California San Francisco, San Francisco, CA USA
| | - Izac J. Findlay
- grid.266842.c0000 0000 8831 109XCancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales Australia ,grid.413648.cPrecision Medicine Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales Australia
| | - Matthew D. Dun
- grid.266842.c0000 0000 8831 109XCancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales Australia ,grid.413648.cPrecision Medicine Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales Australia
| | - Adam Resnick
- grid.239552.a0000 0001 0680 8770Center for Data Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA USA
| | - Mario L. Suvà
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.32224.350000 0004 0386 9924Department of Pathology, Center for Cancer Research, Massachusetts General Hospital, Boston, MA USA
| | - David T. W. Jones
- grid.7497.d0000 0004 0492 0584Hopp Children’s Cancer Center Heidelberg (KiTZ), Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sameer Agnihotri
- grid.21925.3d0000 0004 1936 9000Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA USA ,grid.239553.b0000 0000 9753 0008John G. Rangos Sr. Research Center, Children’s Hospital of Pittsburgh, Pittsburgh, PA USA
| | - Jessica Svedlund
- grid.10548.380000 0004 1936 9377Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Carl Koschmann
- grid.412590.b0000 0000 9081 2336Division of Pediatric Hematology/Oncology, Department of Pediatrics, Michigan Medicine, Ann Arbor, MI USA
| | - Christine Haberler
- grid.22937.3d0000 0000 9259 8492Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Thomas Czech
- grid.22937.3d0000 0000 9259 8492Department of Neurosurgery, Medical University of Vienna, Vienna, Austria
| | - Irene Slavc
- grid.22937.3d0000 0000 9259 8492Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Jennifer A. Cotter
- grid.239546.f0000 0001 2153 6013Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Keck School of Medicine of University of Southern California, Los Angeles, CA USA
| | - Keith L. Ligon
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.62560.370000 0004 0378 8294Department of Pathology, Brigham and Women’s Hospital, Boston, MA USA ,grid.2515.30000 0004 0378 8438Department of Pathology, Boston Children’s Hospital, Boston, MA USA
| | - Sanda Alexandrescu
- grid.2515.30000 0004 0378 8438Department of Pathology, Boston Children’s Hospital, Boston, MA USA
| | - W. K. Alfred Yung
- grid.240145.60000 0001 2291 4776Department of Neuro-Oncology, Brain Tumor Center, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Isabel Arrillaga-Romany
- grid.32224.350000 0004 0386 9924Massachusetts General Hospital, Cancer Center, Boston, MA USA
| | - Johannes Gojo
- grid.511177.4Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA USA ,grid.22937.3d0000 0000 9259 8492Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Michelle Monje
- grid.168010.e0000000419368956Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA USA ,grid.413575.10000 0001 2167 1581Howard Hughes Medical Institute, Stanford, CA USA
| | - Mats Nilsson
- grid.10548.380000 0004 1936 9377Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Mariella G. Filbin
- grid.511177.4Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA USA ,grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
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10
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Tabatneck M, Umaretiya P, Sousa C, Vogelzang J, Ligon K, Baird L, Cooney T. QLTI-24. ANALYSIS OF DISPARITIES IN PEDIATRIC BRAIN TUMOR BANK ENROLLMENT AS FOUNDATION FOR QUALITY IMPROVEMENT INITIATIVES AT DANA-FARBER CANCER INSTITUTE/BOSTON CHILDREN’S CANCER AND BLOOD DISORDERS CENTER. Neuro Oncol 2022. [PMCID: PMC9660686 DOI: 10.1093/neuonc/noac209.926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract
BACKGROUND
Tissue biobanks play a vital role in oncology research; however, disparities have been reported in enrollment. The representativeness of biobanks is an important consideration in the extrapolation of research to the broader population. We sought to identify associations between sociodemographic characteristics and pediatric brain tumor bank enrollment at Dana-Farber Cancer Institute and Boston Children’s Cancer and Blood Disorders Center (DFCI/BCCBDC) to identify opportunities for improving equitable and representative enrollment.
METHODS
We conducted a retrospective cohort study of all patients qualified for enrollment in DFCI/BCCBDC Integrated Tissue and Clinical Data Bank for Patients with Neurological Disorders from 2014-2017 and extracted sociodemographic information from the medical record. The primary outcome was biobank enrollment, and the secondary outcome was approach for enrollment among non-enrolled patients. Exposures of interest included sex, language, interpreter need, race, and ethnicity.
RESULTS
We identified 652 eligible patients of which 580 (89%) enrolled and 72 (11%) were non-enrolled. Non-enrolled patients were more likely to be non-English speaking compared to enrolled patients (20% vs 11%; p = 0.0019) and were more likely to require an interpreter (15% vs. 8%; p = 0.025). Non-enrolled patients were more likely to identify as non-white/other/multiple races compared to enrolled patients (29% and 17%; p = 0.0023). Sex and ethnicity were not associated with enrollment. Of the 72 non-enrolled patients, 19 (26%) were approached to discuss enrollment but declined consent. There were no sociodemographic differences between approached and not approached patients.
CONCLUSION
While overall enrollment rates in this single center pediatric brain tumor bank were high, non-English primary language, interpreter need, and non-white race were significantly associated with non-enrollment. There were no differences in terms of approach for enrollment, suggesting that opportunities to improve representation may include understanding the reasons for declining enrollment and improving the consent process for patients from historically marginalized groups.
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Affiliation(s)
| | - Puja Umaretiya
- Dana Farber / Boston Children’s Cancer and Blood Disorder Center , Boston , USA
| | - Cecilia Sousa
- Dana Farber / Boston Children’s Cancer and Blood Disorder Center , Boston , USA
| | - Jayne Vogelzang
- Dana Farber / Boston Children’s Cancer and Blood Disorder Center , Boston , USA
| | - Keith Ligon
- Dana-Farber Cancer Institute , Boston, MA , USA
| | - Lissa Baird
- Dana Farber / Boston Children’s Cancer and Blood Disorder Center , Boston , USA
| | - Tabitha Cooney
- Dana Farber / Boston Children’s Cancer and Blood Disorder Center , Boston, MA , USA
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11
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Youssef G, Aquilanti E, Muzikansky A, Miller J, Vogelzang J, Lapinskas E, Lim-Fat MJ, Rahman R, Beroukhim R, Bi WL, Chukwueke U, Castro LNG, Lee E, McFaline-Figueroa JR, Nayak L, Reardon DA, Ligon K, Wen PY. PATH-15. THE PROGNOSTIC IMPLICATION OF MGMT PROMOTER METHYLATION IN IDH-MUTANT GLIOMAS. Neuro Oncol 2022. [PMCID: PMC9660908 DOI: 10.1093/neuonc/noac209.588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract
BACKGROUND
MGMT promoter methylation in IDH-mutant gliomas was associated with improved survival in a recent study (PMID 35386566) but did not account for the updated WHO classification of CNS tumors. We evaluated the prognostic value of MGMT methylation in IDH-mutant gliomas incorporating the 2021 WHO classification.
METHODS
We retrospectively identified 431 patients with IDH-mutant gliomas treated at a single institution from 2010-2020. Kaplan-Meier method was used to estimate OS and PFS rates. Log-Rank test was used to evaluate differences between groups.
RESULTS
Median age was 36.2 years. MGMT promoter was methylated in 49.6%, unmethylated in 17.2%, partially methylated in 6.7%, and untested in 26.5%. Histological diagnosis was consistent with astrocytoma in 45.7%, oligodendroglioma in 33.9%, glioblastoma in 16.4%, and oligoastrocytoma in 4%. After accounting for 1p/19q and CDKN2A statuses, 190 patients had an integrated diagnosis of astrocytoma, grade 2 or 3; 94 had astrocytoma, grade 4; and 147 had oligodendroglioma, grade 2 or 3. There were 101 death events. Median OS was 33.36 years and median PFS was 5.67 years in MGMT methylated gliomas, compared to median OS of 12.54 years (p=0.0064) and median PFS of 3.91 years (p=0.0034) in unmethylated tumors. Upon univariate subgroup analysis, MGMT methylation was associated with significantly longer OS in histological astrocytomas, grade 2 or 4. However, when stratifying patients according to 2021 WHO classification of CNS tumors, there was no significant difference in OS between MGMT methylated and unmethylated astrocytomas or oligodendrogliomas, irrespective of WHO grade.
CONCLUSION
MGMT promoter methylation was associated with prolonged OS in histological astrocytomas, IDH-mutant. However, MGMT status did not impact survival after incorporating 2021 WHO classification of CNS tumors, suggesting that 1p/19q co-deletion and CDKN2A homozygous deletion are stronger prognostic factors in our cohort. The number of survival events was limited; larger datasets are required for more definitive conclusions.
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Affiliation(s)
| | | | | | - Julie Miller
- Department of Neurology, Pappas Center for Neuro-Oncology, Massachusetts General Hospital, Harvard Medical School , Boston , USA
| | - Jayne Vogelzang
- Dana Farber / Boston Children’s Cancer and Blood Disorder Center , Boston , USA
| | | | - Mary Jane Lim-Fat
- Sunnybrook Health Sciences Centre, University of Toronto , Toronto , Canada
| | | | | | | | | | | | | | | | | | | | - Keith Ligon
- Dana-Farber Cancer Institute , Boston, MA , USA
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12
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Tsai JW, Cejas P, Wang DK, Patel S, Wu DW, Arounleut P, Wei X, Zhou N, Syamala S, Dubois FP, Crane A, Pelton K, Vogelzang J, Sousa C, Baguette A, Chen X, Condurat AL, Dixon-Clarke SE, Zhou KN, Lu SD, Gonzalez EM, Chacon MS, Digiacomo JJ, Kumbhani R, Novikov D, Hunter J, Tsoli M, Ziegler DS, Dirksen U, Jager N, Balasubramanian GP, Kramm CM, Nathrath M, Bielack S, Baker SJ, Zhang J, McFarland JM, Getz G, Aguet F, Jabado N, Witt O, Pfister SM, Ligon KL, Hovestadt V, Kleinman CL, Long H, Jones DT, Bandopadhayay P, Phoenix TN. FOXR2 Is an Epigenetically Regulated Pan-Cancer Oncogene That Activates ETS Transcriptional Circuits. Cancer Res 2022; 82:2980-3001. [PMID: 35802025 PMCID: PMC9437574 DOI: 10.1158/0008-5472.can-22-0671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/11/2022] [Accepted: 06/28/2022] [Indexed: 11/16/2022]
Abstract
Forkhead box R2 (FOXR2) is a forkhead transcription factor located on the X chromosome whose expression is normally restricted to the testis. In this study, we performed a pan-cancer analysis of FOXR2 activation across more than 10,000 adult and pediatric cancer samples and found FOXR2 to be aberrantly upregulated in 70% of all cancer types and 8% of all individual tumors. The majority of tumors (78%) aberrantly expressed FOXR2 through a previously undescribed epigenetic mechanism that involves hypomethylation of a novel promoter, which was functionally validated as necessary for FOXR2 expression and proliferation in FOXR2-expressing cancer cells. FOXR2 promoted tumor growth across multiple cancer lineages and co-opted ETS family transcription circuits across cancers. Taken together, this study identifies FOXR2 as a potent and ubiquitous oncogene that is epigenetically activated across the majority of human cancers. The identification of hijacking of ETS transcription circuits by FOXR2 extends the mechanisms known to active ETS transcription factors and highlights how transcription factor families cooperate to enhance tumorigenesis. SIGNIFICANCE This work identifies a novel promoter that drives aberrant FOXR2 expression and delineates FOXR2 as a pan-cancer oncogene that specifically activates ETS transcriptional circuits across human cancers. See related commentary by Liu and Northcott, p. 2977.
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Affiliation(s)
- Jessica W. Tsai
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
| | - Paloma Cejas
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, Cancer Program, Broad Institute, Cambridge, Massachusetts
| | - Dayle K. Wang
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
| | - Smruti Patel
- Division of Pharmaceutical Sciences, James L. Winkle College of Pharmacy, University of Cincinnati, Cincinnati, Ohio
- Division of Pediatric Neurosurgery, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
- Department of Neurosurgery, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - David W. Wu
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Phonepasong Arounleut
- Division of Pharmaceutical Sciences, James L. Winkle College of Pharmacy, University of Cincinnati, Cincinnati, Ohio
| | - Xin Wei
- Division of Pharmaceutical Sciences, James L. Winkle College of Pharmacy, University of Cincinnati, Cincinnati, Ohio
| | - Ningxuan Zhou
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, Cancer Program, Broad Institute, Cambridge, Massachusetts
| | - Sudeepa Syamala
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, Cancer Program, Broad Institute, Cambridge, Massachusetts
| | - Frank P.B. Dubois
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Alexander Crane
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Kristine Pelton
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Jayne Vogelzang
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Cecilia Sousa
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Audrey Baguette
- Quantitative Life Sciences, McGill University, Montreal, Quebec H3A 2A7, Canada
- Lady Davis Research Institute, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
| | - Xiaolong Chen
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Alexandra L. Condurat
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
| | - Sarah E. Dixon-Clarke
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Biological Chemistry and Molecular Pharmacology, Boston, Massachusetts
| | - Kevin N. Zhou
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
| | - Sophie D. Lu
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
| | - Elizabeth M. Gonzalez
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
| | - Madison S. Chacon
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
| | - Jeromy J. Digiacomo
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
| | - Rushil Kumbhani
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
| | - Dana Novikov
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
| | - J'Ya Hunter
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
| | - Maria Tsoli
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Sydney, NSW, Australia
| | - David S. Ziegler
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Sydney, NSW, Australia
- School of Women's and Children's Health, University of New South Wales, Sydney, NSW, Australia
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW, Australia
| | - Uta Dirksen
- West German Cancer Center, Pediatrics III, University Hospital Essen, Essen, Germany
- German Cancer Consortium (DKTK), Essen/Düsseldorf, Germany
| | - Natalie Jager
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg University Hospital and German Cancer Research Center (DKFZ) Heidelberg, Germany
- Division of Pediatric Neuro-Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Gnana Prakash Balasubramanian
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg University Hospital and German Cancer Research Center (DKFZ) Heidelberg, Germany
- Division of Pediatric Neuro-Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christof M. Kramm
- Division of Pediatric Hematology and Oncology, University Medical Center Göttingen, Göttingen, Germany
| | - Michaela Nathrath
- Department of Pediatric Hematology and Oncology, Klinikum Kassel, Kassel, Germany
- Children's Cancer Research Centre and Department of Pediatrics, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | | | - Suzanne J. Baker
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | | | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
- Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts
| | - François Aguet
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Nada Jabado
- Department of Human Genetics, McGill University, Montreal, H3A 0C7, Canada
- Department of Pediatrics, McGill University, and The Research Institute of the McGill University Health Centre, Montreal, H4A 3J1, Canada
| | - Olaf Witt
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg University Hospital and German Cancer Research Center (DKFZ) Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology, and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
- National Center for Tumor Disease (NCT) Network, Germany
| | - Stefan M. Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg University Hospital and German Cancer Research Center (DKFZ) Heidelberg, Germany
- Division of Pediatric Neuro-Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology, and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
- National Center for Tumor Disease (NCT) Network, Germany
| | - Keith L. Ligon
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Volker Hovestadt
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
| | - Claudia L. Kleinman
- Lady Davis Research Institute, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
- Department of Human Genetics, McGill University, Montreal, H3A 0C7, Canada
| | - Henry Long
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, Cancer Program, Broad Institute, Cambridge, Massachusetts
| | - David T.W. Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg University Hospital and German Cancer Research Center (DKFZ) Heidelberg, Germany
- Division of Pediatric Neuro-Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Pratiti Bandopadhayay
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
| | - Timothy N. Phoenix
- Division of Pharmaceutical Sciences, James L. Winkle College of Pharmacy, University of Cincinnati, Cincinnati, Ohio
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Dubois FPB, Shapira O, Greenwald NF, Zack T, Wala J, Tsai JW, Crane A, Baguette A, Hadjadj D, Harutyunyan AS, Kumar KH, Blattner-Johnson M, Vogelzang J, Sousa C, Kang KS, Sinai C, Wang DK, Khadka P, Lewis K, Nguyen L, Malkin H, Ho P, O'Rourke R, Zhang S, Gold R, Deng D, Serrano J, Snuderl M, Jones C, Wright KD, Chi SN, Grill J, Kleinman CL, Goumnerova LC, Jabado N, Jones DTW, Kieran MW, Ligon KL, Beroukhim R, Bandopadhayay P. Structural variants shape driver combinations and outcomes in pediatric high-grade glioma. Nat Cancer 2022; 3:994-1011. [PMID: 35788723 PMCID: PMC10365847 DOI: 10.1038/s43018-022-00403-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 05/23/2022] [Indexed: 12/13/2022]
Abstract
We analyzed the contributions of structural variants (SVs) to gliomagenesis across 179 pediatric high-grade gliomas (pHGGs). The most recurrent SVs targeted MYC isoforms and receptor tyrosine kinases (RTKs), including an SV amplifying a MYC enhancer in 12% of diffuse midline gliomas (DMG), indicating an underappreciated role for MYC in pHGG. SV signature analysis revealed that tumors with simple signatures were TP53 wild type (TP53WT) but showed alterations in TP53 pathway members PPM1D and MDM4. Complex signatures were associated with direct aberrations in TP53, CDKN2A and RB1 early in tumor evolution and with later-occurring extrachromosomal amplicons. All pHGGs exhibited at least one simple-SV signature, but complex-SV signatures were primarily restricted to subsets of H3.3K27M DMGs and hemispheric pHGGs. Importantly, DMGs with complex-SV signatures were associated with shorter overall survival independent of histone mutation and TP53 status. These data provide insight into the impact of SVs on gliomagenesis and the mechanisms that shape them.
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Affiliation(s)
- Frank P B Dubois
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ofer Shapira
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Noah F Greenwald
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Travis Zack
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jeremiah Wala
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jessica W Tsai
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Alexander Crane
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Audrey Baguette
- Quantitative Life Sciences, McGill University, Montreal, QC, Canada
| | - Djihad Hadjadj
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | | | - Kiran H Kumar
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mirjam Blattner-Johnson
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jayne Vogelzang
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Cecilia Sousa
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Kyung Shin Kang
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Claire Sinai
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Dayle K Wang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Prasidda Khadka
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Lan Nguyen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hayley Malkin
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Patricia Ho
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ryan O'Rourke
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Shu Zhang
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rose Gold
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Davy Deng
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Chris Jones
- Division of Cancer Therapeutics and Department of Molecular Pathology, Institute of Cancer Research 15 Cotswold Road, Sutton, London, UK
| | - Karen D Wright
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Susan N Chi
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Jacques Grill
- Department of Pediatric and Adolescent Oncology and INSERM Unit 981, Gustave Roussy Institute and University of Paris Saclay, Villejuif, France
| | - Claudia L Kleinman
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Lady Davis Research Institute, Jewish General Hospital, Montreal, QC, Canada
| | - Liliana C Goumnerova
- Department of Neurosurgery, Boston Children's Hospital; Dana Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- LCG: Tromboprotea, MWK: Day One Biopharmaceuticals, San Francisco, CA, USA
| | - Nada Jabado
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Division of Experimental Medicine, Department of Medicine and Department of Pediatrics, McGill University, and The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - David T W Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mark W Kieran
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- LCG: Tromboprotea, MWK: Day One Biopharmaceuticals, San Francisco, CA, USA
| | - Keith L Ligon
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
- Department of Pathology, Brigham & Women's Hospital and Boston Children's Hospital, Boston, USA.
- Center for Patient Derived Models, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Rameen Beroukhim
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.
| | - Pratiti Bandopadhayay
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA.
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14
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Tobochnik S, Lapinskas E, Vogelzang J, Ligon KL, Lee JW. Correction to: Early EEG hyperexcitability is associated with decreased survival in newly diagnosed IDH-wildtype glioma. J Neurooncol 2022; 159:219. [PMID: 35794506 DOI: 10.1007/s11060-022-04086-5] [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: 11/24/2022]
Affiliation(s)
- Steven Tobochnik
- Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA. .,VA Boston Healthcare System, Boston, MA, USA.
| | - Emily Lapinskas
- Department of Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jayne Vogelzang
- Department of Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Keith L Ligon
- Department of Pathology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Jong Woo Lee
- Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
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15
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Tobochnik S, Lapinskas E, Vogelzang J, Ligon KL, Lee JW. Early EEG hyperexcitability is associated with decreased survival in newly diagnosed IDH-wildtype glioma. J Neurooncol 2022; 159:211-218. [PMID: 35715666 PMCID: PMC9329255 DOI: 10.1007/s11060-022-04059-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Received: 04/14/2022] [Accepted: 06/06/2022] [Indexed: 11/29/2022]
Abstract
PURPOSE The relationship between peritumoral neuronal activity, early onset clinical seizures, and glioma survival outcomes remains poorly understood. Hyperexcitability on continuous EEG in the peri-operative period was studied as a prognostic biomarker in patients with newly diagnosed IDH-wildtype diffuse glioma. METHODS A retrospective observational cohort study was performed including adults with newly diagnosed diffuse glioma, absence of IDH1/2 mutations, and continuous EEG monitoring prior to chemoradiation and within 1 month of initial resection. EEG hyperexcitability was defined by the presence of lateralized periodic discharges and/or electrographic seizures. The primary outcome of overall survival was estimated using the Kaplan-Meier method and compared between groups using multivariate Cox proportional hazards model. RESULTS There were 424 patients without continuous EEG and 32 with continuous EEG, of whom lateralized periodic discharges and/or electrographic seizures were seen in 17 (53%). Peri-operative EEG hyperexcitability was associated with decreased overall survival in multivariate analysis [median 12.5 (95% CI 6.2-25.6] months with hyperexcitability versus median 19.9 [95% CI 8.9-53.5] months without hyperexcitability, p = 0.043). Compared to patients without continuous EEG, overall survival was decreased in patients with hyperexcitability (p < 0.0001) and similar in patients without hyperexcitability (p = 0.193). Patients with and without hyperexcitability had similar rates of exposure to anti-seizure medication at baseline, and in long-term follow-up had no difference in number of medications required for seizure control. CONCLUSIONS These findings indicate the potential prognostic value of a clinical EEG biomarker of glioma aggressiveness prior to the initiation of chemoradiation.
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Affiliation(s)
- Steven Tobochnik
- Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA. .,VA Boston Healthcare System, Boston, MA, USA.
| | - Emily Lapinskas
- Department of Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jayne Vogelzang
- Department of Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Keith L Ligon
- Department of Pathology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Jong Woo Lee
- Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
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Jomaa D, Khadka P, Novikov D, Condurat AL, Tsai JW, Dubois F, Zhang S, Zhou K, Gold R, Sousa C, Vogelzang J, Prince E, Lu S, Slivova V, Otto GW, Hereza SC, Ashley D, Cohen-Gadol AA, Thompson E, Beroukhim R, Apps J, Martinez-Barbera JP, Hankinson T, Bandopadhayay P. RARE-22 Characterizing the landscape of structural variants in adamantinomatous craniopharyngioma. Neuro Oncol 2022. [PMCID: PMC9164984 DOI: 10.1093/neuonc/noac079.047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
INTRODUCTION: Adamantinomatous craniopharyngiomas (ACPs) are rare brain tumors that primarily occur in children and impact long-term morbidity and mortality. The canonical driver mutation for ACP growth occurs in CTNNB1 and leads to constitutive activation of the Wnt/β-catenin signaling pathway. In this study, we outline the genomic, transcriptomic, and structural variant (SV) landscape in a cohort of 41 ACP samples. METHODS: We performed whole-genome sequencing (WGS) and RNA-sequencing of 41 ACP samples. Matched normal samples were also characterized by WGS. Mutect2 was used to detect single nucleotide variants (SNVs) and indels, and copy number data was generated using the GATK pipeline. SvABA was used to perform SV analysis and to identify significantly recurrent breakpoints and juxtapositions. DESeq2 was used to perform differential gene expression analysis based on clinical and molecular annotation data. RESULTS: 29/41 (70%) of the ACP samples harbored missense mutations in exon 3 of CTNNB1, all of which have previously been reported in ACP tumors. SV analysis identified a median of 11.5 events per tumor. Overall, 9.7% of events were interchromosomal. Of the remainder, the majority (78.6%) were deletions. No SVs occurred within CTNNB1. A positive correlation (r = 0.533) was observed between the frequency of SVs and SNVs within samples. Analysis of significantly recurring breakpoints (SRBs) did not identify recurrent breakpoint events. Differential gene expression analysis comparing samples with and without CTNNB1 variants identified 2,143 differentially expressed genes with q-value < 0.05. CONCLUSION: This study identifies activating mutations in exon 3 of CTNNB1 in a large cohort of ACP samples. We also integrate SV and transcriptomic data to comprehensively investigate ACP tumor genomes and identify putative novel tumorigenic mechanisms that advance our understanding of ACP biology.
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Affiliation(s)
- Danny Jomaa
- Harvard Medical School , Boston, MA , USA
- Dana-Farber Cancer Institute , Boston, MA , USA
| | - Prasidda Khadka
- Harvard Medical School , Boston, MA , USA
- Dana-Farber Cancer Institute , Boston, MA , USA
| | | | | | - Jessica W Tsai
- Dana-Farber Cancer Institute , Boston, MA , USA
- Boston Children's Hospital , Boston, MA , USA
| | | | - Shu Zhang
- Dana-Farber Cancer Institute , Boston, MA , USA
| | - Kevin Zhou
- Dana-Farber Cancer Institute , Boston, MA , USA
| | - Rose Gold
- Dana-Farber Cancer Institute , Boston, MA , USA
| | | | | | - Eric Prince
- Department of Neurosurgery, University of Colorado School of Medicine , Aurora, CO , USA
- Morgan Adams Foundation for Pediatric Brain Tumor Research Program, University of Colorado School of Medicine , Aurora, CO , USA
| | - Sophie Lu
- Milken Institute of Public Health, George Washington University , Washington, DC , USA
| | | | - Georg W Otto
- University College London, London , England , United Kingdom
| | | | - David Ashley
- Department of Neurosurgery, Duke University , Durham, NC , USA
| | | | - Eric Thompson
- Department of Neurosurgery, Duke University , Durham, NC , USA
| | - Rameen Beroukhim
- Dana-Farber Cancer Institute , Boston, MA , USA
- Brigham and Women's Hospital , Boston, MA , USA
| | - John Apps
- University College London, London , England , United Kingdom
- University of Birmingham, Birmingham , England , United Kingdom
| | | | - Todd Hankinson
- Department of Neurosurgery, University of Colorado School of Medicine , Aurora, CO , USA
- Morgan Adams Foundation for Pediatric Brain Tumor Research Program, University of Colorado School of Medicine , Aurora, CO , USA
| | - Pratiti Bandopadhayay
- Dana-Farber Cancer Institute , Boston, MA , USA
- Boston Children's Hospital , Boston, MA , USA
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17
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Dubois F, Shapira O, Greenwald N, Zack T, Wala J, Tsai J, Crane A, Baguette A, Hadjadj D, Harutyunyan A, Kumar K, Blattner-Johnson M, Vogelzang J, Sousa C, Kang KS, Sinai C, Wang D, Khadka P, Malkin H, Ho P, O'Rourke R, Zhang S, Gold R, Deng D, Serrano J, Snuderl M, Jones C, Wright K, Chi S, Grill J, Kleinman C, Goumnerova L, Jabado N, Jones D, Kieran M, Ligon K, Beroukhim R, Bandopadhayay P. HGG-60. Structural variants shape driver combinations and outcomes in pediatric high-grade glioma. Neuro Oncol 2022. [DOI: 10.1093/neuonc/noac079.275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Pediatric high-grade gliomas (pHGGs), encompassing hemispheric and diffuse midline gliomas (DMGs), remain a devastating disease. The last decade has revealed oncogenic drivers including single nucleotide variants (SNVs) in histones. However, the contribution of structural variants (SVs) to gliomagenesis has not been systematically explored due to limitations in early SV analysis approaches. Using SV algorithms, we recently created, we analyzed SVs in whole-genome sequences of 179 pHGGs including a novel cohort of treatment naïve samples–the largest WGS cohort assembled in adult or pediatric glioma. The most recurrent SVs targeted MYC isoforms and receptor tyrosine kinases, including a novel SV amplifying a MYC enhancer in the lncRNA CCDC26 in 12% of DMGs and revealing a more central role for MYC in these cancers than previously known. Applying de novo SV signature discovery, we identified five signatures including three (SVsig1-3) involving primarily simple SVs, and two (SVsig4-5) involving complex, clustered SVs. These SV signatures associated with genetic variants that differed from what was observed for SV signatures in other cancers, suggesting different links to underlying biology. Tumors with simple SV signatures were TP53 wild-type but were enriched with alterations in TP53 pathway members PPM1D and MDM4. Complex signatures were associated with direct aberrations in TP53, CDKN2A, and RB1 early in tumor evolution, and with extrachromosomal amplicons that likely occurred later. All pHGGs exhibited at least one simple SV signature but complex SV signatures were primarily restricted to subsets of H3.3K27M DMGs and hemispheric pHGGs. Importantly, DMGs with the complex SV signatures SVsig4-5 were associated with shorter overall survival independent of histone type and TP53 status. These data inform the role and impact of SVs in gliomagenesis and mechanisms that shape them.
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Affiliation(s)
- Frank Dubois
- Dana-Farber Cancer Institute , Boston, MA , USA
- Broad Institute , Boston, MA , USA
| | | | - Noah Greenwald
- Dana-Farber Cancer Institute , Boston, MA , USA
- Broad Institute , Boston, MA , USA
| | - Travis Zack
- Dana-Farber Cancer Institute , Boston, MA , USA
- Broad Institute , Boston, MA , USA
| | - Jeremiah Wala
- Dana-Farber Cancer Institute , Boston, MA , USA
- Broad Institute , Boston, MA , USA
| | - Jessica Tsai
- Dana-Farber/Boston Childrens Cancer and Blood Disorder Center , Boston, MA , USA
- Broad Institute , Boston, MA , USA
| | - Alexander Crane
- Dana-Farber Cancer Institute , Boston, MA , USA
- Broad Institute , Boston, MA , USA
| | | | | | | | | | - Mirjam Blattner-Johnson
- Hopp Children's Cancer Center Heidelberg (KiTZ); Pediatric Glioma Research Group, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | | | | | | | | | - Dayle Wang
- Dana-Farber/Boston Childrens Cancer and Blood Disorder Center , Boston, MA , USA
| | - Prasidda Khadka
- Dana-Farber/Boston Childrens Cancer and Blood Disorder Center , Boston, MA , USA
- Broad Institute , Boston, MA , USA
| | | | - Patricia Ho
- Dana-Farber/Boston Childrens Cancer and Blood Disorder Center , Boston, MA , USA
- Broad Institute , Boston, MA , USA
| | - Ryan O'Rourke
- Dana-Farber/Boston Childrens Cancer and Blood Disorder Center , Boston, MA , USA
- Broad Institute , Boston, MA , USA
| | | | | | | | | | | | - Chris Jones
- Institute of Cancer Research , London , United Kingdom
| | - Karen Wright
- Dana-Farber/Boston Childrens Cancer and Blood Disorder Center , Boston, MA , USA
| | - Susan Chi
- Dana-Farber/Boston Childrens Cancer and Blood Disorder Center , Boston, MA , USA
| | - Jacques Grill
- Department of Pediatric and Adolescent Oncology and INSERM Unit 981, Gustave Roussy Institute and University of Paris Saclay , Villejuif , France
| | | | | | | | - David Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ); Pediatric Glioma Research Group, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Mark Kieran
- Dana-Farber/Boston Childrens Cancer and Blood Disorder Center , Boston, MA , USA
| | - Keith Ligon
- Dana-Farber Cancer Institute , Boston, MA , USA
- Broad Institute , Boston, MA , USA
| | - Rameen Beroukhim
- Dana-Farber Cancer Institute , Boston, MA , USA
- Broad Institute , Boston, MA , USA
| | - Pratiti Bandopadhayay
- Dana-Farber/Boston Childrens Cancer and Blood Disorder Center , Boston, MA , USA
- Broad Institute , Boston, MA , USA
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18
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Tsai JW, Choi JJ, Ouaalam H, Murrillo EA, Yeo KK, Vogelzang J, Sousa C, Woods JK, Ligon KL, Warfield SK, Bandopadhayay P, Cooney TM. LGG-32. Integrated biologic, radiologic and clinical analysis of pediatric low-grade gliomas during and after targeted therapy treatment. Neuro Oncol 2022. [PMCID: PMC9165407 DOI: 10.1093/neuonc/noac079.344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND: Pediatric low grade gliomas (pLGGs) are the most common central nervous system tumor in children, characterized by driver alterations in the RAS and MAPK pathways. Genomic advances have facilitated use of molecular targeted therapies, however their long-term impact on tumor behavior remains critically unanswered. METHODS: We performed an IRB-approved, retrospective chart and imaging review of pLGGs treated with off-label targeted therapy at Dana-Farber/Boston Children’s Cancer and Blood Disorders Center from 2010 to 2020. Volumetric analysis was performed for BRAFV600E and BRAF fusion/duplication driven pLGG subsets. RESULTS: Fifty-five patients were identified (dabrafenib n = 15, everolimus n = 26, trametinib n = 11, and vemurafenib n = 3). Targeted agent was used as first or second-line therapy for 58% (32/55). Median duration of targeted therapy was 0.79 years (0.01 – 4.87), and overall median follow-up was 2.50 years (0.01 – 7.39). The 1-year, 3-year, and 5-year EFS from targeted therapy initiation were 62.1%, 38.2%, and 31.8%, respectively. Mean volumetric change for BRAFV600E mutated pLGG on BRAF inhibitors was -54.11%, and median time to best volumetric response was 8.28 months (n = 12). Median time to largest volume post-treatment was 2.86 months. Mean volumetric change for BRAF fusion/duplication pLGG on MEK inhibitors was +7.34% with median time to best volumetric response of 6.71 months (n = 7). Median time to largest volume post-treatment was 2.38 months. CONCLUSIONS: Our integrated clinical and volumetric data suggest the majority of patients receiving BRAF inhibitors or trametinib achieve reduction in tumor volume while on therapy and that tumor stability can be achieved following targeted therapy cessation. Moreover, volumetric analysis shows promise as a tool to assess targeted therapeutic response in pLGGs.
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Affiliation(s)
- Jessica W Tsai
- Dana-Farber/Boston Children’s Cancer and Blood Disorder Center , Boston, MA , USA
| | - Jungwhan John Choi
- Department of Radiology, Boston Children's Hospital , Boston, MA , USA
- Department of Radiology and Medical Imaging, Cincinnati Children’s Hospital , Cincinnati, OH , USA
| | - Hakim Ouaalam
- Department of Radiology, Boston Children's Hospital , Boston, MA , USA
| | - Efrain Aguilar Murrillo
- Department of Radiology, Division of Neuroradiology and Neurointervention, , Brigham and Women’s Hospital , Boston, MA , USA
| | - Kee Kiat Yeo
- Dana-Farber/Boston Children’s Cancer and Blood Disorder Center , Boston, MA , USA
| | - Jayne Vogelzang
- Department of Pathology, Brigham and Women's Hospital , Boston, MA , USA
| | - Cecilia Sousa
- Department of Pathology, Brigham and Women's Hospital , Boston, MA , USA
| | - Jared K Woods
- Department of Pathology, Brigham and Women's Hospital , Boston, MA , USA
| | - Keith L Ligon
- Department of Pathology, Brigham and Women's Hospital , Boston, MA , USA
| | - Simon K Warfield
- Department of Radiology, Boston Children's Hospital , Boston, MA , USA
| | | | - Tabitha M Cooney
- Dana-Farber/Boston Children’s Cancer and Blood Disorder Center , Boston, MA , USA
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19
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Yeo KK, Alexandrescu S, Cotter JA, Vogelzang J, Bhave V, Li MM, Ji J, Benhamida JK, Rosenblum MK, Bale TA, Bouvier N, Kaneva K, Rosenberg T, Lim-Fat MJ, Ghosh H, Martinez M, Aguilera D, Smith A, Goldman S, Diamond EL, Gavrilovic I, MacDonald TJ, Wood MD, Nazemi KJ, Truong A, Cluster A, Ligon KL, Cole K, Bi WL, Margol AS, Karajannis MA, Wright KD. Multi-institutional study of the frequency, genomic landscape, and outcome of IDH-mutant glioma in pediatrics. Neuro Oncol 2022; 25:199-210. [PMID: 35604410 PMCID: PMC9825351 DOI: 10.1093/neuonc/noac132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND The incidence and biology of IDH1/2 mutations in pediatric gliomas are unclear. Notably, current treatment approaches by pediatric and adult providers vary significantly. We describe the frequency and clinical outcomes of IDH1/2-mutant gliomas in pediatrics. METHODS We performed a multi-institutional analysis of the frequency of pediatric IDH1/2-mutant gliomas, identified by next-generation sequencing (NGS). In parallel, we retrospectively reviewed pediatric IDH1/2-mutant gliomas, analyzing clinico-genomic features, treatment approaches, and outcomes. RESULTS Incidence: Among 851 patients with pediatric glioma who underwent NGS, we identified 78 with IDH1/2 mutations. Among patients 0-9 and 10-21 years old, 2/378 (0.5%) and 76/473 (16.1%) had IDH1/2-mutant tumors, respectively. Frequency of IDH mutations was similar between low-grade glioma (52/570, 9.1%) and high-grade glioma (25/277, 9.0%). Four tumors were graded as intermediate histologically, with one IDH1 mutation. Outcome: Seventy-six patients with IDH1/2-mutant glioma had outcome data available. Eighty-four percent of patients with low-grade glioma (LGG) were managed observantly without additional therapy. For low-grade astrocytoma, 5-year progression-free survival (PFS) was 42.9% (95%CI:20.3-63.8) and, despite excellent short-term overall survival (OS), numerous disease-related deaths after year 10 were reported. Patients with high-grade astrocytoma had a 5-year PFS/OS of 36.8% (95%CI:8.8-66.4) and 84% (95%CI:50.1-95.6), respectively. Patients with oligodendroglioma had excellent OS. CONCLUSIONS A subset of pediatric gliomas is driven by IDH1/2 mutations, with a higher rate among adolescents. The majority of patients underwent upfront observant management without adjuvant therapy. Findings suggest that the natural history of pediatric IDH1/2-mutant glioma may be similar to that of adults, though additional studies are needed.
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Affiliation(s)
- Kee Kiat Yeo
- Corresponding Author: Kee Kiat Yeo, MD, Department of Pediatric Oncology, Dana-Farber/Boston Children’s Cancer and Blood Disorder Center, 450 Brookline Ave, Boston, MA 02215, USA ()
| | | | | | - Jayne Vogelzang
- Department of Pediatric Oncology, Dana-Farber/Boston Children’s Cancer and Blood Disorder Center, Boston, MA, USA
| | | | - Marilyn M Li
- Division of Genomic Diagnostics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jianling Ji
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA,USA
| | - Jamal K Benhamida
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marc K Rosenblum
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tejus A Bale
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nancy Bouvier
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kristiyana Kaneva
- Department of Pediatrics, Ann & Robert H. Lurie Children’s Hospital of Chicago, USA,Tempus Labs, Inc., Chicago, IL, USA
| | - Tom Rosenberg
- Department of Pediatric Oncology, Dana-Farber/Boston Children’s Cancer and Blood Disorder Center, Boston, MA, USA,Harvard Medical School, Boston, MA, USA
| | - Mary Jane Lim-Fat
- Department of Medical Oncology, Dana-Farber/Brigham and Women’s Hospital Cancer Center, Boston, MA, USA
| | - Hia Ghosh
- Department of Neurosurgery, Brigham and Women’s Hospital, Boston, MA, USA
| | - Migdalia Martinez
- Department of Pediatrics, Arnold Palmer Hospital for Children, Orlando, FL, USA
| | - Dolly Aguilera
- Department of Pediatrics, Children’s Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA, USA
| | - Amy Smith
- Department of Pediatrics, Arnold Palmer Hospital for Children, Orlando, FL, USA
| | - Stewart Goldman
- Department of Child Health, Phoenix Children’s Hospital, University of Arizona College of Medicine, Phoenix, AZ, USA
| | - Eli L Diamond
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Igor Gavrilovic
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tobey J MacDonald
- Department of Pediatrics, Children’s Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA, USA
| | - Matthew D Wood
- Department of Pathology and Laboratory Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Kellie J Nazemi
- Department of Pediatrics, Doernbecher Children’s Hospital, Portland, OR, USA
| | - AiLien Truong
- Department of Pediatrics, Doernbecher Children’s Hospital, Portland, OR, USA
| | - Andrew Cluster
- Department of Pediatrics, St. Louis Children’s Hospital, St. Louis, MO, USA
| | - Keith L Ligon
- Department of Pathology, Dana-Farber/Brigham and Women’s Hospital Cancer Center, Boston, MA, USA
| | - Kristina Cole
- Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Ashley S Margol
- Department of Pediatrics, Children’s Hospital Los Angeles, Los Angeles, CA, USA
| | | | - Karen D Wright
- Department of Pediatric Oncology, Dana-Farber/Boston Children’s Cancer and Blood Disorder Center, Boston, MA, USA,Harvard Medical School, Boston, MA, USA
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20
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Khadka P, Reitman ZJ, Lu S, Buchan G, Gionet G, Dubois F, Carvalho DM, Shih J, Zhang S, Greenwald NF, Zack T, Shapira O, Pelton K, Hartley R, Bear H, Georgis Y, Jarmale S, Melanson R, Bonanno K, Schoolcraft K, Miller PG, Condurat AL, Gonzalez EM, Qian K, Morin E, Langhnoja J, Lupien LE, Rendo V, Digiacomo J, Wang D, Zhou K, Kumbhani R, Guerra Garcia ME, Sinai CE, Becker S, Schneider R, Vogelzang J, Krug K, Goodale A, Abid T, Kalani Z, Piccioni F, Beroukhim R, Persky NS, Root DE, Carcaboso AM, Ebert BL, Fuller C, Babur O, Kieran MW, Jones C, Keshishian H, Ligon KL, Carr SA, Phoenix TN, Bandopadhayay P. PPM1D mutations are oncogenic drivers of de novo diffuse midline glioma formation. Nat Commun 2022; 13:604. [PMID: 35105861 PMCID: PMC8807747 DOI: 10.1038/s41467-022-28198-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 01/07/2022] [Indexed: 12/23/2022] Open
Abstract
The role of PPM1D mutations in de novo gliomagenesis has not been systematically explored. Here we analyze whole genome sequences of 170 pediatric high-grade gliomas and find that truncating mutations in PPM1D that increase the stability of its phosphatase are clonal driver events in 11% of Diffuse Midline Gliomas (DMGs) and are enriched in primary pontine tumors. Through the development of DMG mouse models, we show that PPM1D mutations potentiate gliomagenesis and that PPM1D phosphatase activity is required for in vivo oncogenesis. Finally, we apply integrative phosphoproteomic and functional genomics assays and find that oncogenic effects of PPM1D truncation converge on regulators of cell cycle, DNA damage response, and p53 pathways, revealing therapeutic vulnerabilities including MDM2 inhibition.
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Affiliation(s)
- Prasidda Khadka
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Harvard Biological and Biomedical Sciences PhD Program, Harvard University, Cambridge, MA, 02138, USA
| | - Zachary J Reitman
- Department of Radiation Oncology, Duke University, Durham, NC, 27710, USA
- Duke Cancer Institute, Duke University, Durham, NC, 27710, USA
- The Preston Robert Tisch Brain Tumor Center at Duke, Duke University, Durham, NC, 27710, USA
| | - Sophie Lu
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02215, USA
| | - Graham Buchan
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02215, USA
| | - Gabrielle Gionet
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02215, USA
| | - Frank Dubois
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Diana M Carvalho
- Division of Molecular Pathology, Institute of Cancer Research, London, UK
| | - Juliann Shih
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Shu Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Noah F Greenwald
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, 02215, USA
| | - Travis Zack
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, 02215, USA
| | - Ofer Shapira
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, 02215, USA
| | - Kristine Pelton
- Department of Oncologic Pathology, Dana Farber Cancer Institute, Boston, MA, 02215, USA
| | - Rachel Hartley
- Division of Pharmaceutical Sciences, James L. Winkle College of Pharmacy, University of Cincinnati, Cincinnati, OH, 45267, USA
| | - Heather Bear
- Research in Patient Services, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45267, USA
| | - Yohanna Georgis
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02215, USA
| | - Spandana Jarmale
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02215, USA
| | - Randy Melanson
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Kevin Bonanno
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Kathleen Schoolcraft
- Department of Oncologic Pathology, Dana Farber Cancer Institute, Boston, MA, 02215, USA
| | - Peter G Miller
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Alexandra L Condurat
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02215, USA
| | - Elizabeth M Gonzalez
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02215, USA
| | - Kenin Qian
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02215, USA
| | - Eric Morin
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02215, USA
| | - Jaldeep Langhnoja
- Division of Pharmaceutical Sciences, James L. Winkle College of Pharmacy, University of Cincinnati, Cincinnati, OH, 45267, USA
| | - Leslie E Lupien
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02215, USA
| | - Veronica Rendo
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, 02215, USA
| | - Jeromy Digiacomo
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02215, USA
| | - Dayle Wang
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02215, USA
| | - Kevin Zhou
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02215, USA
| | - Rushil Kumbhani
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02215, USA
| | | | - Claire E Sinai
- Department of Oncologic Pathology, Dana Farber Cancer Institute, Boston, MA, 02215, USA
| | - Sarah Becker
- Department of Oncologic Pathology, Dana Farber Cancer Institute, Boston, MA, 02215, USA
| | - Rachel Schneider
- Department of Oncologic Pathology, Dana Farber Cancer Institute, Boston, MA, 02215, USA
| | - Jayne Vogelzang
- Department of Oncologic Pathology, Dana Farber Cancer Institute, Boston, MA, 02215, USA
| | - Karsten Krug
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Amy Goodale
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Tanaz Abid
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Zohra Kalani
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | | | - Rameen Beroukhim
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Nicole S Persky
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - David E Root
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Angel M Carcaboso
- Department of Pediatric Hematology and Oncology, Hospital Sant Joan de Deu, Institut de Recerca Sant Joan de Deu, Barcelona, 08950, Spain
| | - Benjamin L Ebert
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - Christine Fuller
- Department of Pathology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45267, USA
| | - Ozgun Babur
- College of Science and Mathematics, University of Massachusetts Boston, Boston, MA, 02125, USA
| | - Mark W Kieran
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02215, USA
- Bristol Myers Squibb, Boston, Devens, MA, 01434, USA
| | - Chris Jones
- Division of Molecular Pathology, Institute of Cancer Research, London, UK
| | | | - Keith L Ligon
- Department of Oncologic Pathology, Dana Farber Cancer Institute, Boston, MA, 02215, USA
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Timothy N Phoenix
- Division of Pharmaceutical Sciences, James L. Winkle College of Pharmacy, University of Cincinnati, Cincinnati, OH, 45267, USA.
- Research in Patient Services, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45267, USA.
| | - Pratiti Bandopadhayay
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02215, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02215, USA.
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21
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Tsai J, Vogelzang J, Sousa C, Yeo KK, Ligon K, Bandopadhayay P, Cooney T. LGG-03. LONG-TERM FOLLOW UP OF TARGETED THERAPY IN PEDIATRIC LOW-GRADE GLIOMAS: THE DANA-FARBER/BOSTON CHILDREN’S EXPERIENCE. Neuro Oncol 2021. [PMCID: PMC8168155 DOI: 10.1093/neuonc/noab090.127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
Pediatric low grade gliomas (pLGGs) are the most common central nervous system (CNS) tumor in children and characterized by alterations in the MAPK pathway. Standard of care is not well defined, and treatment has evolved over the last decade to include molecular targeted therapies. The impact of targeted agents on the natural history of pLGGs remains unknown. We present a retrospective review of patients receiving targeted agents integrated with molecular profiling.
Methods
We performed an IRB-approved, retrospective chart review of pLGGs treated with off-label use of dabrafenib, vemurafenib, everolimus, and trametinib at Dana-Farber/Boston Children’s Cancer and Blood Disorders Center from 2010 to 2020.
Results
Forty-nine patients were identified (dabrafenib n=9, everolimus n=27, trametinib n=10, and vemurafenib n=3). All patients receiving BRAF inhibitors harbored BRAF V600E mutation. Targeted agent was used as first-line therapy for 25% of patients, while for 31% of patients, targeted agent was second-line therapy. The median time from diagnosis to targeted therapy initiation was 4.76 years (0.10 – 23.77), median duration of targeted therapy was 0.79 years (0.01 – 4.87), median time to subsequent therapy post first-line targeted therapy was 0.2 years (0.01 – 3.33), and overall median follow-up for the entire cohort was 3.09 years (0.36 – 11.87). The 1-year, 3-year, and 5-year EFS from targeted therapy initiation was 58.0%, 32.2%, and 26.9%, respectively. Survival analyses by molecular subgroup and agent were performed. Reasons for cessation of targeted therapy included toxicities, progression, and/or planned end of therapy.
Conclusions
Further efforts are ongoing to perform volumetric analysis of growth rates before, during, and after treatment. While targeted molecular therapies show great promise, it will be critical to understand how these agents alter the natural history of pLGGs, particularly in the context of genomic profiling.
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Affiliation(s)
- Jessica Tsai
- Dana-Farber/Boston Children’s Cancer and Blood Disorder Center, Boston, MA, USA
| | - Jayne Vogelzang
- Dana-Farber/Boston Children’s Cancer and Blood Disorder Center, Boston, MA, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Cecilia Sousa
- Dana-Farber/Boston Children’s Cancer and Blood Disorder Center, Boston, MA, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Kee Kiat Yeo
- Dana-Farber/Boston Children’s Cancer and Blood Disorder Center, Boston, MA, USA
| | - Keith Ligon
- Dana-Farber/Boston Children’s Cancer and Blood Disorder Center, Boston, MA, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | | | - Tabitha Cooney
- Dana-Farber/Boston Children’s Cancer and Blood Disorder Center, Boston, MA, USA
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Jane Lim-Fat M, Youssef G, Touat M, Iorgulescu B, Woodward E, Whorral S, Allen M, Vogelzang J, Pisano W, Rahman R, Chukwueke U, Mcfaline-Figueroa J, Nayak L, Lee E, Batchelor T, Chiocca EA, Meredith D, Santagata S, Reardon D, Beroukhim R, Bi WL, Ligon K, Wen P. PATH-03. CLINICAL UTILITY OF NEXT GENERATION SEQUENCING IN IDH-WILDTYPE GLIOBLASTOMA: THE DANA-FARBER CANCER INSTITUTE EXPERIENCE. Neuro Oncol 2020. [DOI: 10.1093/neuonc/noaa215.685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
BACKGROUND
Comprehensive next generation sequencing (NGS) is available through many academic institutions and commercial entities, and is incorporated in practice guidelines for glioblastoma (GBM). We retrospective evaluated the practice patterns and utility of incorporating NGS data into routine care of GBM patients at a clinical trials-focused academic center.
METHODS
We identified 1,011 consecutive adult patients with histologically confirmed GBM with OncoPanel testing, a targeted exome NGS platform of 447 cancer-associated genes at Dana Farber Cancer Institute (DFCI), from 2013-2019. We selected and retrospectively reviewed clinical records of all IDH-wildtype GBM patients treated at DFCI.
RESULTS
We identified 557 GBM IDH-wildtype patients, of which 227 were male (40.7%). OncoPanel testing revealed 833 single nucleotide variants and indels in 44 therapeutically relevant genes (Tier 1 or 2 mutations) including PIK3CA (n=51), BRAF (n=9), FGFR1 (n=8), MSH2 (n=4), MSH6 (n=2) and MLH1 (n=1). Copy number analysis revealed 509 alterations in 18 therapeutically relevant genes including EGFR amplification (n= 186), PDGFRA amplification (N=39) and CDKN2A/2B homozygous loss (N=223). Median overall survival was 17.5 months for the whole cohort. Seventy-four therapeutic clinical trials accrued 144 patients in the upfront setting (25.9%) and 203 patients (36.4%) at recurrence. Altogether, NGS data for 107 patients (19.2%) were utilized for clinical trial enrollment or targeted therapy indications. High mutational burden (>17mutations/Mb) was identified in 11/464 samples (2.4%); of whom 3/11 received immune checkpoint blockade. Four patients received compassionate use therapy targeting EGFRvIII (rindopepimut, n=2), CKD4/6 (abemaciclib, n=1) and BRAFV600E (dabrafenib/trametinib, n=1).
CONCLUSION
While NGS has greatly improved diagnosis and molecular classification, we highlight that NGS remains underutilized in selecting therapy in GBM, even in a setting where clinical trials and off-label therapies are relatively accessible. Continued efforts to develop better targeted therapies and efficient clinical trial design are required to maximize the potential benefits of genomically-stratified data.
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Affiliation(s)
| | | | - Mehdi Touat
- AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neurologie 2-Mazarin, Paris, France
| | | | | | | | - Marie Allen
- Dana Farber Cancer Institute, Boston, MA, USA
| | | | - William Pisano
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Rifaquat Rahman
- Brigham and Women’s/Dana-Farber Cancer Center, Boston, MA, USA
| | | | | | | | - Eudocia Lee
- Dana Farber Cancer Institute, Boston, MA, USA
| | | | - E Antonio Chiocca
- Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - David Meredith
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Sandro Santagata
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - David Reardon
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Wenya Linda Bi
- Department of Neurosurgery, Brigham and Women’s Hospital, Boston, MA, USA
| | - Keith Ligon
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Patrick Wen
- Dana Farber Cancer Institute, Boston, MA, USA
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Jane Lim-Fat M, Vogelzang J, Woodward E, McGovern A, Ma C, Al-sayegh H, Alexandrescu S, Margol A, Cotter J, Cole K, Li M, Owens E, Smith A, Goldman S, Kaneva K, Burton E, Nazemi K, Wright K, Wen P, Warren K, Touat M, Reardon D, Bi WL, Ligon K, Yeo KK. EPID-11. A MULTI-INSTITUTIONAL COMPARATIVE ANALYSIS OF THE CLINICAL, GENOMIC, AND SURVIVAL CHARACTERISTICS OF PEDIATRIC, YOUNG ADULT AND OLDER ADULT PATIENTS WITH IDH-MUTANT GLIOMA. Neuro Oncol 2020. [DOI: 10.1093/neuonc/noaa215.329] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
BACKGROUND
Prognostic significance of IDH-mutation in glioma is incompletely understood in children and adolescents/young adults (YAs). We compared the clinico-genomic features, outcomes and prognostic factors observed in IDH-mutant gliomas across age groups.
METHODS
Clinical, histologic and molecular data of patients with IDH-mutant gliomas from 8 pediatric institutions (spanning twenty years) and adult patients from two institutions (from 2013–2019) were identified. Patients were grouped as pediatric (< 19y), YA (19y to < 40y) or older adult (≥ 40y). Genomic alterations, including somatic mutations and copy number variants, were captured with institutional next generation sequencing. Factors were compared across age categories using Fisher’s exact test or analysis-of-variance. Cox proportional-hazards regression tested factors for association with overall (OS) and progression-free survival (PFS).
RESULTS
Of 379 patients, 48(13%) were pediatric, 204(54%) YA and 127(33%) older adult. Histological subtype differed significantly by age group (p< 0.0001). YAs had higher rates of malignant transformation (p=0.01) and shorter time-from-diagnosis-to-malignant transformation (p=0.01) compared to other age groups. Analysis of genomic alterations revealed an age-related difference in distribution in ATRX mutations only (p=0.0018). Median PFS and OS for the entire cohort were 4.62 and 17.19 years. In univariate models, PFS differed by age group (p=0.0012), with YAs having the worst outcomes. Lack of MGMT methylation (p=0.024) predicted poorer OS. Upfront observant management was predictive of poorer PFS. Gene mutations were not associated with PFS. In multi-variable models, YAs had shorter PFS compared to pediatric (hazard ratio [HR]=2.03, p=0.01) and older adults (HR=1.59, p=0.003) after adjusting for histology, extent of resection, and initial therapy. Age at diagnosis was not associated with OS in multi-variable analysis.
CONCLUSIONS
Within our cohort, YA with IDH-mutant tumors progressed more quickly compared to their pediatric counterparts. Further study of YA patients with IDH-mutant glioma is critical to better define best practices for this group.
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Affiliation(s)
| | | | | | | | - Clement Ma
- Boston Children’s Hospital, Boston, MA, USA
| | | | | | - Ashley Margol
- Children’s Hospital Los Angeles, Los Angeles, CA, USA
| | | | - Kristina Cole
- Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Marilyn Li
- Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Emily Owens
- Orlando Health Arnold Palmer Hospital for Children, Orlando, FL, USA
| | - Amy Smith
- Orlando Health Arnold Palmer Hospital for Children, Orlando, FL, USA
| | - Stewart Goldman
- Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL, USA
| | - Kristiyana Kaneva
- Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL, USA
| | - Emily Burton
- OHSU Doernbecher Children’s Hospital, Portland, OR, USA
| | - Kellie Nazemi
- OHSU Doernbecher Children’s Hospital, Portland, OR, USA
| | - Karen Wright
- Dana-Farber Cancer Institute/Boston Children’s Hospital, Boston, MA, USA
| | - Patrick Wen
- Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Mehdi Touat
- AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neurologie 2-Mazarin, Paris, France
| | - David Reardon
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Wenya Linda Bi
- Department of Neurosurgery, Brigham and Women’s Hospital, Boston, MA, USA
| | - Keith Ligon
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
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Vogelzang J. Unaccompanied Minor Refugee Life Skills: Navigating the U.S. Food Landscape. J Acad Nutr Diet 2016. [DOI: 10.1016/j.jand.2016.06.353] [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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Van Der Laan L, Vogelzang J, Schalke R. Commuting in multi-nodal urban systems: an empirical comparison of three alternative models. Tijdschr Econ Soc Geogr 1998; 89:384-400. [PMID: 12294778 DOI: 10.1111/1467-9663.00037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
"This paper analyses whether the basic monocentric model of urban structure and commuting explains actual commuting in Europe, i.e. The Netherlands. As in the USA much wasteful commuting is established. The basic model has a low degree of explanatory power. In order to get more in line with actual commuting, the paper elaborates two alternatives to the basic model. Besides a deconcentrated model, a cross-traffic model is developed. Particularly the latter is quite successful in explaining actual commuting. The paper pleads for endogenising employment and stresses heterogeneity in labour demand and supply."
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van der Kooij MWA, Vogelzang J, Calkoen CJ. A simple analytical model for brightness modulations caused by submarine sand waves in radar imagery. ACTA ACUST UNITED AC 1995. [DOI: 10.1029/94jc00957] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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