1
|
Roy DM, Walsh LA, Desrichard A, Huse JT, Wu W, Gao J, Bose P, Lee W, Chan TA. Integrated Genomics for Pinpointing Survival Loci within Arm-Level Somatic Copy Number Alterations. Cancer Cell 2016; 29:737-750. [PMID: 27165745 PMCID: PMC4864611 DOI: 10.1016/j.ccell.2016.03.025] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 12/22/2015] [Accepted: 03/24/2016] [Indexed: 01/04/2023]
Abstract
The identification of driver loci underlying arm-level somatic copy number alterations (SCNAs) in cancer has remained challenging and incomplete. Here, we assess the relative impact and present a detailed landscape of arm-level SCNAs in 10,985 patient samples across 33 cancer types from The Cancer Genome Atlas (TCGA). Furthermore, using chromosome 9p loss in lower grade glioma (LGG) as a model, we employ a unique multi-tiered genomic dissection strategy using 540 patients from three independent LGG datasets to identify genetic loci that govern tumor aggressiveness and poor survival. This comprehensive approach uncovered several 9p loss-specific prognostic markers, validated existing ones, and redefined the impact of CDKN2A loss in LGG.
Collapse
Affiliation(s)
- David M Roy
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY 10065, USA
| | - Logan A Walsh
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Alexis Desrichard
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jason T Huse
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Brain Tumor Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Wei Wu
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - JianJiong Gao
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Promita Bose
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - William Lee
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Timothy A Chan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Brain Tumor Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Cellular and Developmental Biology, Weill Cornell Medical College, New York, NY 10065, USA.
| |
Collapse
|
2
|
Mwita CC, Muthoka J, Maina S, Mulingwa P, Gwer S. Early management of traumatic brain injury in a Tertiary hospital in Central Kenya: A clinical audit. J Neurosci Rural Pract 2016; 7:97-101. [PMID: 26933354 PMCID: PMC4750351 DOI: 10.4103/0976-3147.165390] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Background: Traumatic brain injury (TBI) is a major cause of death and disability worldwide and is mostly attributed to road traffic accidents in resource-poor areas. However, access to neurosurgical care is poor in these settings and patients in need of neurosurgical procedures are often managed by general practitioners or surgeons. Materials and Methods: A retrospective clinical audit of the initial management of patients with TBI in Thika Level 5 Hospital (TL5H), a Tertiary Hospital in Central Kenya. Seventeen audit criteria divided into five clinical domains were identified and patient case notes reviewed for compliance with each criterion. Data were analyzed separately for those below 13 years owing to differences in response to brain trauma in those below this age. Results: Overall, there was poor compliance with audit criteria in both groups. Among those below 13 years of age, only 3 out of 17 criteria achieved compliance and 4 out of 17 criteria achieved compliance for those above 13 years of age. Assessment for the need for a cervical radiograph (7.1% and 8.8% compliance) and administration of oxygen (21.4% and 20.6% compliance) had the worst performance in both groups. Conclusion: Poor compliance to audit criteria indicates the low quality of care for patients with TBI in TL5H. Quality improvement strategies with follow-up audits are needed to improve care. There is a need to develop and enforce evidence-based protocols and guidelines for use in the management of patients with TBI in sub-Saharan Africa.
Collapse
Affiliation(s)
- Clifford Chacha Mwita
- Department of Surgery, Thika Level 5 Hospital, Thika, Kenya; Evidence and Translation Unit, Afya Research Africa, Africa; Department of Surgery, Moi University, Eldoret, Kenya
| | - Johnstone Muthoka
- Department of Surgery, Thika Level 5 Hospital, Thika, Kenya; Department of Human Anatomy, Kenya Methodist University, Meru, Kenya
| | - Stephen Maina
- Department of Surgery, Thika Level 5 Hospital, Thika, Kenya
| | | | - Samson Gwer
- Department of Human Physiology, Kenyatta University, Nairobi, Kenya
| |
Collapse
|
3
|
Loss of Heterozygosity of 9p Is Associated with Poorer Survival in Patients with Gliomas. Mol Neurobiol 2015; 53:6407-6412. [PMID: 26582467 DOI: 10.1007/s12035-015-9523-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Accepted: 11/03/2015] [Indexed: 01/11/2023]
Abstract
The prognostic factors associated with the survival of glioma patients have not been well established. Loss of heterozygosity (LOH) of 9p was known to be a typical molecular signature of gliomas, but it was still unclear whether LOH of 9p was associated with poorer survival in patients with gliomas. We searched PubMed and Embase databases from the earliest records to May 2015 to identify studies that met the inclusion criteria. Either a fixed- or a random-effects model was used to calculate the pooled hazard ratio (HR) according to the between-study heterogeneity. Thirteen eligible studies involving 1465 cases of gliomas were included in the meta-analysis. There was little between-study heterogeneity (I 2 = 15 %), and the fixed-effects model was used to calculate the pooled HR. Meta-analysis of total 13 studies showed that LOH of 9p was significantly associated with poorer prognosis of glioma patients (HR = 1.39, 95%CI 1.17-1.64, P = 0.0002). Meta-analysis of eight studies reporting adjusted estimates showed that LOH of 9p was independently associated with poorer prognosis of glioma patients (HR = 1.40, 95%CI 1.14-1.72, P = 0.001). Subgroup analysis by types of gliomas showed that LOH of 9p was significantly associated with poorer prognosis in patients with glioblastoma (HR = 1.34, 95%CI 1.01-1.78, P = 0.04). There was no obvious risk of publication bias shown in the funnel plot. LOH of 9p is significantly associated with poorer prognosis of glioma patients, which is a useful biomarker in predicting patients' survival.
Collapse
|
4
|
Lhotska H, Zemanova Z, Cechova H, Ransdorfova S, Lizcova L, Kramar F, Krejcik Z, Svobodova K, Bystricka D, Hrabal P, Dohnalova A, Michalova K. Genetic and epigenetic characterization of low-grade gliomas reveals frequent methylation of the MLH3 gene. Genes Chromosomes Cancer 2015; 54:655-67. [PMID: 26303387 DOI: 10.1002/gcc.22266] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 04/30/2015] [Accepted: 04/30/2015] [Indexed: 12/31/2022] Open
Abstract
Diffuse astrocytomas and oligodendrogliomas (WHO grade II) are the most common histological subtypes of low-grade gliomas (LGGs). Several molecular and epigenetic markers have been identified that predict tumor progression. Our aim was in detail to investigate the genetic and epigenetic background of LGGs and to identify new markers that might play a role in tumor behavior. Twenty-three patients with oligodendroglioma or oligoastrocytoma (LGO) and 22 patients with diffuse astrocytoma (LGA) were investigated using several molecular-cytogenetic and molecular methods to assess their copy number variations, mutational status and level of promoter methylation. The most frequent findings were a 1p/19q codeletion in 83% of LGO and copy-neutral loss of heterozygosity (CN-LOH) of 17p in 72% of LGA. Somatic mutations in the isocitrate dehydrogenase 1 or 2 (IDH1/IDH2) genes were detected in 96% of LGO and 91% of LGA. The O-6-methylguanine-DNA-methyltransferase (MGMT) promoter was methylated in 83% of LGO and 59% of LGA. MutL homolog 3 (MLH3) promoter methylation was observed in 61% of LGO and 27% of LGA. Methylation of the MGMT promoter, 1p/19q codeletion, mutated IDH1, and CN-LOH of 17p were the most frequent genetic aberrations in LGGs. The findings were more diverse in LGA than in LGO. To the best of our knowledge, this is the first time description of methylation of the MLH3 gene promoter in LGGs. Further studies are required to determine the role of the methylated MLH3 promoter and the other aberrations detected.
Collapse
Affiliation(s)
- Halka Lhotska
- Center of Oncocytogenetics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and 1st Faculty of Medicine, Charles University, Prague 2, Czech Republic
| | - Zuzana Zemanova
- Center of Oncocytogenetics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and 1st Faculty of Medicine, Charles University, Prague 2, Czech Republic
| | - Hana Cechova
- Department of Molecular Genetics, Institute of Hematology and Blood Transfusion, Prague 2, Czech Republic
| | - Sarka Ransdorfova
- Cytogenetic Department, Institute of Hematology and Blood transfusion, Prague 2, Czech Republic
| | - Libuse Lizcova
- Center of Oncocytogenetics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and 1st Faculty of Medicine, Charles University, Prague 2, Czech Republic
| | - Filip Kramar
- Department of Neurosurgery, Central Military Hospital and 1st Faculty of Medicine, Charles University, Prague 6, Czech Republic
| | - Zdenek Krejcik
- Department of Molecular Genetics, Institute of Hematology and Blood Transfusion, Prague 2, Czech Republic
| | - Karla Svobodova
- Center of Oncocytogenetics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and 1st Faculty of Medicine, Charles University, Prague 2, Czech Republic
| | - Dagmar Bystricka
- Center of Oncocytogenetics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and 1st Faculty of Medicine, Charles University, Prague 2, Czech Republic
| | - Petr Hrabal
- Department of Neurosurgery, Central Military Hospital and 1st Faculty of Medicine, Charles University, Prague 6, Czech Republic
| | - Alena Dohnalova
- Institute of Physiology, 1st Faculty of Medicine, Charles University, Prague 2, Czech Republic
| | - Kyra Michalova
- Center of Oncocytogenetics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and 1st Faculty of Medicine, Charles University, Prague 2, Czech Republic.,Cytogenetic Department, Institute of Hematology and Blood transfusion, Prague 2, Czech Republic
| |
Collapse
|
5
|
Cohen A, Sato M, Aldape K, Mason CC, Alfaro-Munoz K, Heathcock L, South ST, Abegglen LM, Schiffman JD, Colman H. DNA copy number analysis of Grade II-III and Grade IV gliomas reveals differences in molecular ontogeny including chromothripsis associated with IDH mutation status. Acta Neuropathol Commun 2015; 3:34. [PMID: 26091668 PMCID: PMC4474351 DOI: 10.1186/s40478-015-0213-3] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 05/13/2015] [Indexed: 12/21/2022] Open
Abstract
Introduction Isocitrate dehydrogenase (IDH) mutation status and grade define subgroups of diffuse gliomas differing based on age, tumor location, presentation, and prognosis. While some biologic differences between IDH mutated (IDHmut) and wild-type (IDHwt) gliomas are clear, the distinct alterations associated with progression of the two subtypes to glioblastoma (GBM, Grade IV) have not been well described. We analyzed copy number alterations (CNAs) across grades (Grade II–III and GBM) in both IDHmut and IDHwt infiltrating gliomas using molecular inversion probe arrays. Results Ninety four patient samples were divided into four groups: Grade II–III IDHwt (n = 17), Grade II–III IDHmut (n = 28), GBM IDHwt (n = 25), and GBM IDHmut (n = 24). We validated prior observations that IDHwt GBM have a high frequency of chromosome 7 gain (including EGFR) and chromosome 10 loss (including PTEN) compared with IDHmut GBM. Hierarchical clustering of IDHmut gliomas demonstrated distinct CNA patterns distinguishing lower grade gliomas versus GBM. However, similar hierarchical clustering of IDHwt gliomas demonstrated no CNA distinction between lower grade glioma and GBM. Functional analyses showed that IDHwt gliomas had more chromosome gains in regions containing receptor tyrosine kinase pathways. In contrast, IDHmut gliomas more commonly demonstrated amplification of cyclins and cyclin dependent kinase genes. One of the most common alterations associated with transformation of lower grade to GBM IDHmut gliomas was the loss of chromosomal regions surrounding PTEN. IDHmut GBM tumors demonstrated significantly higher levels of overall CNAs compared to lower grade IDHmut tumors and all grades of IDHwt tumors, and IDHmut GBMs also demonstrated significant increase in incidence of chromothripsis. Conclusions Taken together, these analyses demonstrate distinct molecular ontogeny between IDHwt and IDHmut gliomas. Our data also support the novel findings that malignant progression of IDHmut gliomas to GBM involves increased genomic instability and genomic catastrophe, while IDHwt lower grade tumors are virtually identical to GBMs at the level of DNA copy number alterations. Electronic supplementary material The online version of this article (doi:10.1186/s40478-015-0213-3) contains supplementary material, which is available to authorized users.
Collapse
|
6
|
Thuy MN, Kam JK, Lee GC, Tao PL, Ling DQ, Cheng M, Goh SK, Papachristos AJ, Shukla L, Wall KL, Smoll NR, Jones JJ, Gikenye N, Soh B, Moffat B, Johnson N, Drummond KJ. A novel literature-based approach to identify genetic and molecular predictors of survival in glioblastoma multiforme: Analysis of 14,678 patients using systematic review and meta-analytical tools. J Clin Neurosci 2015; 22:785-99. [DOI: 10.1016/j.jocn.2014.10.029] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2014] [Revised: 10/21/2014] [Accepted: 10/25/2014] [Indexed: 01/08/2023]
|
7
|
Pierscianek D, Kim YH, Motomura K, Mittelbronn M, Paulus W, Brokinkel B, Keyvani K, Wrede K, Nakazato Y, Tanaka Y, Mariani L, Vital A, Sure U, Ohgaki H. MET gain in diffuse astrocytomas is associated with poorer outcome. Brain Pathol 2012; 23:13-8. [PMID: 22672415 DOI: 10.1111/j.1750-3639.2012.00609.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 05/11/2012] [Indexed: 12/01/2022] Open
Abstract
Glioblastoma may develop rapidly without evidence for precursor lesions (primary glioblastomas), or progress from diffuse or anaplastic astrocytomas (secondary glioblastomas). Despite having distinct genetic profiles, these glioblastoma subtypes have similar histological features. We hypothesized that the highly malignant phenotype of glioblastoma may be attributable to genetic alterations that are common to both glioblastoma subtypes. In the present study, we first searched for commonly (>35%) amplified genes in glioblastomas with IDH1 mutation (a hallmark of secondary glioblastoma) and those without IDH1 mutation (typical for primary glioblastoma) in data from The Cancer Genome Atlas (TCGA). A total of 25 genes were identified, of which 21 were located at 7q31-34. We then screened 264 gliomas (70 glioblastomas, 112 diffuse astrocytomas, 82 oligodendrogliomas) for gain of the MET at 7q31.2 with quantitative polymerase chain reaction (PCR). MET gain was detected in primary glioblastomas (47%) and secondary glioblastomas (44%), suggesting that this genetic alteration plays a role in the pathogenesis of both glioblastoma subtypes. MET gain was also common in diffuse astrocytomas (38%), but less frequent in oligodendrogliomas (16%). MET gain in diffuse astrocytomas was associated with shorter survival (median, 43.0 vs. 70.7 months; P = 0.004), suggesting that MET gain is a useful prognostic marker for diffuse astrocytomas.
Collapse
Affiliation(s)
- Daniela Pierscianek
- Molecular Pathology, International Agency for Research on Cancer, Lyon, France
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
8
|
Masselli M, Laise P, Tonini G, Fanelli D, Pillozzi S, Cetica V, Da Ros M, Sardi I, Buccoliero AM, Aricò M, Genitori L, Becchetti A, Arcangeli A. Deregulation of ion channel and transporter encoding genes in pediatric gliomas. Front Oncol 2012; 2:53. [PMID: 22662319 PMCID: PMC3362739 DOI: 10.3389/fonc.2012.00053] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Accepted: 05/08/2012] [Indexed: 02/05/2023] Open
Abstract
Brain tumors, including the majority gliomas, are the leading cause of cancer-related death in children. World Health Organization has divided pediatric brain tumors into different grades and, based upon cDNA microarray data identifying gene expression profiles (GEPs), it has become evident in the last decade that the various grades involve different types of genetic alterations. However, it is not known whether ion channel and transporter genes, intimately involved in brain functioning, are associated with such GEPs. We determined the GEPs in an available cohort of 10 pediatric brain tumors initially by comparing the data obtained from four primary tumor samples and corresponding short-term cultures. The correspondence between the two types of samples was statistically significant. We then performed bioinformatic analyses on those samples (a total of nine) which corresponded to tumors of glial origin, either tissues or cell cultures, depending on the best "RNA integrity number." We used R software to evaluate the genes which were differentially expressed (DE) in gliomas compared with normal brain. Applying a p-value below 0.01 and fold change ≥4, led to identification of 2284 DE genes. Through a Functional Annotation Analysis (FAA) using the NIH-DAVID software, the DE genes turned out to be associated mainly with: immune/inflammatory response, cell proliferation and survival, cell adhesion and motility, neuronal phenotype, and ion transport. We have shown that GEPs of pediatric brain tumors can be studied using either primary tumor samples or short-term cultures with similar results. From FAA, we concluded that, among DE genes, pediatric gliomas show a strong deregulation of genes related to ion channels and transporters.
Collapse
Affiliation(s)
- Marika Masselli
- Department of Experimental Pathology and Oncology, University of Firenze Firenze, Italy
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
9
|
Dobson NR, Moore RT, Tobin JE, Armstrong RC. Leukemia/lymphoma-related factor regulates oligodendrocyte lineage cell differentiation in developing white matter. Glia 2012; 60:1378-90. [PMID: 22615173 DOI: 10.1002/glia.22356] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Accepted: 04/25/2012] [Indexed: 11/10/2022]
Abstract
Leukemia/lymphoma-related factor (LRF) is a zinc-finger transcription factor that regulates differentiation and oncogenesis in multiple tissues and cell lineages. The potential role for LRF in cells of the CNS has not been examined to date. This study shows prominent nuclear expression of LRF in diverse neuronal populations and in oligodendrocytes. We focused on examining the function of LRF during the transition from oligodendrocyte progenitor (OP) to mature oligodendrocyte that is associated with myelination in the postnatal spinal cord. During spinal cord myelination, LRF is expressed in only a minority of OP cells whereas most mature oligodendrocytes exhibited nuclear LRF immunoreactivity. Mice with floxed alleles of the Zbtb7a gene, which encodes for LRF protein, were used for in vivo analysis of LRF function. Lentiviral driven Cre recombinase inactivation of LRF at postnatal day 7 reduced the proportion of OP cells that differentiated into mature oligodendrocytes by postnatal day 28. Astrocyte populations were not altered by LRF deletion in the same tissues. These results indicate that LRF deletion reduces differentiation within the oligodendrocyte lineage and does not alter OP lineage choice. In vitro analysis confirmed a specific effect of LRF on OP differentiation. In neonatal OP cultures, RNA interference targeting LRF inhibited OP differentiation while LRF transduction was sufficient to induce differentiation into oligodendrocytes. These results support a critical role for LRF in transcriptional control of differentiation in oligodendrocyte lineage cells during developmental myelination in the CNS.
Collapse
Affiliation(s)
- Nicole R Dobson
- Department of Pediatrics, Uniformed Services University of Health Sciences, Bethesda, MD 20814, USA
| | | | | | | |
Collapse
|
10
|
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.
Collapse
|
11
|
Phillips JJ, Huillard E, Robinson AE, Ward A, Lum DH, Polley MY, Rosen SD, Rowitch DH, Werb Z. Heparan sulfate sulfatase SULF2 regulates PDGFRα signaling and growth in human and mouse malignant glioma. J Clin Invest 2012; 122:911-22. [PMID: 22293178 DOI: 10.1172/jci58215] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Accepted: 12/14/2011] [Indexed: 11/17/2022] Open
Abstract
Glioblastoma (GBM), a uniformly lethal brain cancer, is characterized by diffuse invasion and abnormal activation of multiple receptor tyrosine kinase (RTK) signaling pathways, presenting a major challenge to effective therapy. The activation of many RTK pathways is regulated by extracellular heparan sulfate proteoglycans (HSPG), suggesting these molecules may be effective targets in the tumor microenvironment. In this study, we demonstrated that the extracellular sulfatase, SULF2, an enzyme that regulates multiple HSPG-dependent RTK signaling pathways, was expressed in primary human GBM tumors and cell lines. Knockdown of SULF2 in human GBM cell lines and generation of gliomas from Sulf2(-/-) tumorigenic neurospheres resulted in decreased growth in vivo in mice. We found a striking SULF2 dependence in activity of PDGFRα, a major signaling pathway in GBM. Ablation of SULF2 resulted in decreased PDGFRα phosphorylation and decreased downstream MAPK signaling activity. Interestingly, in a survey of SULF2 levels in different subtypes of GBM, the proneural subtype, characterized by aberrations in PDGFRα, demonstrated the strongest SULF2 expression. Therefore, in addition to its potential as an upstream target for therapy of GBM, SULF2 may help identify a subset of GBMs that are more dependent on exogenous growth factor-mediated signaling. Our results suggest the bioavailability of growth factors from the microenvironment is a significant contributor to tumor growth in a major subset of human GBM.
Collapse
Affiliation(s)
- Joanna J Phillips
- Department of Neurological Surgery, UCSF, San Francisco, California 94158, USA.
| | | | | | | | | | | | | | | | | |
Collapse
|
12
|
Hirose Y, Sasaki H, Miwa T, Ohba S, Ikeda E, Abe M, Ikeda S, Kobayashi M, Kawase T, Hasegawa M, Yoshida K. Whole Genome Analysis From Microdissected Tissue Revealed Adult Supratentorial Grade II-III Gliomas Are Divided Into Clinically Relevant Subgroups by Genetic Profile. Neurosurgery 2011; 69:376-90. [PMID: 21358357 DOI: 10.1227/neu.0b013e318212bcd8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Yuichi Hirose
- Department of Neurosurgery, Fujita Health University, Toyoake, Japan.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Dahlback HSS, Brandal P, Meling TR, Gorunova L, Scheie D, Heim S. Genomic aberrations in 80 cases of primary glioblastoma multiforme: Pathogenetic heterogeneity and putative cytogenetic pathways. Genes Chromosomes Cancer 2009; 48:908-24. [PMID: 19603525 DOI: 10.1002/gcc.20690] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Screening the whole glioblastoma multiforme (GBM) genome for aberrations is a good starting point when looking for molecular markers that could potentially stratify patients according to prognosis and optimal treatment. We investigated 80 primary untreated GBM using both G-banding analysis and high-resolution comparative genomic hybridization (HR-CGH). Abnormal karyotypes were found in 83% of the tumors. The most common numerical chromosome aberrations were +7, -10, -13, -14, -15, +20, and -22. Structural abnormalities most commonly involved chromosomes 1 and 3, and the short arm of chromosome 9. HR-CGH verified these findings and revealed additional frequent losses at 1p34-36, 6q22-27, and 19q12-13 and gains of 3q26 and 12q13-15. Although most karyotypes and gain/loss patterns were complex, there was also a distinct subset of tumors displaying simple karyotypic changes only. There was a statistically significant association between trisomy 7 and monosomy 10, and also between +7/-10 as putative primary aberrations and secondary losses of 1p, 9p, 13q, and 22q. The low number of tumors in the rarer histological tumor subgroups precludes definite conclusions, but there did not seem to be any clear-cut cytogenetic-pathological correlations, perhaps with the exception of ring chromosomes in giant cell glioblastomas. Our findings demonstrate that although GBM is a pathogenetically very heterogeneous group of diseases, distinct genomic aberration patterns exist.
Collapse
Affiliation(s)
- Hanne-Sofie S Dahlback
- Department of Medical Genetics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.
| | | | | | | | | | | |
Collapse
|
14
|
Integrated molecular analysis suggests a three-class model for low-grade gliomas: a proof-of-concept study. Genomics 2009; 95:16-24. [PMID: 19835948 DOI: 10.1016/j.ygeno.2009.09.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2009] [Revised: 09/11/2009] [Accepted: 09/29/2009] [Indexed: 11/22/2022]
Abstract
INTRODUCTION We used an integrated molecular analysis strategy to perform class discovery on a population of low-grade gliomas (astrocytomas, oligodendrogliomas, and mixed gliomas) to improve our understanding of the molecular relationships among these tumors and to reconcile genotypic relationships with current histologic and molecular strategies for tumor classification. METHODS Gene expression profiling was performed on a cross-section of World Health Organization (WHO) grades I-II gliomas. Unsupervised class discovery algorithms identified and validated tumor clusters with genotypic similarity, and these data were integrated with chromosomal copy number assays and RT-PCR data to define molecular tumor subclasses. Machine learning models allowed accurate, prospective classification of unknown tumors into these molecular subgroups. This molecular classification model was compared to current histologic (WHO) and molecular pathologic (chromosome 1p and 19q deletions, p53 alterations, and Ki-67 expression) methods for glioma classification. RESULTS Molecular class discovery suggested a three-class model for low-grade gliomas. One discrete cluster of gliomas identified the pilocytic astrocytomas, a second grouped the 1p/19q codeleted oligodendrogliomas, and the mixture of remaining 1p/19q intact gliomas, including astrocytomas, oligodendrogliomas, and oligoastrocytomas, formed a third cluster with a discrete pattern of expression. CONCLUSIONS Integration of genomic, transcriptomic, and morphologic data for class discovery suggests a three-class model for low-grade gliomas. Class I represents tumors with molecular similarity to pilocytic astrocytomas, class II tumors are similar to 1p/19q codeleted oligodendrogliomas, and class III represents infiltrative low-grade gliomas. This classification is similar to current clinical paradigms for low-grade gliomas; our work suggests a molecular basis for such models. This classification may supplement or may serve as the basis for a molecular pathologic alternative to current grading schemes for low-grade gliomas and may highlight potential targets for future biologically based treatments or strategies for future clinical trials.
Collapse
|
15
|
Vital AL, Tabernero MD, Crespo I, Rebelo O, Tão H, Gomes F, Lopes MC, Orfao A. Intratumoral patterns of clonal evolution in gliomas. Neurogenetics 2009; 11:227-39. [DOI: 10.1007/s10048-009-0217-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2009] [Accepted: 08/21/2009] [Indexed: 12/12/2022]
|
16
|
Caveolin 1 Expression Independently Predicts Shorter Survival in Oligodendrogliomas. J Neuropathol Exp Neurol 2009; 68:425-31. [DOI: 10.1097/nen.0b013e31819ed0b7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
|
17
|
Grau E, Balaguer J, Canete A, Martinez F, Orellana C, Oltra S, Hernandez M, Castel V. Subtelomeric analysis of pediatric astrocytoma: subchromosomal instability is a distinctive feature of pleomorphic xanthoastrocytoma. J Neurooncol 2008; 93:175-82. [PMID: 19099200 DOI: 10.1007/s11060-008-9763-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2008] [Accepted: 12/08/2008] [Indexed: 10/21/2022]
Abstract
Astrocytic neoplasms are genetically heterogeneous; however a low frequency of genomic changes has been found in juvenile pilocytic astrocytoma (PA) in molecular studies. Concerning pleomorphic xanthoastrocytomas (PXA), recent studies have given heterogeneous results for chromosomal alterations. We studied the subtelomeric regions of 19 primary astrocytoma tumors. Results were near normality for the PA group with relative scarcity of chromosomal imbalances, except for the duplication of 3pter in 4/15 and deletion of 21qter in 5/15 of them. In contrast, a specific profile was observed in the 4 PXA tumoral samples. This involved 3pter, 14qter and 19pter duplication and 4qter, 6qter, 9qter, 13cen, 17pter, 18qter and 21qter deletion. Our results indicate that the chromosomal and genetic aberrations in PXAs differed from those typically associated with the diffusely infiltrating astrocytic and oligodendroglial gliomas. These genetic differences would likely contribute to the more favorable behavior of PXAs and may be helpful for molecular differential diagnosis of pediatric cerebral tumors.
Collapse
Affiliation(s)
- Elena Grau
- Hospital Universitario La Fe, Valencia, Spain.
| | | | | | | | | | | | | | | |
Collapse
|
18
|
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.
Collapse
|
19
|
Takahashi S, Hirose Y, Ikeda E, Fukaya R, Kawase T. Chromosome arm 1q gain associated with good response to chemotherapy in a malignant glioma. Case report. J Neurosurg 2007; 106:488-94. [PMID: 17367075 DOI: 10.3171/jns.2007.106.3.488] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The authors describe the case of a patient with a glioblastoma multiforme who showed remarkably good response to chemotherapy. A genetic analysis using comparative genomic hybridization (CGH) revealed that the tumor had a gain on the q arm of chromosome 1 (1q). Using CGH for a series of genetic analyses of more than 180 patients with gliomas, six were found to have a demonstrated 1q gain. Although the tumors in all six of these cases were histopathologically diagnosed as high-grade gliomas, compared with other malignant gliomas they demonstrated a good prognosis because of their favorable chemotherapeutic sensitivity. In immunohistochemical tests, most of the tumor cells in these cases were negative for O6-methylguanine-DNA methyltransferase, which antagonizes the effect of DNA-alkylating chemotherapeutic agents. The authors believed that a gain of 1q could be produced through the genetic events that cause loss of 1p, because these chromosomal aberrations have an imbalance of DNA copy number in common (1p < 1q). A gain of 1q is an infrequent chromosomal aberration and its clinical importance should be investigated in a larger study; however, patients with malignant gliomas demonstrating a 1q gain possibly show longer survival and good response to chemotherapy similar to patients with tumors demonstrating 1p loss. The importance of using genetic analysis for gliomas is emphasized in this report because it may help in selecting cases responsive to chemotherapy and because appropriate treatment for these patients will lead to progress in the treatment of malignant gliomas.
Collapse
Affiliation(s)
- Satoshi Takahashi
- Department of Neurosurgery, Keio University School of Medicine, Tokyo, Japan.
| | | | | | | | | |
Collapse
|
20
|
Wrensch M, Wiencke JK, Wiemels J, Miike R, Patoka J, Moghadassi M, McMillan A, Kelsey KT, Aldape K, Lamborn KR, Parsa AT, Sison JD, Prados MD. Serum IgE, tumor epidermal growth factor receptor expression, and inherited polymorphisms associated with glioma survival. Cancer Res 2006; 66:4531-41. [PMID: 16618782 DOI: 10.1158/0008-5472.can-05-4032] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In population-based glioma patients, we examined survival in relation to potentially pertinent constitutive polymorphisms, serologic factors, and tumor genetic and protein alterations in epidermal growth factor receptor (EGFR), MDM2, and TP53. Subjects were newly diagnosed adults residing in the San Francisco Bay Surveillance Epidemiology and End Results Area during 1991 to 1994 and 1997 to 1999 with central neuropathology review (n = 873). Subjects provided blood for serologic studies of IgE and IgG to four herpes viruses and constitutive specimens for genotyping 22 polymorphisms in 13 genes (n = 471). We obtained 595 of 697 astrocytic tumors for marker studies. We determined treatments, vital status, and other factors using registry, interview, medical record, and active follow-up data. Cox regressions for survival were adjusted for age, gender, ethnicity, study series, resection versus biopsy only, radiation, and chemotherapy. Using a stringent P < 0.001, glioma survival was associated with ERCC1 C8092A [hazard ratio (HR), 0.72; 95% confidence limits (95% CL), 0.60-0.86; P = 0.0004] and GSTT1 deletion (HR, 1.64; 95% CL, 1.25-2.16; P = 0.0004); glioblastoma patients with elevated IgE had 9 months longer survival than those with normal or borderline IgE levels (HR, 0.62; 95% CL, 0.47-0.82; P = 0.0007), and EGFR expression in anaplastic astrocytoma was associated with nearly 3-fold poorer survival (HR, 2.97; 95% CL, 1.70-5.19; P = 0.0001). Based on our and others' findings, we recommend further studies to (a) understand relationships of elevated IgE levels and other immunologic factors with improved glioblastoma survival potentially relevant to immunologic therapies and (b) determine which inherited ERCC1 variants or other variants in the 19q13.3 region influence survival. We also suggest that tumor EGFR expression be incorporated into clinical evaluation of anaplastic astrocytoma patients.
Collapse
Affiliation(s)
- Margaret Wrensch
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California 94102, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
21
|
Korshunov A, Sycheva R, Golanov A. Genetically distinct and clinically relevant subtypes of glioblastoma defined by array-based comparative genomic hybridization (array-CGH). Acta Neuropathol 2006; 111:465-74. [PMID: 16557391 DOI: 10.1007/s00401-006-0057-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2005] [Revised: 02/15/2006] [Accepted: 02/16/2006] [Indexed: 10/24/2022]
Abstract
To optimize treatment strategies for patients with glioblastoma, a more precise understanding of the molecular basis of this disease clearly is necessary. Therefore, numerous studies have focused on the molecular biology of glioblastoma and its linkage to clinical behavior. Here we investigated 70 glioblastomas using the array-based comparative genomic hybridization (array-CGH) with GenoSensor Array 300 to identify recurrent DNA copy number imbalances associated with patient outcomes. Univariate log-rank analysis of array-CGH data revealed 46 copy number aberrations (CNAs) associated with outcome. Among them, 26 CNAs were associated with shortened survival whereas the remaining 20 CNAs correlated with good prognosis. A hierarchical cluster analysis disclosed two genetically distinct groups of glioblastomas (1 and 2; 56 and 14 tumors, respectively). Univariate log-rank test discerned significant difference in survival between both genetic subsets while the 5-year survival rate consisted of 0 for group 1 and 63% for group 2. Multivariate analysis revealed that unfavorable genetic signature is an independent prognostic factor increasing a risk of patient death (hazard ratio, 4.38; P=0.00001). In conclusion, our current study suggests that glioblastomas can be subdivided into clinically relevant genetic subsets. Therefore, array-CGH screening of glioblastomas could provide clinically useful information and, perhaps, potentially improve the quality of treatment.
Collapse
Affiliation(s)
- Andrey Korshunov
- Department of Neuropathology, NN Burdenko Neurosurgical Institute, Fadeeva Str. 5, 125047, Moscow, Russia.
| | | | | |
Collapse
|
22
|
Reardon DA, Quinn JA, Vredenburgh JJ, Gururangan S, Friedman AH, Desjardins A, Sathornsumetee S, Herndon JE, Dowell JM, McLendon RE, Provenzale JM, Sampson JH, Smith RP, Swaisland AJ, Ochs JS, Lyons P, Tourt-Uhlig S, Bigner DD, Friedman HS, Rich JN. Phase 1 Trial of Gefitinib Plus Sirolimus in Adults with Recurrent Malignant Glioma. Clin Cancer Res 2006; 12:860-8. [PMID: 16467100 DOI: 10.1158/1078-0432.ccr-05-2215] [Citation(s) in RCA: 159] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE To determine the maximum tolerated dose (MTD) and dose-limiting toxicity (DLT) of gefitinib, a receptor tyrosine kinase inhibitor of the epidermal growth factor receptor, plus sirolimus, an inhibitor of the mammalian target of rapamycin, among patients with recurrent malignant glioma. PATIENTS AND METHODS Gefitinib and sirolimus were administered on a continuous daily dosing schedule at dose levels that were escalated in successive cohorts of malignant glioma patients at any recurrence who were stratified based on concurrent use of CYP3A-inducing anticonvulsants [enzyme-inducing antiepileptic drugs, (EIAED)]. Pharmacokinetic and archival tumor biomarker data were also assessed. RESULTS Thirty-four patients with progressive disease after prior radiation therapy and chemotherapy were enrolled, including 29 (85%) with glioblastoma multiforme and 5 (15%) with anaplastic glioma. The MTD was 500 mg of gefitinib plus 5 mg of sirolimus for patients not on EIAEDs and 1,000 mg of gefitinib plus 10 mg of sirolimus for patients on EIAEDs. DLTs included mucositis, diarrhea, rash, thrombocytopenia, and hypertriglyceridemia. Gefitinib exposure was not affected by sirolimus administration but was significantly lowered by concurrent EIAED use. Two patients (6%) achieved a partial radiographic response, and 13 patients (38%) achieved stable disease. CONCLUSION We show that gefitinib plus sirolimus can be safely coadministered on a continuous, daily dosing schedule, and established the recommended dose level of these agents in combination for future phase 2 clinical trials.
Collapse
|
23
|
Hirose Y, Yoshida K. Chromosomal abnormalities subdivide neuroepithelial tumors into clinically relevant groups. Keio J Med 2006; 55:52-8. [PMID: 16823260 DOI: 10.2302/kjm.55.52] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Gliomas are the most common primary brain tumor, and are histopathologically classified according to their cell type and the degree of malignancy. However, sometimes diagnosis can be controversial,and tumors of the same entity possibly have a wide range of survival. Genetic analysis of these tumors is considered to have great importance in terms that it can provide clinically relevant classification of the tumors and compensate for the limitation of the histological classification. Previous studies using comparative genomic hybridization (CGH) demonstrated that copy number aberrations(CNAs) were frequently recognized in these tumors, and revealed that a gain on chromosomal arm 7q was the most common CNA in diffuse astrocytomas, whereas a small population of the tumor showed losses on 1p/19q which characterizes oligodendrogliomas with good responsiveness to chemotherapeutic regime using procarbazine, nitrosourea and vincristine. High grade (malignant) gliomas(i.e. anaplastic astrocytomas, anaplastic oligodendrogliomas and glioblastomas) have been reported to have a gain on 7p and losses on 9p and 10q. In case of ependymomas, frequent chromosomal aberrations in intracranial tumors were a gain on 1q and losses on 6q, and, on the other hand, a gain on chromosome 7 was recognized almost exclusively in spinal cord tumors. These data suggest that intracranial and spinal cord ependymomas are different genetic diseases and comprise different subgroups within one histological entity. In conclusion, genetic analysis of gliomas may help to classify these tumors and provide leads concerning their initiation and progression. The relationship of these aberrations to patient outcome needs to be addressed.
Collapse
Affiliation(s)
- Yuichi Hirose
- Division of Neurosurgery, Department of Surgery, Keio University School of Medicine, Tokyo, Japan
| | | |
Collapse
|
24
|
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.
Collapse
Affiliation(s)
- Jane Bayani
- Department of Applied Molecular Oncology, Ontario Cancer Institute, Princess Margaret Hospital, University Health Network, Ontario, Canada.
| | | | | |
Collapse
|
25
|
Nutt CL. Molecular genetics of oligodendrogliomas: a model for improved clinical management in the field of neurooncology. Neurosurg Focus 2005; 19:E2. [PMID: 16398466 DOI: 10.3171/foc.2005.19.5.3] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Over the last several years, oligodendroglial tumors have become a model for the positive role of molecular genetics in improved treatment of patients with brain tumors. Oligodendrogliomas, in contrast to astrocytic gliomas, frequently respond to chemotherapy and have a better overall prognosis. Combined loss of chromosomes 1p and 19q has proven to be a powerful predictor of chemotherapeutic response and survival in oligodendrogliomas. In contrast, other genetic alterations, such as TP53 and PTEN mutations, EGFR amplification, and homozygous deletion of CDKN2A have been correlated with worse outcome in these tumors. Furthermore, 1p/19q loss has been shown to correlate with unequivocal oligodendroglial tumor histology, location and growth pattern of tumors within the brain, and magnetic resonance imaging characteristics. Although much is also known about the molecular pathological characteristics of astrocytic gliomas, the significance of this information to clinical management in patients with these tumors has not been as striking as has been the case for oligodendrogliomas; possible reasons for this are discussed. In this paper the author will summarize these advances, thus attempting to highlight the molecular genetic study of oligodendrogliomas as a model for improved clinical management in the field of neurooncology.
Collapse
Affiliation(s)
- Catherine L Nutt
- Department of Pathology, Neurosurgical Service and Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA.
| |
Collapse
|
26
|
McLendon RE, Herndon JE, West B, Reardon D, Wiltshire R, Rasheed BKA, Quinn J, Friedman HS, Friedman AH, Bigner DD. Survival analysis of presumptive prognostic markers among oligodendrogliomas. Cancer 2005; 104:1693-9. [PMID: 16116609 DOI: 10.1002/cncr.21362] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Allelic losses of 1p and 19q arms correlate with the oligodendroglial phenotype as well as with sensitivity to radiotherapy and chemotherapy. Furthermore, the DNA repair gene, methylguanine methyltransferase (MGMT), is diminished in 80% of oligodendroglial tumors and represents a possible mechanism for this therapeutic sensitivity. However, the authors questioned the relevance of genetic testing and measuring MGMT levels in tumors that were diagnostic of oligodendroglioma. METHODS The authors performed a retrospective analysis of 1p, 19q, 9p21, TP53, and MGMT status in 46 patients with oligodendrogliomas to address any relations that may exist among these markers with regard to progression-free survival (PFS) and total survival. Methodologies included comparative genomic hybridization; loss of heterozygosity (LOH) on 1p, 19q, and 9p21; TP53 mutational analysis; and immunohistochemistry for MGMT. RESULTS The authors found that survival among patients with light microscopically diagnosed oligodendroglial tumors demonstrating LOH of 1p and 19q trended toward statistical significance (P = 0.102 and P = 0.058, respectively). 9p21 LOH was significant as a predictor of PFS only among anaplastic oligodendrogliomas in this cohort (P = 0.033). TP53 mutation was found to be significantly predictive of a shorter survival (P = 0.027) among all patients and exhibited a strong trend toward a shorter PFS (P = 0.060). Low-level MGMT labeling index (LI) (< 20%) was noted in 86% of all oligodendroglial tumors. MGMT LI was not found to correlate with an improved PFS or total survival in this cohort, recognizing that median survival was not reached after a median follow-up of 104 months. CONCLUSIONS 9p21 and TP53 mutational status assisted in developing a stricter subclassification of these tumors with prognostic significance. MGMT levels were decreased in a majority of oligodendrogliomas.
Collapse
Affiliation(s)
- Roger E McLendon
- Department of Pathology, Duke University Medical Center, Durham, North Carolina 27710, USA.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Rovin RA, Winn R. Pokemon expression in malignant glioma: an application of bioinformatics methods. Neurosurg Focus 2005; 19:E8. [PMID: 16241110 DOI: 10.3171/foc.2005.19.4.9] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
OBJECT In this report the authors review the role of bioinformatics in the design of a research project in which the molecular genetics of malignant glioma were studied. A project to characterize Pokemon expression in malignant glioma was developed, refined, and implemented using bioinformatics methods. METHODS Using the resources available from the National Center for Biotechnology Information, the messenger RNA (mRNA) sequence for Pokemon was determined. With this information and online primer design tools, novel primers were designed that would specifically amplify Pokemon mRNA by using reverse transcription-polymerase chain reaction assays. CONCLUSIONS The promise of bioinformatics is in the rapid and widespread dissemination and analysis of genomic information. This information is then used in research investigating the genetic basis of disease. In this paper the authors review the bioinformatics methods used in their study of Pokemon expression in malignant glioma.
Collapse
Affiliation(s)
- Richard A Rovin
- Marquette General Hospital, Department of Biology, Northern Michigan University, Marquette, Michigan, USA.
| | | |
Collapse
|
28
|
Korshunov A, Sycheva R, Golanov A. The prognostic relevance of molecular alterations in glioblastomas for patients age < 50 years. Cancer 2005; 104:825-32. [PMID: 15981281 DOI: 10.1002/cncr.21221] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
BACKGROUND In patients with glioblastoma, age < 50 years was identified as a consistent prognostic variable. In addition, the prognosis for these patients may be determined by a complex interaction between age and genetic alterations. The objective of the current study was the molecular analysis of glioblastomas from adult patients age < 50 years ("young adults"). METHODS The authors analyzed a set of 189 glioblastoma specimens. Fluorescence in situ hybridization was performed with a set of 10 chromosome probes (1p36, 1q25, centomere probe 7 [CEP7], 7p12/epidermal growth factor receptor gene (EGFR), CEP9, 9p21/p16, CEP10, 10q23/phosphatase and tesnin homolog gene (PTEN), 19p13, and 19q13). RESULTS Patient age < 40 years was associated strongly with a favorable prognosis. Patients age > or = 40 years frequently showed EGFR amplification, loss of 9p, loss of 10q, and gain of chromosome 19. The patients with - 19q were age < 40 years. The survival was shorter for patients with EGFR amplification, gain of chromosome 7, loss of 9p, loss of 10q, and gain of chromosome 19. In contrast, the patients who had tumors with gain of chromosome 9 or loss of 19q had more favorable outcomes. In a multivariate analysis, gain of chromosome 9 (P = 0.026) and loss of 10q23 (P = 0.007) reached the level of independent prognostic value. In addition, the prognostic value of molecular alterations in patients age < 40 years and patients age > 40 years were examined separately. Consequently, EGFR amplification, - 9p, and + 9 were significant for both age groups, whereas gain of chromosome 7 and loss of 10q showed clinical importance only among patients age > 40 years. CONCLUSIONS Adult patients age < 50 years with glioblastoma had molecularly distinct disease, and the age-dependent heterogeneity seen on the chromosomal level also applied at the clinical level.
Collapse
Affiliation(s)
- Andrey Korshunov
- Department of Neuropathology, N. N. Burdenko Neurosurgical Institute, Moscow, Russia.
| | | | | |
Collapse
|
29
|
Díaz de Ståhl T, Hartmann C, de Bustos C, Piotrowski A, Benetkiewicz M, Mantripragada KK, Tykwinski T, von Deimling A, Dumanski JP. Chromosome 22 tiling-path array-CGH analysis identifies germ-line- and tumor-specific aberrations in patients with glioblastoma multiforme. Genes Chromosomes Cancer 2005; 44:161-9. [PMID: 15945096 DOI: 10.1002/gcc.20226] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Gliomas are common and frequently malignant tumors of the central nervous system. Recurrent allelic losses of chromosome 22 have been reported in gliomas, indicating tumor-suppressor genes at this location. However, the target genes are still unknown. We applied a high resolution tiling-path chromosome 22 array to a series of 50 glioblastoma samples, with the aim of investigating the underlying abnormalities in both constitutional and tumor-derived DNA. We detected hemizygous deletions in 28% of the tumors (14 of 50), with monosomy 22 (10 of 50) being the predominant pattern. The distribution of overlapping hemizygous deletions delineated two putative tumor-suppressor loci (11.1 and 3.08 Mb in size) across 22q. Most strikingly, we identified two distinct loci affected by regional gains. Both alterations were of germ-line origin and were unique to samples from patients affected with tumors. Analysis of these two amplified regions revealed the presence of two interesting candidate genes: TOP3B and TAFA5. The TOP3B gene encodes a protein that seems to function in the unlinking of parental strands at the final stage of DNA replication and/or in the dissociation of structures in mitotic cells that could lead to recombination. The TAFA5 gene belongs to a novel family of proteins with similarity to chemokines and brain-specific expression. The role of the identified candidate loci should be studied further. Our results demonstrated the power of array-CGH to determine DNA copy number alterations in the context of germ-line- and tumor-specific aberrations.
Collapse
Affiliation(s)
- Teresita Díaz de Ståhl
- Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Bredel M, Bredel C, Juric D, Harsh GR, Vogel H, Recht LD, Sikic BI. High-resolution genome-wide mapping of genetic alterations in human glial brain tumors. Cancer Res 2005; 65:4088-96. [PMID: 15899798 DOI: 10.1158/0008-5472.can-04-4229] [Citation(s) in RCA: 124] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
High-resolution genome-wide mapping of exact boundaries of chromosomal alterations should facilitate the localization and identification of genes involved in gliomagenesis and may characterize genetic subgroups of glial brain tumors. We have done such mapping using cDNA microarray-based comparative genomic hybridization technology to profile copy number alterations across 42,000 mapped human cDNA clones, in a series of 54 gliomas of varying histogenesis and tumor grade. This gene-by-gene approach permitted the precise sizing of critical amplicons and deletions and the detection of multiple new genetic aberrations. It has also revealed recurrent patterns of occurrence of distinct chromosomal aberrations as well as their interrelationships and showed that gliomas can be clustered into distinct genetic subgroups. A subset of detected alterations was shown predominantly associated with either astrocytic or oligodendrocytic tumor phenotype. Finally, five novel minimally deleted regions were identified in a subset of tumors, containing putative candidate tumor suppressor genes (TOPORS, FANCG, RAD51, TP53BP1, and BIK) that could have a role in gliomagenesis.
Collapse
Affiliation(s)
- Markus Bredel
- Division of Oncology, Center for Clinical Sciences Research, Stanford University School of Medicine, Stanford, California 94305-5151, USA.
| | | | | | | | | | | | | |
Collapse
|