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Filbin MG, Suvà ML. Gliomas Genomics and Epigenomics: Arriving at the Start and Knowing It for the First Time. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2016; 11:497-521. [DOI: 10.1146/annurev-pathol-012615-044208] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Mariella G. Filbin
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114;
- Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts 02114;
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, Massachusetts 02215
| | - Mario L. Suvà
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114;
- Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts 02114;
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142
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Bergthold G, Bandopadhayay P, Bi WL, Ramkissoon L, Stiles C, Segal RA, Beroukhim R, Ligon KL, Grill J, Kieran MW. Pediatric low-grade gliomas: how modern biology reshapes the clinical field. Biochim Biophys Acta Rev Cancer 2014; 1845:294-307. [PMID: 24589977 DOI: 10.1016/j.bbcan.2014.02.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 02/20/2014] [Indexed: 12/17/2022]
Abstract
Low-grade gliomas represent the most frequent brain tumors arising during childhood. They are characterized by a broad and heterogeneous group of tumors that are currently classified by the WHO according to their morphological appearance. Here we review the clinical features of these tumors, current therapeutic strategies and the recent discovery of genomic alterations characteristic to these tumors. We further explore how these recent biological findings stand to transform the treatment for these tumors and impact the diagnostic criteria for pediatric low-grade gliomas.
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Affiliation(s)
| | - Pratiti Bandopadhayay
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Division of Pediatric Hematology and Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Boston Children's Hospital, Boston, MA, USA
| | - Wenya Linda Bi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Lori Ramkissoon
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA; Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Charles Stiles
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Rosalind A Segal
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Rameen Beroukhim
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Keith L Ligon
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA; Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jacques Grill
- Departement de Cancerologie de l'enfant et de l'adolescent, Gustave Roussy and Unité Mixte de Recherche 8203 du Centre National de la Recherche Scientifique, Université Paris-Sud, Villejuif, France
| | - Mark W Kieran
- Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA; Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA.
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Kim JH, Huse JT, Huang Y, Lyden D, Greenfield JP. Molecular diagnostics in paediatric glial tumours. Lancet Oncol 2013; 14:e19-27. [PMID: 23276367 DOI: 10.1016/s1470-2045(12)70577-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Glial tumours in children have distinct patterns of epigenetic alteration, chromosomal structure, and gene and protein expression that differentiate them from their histological counterparts in adults. Understanding paediatric gliomas at the molecular level provides important prognostic and therapeutic insights, such as which genetic alterations confer a favourable response to adjuvant therapy, or which signalling pathways might be amenable to specific molecularly targeted agents. For clinicians, the ultimate goal is to individualise therapeutic regimens on the basis of the molecular fingerprint of a particular tumour and the prognosis conferred by this profile. In this Review, we examine a series of studies of molecular and genomic analysis of glial tumours in children, and discuss the many clinical insights that these molecular features provide.
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Affiliation(s)
- Joon-Hyung Kim
- Department of Neurological Surgery, Weill Cornell Medical College, New York, NY 10065, USA
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Abstract
PURPOSE The aim is to describe the behavior of pilocytic astrocytoma (PAs) and its effects on patient prognosis by using flow cytometric, immunohistochemical and cytogenetic methods. We also aim to find out whether there is any difference between differently localized tumors by the above mentioned analyses. METHODS We studied DNA index, expression of p53, p16, pRb, MMAC/PTEN1, VEGF, MIB-1 index and chromosomal anomalies which can be detected by array comparative genomic hybridization (CGH) technique. We analyzed the association of the results of these studies with clinical prognosis and tumor localization. We included 53 patients (18 cerebellar, 20 chiasmatic/hypothalamic and 15 hemispheric). Samples were studied from paraffin embedded tumors. RESULTS We found that PAs are mostly diploid and ploidy pattern does not affect the prognosis. The expression of p53, p16, pRb, MMAC/PTEN1 and VEGF was not significantly different between different localizations and could not predict the prognosis. Frequently seen copy number aberrations (CNAs) are: amplification in 1p36.33, 2p11.2, 9p11.2, 9q12, 16p11.2, 19q13.12-q13.2, Xp22.2-p21.3, Xp11.3-p11.22, Xq11.1-q12, Xq13.1, Xq21.1-q21.31, Xq22.3, Xq26.3 and homozygous deletion in 2p11.2, 8p23.1, 16p12.3. Among them, 2p11.2 amp, 9p11.2 amp and 1p36.21 hom del were correlated with prognosis. Moreover, we found a significant correlation between 16p11.2 amp and tumor localization. CONCLUSIONS Differently localized PAs have different properties which make them behave with different biological aggressiveness. PAs demonstrate a significant amount of CNAs that can be detected by a high-resolution study. However, tumor suppressor genes p53, p16, pRb, MMAC/PTEN1 and expression patterns do not play a significant role in PAs.
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Crouse NR, Dahiya S, Gutmann DH. Rethinking Pediatric Gliomas as Developmental Brain Abnormalities. Curr Top Dev Biol 2011; 94:283-308. [DOI: 10.1016/b978-0-12-380916-2.00009-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Tung JN, Tsao TY, Tai CJ, Yeh KT, Cheng YW, Jiang MC. Distribution of lysosome-associated membrane proteins-1 and -2, and cathepsin D in eosinophilic granular bodies: possible relationship to cyst development in pilocytic astrocytomas. J Int Med Res 2010; 38:1354-64. [PMID: 20926008 DOI: 10.1177/147323001003800417] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023] Open
Abstract
Pilocytic astrocytomas are usually cystic; cyst formation within these tumours may result in increased intracranial pressure, due to the effect of their mass, and contribute to cerebral damage. Eosinophilic granular bodies (EGBs) are produced abundantly in pilocytic astrocytomas but their role in disease progression remains unknown. Immunohistochemistry studies showed EGBs to exhibit pronounced reactivity to antibodies against lysosome-associated membrane proteins (LAMP)-1 and LAMP-2, and the lysosomal enzyme cathepsin D. Both LAMP-1 and LAMP-2 showed peripheral rim and granular staining patterns. The EGBs were scattered widely across cysts and, where EGBs aggregated in clusters, were usually close to areas of fluid in the cysts. Most EGBs had nuclei either attached or close by, indicating that the EGBs may be derived from anucleated astrocytes. The results suggest that EGBs, together with other factors, may play a role in the development of cysts in pilocytic astrocytomas.
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Affiliation(s)
- J-N Tung
- Institutes of Medicine, Chung Shan Medical University, Taichung, Taiwan
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Yu J, Deshmukh H, Gutmann RJ, Emnett RJ, Rodriguez FJ, Watson MA, Nagarajan R, Gutmann DH. Alterations of BRAF and HIPK2 loci predominate in sporadic pilocytic astrocytoma. Neurology 2009; 73:1526-31. [PMID: 19794125 DOI: 10.1212/wnl.0b013e3181c0664a] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
OBJECTIVE Independent studies have previously demonstrated that both the HIPK2 and BRAF genes are amplified and rearranged, respectively, in pilocytic astrocytomas (PAs). The purpose of this study was to further investigate the frequency of BRAF and HIPK2 alterations in PAs, the concordance of these events, and their relationship to clinical phenotype. METHODS We performed extensive characterization by array-based copy number assessment (aCGH), HIPK2 copy number analysis, and BRAF rearrangement and mutation analysis in a set of 79 PAs, including 9 tumors from patients with neurofibromatosis type 1 (NF1). RESULTS We identified 1 of 3 previously identified BRAF rearrangements in 42/70 sporadic PAs. An additional 2 tumors with no rearrangement also exhibited BRAF mutation, including a novel 3-base insertion. As predicted from the genomic organization at this locus, 22/36 tumors with BRAF rearrangement also exhibited corresponding HIPK2 amplification. However, 14/36 tumors with BRAF rearrangement had no detectable HIPK2 gene amplification and 6/20 tumors demonstrated HIPK2 amplification without apparent BRAF rearrangement or mutation. Only 12/70 PAs lacked detectable BRAF or HIPK2 alterations. Importantly, none of the 9 PA tumors from NF1 patients exhibited BRAF rearrangement or mutation. CONCLUSIONS BRAF rearrangement represents the most common genetic alteration in sporadic, but not neurofibromatosis type 1-associated, pilocytic astrocytomas (PAs). These findings implicate BRAF in the pathogenesis of these common low-grade astrocytomas in children, and suggest that PAs arise either from NF1 inactivation or BRAF gain of function.
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Affiliation(s)
- J Yu
- Department of Pathology, Washington University School of Medicine, Box 8111, 660 South Euclid Avenue, Saint Louis, MO 63110, USA
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Low-grade astrocytoma in a child with encephalocraniocutaneous lipomatosis. J Neurooncol 2009; 96:437-41. [PMID: 19652916 DOI: 10.1007/s11060-009-9978-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2009] [Accepted: 07/13/2009] [Indexed: 10/20/2022]
Abstract
Encephalocutaneous lipomatosis (ECCL), or Haberland syndrome, is an uncommon congenital disorder with unique cutaneous, ocular and neurological features. In the present article, we describe a 3-year-old boy with ECCL who developed an extensive and recurring intraventricular low-grade glioma with atypical pathological features and elevated mitotic index. Cytogenetic analysis from tumor sample was also performed. This is the first report of a low-grade astrocytoma occurring in a child with ECCL. Whether or not the origin of the tumor is associated to the pathogenesis of the underlying syndrome is a matter for further investigation.
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Mueller S, Chang S. Pediatric brain tumors: current treatment strategies and future therapeutic approaches. Neurotherapeutics 2009; 6:570-86. [PMID: 19560746 PMCID: PMC5084192 DOI: 10.1016/j.nurt.2009.04.006] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2009] [Revised: 04/11/2009] [Accepted: 04/13/2009] [Indexed: 01/19/2023] Open
Abstract
Pediatric CNS tumors are the most common solid tumors of childhood and the second most common cancer after hematological malignancies accounting for approximate 20 to 25% of all primary pediatric tumors. With over 3,000 new cases per year in the United States, childhood CNS tumors are the leading cause of death related to cancer in this population. The prognosis for these patients has improved over the last few decades, but current therapies continue to carry a high risk of significant side effects, especially for the very young. Currently a combination of surgery, radiation, and chemotherapy is often used in children greater than 3 years of age. This article will outline current and future therapeutic strategies for the most common pediatric CNS tumors, including primitive neuroectodermal tumors such as medulloblastoma, as well as astrocytomas and ependymomas.
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Affiliation(s)
- Sabine Mueller
- Department of Neurology, Division of Child Neurology, University of San Francisco, San Francisco, California, USA.
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Forshew T, Tatevossian RG, Lawson ARJ, Ma J, Neale G, Ogunkolade BW, Jones TA, Aarum J, Dalton J, Bailey S, Chaplin T, Carter RL, Gajjar A, Broniscer A, Young BD, Ellison DW, Sheer D. Activation of the ERK/MAPK pathway: a signature genetic defect in posterior fossa pilocytic astrocytomas. J Pathol 2009; 218:172-81. [PMID: 19373855 DOI: 10.1002/path.2558] [Citation(s) in RCA: 216] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
We report genetic aberrations that activate the ERK/MAP kinase pathway in 100% of posterior fossa pilocytic astrocytomas, with a high frequency of gene fusions between KIAA1549 and BRAF among these tumours. These fusions were identified from analysis of focal copy number gains at 7q34, detected using Affymetrix 250K and 6.0 SNP arrays. PCR and sequencing confirmed the presence of five KIAA1549-BRAF fusion variants, along with a single fusion between SRGAP3 and RAF1. The resulting fusion genes lack the auto-inhibitory domains of BRAF and RAF1, which are replaced in-frame by the beginning of KIAA1549 and SRGAP3, respectively, conferring constitutive kinase activity. An activating mutation of KRAS was identified in the single pilocytic astrocytoma without a BRAF or RAF1 fusion. Further fusions and activating mutations in BRAF were identified in 28% of grade II astrocytomas, highlighting the importance of the ERK/MAP kinase pathway in the development of paediatric low-grade gliomas.
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Affiliation(s)
- Tim Forshew
- Neuroscience Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Institute of Cell and Molecular Science, London, UK
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Qaddoumi I, Sultan I, Broniscer A. Pediatric low-grade gliomas and the need for new options for therapy: Why and how? Cancer Biol Ther 2009; 8:4-10. [PMID: 19164945 DOI: 10.4161/cbt.8.1.7237] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Pediatric low-grade gliomas are the most common tumors of the central nervous system in children, accounting for almost 50% of all childhood brain tumors. They are a heterogeneous group of tumors with different histologic subtypes. Most treatment studies address low-grade gliomas as a single entity, depriving us of histology-specific treatment outcomes. This is mostly due to a lack of understanding of tumor biology at the molecular level. Pediatric low-grade gliomas are not benign, and most incompletely resected tumors will progress and negatively affect quality of life. The advancements made in understanding sporadic pilocytic astrocytoma and neurofibromatosis 1-associated pilocytic astrocytoma in particular have paved the way for potential targeted therapy and biological stratification. Such progress in pilocytic astrocytoma needs to be consolidated and expanded to other histologic varieties of pediatric low-grade gliomas.
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Affiliation(s)
- Ibrahim Qaddoumi
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.
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Abstract
Pediatric gliomas comprise a clinically, histologically, and molecularly very heterogeneous group of CNS tumors. In addition, these tumors are largely different from their counterparts occurring in adults, although they are histologically indistinguishable and uniformly classified by the current WHO classification for CNS tumors. Pilocytic astrocytoma (WHO grade I), mainly arising in the posterior fossa, is the most common representative in children, whereas glioblastoma multiforme (WHO grade IV) predominates in adults. When radical surgical resection is possible in low-grade gliomas, it will likely cure the patient. If complete surgical resection is not possible, however, for example in brainstem gliomas, which are defined by their anatomic localization rather than by their histological or molecular features, therapeutic options are limited and prognosis is usually poor. Recent genome-wide analyses applying different microarray-based methods to investigate DNA copy-number aberrations, mRNA expression signatures, and methylation patterns have shed some light on the pathways involved in the pathogenesis of pediatric glio-mas. Mitogen-activated protein kinase (MAPK) and PI3K/AKT signaling were identified as prominent oncogenic pathways in astrocytic tumors in several studies, whereas NOTCH signaling was implicated in the pathogenesis of a subset of intracranial ependymomas. Future therapeutic strategies targeting these (and other) pathways or conferring epigenetic modifications in the tumor might contribute to a better treatment outcome of patients with unresectable or disseminated tumors at diagnosis. Consideration of reliable molecular markers for outcome prediction will most likely result in a better stratification of patients into different risk groups with adjusted treatment intensity in the future.
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Jones DTW, Kocialkowski S, Liu L, Pearson DM, Bäcklund LM, Ichimura K, Collins VP. Tandem duplication producing a novel oncogenic BRAF fusion gene defines the majority of pilocytic astrocytomas. Cancer Res 2008; 68:8673-7. [PMID: 18974108 DOI: 10.1158/0008-5472.can-08-2097] [Citation(s) in RCA: 654] [Impact Index Per Article: 40.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Brain tumors are the most common solid tumors of childhood, and pilocytic astrocytomas (PA) are the most common central nervous system tumor in 5 to 19 year olds. Little is known about the genetic alterations underlying their development. Here, we describe a tandem duplication of approximately 2 Mb at 7q34 occurring in 66% of PAs. This rearrangement, which was not observed in a series of 244 higher-grade astrocytomas, results in an in-frame fusion gene incorporating the kinase domain of the BRAF oncogene. We further show that the resulting fusion protein has constitutive BRAF kinase activity and is able to transform NIH3T3 cells. This is the first report of BRAF activation through rearrangement as a frequent feature in a sporadic tumor. The frequency and specificity of this change underline its potential both as a therapeutic target and as a diagnostic tool.
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Affiliation(s)
- David T W Jones
- Department of Pathology, Division of Molecular Histopathology, University of Cambridge, Cambridge, United Kingdom.
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Clinicopathological features and global genomic copy number alterations of pilomyxoid astrocytoma in the hypothalamus/optic pathway: comparative analysis with pilocytic astrocytoma using array-based comparative genomic hybridization. Mod Pathol 2008; 21:1345-56. [PMID: 18622384 DOI: 10.1038/modpathol.2008.88] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Pilomyxoid astrocytoma is a recently identified variant of pilocytic astrocytoma. We studied 11 circumscribed astrocytomas with focal (n=5) or diffuse (n=6) pilomyxoid features and compared them with 17 pilocytic astrocytomas from the hypothalamic/chiasmatic region in children. In one patient, a tumor that recurred after initial surgery had changed from pure-form pilomyxoid astrocytoma to the mixed form. The presence of a pilomyxoid area was associated with shorter survival. Next, we compared the comprehensive genome copy number changes in the pilomyxoid astrocytoma (n=4) with those in pilocytic astrocytoma (n=6) cases by array-based comparative genomic hybridization. The number of lost clones was larger in pilomyxoid astrocytoma than in pilocytic astrocytoma. Clones located in chromosome 8q24.3 were frequently gained in pilocytic astrocytoma (four of six) and in pilomyxoid astrocytoma (one of four). Clones located in 9p24.3 and 15q26.3 were lost in all of the pilomyxoid astrocytomas and in five of the pilocytic astrocytomas. Those in 8p23.3 showed a copy number loss in three of the pilomyxoid astrocytomas and four of the pilocytic astrocytomas. The frequency of copy number changes was significantly different between pilomyxoid astrocytoma and pilocytic astrocytoma in 47 (3.6%) clones, 20 of them having been located in 2p, 10 in 2q, and 11 in 3q. An unsupervised hierarchical clustering analysis classified the cases into three clusters: one pilomyxoid astrocytoma patient into one cluster, two pilomyxoid astrocytoma patients into another cluster, and six pilocytic astrocytoma patients and one pilomyxoid astrocytoma patient into the third cluster. In conclusion, the presence of mixed-form pilomyxoid astrocytoma, the acquisition of pilocytic astrocytoma features in a recurrent tumor in pure-form pilomyxoid astrocytoma, and the above results of the genome-wide gene copy number analysis suggest that pilomyxoid astrocytoma might be a pathologically and genetically related, aggressive variant of pilocytic astrocytoma with partially different genetic alterations.
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Genomic deletions correlate with underexpression of novel candidate genes at six loci in pediatric pilocytic astrocytoma. Neoplasia 2008; 10:757-72. [PMID: 18670637 DOI: 10.1593/neo.07914] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2007] [Revised: 05/09/2008] [Accepted: 05/11/2008] [Indexed: 01/24/2023] Open
Abstract
The molecular pathogenesis of pediatric pilocytic astrocytoma (PA) is not well defined. Previous cytogenetic and molecular studies have not identified nonrandom genetic aberrations. To correlate differential gene expression and genomic copy number aberrations (CNAs) in PA, we have used Affymetrix GeneChip HG_U133A to generate gene expression profiles of 19 pediatric patients and the SpectralChip 2600 to investigate CNAs in 11 of these tumors. Hierarchical clustering according to expression profile similarity grouped tumors and controls separately. We identified 1844 genes that showed significant differential expression between tumor and normal controls, with a large number clearly influencing phosphatidylinositol and mitogen-activated protein kinase signaling in PA. Most CNAs identified in this study were single-clone alterations. However, a small region of loss involving up to seven adjacent clones at 7q11.23 was observed in seven tumors and correlated with the underexpression of BCL7B. Loss of four individual clones was also associated with reduced gene expression including SH3GL2 at 9p21.2-p23, BCL7A (which shares 90% sequence homology with BCL7B) at 12q24.33, DRD1IP at 10q26.3, and TUBG2 and CNTNAP1 at 17q21.31. Moreover, the down-regulation of FOXG1B at 14q12 correlated with loss within the gene promoter region in most tumors. This is the first study to correlate differential gene expression with CNAs in PA.
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Abstract
Relatively little is known about the molecular changes that promote the formation or growth of pilocytic astrocytomas. We investigated genomic alterations in 25 pilocytic astrocytomas, including 5 supratentorial and 20 posterior fossa tumors, using oligonucleotide array comparative genomic hybridization. Large changes were identified in 7 tumors and included gains of chromosomes 5, 6, and 7 and losses of chromosomes 16, 17, 19, and 22. The most common alteration was a 1.9-MB region of low-level gain at chromosome 7q34 identified in 17 of 20 posterior fossa tumors. In most tumors, the region of gain ended within the BRAF locus and encompassed only exons that encode the BRAF kinase domain. We confirmed copy number increase at the 7q34 locus using quantitative polymerase chain reaction with primers adjacent to the HIPK2, RAB19B, and BRAF genes. Western blot analysis revealed that 3 of 6 pilocytic astrocytomas with 7q34 gain contained high levels of phosphorylated extracellular signal-related kinase (ERK) and nitrogen-activated protein kinase/ERK kinase (MEK), while 1 tumor lacking 7q34 gain and 2 normal brain specimens did not. Immunohistochemical stains of a tissue microarray containing 43 pilocytic astrocytoma identified ERK phosphorylation in 35 (81%). These data indicate that focal gains at chromosome 7q34 and increased BRAF-MEK-ERK signaling are common findings in sporadic pilocytic astrocytomas.
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Pfister S, Janzarik WG, Remke M, Ernst A, Werft W, Becker N, Toedt G, Wittmann A, Kratz C, Olbrich H, Ahmadi R, Thieme B, Joos S, Radlwimmer B, Kulozik A, Pietsch T, Herold-Mende C, Gnekow A, Reifenberger G, Korshunov A, Scheurlen W, Omran H, Lichter P. BRAF gene duplication constitutes a mechanism of MAPK pathway activation in low-grade astrocytomas. J Clin Invest 2008; 118:1739-49. [PMID: 18398503 DOI: 10.1172/jci33656] [Citation(s) in RCA: 360] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2007] [Accepted: 02/13/2008] [Indexed: 12/30/2022] Open
Abstract
The molecular pathogenesis of pediatric astrocytomas is still poorly understood. To further understand the genetic abnormalities associated with these tumors, we performed a genome-wide analysis of DNA copy number aberrations in pediatric low-grade astrocytomas by using array-based comparative genomic hybridization. Duplication of the BRAF protooncogene was the most frequent genomic aberration, and tumors with BRAF duplication showed significantly increased mRNA levels of BRAF and a downstream target, CCND1, as compared with tumors without duplication. Furthermore, denaturing HPLC showed that activating BRAF mutations were detected in some of the tumors without BRAF duplication. Similarly, a marked proportion of low-grade astrocytomas from adult patients also had BRAF duplication. Both the stable silencing of BRAF through shRNA lentiviral transduction and pharmacological inhibition of MEK1/2, the immediate downstream phosphorylation target of BRAF, blocked the proliferation and arrested the growth of cultured tumor cells derived from low-grade gliomas. Our findings implicate aberrant activation of the MAPK pathway due to gene duplication or mutation of BRAF as a molecular mechanism of pathogenesis in low-grade astrocytomas and suggest inhibition of the MAPK pathway as a potential treatment.
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Affiliation(s)
- Stefan Pfister
- Division Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
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High-resolution, dual-platform aCGH analysis reveals frequent HIPK2 amplification and increased expression in pilocytic astrocytomas. Oncogene 2008; 27:4745-51. [DOI: 10.1038/onc.2008.110] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Sharma MK, Mansur DB, Reifenberger G, Perry A, Leonard JR, Aldape KD, Albin MG, Emnett RJ, Loeser S, Watson MA, Nagarajan R, Gutmann DH. Distinct genetic signatures among pilocytic astrocytomas relate to their brain region origin. Cancer Res 2007; 67:890-900. [PMID: 17283119 DOI: 10.1158/0008-5472.can-06-0973] [Citation(s) in RCA: 141] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Pilocytic astrocytomas (PAs) are the most common glioma in children. Whereas many PAs are slow-growing or clinically indolent, others exhibit more aggressive features with tumor recurrence and death. To identify genetic signatures that might predict PA clinical behavior, we did gene expression profiling on 41 primary PAs arising sporadically and in patients with neurofibromatosis type 1 (NF1). Whereas no expression signature was found that could discriminate clinically aggressive or recurrent tumors from more indolent cases, PAs arising in patients with NF1 did exhibit a unique gene expression pattern. In addition, we identified a gene expression signature that stratified PAs by location (supratentorial versus infratentorial). Lastly, we also identified a gene expression pattern common to PAs and normal mouse astrocytes and neural stem cells from these distinct brain regions as well as a gene expression pattern shared between PAs and another human glial tumor (ependymoma) arising supratentorially compared with those originating in the posterior fossa. These results suggest that glial tumors share an intrinsic, lineage-specific molecular signature that reflects the brain region in which their nonmalignant predecessors originated.
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Affiliation(s)
- Mukesh K Sharma
- Department of Neurology, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA
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Jones DTW, Ichimura K, Liu L, Pearson DM, Plant K, Collins VP. Genomic analysis of pilocytic astrocytomas at 0.97 Mb resolution shows an increasing tendency toward chromosomal copy number change with age. J Neuropathol Exp Neurol 2006; 65:1049-58. [PMID: 17086101 PMCID: PMC2761618 DOI: 10.1097/01.jnen.0000240465.33628.87] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Brain tumors are the most common solid tumors of childhood, accounting for over 20% of cancers in children under 15 years of age. Pilocytic astrocytomas (PAs), World Health Organization grade I, are one of the most frequently occurring childhood brain tumors, yet little is known about genetic changes characterizing this entity. We have used microarray comparative genomic hybridization at 0.97 Mb resolution to study a series of PAs (n = 44). No copy number abnormality was seen in 64% of cases at this resolution. However, whole chromosomal gain (median 5 chromosomes affected) occurred in 32% of tumors. The most frequently affected chromosomes were 5 and 7 (11 of 44 cases each) followed by 6, 11, 15, and 20 (greater than 10% of cases each). Findings were confirmed by fluorescence in situ hybridization and microsatellite analysis in a subset of tumors. Chromosomal gain was significantly more frequent in PAs from patients over 15 years old (p = 0.03, Fisher exact test). The number of chromosomes involved was also significantly greater in the older group (p = 0.02, Mann-Whitney U test). One case (2%) showed a region of gain on chromosome 3 and one (2%) a deletion on 6q as their sole abnormalities. This is the first genomewide study to show this nonrandom pattern of genetic alteration in pilocytic astrocytomas.
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Affiliation(s)
- David T W Jones
- Department of Pathology, Division of Molecular Histopathology, Cambridge University, Cambridge, UK.
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21
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Tamber MS, Bansal K, Liang ML, Mainprize TG, Salhia B, Northcott P, Taylor M, Rutka JT. Current concepts in the molecular genetics of pediatric brain tumors: implications for emerging therapies. Childs Nerv Syst 2006; 22:1379-94. [PMID: 16951964 DOI: 10.1007/s00381-006-0187-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2006] [Indexed: 12/18/2022]
Abstract
BACKGROUND The revolution in molecular biology that has taken place over the past 2 decades has provided researchers with new and powerful tools for detailed study of the molecular mechanisms giving rise to the spectrum of pediatric brain tumors. Application of these tools has greatly advanced our understanding of the molecular pathogenesis of these lesions. REVIEW After familiarizing readers with some promising new techniques in the field of oncogenomics, this review will present the current state of knowledge as it pertains to the molecular biology of pediatric brain neoplasms. Along the way, we hope to highlight specific instances where the detailed mechanistic knowledge acquired thus far may be exploited for therapeutic advantage.
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Affiliation(s)
- Mandeep S Tamber
- Division of Neurosurgery, The Hospital for Sick Children, The University of Toronto, Toronto, Ontario, Canada
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22
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Koeller KK, Rushing EJ. From the archives of the AFIP: pilocytic astrocytoma: radiologic-pathologic correlation. Radiographics 2005; 24:1693-708. [PMID: 15537977 DOI: 10.1148/rg.246045146] [Citation(s) in RCA: 137] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Pilocytic astrocytoma is the most common pediatric central nervous system glial neoplasm and the most common pediatric cerebellar tumor. This tumor has a noteworthy benign biologic behavior that translates into an extremely high survival rate-94% at 10 years-that is by far the best of any glial tumor. Most patients present in the first 2 decades, and clinical symptoms and signs are usually of several months duration and directly related to the specific location of the tumor. The cerebellum, optic nerve and chiasm, and hypothalamic region are the most common locations, but the tumor can also be found in the cerebral hemisphere, ventricles, and spinal cord. Surgical resection is the treatment of choice for all tumors, except for those involving the optic pathway and hypothalamic region, which may be treated with radiation therapy and chemotherapy. Cross-sectional imaging often demonstrates a classic appearance: a cystic mass with an enhancing mural nodule. Less common appearances are quite nonspecific. Surrounding vasogenic edema is rarely present, and this feature provides a valuable clue to the correct diagnosis. Accurate interpretation of imaging studies plays an essential role in directing treatment of these tumors, particularly when they arise in the optic pathway of patients with neurofibromatosis type 1. Disseminated disease and recurrence are extremely rare.
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Affiliation(s)
- Kelly K Koeller
- Department of Radiologic Pathology, Armed Forces Institute of Pathology, 14th St at Alaska Ave, Bldg 54, Rm M-121, Washington, DC 20306-6000, USA.
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Bayani J, Pandita A, Squire JA. Molecular cytogenetic analysis in the study of brain tumors: findings and applications. Neurosurg Focus 2005; 19:E1. [PMID: 16398459 DOI: 10.3171/foc.2005.19.5.2] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Classic cytogenetics has evolved from black and white to technicolor images of chromosomes as a result of advances in fluorescence in situ hybridization (FISH) techniques, and is now called molecular cytogenetics. Improvements in the quality and diversity of probes suitable for FISH, coupled with advances in computerized image analysis, now permit the genome or tissue of interest to be analyzed in detail on a glass slide. It is evident that the growing list of options for cytogenetic analysis has improved the understanding of chromosomal changes in disease initiation, progression, and response to treatment. The contributions of classic and molecular cytogenetics to the study of brain tumors have provided scientists and clinicians alike with new avenues for investigation. In this review the authors summarize the contributions of molecular cytogenetics to the study of brain tumors, encompassing the findings of classic cytogenetics, interphase- and metaphase-based FISH studies, spectral karyotyping, and metaphase- and array-based comparative genomic hybridization. In addition, this review also details the role of molecular cytogenetic techniques in other aspects of understanding the pathogenesis of brain tumors, including xenograft, cancer stem cell, and telomere length studies.
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Affiliation(s)
- Jane Bayani
- Department of Applied Molecular Oncology, Ontario Cancer Institute, Princess Margaret Hospital, University Health Network, Ontario, Canada.
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Abstract
In the last decade, the molecular biology revolution has advanced considerably. These advances have enhanced our understanding of the genetic underpinnings of human brain tumors in general, and pediatric brain tumors in particular. We now know that many pediatric brain tumors arise from disturbances in developmentally regulated signaling pathways. The medulloblastoma, a tumor in which the developmental Hedgehog and WNT pathways have gone awry, is a prime example of this. New techniques in genetic engineering have allowed for the creation of sophisticated mouse models of brain tumors that recapitulate the human disease. Many laboratories are now using cDNA microarrays to study the expression level of thousands of genes that may be aberrantly expressed in brain tumors when compared to normal control cells. In the next decade, the use of several new molecular techniques to establish brain tumor diagnoses will likely become standard tools in the diagnostics and treatment stratification of children with central nervous system tumors.
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Affiliation(s)
- Torsten Pietsch
- Department of Neuropathology, University of Bonn Medical Center, Bonn, Germany
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25
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Abstract
Our current knowledge of the molecular pathogenesis of the diffuse adult astrocytic tumours is vast if compared to 20 years ago, yet we are far from understanding the details of this process at the molecular level and using such an understanding to logically and specifically treat patients' tumours. In other astrocytic tumours we have little or no knowledge of the molecular processes. This article will attempt to summarise the histological classification criteria and genetic data for all the astrocytic tumours. The current World Health Organisation classification lists six entities, some with subgroups. Common problems associated with the diagnosis of these tumours are outlined. While the molecular findings are not as yet used clinically, we are approaching a time when the histological investigation will have to be supplemented with molecular data to ensure the best choice of treatment for the patient and as an accurate indicator of prognosis.
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Affiliation(s)
- Koichi Ichimura
- Department of Pathology, University of Cambridge, Cambridge, UK
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26
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Affiliation(s)
- V P Collins
- Department of Histopathology, University of Cambridge, Addenbrooke's Hospital, UK.
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Pollack IF, Hamilton RL, Finkelstein SD, Lieberman F. Molecular abnormalities and correlations with tumor response and outcome in glioma patients. Neuroimaging Clin N Am 2002; 12:627-39. [PMID: 12687916 DOI: 10.1016/s1052-5149(02)00030-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular analysis approaches hold promise to refine the management of patients with malignant gliomas. An important step in the application of these techniques to guide clinical decision-making involves transitioning these approaches from the research setting into the clinical diagnostic arena, using methods that can be performed rapidly and reliably on surgically obtained tumor specimens. Many centers have begun this process for the detection of chromosome 1p and 19q deletions in oligodendroglial neoplasms. It is likely that the current limited portfolio of prognostic markers will be increased substantially during the next several years as innovative techniques for tumor genotyping and gene expression profiling help to identify additional correlates of tumor prognosis. An associated challenge involves demonstrating that biological stratification can support therapeutic stratification that will influence, rather than merely predict, the outcome of patients with brain tumors. The realization of this long-range goal will require the identification of novel therapeutic strategies that hold promise for improving the outcome of molecularly defined subsets of high-grade gliomas, which as a group remain largely resistant to conventional therapies.
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Affiliation(s)
- Ian F Pollack
- Department of Neurosurgery, University of Pittsburgh Medical Center and the Children's Hospital of Pittsburgh, 3705 Fifth Avenue, Pittsburgh, PA 15213, USA
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Gutmann DH, Giovannini M. Mouse models of neurofibromatosis 1 and 2. Neoplasia 2002; 4:279-90. [PMID: 12082543 PMCID: PMC1531708 DOI: 10.1038/sj.neo.7900249] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2002] [Accepted: 03/08/2002] [Indexed: 11/08/2022]
Abstract
The neurofibromatoses represent two of the most common inherited tumor predisposition syndromes affecting the nervous system. Individuals with neurofibromatosis 1 (NF1) are prone to the development of astrocytomas and peripheral nerve sheath tumors whereas those affected with neurofibromatosis 2 (NF2) develop schwannomas and meningiomas. The development of traditional homozygous knockout mice has provided insights into the roles of the NF1 and NF2 genes during development and in differentiation, but has been less instructive regarding the contribution of NF1 and NF2 dysfunction to the pathogenesis of specific benign and malignant tumors. Recent progress employing novel mouse targeting strategies has begun to illuminate the roles of the NF1 and NF2 gene products in the molecular pathogenesis of NF-associated tumors.
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Affiliation(s)
- David H Gutmann
- Department of Neurology, Washington University School of Medicine, Box 8111, 660 S. Euclid Avenue, St. Louis, MO 63110, USA.
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Bajenaru ML, Zhu Y, Hedrick NM, Donahoe J, Parada LF, Gutmann DH. Astrocyte-specific inactivation of the neurofibromatosis 1 gene (NF1) is insufficient for astrocytoma formation. Mol Cell Biol 2002; 22:5100-13. [PMID: 12077339 PMCID: PMC139771 DOI: 10.1128/mcb.22.14.5100-5113.2002] [Citation(s) in RCA: 239] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2002] [Revised: 04/04/2002] [Accepted: 04/19/2002] [Indexed: 11/20/2022] Open
Abstract
Individuals with the neurofibromatosis 1 (NF1) inherited tumor syndrome develop low-grade gliomas (astrocytomas) at an increased frequency, suggesting that the NF1 gene is a critical growth regulator for astrocytes. In an effort to determine the contribution of the NF1 gene product, neurofibromin, to astrocyte growth regulation and NF1-associated astrocytoma formation, we generated astrocyte-specific Nf1 conditional knockout mice (Nf1(GFAP)CKO) by using Cre/LoxP technology. Transgenic mice were developed in which Cre recombinase was specifically expressed in astrocytes by embryonic day 14.5. Successive intercrossing with mice bearing a conditional Nf1 allele (Nf1flox) resulted in GFAP-Cre Nf1flox/flox (Nf1(GFAP)CKO) animals. No astrocytoma formation or neurological impairment was observed in Nf1(GFAP)CKO mice after 20 months, but increased numbers of proliferating astrocytes were observed in several brain regions. To determine the consequence of Nf1 inactivation at different developmental times, the growth properties of embryonic day 12.5 and postnatal day 2 Nf1 null astrocytes were analyzed. Nf1 null astrocytes exhibited increased proliferation but lacked tumorigenic properties in vitro and did not form tumors when injected into immunocompromised mouse brains in vivo. Collectively, our results suggest that loss of neurofibromin is not sufficient for astrocytoma formation in mice and that other genetic or environmental factors might influence NF1-associated glioma tumorigenesis.
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Affiliation(s)
- Michaela Livia Bajenaru
- Department of Neurology, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA
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Abstract
Under the current World Health Organization (WHO) classification, gliomas can be divided into diffuse variants such as astrocytoma, oligodendroglioma, and mixed oligo-astrocytoma versus more discrete subtypes such as pilocytic astrocytoma and other less common entities. These tumors have been assigned histologic grades ranging from I to IV to reflect expected biological behavior. The ever-growing body of literature on genetic alterations of glial neoplasms promises to augment therapeutic and prognostic information in the future. An important example is the 1p and 19q deletions in oligodendrogliomas that recently have been associated with chemosensitivity and prolonged patient survival. This article reviews the pathology of low- and intermediate-grade gliomas, highlighting practical diagnostic and prognostic issues.
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Affiliation(s)
- C E Fuller
- Division of Neuropathology, Washington University School of Medicine, St. Louis, MO, USA
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31
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Szymas J, Wolf G, Petersen S, Schluens K, Nowak S, Petersen I. Comparative genomic hybridization indicating two distinct subgroups of pilocytic astrocytomas. Neurosurg Focus 2000. [DOI: 10.3171/foc.2000.8.4.9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Object
The authors investigated the spectrum of chromosomal imbalances of pilocytic astrocytoma by using comparative genomic hybridization (CGH).
Methods
Tumor DNA was extracted from surgically obtained samples of 18 pilocytic astrocytomas that were examined for the presence of neoplastic tissue on frozen sections. Comparative genomic hybridization was performed using standard procedures, and digital image analysis was conducted using out by custom-made software. The chromosomal alterations were determined by a statistical procedure in which Student's t-test (99% confidence interval) was used. Details on CGH analysis and individual ratio profiles are available at http://amba.charite.de/cgh/.
Conclusions
The results suggests the presence of two distinct genetic subgroups of pilocytic astrocytoma, with imbalances of chromosome 19 being the major change for differentiation. In the first group (10 samples), deletions on chromosome 19 were shown as well as multiple gains mainly on chromosomes 5 and 6q but also on chromosomes 4, 7, 8, 10, and 11. The second group (eight samples) was characterized by overrepresentation on chromosomes 19p and 22q, which were associated with deletions on 4q, 5q, 6q, 9p, 13q, and 18q. To understand the diverse biological and clinical behavior exhibited by this tumor type, it is important that pilocytic astrocytomas be classified into distinct subgroups according to their genetic makeup.
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Fontes P, Marques M, Costa M, Fernandes T. External beam radiation therapy in pilocytic astrocytoma of cerebellum. Neurocirugia (Astur) 2000. [DOI: 10.1016/s1130-1473(00)70748-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Abstract
The last 10 years has seen major improvements in our understanding of the genetic anomalies that lie behind the development and progression of human astrocytic tumors. The least aggressive astrocytomas frequently show loss of wild type p53 as well as losses of alleles from a number of regions of the genome. The genes targeted have yet to be identified. The most aggressive tumors, the glioblastomas, show mutations affecting the cellular mechanisms controlling entry into the S-phase of the cell cycle. The picture has become more complex as regards the mechanisms targeted. The heterogeneous genetic abnormalities reported previously in individual tumors of the same type have become easier to understand with the realization that they represent the mutation of different genes that code for components of the same cellular control mechanisms. There remain many routes to explore before we understand in detail the molecular mechanisms behind the phenotype of these tumors.
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Affiliation(s)
- V P Collins
- Division of Clinical Molecular Pathology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 2QQ, UK
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Abstract
Conventional therapies such as surgery, radiotherapy and, to a lesser extent, chemotherapy have produced significant increases in survival in patients with some types of brain tumours such as medulloblastoma. However, in many other types of brain tumour in both adults and children, the effect of these modalities has been more modest. A thorough understanding of the biology of malignant brain tumours is likely to provide the background for the development of new leads that might be amenable to therapeutic exploitation. This review examines some aspects of glioma biology that have been reported in the past 12 months, and which might be translated into clinical application.
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Affiliation(s)
- J L Darling
- University Department of Neurosurgery, Institute of Neurology, National Hospital for Neurology and Neurosurgery, London, UK
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