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Parker M, Chen X, Bahrami A, Dalton J, Rusch M, Wu G, Easton J, Cheung NK, Dyer M, Mardis ER, Wilson RK, Mullighan C, Gilbertson R, Baker SJ, Zambetti G, Ellison DW, Downing JR, Zhang J. Assessing telomeric DNA content in pediatric cancers using whole-genome sequencing data. Genome Biol 2012; 13:R113. [PMID: 23232254 PMCID: PMC3580411 DOI: 10.1186/gb-2012-13-12-r113] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Revised: 11/22/2012] [Accepted: 12/11/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Telomeres are the protective arrays of tandem TTAGGG sequence and associated proteins at the termini of chromosomes. Telomeres shorten at each cell division due to the end-replication problem and are maintained above a critical threshold in malignant cancer cells to prevent cellular senescence or apoptosis. With the recent advances in massive parallel sequencing, assessing telomere content in the context of other cancer genomic aberrations becomes an attractive possibility. We present the first comprehensive analysis of telomeric DNA content change in tumors using whole-genome sequencing data from 235 pediatric cancers. RESULTS To measure telomeric DNA content, we counted telomeric reads containing TTAGGGx4 or CCCTAAx4 and normalized to the average genomic coverage. Changes in telomeric DNA content in tumor genomes were clustered using a Bayesian Information Criterion to determine loss, no change, or gain. Using this approach, we found that the pattern of telomeric DNA alteration varies dramatically across the landscape of pediatric malignancies: telomere gain was found in 32% of solid tumors, 4% of brain tumors and 0% of hematopoietic malignancies. The results were validated by three independent experimental approaches and reveal significant association of telomere gain with the frequency of somatic sequence mutations and structural variations. CONCLUSIONS Telomere DNA content measurement using whole-genome sequencing data is a reliable approach that can generate useful insights into the landscape of the cancer genome. Measuring the change in telomeric DNA during malignant progression is likely to be a useful metric when considering telomeres in the context of the whole genome.
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Affiliation(s)
- Matthew Parker
- Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Xiang Chen
- Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Armita Bahrami
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - James Dalton
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Michael Rusch
- Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Gang Wu
- Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - John Easton
- The Pediatric Cancer Genome Project, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Nai-Kong Cheung
- Department of Pediatrics, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Michael Dyer
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Elaine R Mardis
- The Genome Center at Washington University, Washington University, 4444 Forest Park Ave, St Louis, Missouri 63108, USA
- Department of Genetics, Washington University, 4444 Forest Park Ave, St Louis, Missouri 63108, USA
| | - Richard K Wilson
- The Genome Center at Washington University, Washington University, 4444 Forest Park Ave, St Louis, Missouri 63108, USA
- Department of Genetics, Washington University, 4444 Forest Park Ave, St Louis, Missouri 63108, USA
| | - Charles Mullighan
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Richard Gilbertson
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Suzanne J Baker
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Gerard Zambetti
- Department of Biochemistry, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - David W Ellison
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - James R Downing
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Jinghui Zhang
- Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
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307
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Liu XY, Gerges N, Korshunov A, Sabha N, Khuong-Quang DA, Fontebasso AM, Fleming A, Hadjadj D, Schwartzentruber J, Majewski J, Dong Z, Siegel P, Albrecht S, Croul S, Jones DTW, Kool M, Tonjes M, Reifenberger G, Faury D, Zadeh G, Pfister S, Jabado N. Frequent ATRX mutations and loss of expression in adult diffuse astrocytic tumors carrying IDH1/IDH2 and TP53 mutations. Acta Neuropathol 2012; 124:615-25. [PMID: 22886134 DOI: 10.1007/s00401-012-1031-3] [Citation(s) in RCA: 305] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 07/31/2012] [Accepted: 08/02/2012] [Indexed: 12/12/2022]
Abstract
Gliomas are the most common primary brain tumors in children and adults. We recently identified frequent alterations in chromatin remodelling pathways including recurrent mutations in H3F3A and mutations in ATRX (α-thalassemia/mental-retardation-syndrome-X-linked) in pediatric and young adult glioblastoma (GBM, WHO grade IV astrocytoma). H3F3A mutations were specific to pediatric high-grade gliomas and identified in only 3.4 % of adult GBM. Using sequencing and/or immunohistochemical analyses, we investigated ATRX alterations (mutation/loss of expression) and their association with TP53 and IDH1 or IDH2 mutations in 140 adult WHO grade II, III and IV gliomas, 17 pediatric WHO grade II and III astrocytomas and 34 pilocytic astrocytomas. In adults, ATRX aberrations were detected in 33 % of grade II and 46 % of grade III gliomas, as well as in 80 % of secondary and 7 % of primary GBMs. They were absent in the 17 grade II and III astrocytomas in children, and the 34 pilocytic astrocytomas. ATRX alterations closely overlapped with mutations in IDH1/2 (p < 0.0001) and TP53 (p < 0.0001) in samples across all WHO grades. They were prevalent in astrocytomas and oligoastrocytomas, but were absent in oligodendrogliomas (p < 0.0001). No significant association of ATRX mutation/loss of expression and alternative lengthening of telomeres was identified in our cohort. In summary, our data show that ATRX alterations are frequent in adult diffuse gliomas and are specific to astrocytic tumors carrying IDH1/2 and TP53 mutations. Combined alteration of these genes may contribute to drive the neoplastic growth in a major subset of diffuse astrocytomas in adults.
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309
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Jiao Y, Killela PJ, Reitman ZJ, Rasheed BA, Heaphy CM, de Wilde RF, Rodriguez FJ, Rosemberg S, Oba-Shinjo SM, Marie SKN, Bettegowda C, Agrawal N, Lipp E, Pirozzi CJ, Lopez GY, He Y, Friedman HS, Friedman AH, Riggins GJ, Holdhoff M, Burger P, McLendon RE, Bigner DD, Vogelstein B, Meeker AK, Kinzler KW, Papadopoulos N, Diaz LA, Yan H. Frequent ATRX, CIC, FUBP1 and IDH1 mutations refine the classification of malignant gliomas. Oncotarget 2012; 3:709-22. [PMID: 22869205 PMCID: PMC3443254 DOI: 10.18632/oncotarget.588] [Citation(s) in RCA: 435] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 08/02/2012] [Indexed: 11/25/2022] Open
Abstract
Mutations in the critical chromatin modifier ATRX and mutations in CIC and FUBP1, which are potent regulators of cell growth, have been discovered in specific subtypes of gliomas, the most common type of primary malignant brain tumors. However, the frequency of these mutations in many subtypes of gliomas, and their association with clinical features of the patients, is poorly understood. Here we analyzed these loci in 363 brain tumors. ATRX is frequently mutated in grade II-III astrocytomas (71%), oligoastrocytomas (68%), and secondary glioblastomas (57%), and ATRX mutations are associated with IDH1 mutations and with an alternative lengthening of telomeres phenotype. CIC and FUBP1 mutations occurred frequently in oligodendrogliomas (46% and 24%, respectively) but rarely in astrocytomas or oligoastrocytomas ( more than 10%). This analysis allowed us to define two highly recurrent genetic signatures in gliomas: IDH1/ATRX (I-A) and IDH1/CIC/FUBP1 (I-CF). Patients with I-CF gliomas had a significantly longer median overall survival (96 months) than patients with I-A gliomas (51 months) and patients with gliomas that did not harbor either signature (13 months). The genetic signatures distinguished clinically distinct groups of oligoastrocytoma patients, which usually present a diagnostic challenge, and were associated with differences in clinical outcome even among individual tumor types. In addition to providing new clues about the genetic alterations underlying gliomas, the results have immediate clinical implications, providing a tripartite genetic signature that can serve as a useful adjunct to conventional glioma classification that may aid in prognosis, treatment selection, and therapeutic trial design.
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Affiliation(s)
- Yuchen Jiao
- Ludwig Center for Cancer Genetics and Howard Hughes Medical Institutions, The Johns Hopkins Kimmel Cancer Center, the Department of Oncology, the Department of Pathology, the Department of Neurosurgery, the Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Patrick J. Killela
- The Preston Robert Tisch Brain Tumor Center at Duke, The Pediatric Brain Tumor Foundation Institute, the Department of Pathology, the Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Zachary J. Reitman
- The Preston Robert Tisch Brain Tumor Center at Duke, The Pediatric Brain Tumor Foundation Institute, the Department of Pathology, the Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - B. Ahmed Rasheed
- The Preston Robert Tisch Brain Tumor Center at Duke, The Pediatric Brain Tumor Foundation Institute, the Department of Pathology, the Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Christopher M. Heaphy
- Ludwig Center for Cancer Genetics and Howard Hughes Medical Institutions, The Johns Hopkins Kimmel Cancer Center, the Department of Oncology, the Department of Pathology, the Department of Neurosurgery, the Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Roeland F. de Wilde
- Ludwig Center for Cancer Genetics and Howard Hughes Medical Institutions, The Johns Hopkins Kimmel Cancer Center, the Department of Oncology, the Department of Pathology, the Department of Neurosurgery, the Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Fausto J. Rodriguez
- Ludwig Center for Cancer Genetics and Howard Hughes Medical Institutions, The Johns Hopkins Kimmel Cancer Center, the Department of Oncology, the Department of Pathology, the Department of Neurosurgery, the Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Sergio Rosemberg
- The Department of Pathology, the Department of Neurology, School of Medicine, University of Sao Paulo, Sao Paulo, Sao Paulo, Brazil
| | - Sueli Mieko Oba-Shinjo
- The Department of Pathology, the Department of Neurology, School of Medicine, University of Sao Paulo, Sao Paulo, Sao Paulo, Brazil
| | - Suely Kazue Nagahashi Marie
- The Department of Pathology, the Department of Neurology, School of Medicine, University of Sao Paulo, Sao Paulo, Sao Paulo, Brazil
| | - Chetan Bettegowda
- Ludwig Center for Cancer Genetics and Howard Hughes Medical Institutions, The Johns Hopkins Kimmel Cancer Center, the Department of Oncology, the Department of Pathology, the Department of Neurosurgery, the Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Nishant Agrawal
- Ludwig Center for Cancer Genetics and Howard Hughes Medical Institutions, The Johns Hopkins Kimmel Cancer Center, the Department of Oncology, the Department of Pathology, the Department of Neurosurgery, the Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Eric Lipp
- The Preston Robert Tisch Brain Tumor Center at Duke, The Pediatric Brain Tumor Foundation Institute, the Department of Pathology, the Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Christopher J. Pirozzi
- The Preston Robert Tisch Brain Tumor Center at Duke, The Pediatric Brain Tumor Foundation Institute, the Department of Pathology, the Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Giselle Y. Lopez
- The Preston Robert Tisch Brain Tumor Center at Duke, The Pediatric Brain Tumor Foundation Institute, the Department of Pathology, the Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Yiping He
- The Preston Robert Tisch Brain Tumor Center at Duke, The Pediatric Brain Tumor Foundation Institute, the Department of Pathology, the Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Henry S. Friedman
- The Preston Robert Tisch Brain Tumor Center at Duke, The Pediatric Brain Tumor Foundation Institute, the Department of Pathology, the Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Allan H. Friedman
- The Preston Robert Tisch Brain Tumor Center at Duke, The Pediatric Brain Tumor Foundation Institute, the Department of Pathology, the Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Gregory J. Riggins
- Ludwig Center for Cancer Genetics and Howard Hughes Medical Institutions, The Johns Hopkins Kimmel Cancer Center, the Department of Oncology, the Department of Pathology, the Department of Neurosurgery, the Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Matthias Holdhoff
- Ludwig Center for Cancer Genetics and Howard Hughes Medical Institutions, The Johns Hopkins Kimmel Cancer Center, the Department of Oncology, the Department of Pathology, the Department of Neurosurgery, the Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
- The Swim Across America Laboratory at Johns Hopkins, The Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Peter Burger
- Ludwig Center for Cancer Genetics and Howard Hughes Medical Institutions, The Johns Hopkins Kimmel Cancer Center, the Department of Oncology, the Department of Pathology, the Department of Neurosurgery, the Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Roger E. McLendon
- The Preston Robert Tisch Brain Tumor Center at Duke, The Pediatric Brain Tumor Foundation Institute, the Department of Pathology, the Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Darell D. Bigner
- The Preston Robert Tisch Brain Tumor Center at Duke, The Pediatric Brain Tumor Foundation Institute, the Department of Pathology, the Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Bert Vogelstein
- Ludwig Center for Cancer Genetics and Howard Hughes Medical Institutions, The Johns Hopkins Kimmel Cancer Center, the Department of Oncology, the Department of Pathology, the Department of Neurosurgery, the Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Alan K. Meeker
- Ludwig Center for Cancer Genetics and Howard Hughes Medical Institutions, The Johns Hopkins Kimmel Cancer Center, the Department of Oncology, the Department of Pathology, the Department of Neurosurgery, the Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Kenneth W. Kinzler
- Ludwig Center for Cancer Genetics and Howard Hughes Medical Institutions, The Johns Hopkins Kimmel Cancer Center, the Department of Oncology, the Department of Pathology, the Department of Neurosurgery, the Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Nickolas Papadopoulos
- Ludwig Center for Cancer Genetics and Howard Hughes Medical Institutions, The Johns Hopkins Kimmel Cancer Center, the Department of Oncology, the Department of Pathology, the Department of Neurosurgery, the Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Luis A. Diaz
- Ludwig Center for Cancer Genetics and Howard Hughes Medical Institutions, The Johns Hopkins Kimmel Cancer Center, the Department of Oncology, the Department of Pathology, the Department of Neurosurgery, the Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
- The Swim Across America Laboratory at Johns Hopkins, The Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Hai Yan
- The Preston Robert Tisch Brain Tumor Center at Duke, The Pediatric Brain Tumor Foundation Institute, the Department of Pathology, the Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
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