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Bauman MMJ, Harrison DJ, Giesken MB, Daniels DJ. The evolving landscape of pilocytic astrocytoma: a bibliometric analysis of the top-100 most cited publications. Childs Nerv Syst 2022; 38:1271-1280. [PMID: 35352179 DOI: 10.1007/s00381-022-05503-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 03/15/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND Pilocytic astrocytomas are the most common low-grade glioma of the central nervous system that typically occurs in children, and much research has been dedicated to characterizing their molecular features and clinical courses. We provide an overview of the current literature through the use of a bibliometric analysis of the top 100 most cited publications discussing pilocytic astrocytomas. METHODS We identified the top 100 most cited publications discussing pilocytic astrocytomas. Articles were ranked based on the number of citations. Descriptive statistics and univariate analysis were used to determine any trends or significant differences in the data. RESULTS Of the top 100 articles, 50 were basic science (50%), 34 were clinical (34%), and 16 were review (16%). The number of citations ranged from 79 to 921, with 123 being the median. The US had the most first authors and principal authors (n = 53 and n = 54, respectively). Years of publication had a left-skewed distribution and peaked during 2011 with 12 articles published in that year. Sixty percent of basic science articles investigated BRAF/MAPK pathways, while 67.6% of clinical articles focused on evaluating treatment options for pilocytic astrocytomas. Compared to basic science and clinical articles, review articles were published more recently (p < 0.001), had fewer authors (p = 0.025) and were published in journals with higher impact factors (p = 0.022). CONCLUSION Research regarding pilocytic astrocytomas has increased over the past three decades. Future directions of research point towards employing targeted therapies and discovering additional cellular pathways contributing to disease pathogenesis.
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Affiliation(s)
| | | | - Max B Giesken
- Mayo Clinic Alix School of Medicine, Rochester, MN, USA
| | - David J Daniels
- Department of Neurological Surgery, Rochester, MN, USA.
- Department of Neurological Surgery, Mayo Clinic, 200 1st St. SW, Rochester, MN, 55905, USA.
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2
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Unger K, Fleischmann DF, Ruf V, Felsberg J, Piehlmaier D, Samaga D, Hess J, Suresh MP, Mittelbronn M, Lauber K, Budach W, Sabel M, Rödel C, Reifenberger G, Herms J, Tonn JC, Zitzelsberger H, Belka C, Niyazi M. Improved risk stratification in younger IDH wild-type glioblastoma patients by combining a 4-miRNA signature with MGMT promoter methylation status. Neurooncol Adv 2020; 2:vdaa137. [PMID: 33305269 PMCID: PMC7712804 DOI: 10.1093/noajnl/vdaa137] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Background The potential benefit of risk stratification using a 4-miRNA signature in combination with MGMT promoter methylation in IDH1/2 wild-type glioblastoma patients was assessed. Methods Primary tumors from 102 patients with comparable treatment from the LMU Munich (n = 37), the University Hospital Düsseldorf (n = 33), and The Cancer Genome Atlas (n = 32) were included. Risk groups were built using expressions of hsa-let-7a-5p, hsa-let-7b-5p, hsa-miR-615-5p, and hsa-miR-125a-5p to assess prognostic performance in overall survival (OS). MGMT promoter methylation and age were considered as cofactors. Integrated miRNA, DNA methylome, and transcriptome analysis were used to explore the functional impact of signature miRNAs. Results The 4-miRNA signature defined high-risk (n = 46, median OS: 15.8 months) and low-risk patients (n = 56, median OS: 20.7 months; univariable Cox proportional hazard analysis: hazard ratio [HR]: 1.8, 95% confidence interval [CI]: 1.14–2.83, P = .01). The multivariable Cox proportional hazard model including the 4-miRNA signature (P = .161), MGMT promoter methylation (P < .001), and age (P = .034) significantly predicted OS (Log-rank P < .0001). Likewise to clinical routine, analysis was performed for younger (≤60 years, n = 50, median OS: 20.2 months) and older patients (>60 years, n = 52, median OS: 15.8) separately. In younger patients, the 4-miRNA signature had prognostic value (HR: 1.92, 95% CI: 0.93–3.93, P = .076). Particularly, younger, MGMT methylated, 4-miRNA signature low-risk patients (n = 18, median OS: 37.4 months) showed significantly improved survival, compared to other younger patients (n = 32, OS 18.5 months; HR: 0.33, 95% CI: 0.15–0.71, P = .003). Integrated data analysis revealed 4-miRNA signature-associated genes and pathways. Conclusion The prognostic 4-miRNA signature in combination with MGMT promoter methylation improved risk stratification with the potential for therapeutic substratification, especially of younger patients.
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Affiliation(s)
- Kristian Unger
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer," Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany
| | - Daniel F Fleischmann
- Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany.,German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Viktoria Ruf
- Center for Neuropathology and Prion Research LMU Munich, Munich, Germany
| | - Jörg Felsberg
- Institute for Neuropathology, University Hospital Düsseldorf (UKD), Heinrich Heine University, Düsseldorf, Germany.,German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel Piehlmaier
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Daniel Samaga
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Julia Hess
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer," Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Marian Preetham Suresh
- Department of Neurosurgery, University Hospital Düsseldorf (UKD), Heinrich Heine University, Düsseldorf, Germany
| | - Michel Mittelbronn
- National Center of Pathology (NCP), Laboratoire National de Santé (LNS), Dudelange, Luxembourg.,Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg.,Department of Oncology (DONC), Luxembourg Institute of Health (LIH), Luxembourg, Luxembourg.,Luxembourg Center of Neuropathology (LCNP), Luxembourg, Luxembourg
| | - Kirsten Lauber
- Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer," Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany.,German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - Wilfried Budach
- Department of Radiotherapy and Radiation Oncology, University Hospital Düsseldorf (UKD), Heinrich Heine University, Düsseldorf, Germany
| | - Michael Sabel
- Department of Neurosurgery, University Hospital Düsseldorf (UKD), Heinrich Heine University, Düsseldorf, Germany
| | - Claus Rödel
- Department of Radiation Oncology, University Hospital, Frankfurt, Germany
| | - Guido Reifenberger
- Institute for Neuropathology, University Hospital Düsseldorf (UKD), Heinrich Heine University, Düsseldorf, Germany.,German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jochen Herms
- Center for Neuropathology and Prion Research LMU Munich, Munich, Germany
| | - Jörg-Christian Tonn
- Department of Neurosurgery, University Hospital, LMU Munich, Munich, Germany
| | - Horst Zitzelsberger
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer," Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany
| | - Claus Belka
- Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer," Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany.,German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - Maximilian Niyazi
- Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany.,German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
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miR-6086 inhibits ovarian cancer angiogenesis by downregulating the OC2/VEGFA/EGFL6 axis. Cell Death Dis 2020; 11:345. [PMID: 32393810 PMCID: PMC7214437 DOI: 10.1038/s41419-020-2501-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 04/08/2020] [Accepted: 04/14/2020] [Indexed: 12/13/2022]
Abstract
miRNAs have emerged as a pivotal component of gene regulatory networks, mediating cytokines secretion, cell cycle, and differentiation regulation. However, how miRNAs collaborate with transcription factors and downstream effector proteins that determine the fate of ovarian cancer cells remains to be understood, especially regarding to mechanism of tumor angiogenesis regulation. Based on the qRT-PCR and IHC analysis, we found that miR-6086 was maintained a very low level both in ovarian cancer cell lines and tissues. Further, we identified OC2 and EGFL6 as the direct targets of miR-6086 by luciferase assay and we observed an inverse relationship between the expression of miR-6086 and the OC2/VEGFA/EGFL6 axis. The Western blotting analysis suggested that OC2 could directly upregulate VEGFA and indirectly up-regulate EGFL6 through VEGFA. Moreover, miR-6086 could indirectly downregulate VEGFA through OC2. In addition, miR-6086, siOC2 and siEGFL6 could negatively regulate the tumor growth and angiogenesis of ovarian cancer (Skov3) in the animal studies, with the inhibition rates of 77.07%, 69.89%, and 73.62%, respectively (**p < 0.01). Moreover, the tumor cell proliferation, migration, and invasion of ovarian cancer cell lines (Caov3 and Skov3) and vascular formation (HUVECs) were significantly suppressed in vitro, by decreasing the AKT/MAPK pathways (*p < 0.05). Taken together, our results reveal that miR-6086 can suppress the angiogenesis networks in ovarian cancer by down-regulating the OC2/VEGFA/EGFL6 axis, directly or indirectly, which may provide potential targets for tumor therapeutics.
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Central Nervous System-type Neuroepithelial Tumors and Tumor-like Proliferations Developing in the Gynecologic Tract and Pelvis. Am J Surg Pathol 2018; 42:1429-1444. [DOI: 10.1097/pas.0000000000001131] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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5
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Chakraborty S, Ghosh Z. A systemic insight into astrocytoma biology across different grades. J Cell Physiol 2018; 234:4243-4255. [DOI: 10.1002/jcp.27193] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 07/17/2018] [Indexed: 01/05/2023]
Affiliation(s)
| | - Zhumur Ghosh
- Bioinformatics Centre, Bose Institute Kolkata India
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6
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Pan Y, Zhu Y, Yang W, Tycksen E, Liu S, Palucki J, Zhu L, Sasaki Y, Sharma MK, Kim AH, Zhang B, Yano H. The role of Twist1 in mutant huntingtin-induced transcriptional alterations and neurotoxicity. J Biol Chem 2018; 293:11850-11866. [PMID: 29891550 DOI: 10.1074/jbc.ra117.001211] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 05/14/2018] [Indexed: 01/12/2023] Open
Abstract
Huntington's disease (HD) is a fatal neurodegenerative disorder caused by an abnormal expansion of polyglutamine repeats in the huntingtin protein (Htt). Transcriptional dysregulation is an early event in the course of HD progression and is thought to contribute to disease pathogenesis, but how mutant Htt causes transcriptional alterations and subsequent cell death in neurons is not well understood. RNA-Seq analysis revealed that expression of a mutant Htt fragment in primary cortical neurons leads to robust gene expression changes before neuronal death. Basic helix-loop-helix transcription factor Twist1, which is essential for embryogenesis and is normally expressed at low levels in mature neurons, was substantially up-regulated in mutant Htt-expressing neurons in culture and in the brains of HD mouse models. Knockdown of Twist1 by RNAi in mutant Htt-expressing primary cortical neurons reversed the altered expression of a subset of genes involved in neuronal function and, importantly, abrogated neurotoxicity. Using brain-derived neurotrophic factor (Bdnf), which is known to be involved in HD pathogenesis, as a model gene, we found that Twist1 knockdown could reverse mutant Htt-induced DNA hypermethylation at the Bdnf regulatory region and reactivate Bdnf expression. Together, these results suggest that Twist1 is an important upstream mediator of mutant Htt-induced neuronal death and may in part operate through epigenetic mechanisms.
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Affiliation(s)
| | - Ying Zhu
- From the Department of Neurological Surgery
| | - Wei Yang
- Genome Technology Access Center.,Department of Genetics
| | | | | | | | | | | | | | - Albert H Kim
- From the Department of Neurological Surgery.,Department of Genetics.,Department of Developmental Biology.,Center of Regenerative Medicine.,Department of Neurology, and.,Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Bo Zhang
- Department of Developmental Biology.,Center of Regenerative Medicine
| | - Hiroko Yano
- From the Department of Neurological Surgery, .,Department of Genetics.,Center of Regenerative Medicine.,Department of Neurology, and.,Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, Missouri 63110
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7
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Selt F, Hohloch J, Hielscher T, Sahm F, Capper D, Korshunov A, Usta D, Brabetz S, Ridinger J, Ecker J, Oehme I, Gronych J, Marquardt V, Pauck D, Bächli H, Stiles CD, von Deimling A, Remke M, Schuhmann MU, Pfister SM, Brummer T, Jones DTW, Witt O, Milde T. Establishment and application of a novel patient-derived KIAA1549:BRAF-driven pediatric pilocytic astrocytoma model for preclinical drug testing. Oncotarget 2017; 8:11460-11479. [PMID: 28002790 PMCID: PMC5355278 DOI: 10.18632/oncotarget.14004] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 11/23/2016] [Indexed: 11/25/2022] Open
Abstract
Pilocytic astrocytoma (PA) is the most frequent pediatric brain tumor. Activation of the MAPK pathway is well established as the oncogenic driver of the disease. It is most frequently caused by KIAA1549:BRAF fusions, and leads to oncogene induced senescence (OIS). OIS is thought to be a major reason for growth arrest of PA cells in vitro and in vivo, preventing establishment of PA cultures. Hence, valid preclinical models are currently very limited, but preclinical testing of new compounds is urgently needed. We transduced the PA short-term culture DKFZ-BT66 derived from the PA of a 2-year old patient with a doxycycline-inducible system coding for Simian Vacuolating Virus 40 Large T Antigen (SV40-TAg). SV40-TAg inhibits TP53/CDKN1A and CDKN2A/RB1, two pathways critical for OIS induction and maintenance. DNA methylation array and KIAA1549:BRAF fusion analysis confirmed pilocytic astrocytoma identity of DKFZ-BT66 cells after establishment. Readouts were analyzed in proliferating as well as senescent states, including cell counts, viability, cell cycle analysis, expression of SV40-Tag, CDKN2A (p16), CDKN1A (p21), and TP53 (p53) protein, and gene-expression profiling. Selected MAPK inhibitors (MAPKi) including clinically available MEK inhibitors (MEKi) were tested in vitro. Expression of SV40-TAg enabled the cells to bypass OIS and to resume proliferation with a mean doubling time of 45h allowing for propagation and long-term culture. Withdrawal of doxycycline led to an immediate decrease of SV40-TAg expression, appearance of senescent morphology, upregulation of CDKI proteins and a subsequent G1 growth arrest in line with the re-induction of senescence. DKFZ-BT66 cells still underwent replicative senescence that was overcome by TERT expression. Testing of a set of MAPKi revealed differential responses in DKFZ-BT66. MEKi efficiently inhibited MAPK signaling at clinically achievable concentrations, while BRAF V600E- and RAF Type II inhibitors showed paradoxical activation. Taken together, we have established the first patient-derived long term expandable PA cell line expressing the KIAA1549:BRAF-fusion suitable for preclinical drug testing.
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Affiliation(s)
- Florian Selt
- Clinical Cooperation Unit Pediatric Oncology (G340), German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Heidelberg, Germany.,Center for Individualized Pediatric Oncology (ZIPO) and Section of Pediatric Brain Tumors, Department of Pediatric Oncology, Hematology and Immunology, University Hospital Heidelberg, Heidelberg, Germany
| | - Juliane Hohloch
- Clinical Cooperation Unit Pediatric Oncology (G340), German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Thomas Hielscher
- Division of Biostatistics (C060), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Felix Sahm
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology (G380), German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - David Capper
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology (G380), German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Andrey Korshunov
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology (G380), German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Diren Usta
- Clinical Cooperation Unit Pediatric Oncology (G340), German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Sebastian Brabetz
- Division of Pediatric Neurooncology (B062), German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Johannes Ridinger
- Clinical Cooperation Unit Pediatric Oncology (G340), German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Jonas Ecker
- Clinical Cooperation Unit Pediatric Oncology (G340), German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Heidelberg, Germany.,Center for Individualized Pediatric Oncology (ZIPO) and Section of Pediatric Brain Tumors, Department of Pediatric Oncology, Hematology and Immunology, University Hospital Heidelberg, Heidelberg, Germany
| | - Ina Oehme
- Clinical Cooperation Unit Pediatric Oncology (G340), German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Jan Gronych
- Division of Molecular Genetics (B060), German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Heidelberg, Germany.,Current affiliation: AbbVie Deutschland GmbH & Co. KG, Medical Immunology, Wiesbaden, Germany
| | - Viktoria Marquardt
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Germany.,Department of Pediatric Neuro-Oncogenomics, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David Pauck
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Germany.,Department of Pediatric Neuro-Oncogenomics, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Heidi Bächli
- Department of Neurosurgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Charles D Stiles
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Andreas von Deimling
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology (G380), German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Marc Remke
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Germany.,Department of Pediatric Neuro-Oncogenomics, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin U Schuhmann
- Department of Neurosurgery, University Hospital Tübingen, Tübingen, Germany
| | - Stefan M Pfister
- Center for Individualized Pediatric Oncology (ZIPO) and Section of Pediatric Brain Tumors, Department of Pediatric Oncology, Hematology and Immunology, University Hospital Heidelberg, Heidelberg, Germany.,Division of Pediatric Neurooncology (B062), German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Tilman Brummer
- Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University and University Medical Centre, Freiburg, Germany
| | - David T W Jones
- Division of Pediatric Neurooncology (B062), German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Olaf Witt
- Clinical Cooperation Unit Pediatric Oncology (G340), German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Heidelberg, Germany.,Center for Individualized Pediatric Oncology (ZIPO) and Section of Pediatric Brain Tumors, Department of Pediatric Oncology, Hematology and Immunology, University Hospital Heidelberg, Heidelberg, Germany
| | - Till Milde
- Clinical Cooperation Unit Pediatric Oncology (G340), German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Heidelberg, Germany.,Center for Individualized Pediatric Oncology (ZIPO) and Section of Pediatric Brain Tumors, Department of Pediatric Oncology, Hematology and Immunology, University Hospital Heidelberg, Heidelberg, Germany
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Narsia N, Ramagiri P, Ehrmann J, Kolar Z. Transcriptome analysis reveals distinct gene expression profiles in astrocytoma grades II-IV. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 2017; 161:261-271. [PMID: 28452381 DOI: 10.5507/bp.2017.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 04/18/2017] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Astrocytoma is the most prevalent form of primary brain cancer categorized into four histological grades by the World Health Organization. Investigation into individual grades of astrocytoma by previous studies has provided some insight into dysregulation of regulatory networks associated with increasing astrocytoma grades. However, further understanding of key mechanisms that distinguish different astrocytoma grades is required to facilitate targeted therapies. METHODS In this study, we utilized a large cohort of publicly available RNA sequencing data from patients with diffuse astrocytoma (grade II), anaplastic astrocytoma (grade III), primary glioblastoma (grade IV), secondary glioblastoma (grade IV), recurrent glioblastoma (grade IV), and normal brain samples to identify genetic similarities and differences between these grades using bioinformatics applications. RESULTS Our analysis revealed a distinct gene expression pattern between grade II astrocytoma and grade IV glioblastoma (GBM). We also identified genes that were exclusively expressed in each of the astrocytoma grades. Furthermore, we identified known and novel genes involved in key pathways in our study. Gene set enrichment analysis revealed a distinct expression pattern of transcriptional regulators in primary GBM. Further investigation into molecular processes showed that the genes involved in cell proliferation and invasion were shared across all subtypes of astrocytoma. Also, the number of genes involved in metastasis, regulation of cell proliferation, and apoptosis increased with tumor grade. CONCLUSIONS We confirmed existing findings and shed light on some important genes and molecular processes that will improve our understanding of glioma biology.
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Affiliation(s)
- Nato Narsia
- Department of Clinical and Molecular Pathology and Laboratory of Molecular Pathology, Faculty of Medicine and Dentistry, Palacky University Olomouc and University Hospital Olomouc, Czech Republic
| | - Pradeep Ramagiri
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Jiri Ehrmann
- Department of Clinical and Molecular Pathology and Laboratory of Molecular Pathology, Faculty of Medicine and Dentistry, Palacky University Olomouc and University Hospital Olomouc, Czech Republic
| | - Zdenek Kolar
- Department of Clinical and Molecular Pathology and Laboratory of Molecular Pathology, Faculty of Medicine and Dentistry, Palacky University Olomouc and University Hospital Olomouc, Czech Republic
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9
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Grossman R, Ram Z. Posterior Fossa Intra-Axial Tumors in Adults. World Neurosurg 2015; 88:140-145. [PMID: 26743385 DOI: 10.1016/j.wneu.2015.12.066] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 12/21/2015] [Accepted: 12/22/2015] [Indexed: 11/17/2022]
Abstract
BACKGROUND The posterior fossa is the site of many types of tumors, and brain metastases are the most common malignancies in that location among adults. Other brain tumors, such as ependymomas, medulloblastomas, and juvenile pilocytic astrocytomas, mostly occur during childhood and are relatively rare in adults. Most primary malignant brain tumors, such as gliomas and lymphomas, tend to be located in the supratentorial compartment. METHODS This review summarizes prognostic factors, therapeutic management, and molecular data of intra-axial posterior fossa tumors in adults, including ependymomas, medulloblastomas, and pilocytic astrocytomas. RESULTS The literature on intra-axial posterior fossa tumors in adults relies mainly on limited retrospective clinical studies, and such studies employ a wide range of treatment approaches that are usually based on therapies developed specifically for children or for supratentorial brain tumors. CONCLUSIONS The clinical course and surgical outcome of adult patients with intra-axial brain tumors in the posterior fossa are summarized in this review. The prognostic factors and therapeutic management of patients with these tumors are controversial because of their rarity, their heterogeneity, and the lack of sufficient data in the literature.
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Affiliation(s)
- Rachel Grossman
- Department of Neurosurgery, Sackler Faculty of Medicine, Tel-Aviv Medical Center, Tel-Aviv University, Tel-Aviv, Israel.
| | - Zvi Ram
- Department of Neurosurgery, Sackler Faculty of Medicine, Tel-Aviv Medical Center, Tel-Aviv University, Tel-Aviv, Israel
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10
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Comparative transcriptomics reveals similarities and differences between astrocytoma grades. BMC Cancer 2015; 15:952. [PMID: 26673168 PMCID: PMC4682229 DOI: 10.1186/s12885-015-1939-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 11/01/2015] [Indexed: 11/23/2022] Open
Abstract
Background Astrocytomas are the most common primary brain tumors distinguished into four histological grades. Molecular analyses of individual astrocytoma grades have revealed detailed insights into genetic, transcriptomic and epigenetic alterations. This provides an excellent basis to identify similarities and differences between astrocytoma grades. Methods We utilized public omics data of all four astrocytoma grades focusing on pilocytic astrocytomas (PA I), diffuse astrocytomas (AS II), anaplastic astrocytomas (AS III) and glioblastomas (GBM IV) to identify similarities and differences using well-established bioinformatics and systems biology approaches. We further validated the expression and localization of Ang2 involved in angiogenesis using immunohistochemistry. Results Our analyses show similarities and differences between astrocytoma grades at the level of individual genes, signaling pathways and regulatory networks. We identified many differentially expressed genes that were either exclusively observed in a specific astrocytoma grade or commonly affected in specific subsets of astrocytoma grades in comparison to normal brain. Further, the number of differentially expressed genes generally increased with the astrocytoma grade with one major exception. The cytokine receptor pathway showed nearly the same number of differentially expressed genes in PA I and GBM IV and was further characterized by a significant overlap of commonly altered genes and an exclusive enrichment of overexpressed cancer genes in GBM IV. Additional analyses revealed a strong exclusive overexpression of CX3CL1 (fractalkine) and its receptor CX3CR1 in PA I possibly contributing to the absence of invasive growth. We further found that PA I was significantly associated with the mesenchymal subtype typically observed for very aggressive GBM IV. Expression of endothelial and mesenchymal markers (ANGPT2, CHI3L1) indicated a stronger contribution of the micro-environment to the manifestation of the mesenchymal subtype than the tumor biology itself. We further inferred a transcriptional regulatory network associated with specific expression differences distinguishing PA I from AS II, AS III and GBM IV. Major central transcriptional regulators were involved in brain development, cell cycle control, proliferation, apoptosis, chromatin remodeling or DNA methylation. Many of these regulators showed directly underlying DNA methylation changes in PA I or gene copy number mutations in AS II, AS III and GBM IV. Conclusions This computational study characterizes similarities and differences between all four astrocytoma grades confirming known and revealing novel insights into astrocytoma biology. Our findings represent a valuable resource for future computational and experimental studies. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1939-9) contains supplementary material, which is available to authorized users.
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Zakrzewski K, Jarząb M, Pfeifer A, Oczko-Wojciechowska M, Jarząb B, Liberski PP, Zakrzewska M. Transcriptional profiles of pilocytic astrocytoma are related to their three different locations, but not to radiological tumor features. BMC Cancer 2015; 15:778. [PMID: 26497896 PMCID: PMC4619381 DOI: 10.1186/s12885-015-1810-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 10/16/2015] [Indexed: 01/06/2023] Open
Abstract
Background Pilocytic astrocytoma is the most common type of brain tumor in the pediatric population, with a generally favorable prognosis, although recurrences or leptomeningeal dissemination are sometimes also observed. For tumors originating in the supra-or infratentorial location, a different molecular background was suggested, but plausible correlations between the transcriptional profile and radiological features and/or clinical course are still undefined. The purpose of this study was to identify gene expression profiles related to the most frequent locations of this tumor, subtypes based on various radiological features, and the clinical pattern of the disease. Methods Eighty six children (55 males and 31 females) with histologically verified pilocytic astrocytoma were included in this study. Their age at the time of diagnosis ranged from fourteen months to seventeen years, with a mean age of seven years. There were 40 cerebellar, 23 optic tract/hypothalamic, 21 cerebral hemispheric, and two brainstem tumors. According to the radiological features presented on MRI, all cases were divided into four subtypes: cystic tumor with a non-enhancing cyst wall; cystic tumor with an enhancing cyst wall; solid tumor with central necrosis; and solid or mainly solid tumor. In 81 cases primary surgical resection was the only and curative treatment, and in five cases progression of the disease was observed. In 47 cases the analysis was done by using high density oligonucleotide microarrays (Affymetrix HG-U133 Plus 2.0) with subsequent bioinformatic analyses and confirmation of the results by independent RT-qPCR (on 39 samples). Results Bioinformatic analyses showed that the gene expression profile of pilocytic astrocytoma is highly dependent on the tumor location. The most prominent differences were noted for IRX2, PAX3, CXCL14, LHX2, SIX6, CNTN1 and SIX1 genes expression even within different compartments of the supratentorial region. Analysis of the genes potentially associated with radiological features showed much weaker transcriptome differences. Single genes showed association with the tendency to progression. Conclusions Here we have shown that pilocytic astrocytomas of three different locations can be precisely differentiated on the basis of their gene expression level, but their transcriptional profiles does not strongly reflect the radiological appearance of the tumor or the course of the disease. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1810-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Krzysztof Zakrzewski
- Department of Neurosurgery, Polish Mother Memorial Hospital Research Institute, Rzgowska 281/289, 93-338, Lodz, Poland.
| | - Michał Jarząb
- Third Department of Radiotherapy and Chemotherapy, Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, Wybrzeze Armii Krajowej 15, 44-101, Gliwice, Poland.
| | - Aleksandra Pfeifer
- Department of Nuclear Medicine and Endocrine Oncology, Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, Wybrzeze Armii Krajowej 15, 44-101, Gliwice, Poland.
| | - Małgorzata Oczko-Wojciechowska
- Department of Nuclear Medicine and Endocrine Oncology, Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, Wybrzeze Armii Krajowej 15, 44-101, Gliwice, Poland.
| | - Barbara Jarząb
- Department of Nuclear Medicine and Endocrine Oncology, Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, Wybrzeze Armii Krajowej 15, 44-101, Gliwice, Poland.
| | - Paweł P Liberski
- Department of Molecular Pathology and Neuropathology, Medical University of Lodz, Pomorska 251, 92-213, Lodz, Poland.
| | - Magdalena Zakrzewska
- Department of Molecular Pathology and Neuropathology, Medical University of Lodz, Pomorska 251, 92-213, Lodz, Poland.
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Collins VP, Jones DTW, Giannini C. Pilocytic astrocytoma: pathology, molecular mechanisms and markers. Acta Neuropathol 2015; 129:775-88. [PMID: 25792358 PMCID: PMC4436848 DOI: 10.1007/s00401-015-1410-7] [Citation(s) in RCA: 261] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 02/17/2015] [Accepted: 03/06/2015] [Indexed: 01/19/2023]
Abstract
Pilocytic astrocytomas (PAs) were recognized as a discrete clinical entity over 70 years ago. They are relatively benign (WHO grade I) and have, as a group, a 10-year survival of over 90%. Many require merely surgical removal and only very infrequently do they progress to more malignant gliomas. While most show classical morphology, they may present a spectrum of morphological patterns, and there are difficult cases that show similarities to other gliomas, some of which are malignant and require aggressive treatment. Until recently, almost nothing was known about the molecular mechanisms involved in their development. The use of high-throughput sequencing techniques interrogating the whole genome has shown that single abnormalities of the mitogen-activating protein kinase (MAPK) pathway are exclusively found in almost all cases, indicating that PA represents a one-pathway disease. The most common mechanism is a tandem duplication of a ≈2 Mb-fragment of #7q, giving rise to a fusion between two genes, resulting in a transforming fusion protein, consisting of the N-terminus of KIAA1549 and the kinase domain of BRAF. Additional infrequent fusion partners have been identified, along with other abnormalities of the MAP-K pathway, affecting tyrosine kinase growth factor receptors at the cell surface (e.g., FGFR1) as well as BRAF V600E, KRAS, and NF1 mutations among others. However, while the KIAA1549-BRAF fusion occurs in all areas, the incidence of the various other mutations identified differs in PAs that develop in different regions of the brain. Unfortunately, from a diagnostic standpoint, almost all mutations found have been reported in other brain tumor types, although some retain considerable utility. These molecular abnormalities will be reviewed, and the difficulties in their potential use in supporting a diagnosis of PA, when the histopathological findings are equivocal or in the choice of individualized therapy, will be discussed.
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Affiliation(s)
- V Peter Collins
- Department of Pathology, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK,
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Pećina-Šlaus N, Gotovac K, Kafka A, Tomas D, Borovečki F. Genetic changes observed in a case of adult pilocytic astrocytoma revealed by array CGH analysis. Mol Cytogenet 2014; 7:95. [PMID: 25606054 PMCID: PMC4300045 DOI: 10.1186/s13039-014-0095-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 11/27/2014] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND A palette of copy number changes in a case of adult pilocytic astrocytoma analyzed by Array Comparative Genomic Hybridization (aCGH) is presented. Pilocytic astrocytomas are specific gliomas that are benign and biologically distinct and the molecular mechanisms responsible for their development remain unexplained. The aCGH was performed using SurePrint G3 Human CGH microarrays 4 × 180 K (Agilent Technologies). To ascertain whether some of the aberrations were of constitutive nature, we also analyzed the blood sample from the same patient. RESULTS The result of aCGH analysis demonstrated differences in the tumor tissue when compared to normal control on the array and also to autologous DNA from patient's blood. The total number of aberrations found in our case was 41 including 37 deletions and 4 amplifications. Whole chromosomal gains and losses were not observed. Collectively, our results showed three deletions and one amplification at 1p, two deletions at 2q, two deletions at 4q, two deletion at 5q, two deletions at 7p and two deletions at 7q; there were also three deletions at 8q, one deletion at 9p, one deletion at 10p, three deletions and one amplification at 10q. Chromosome 11 showed two deletions at 11p, while there was one deletion at 12p and one at 12q. Four deletions at 14q; two deletions at 15q, one amplification at 17q and one deletion at 17q; one deletion at 18p, two deletions at 22q and finally one deletion at Xp and one deletion and one amplification at Xq. Among the signaling pathways, olfactory transduction, Fc gamma R-mediated phagocytosis and p53 signaling pathway showed significant enrichment ascertained by gene ontology (GO) analysis using the DAVID software. CONCLUSIONS Our aCGH analysis is bringing subtle genomic alterations thus broadening genetic spectrum of adult pilocytic astrocytoma in order to offer new molecular biomarkers that will help in diagnostics and therapeutic decision-making.
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Affiliation(s)
- Nives Pećina-Šlaus
- />Laboratory of Neurooncology, Croatian Institute for Brain Research, School of Medicine University of Zagreb, Šalata 12, 10000 Zagreb, Croatia
- />Department of Biology, School of Medicine, University of Zagreb, Šalata 3, 10000 Zagreb, Croatia
| | - Kristina Gotovac
- />Department for Functional Genomics, Center for Translational and Clinical Research, University of Zagreb School of Medicine, and University Hospital Center Zagreb, Šalata 2, 10 000 Zagreb, Croatia
| | - Anja Kafka
- />Laboratory of Neurooncology, Croatian Institute for Brain Research, School of Medicine University of Zagreb, Šalata 12, 10000 Zagreb, Croatia
- />Department of Biology, School of Medicine, University of Zagreb, Šalata 3, 10000 Zagreb, Croatia
| | - Davor Tomas
- />Department of Pathology, School of Medicine, University of Zagreb, Šalata 10, 10000 Zagreb, Croatia
- />Hospital Center “Sisters of Charity”, Vinogradska 29, 10000 Zagreb, Croatia
| | - Fran Borovečki
- />Department for Functional Genomics, Center for Translational and Clinical Research, University of Zagreb School of Medicine, and University Hospital Center Zagreb, Šalata 2, 10 000 Zagreb, Croatia
- />Department of Neurology, University Hospital Center Zagreb, Kišpatićeva 12, 10000 Zagreb, Croatia
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Structural and expression differences between the vasculature of pilocytic astrocytomas and glioblastomas. J Neuropathol Exp Neurol 2014; 72:1171-81. [PMID: 24226271 DOI: 10.1097/nen.0000000000000015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The identification of differences in vascular architecture and utilization of angiogenic pathways is a first step for identifying specific targets for tailored antiangiogenic therapies of brain tumor patients. Here, we compared the proliferating vasculature of 2 glioma subtypes with entirely different biologic behaviors and molecular background at the immunophenotype and gene expression levels. Proliferating vessels in 13 pilocytic astrocytomas and 8 glioblastomas were compared for differences in the composition of the vascular walls using confocal microscopy for markers of endothelial cells and pericytes/mural cells. Endothelial, pericytic, and mural cells had normal-appearing arrangements in the vessels in pilocytic astrocytomas, whereas those in glioblastomas appeared to be more disorganized. In addition, differences in expression of angiogenesis-related genes were sought in the tumor specimens using RNA expression arrays. There were 114 out of 2,894 differentially expressed angiogenesis-related genes between these 2 glioma subtypes indicating differences in the utilization of various pathways. These results point to the need for detailed information on mechanisms of neoangiogenesis in tumor subtypes to facilitate the development of specific antiangiogenic strategies.
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Differential expression of the tumor suppressor A-kinase anchor protein 12 in human diffuse and pilocytic astrocytomas is regulated by promoter methylation. J Neuropathol Exp Neurol 2013; 72:933-41. [PMID: 24042196 DOI: 10.1097/nen.0b013e3182a59a88] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The scaffold protein A-kinase anchor protein 12 (AKAP12) exerts tumor suppressor activity and is downregulated in several tumor entities. We characterized AKAP12 expression and regulation in astrocytomas, including pilocytic and diffusely infiltrating astrocytomas. We examined 194 human gliomas and 23 normal brain white matter samples by immunohistochemistry or immunoblotting for AKAP12 expression. We further performed quantitative methylation analysis of the AKAP12 promoter by MassARRAY® of normal brain, World Health Organization (WHO) grade I to IV astrocytomas, and glioma cell lines. Our results show that AKAP12 is expressed in a perivascular distribution in normal CNS, strongly upregulated in tumor cells in pilocytic astrocytomas, and weakly expressed in diffuse astrocytomas of WHO grade II to IV. Methylation analyses revealed specific hypermethylation of AKAP12α promoter in WHO grade II to IV astrocytomas. Restoration experiments using 5-aza-2'-deoxycytidine in primary glioblastoma cells decreased AKAP12α promoter methylation and markedly increased AKAP12α mRNA levels. In summary, we demonstrate that AKAP12 is differentially expressed in human astrocytomas showing high expression in pilocytic but low expression in diffuse astrocytomas of all WHO-grades. Our results further indicate that epigenetic mechanisms are involved in silencing AKAP12 in diffuse astrocytomas; however, a tumor suppressive role of AKAP12 in distinct astrocytoma subtypes remains to be determined.
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Abstract
World Health Organization (WHO) grade I astrocytomas include pilocytic astrocytoma (PA) and subependymal giant cell astrocytoma (SEGA). As technologies in pharmacologic neo-adjuvant therapy continue to progress and as molecular characteristics are progressively recognized as potential markers of both clinically significant tumor subtypes and response to therapy, interest in the biology of these tumors has surged. An updated review of the current knowledge of the molecular biology of these tumors is needed. We conducted a Medline search to identify published literature discussing the molecular biology of grade I astrocytomas. We then summarized this literature and discuss it in a logical framework through which the complex biology of these tumors can be clearly understood. A comprehensive review of the molecular biology of WHO grade I astrocytomas is presented. The past several years have seen rapid progress in the level of understanding of PA in particular, but the molecular literature regarding both PA and SEGA remains nebulous, ambiguous, and occasionally contradictory. In this review we provide a comprehensive discussion of the current understanding of the chromosomal, genomic, and epigenomic features of both PA and SEGA and provide a logical framework in which these data can be more readily understood.
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Affiliation(s)
- Nicholas F Marko
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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Ho CY, Bar E, Giannini C, Marchionni L, Karajannis MA, Zagzag D, Gutmann DH, Eberhart CG, Rodriguez FJ. MicroRNA profiling in pediatric pilocytic astrocytoma reveals biologically relevant targets, including PBX3, NFIB, and METAP2. Neuro Oncol 2012; 15:69-82. [PMID: 23161775 DOI: 10.1093/neuonc/nos269] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Pilocytic astrocytoma (PA) is a World Health Organization grade I glioma that occurs most commonly in children and young adults. Specific genetic alterations have been described in PA, but the pathogenesis remains poorly understood. We studied microRNA (miRNA) alterations in a large cohort of patients with PA. A total of 43 PA, including 35 sporadic grade I PA, 4 neurofibromatosis-1 (NF1)-associated PA, and 4 PA with pilomyxoid features, as well as 5 nonneoplastic brain controls were examined. BRAF fusion status was assessed in most cases. RNA was examined using the Agilent Human miRNA Microarray V3 platform. Expression of miRNA subsets was validated using quantitative real-time PCR (qRT-PCR) with Taqman probes. Validation of predicted protein targets was performed on tissue microarrays with the use of immunohistochemistry. We identified a subset of miRNAs that were differentially expressed in pediatric PAs versus normal brain tissue: 13 miRNAs were underexpressed, and 20 miRNAs were overexpressed in tumors. Differences were validated by qRT-PCR in a subset, with mean fold change in tumor versus brain of -17 (miR-124), -15 (miR-129), and 19.8 (miR-21). Searching for predicted protein targets in Targetscan, we identified a number of known and putative oncogenes that were predicted targets of miRNA sets relatively underexpressed in PA. Predicted targets with increased expression at the mRNA and/or protein level in PA included PBX3, METAP2, and NFIB. A unique miRNA profile exists in PA, compared with brain tissue. These miRNAs and their targets may play a role in the pathogenesis of PA.
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Affiliation(s)
- Cheng-Ying Ho
- Division of Neuropathology, Department of Pathology, Johns Hopkins University, Baltimore, Maryland 21231, USA
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Essaghir A, Demoulin JB. A minimal connected network of transcription factors regulated in human tumors and its application to the quest for universal cancer biomarkers. PLoS One 2012; 7:e39666. [PMID: 22761861 PMCID: PMC3382591 DOI: 10.1371/journal.pone.0039666] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Accepted: 05/25/2012] [Indexed: 12/19/2022] Open
Abstract
A universal cancer biomarker candidate for diagnosis is supposed to distinguish, within a broad range of tumors, between healthy and diseased patients. Recently published studies have explored the universal usefulness of some biomarkers in human tumors. In this study, we present an integrative approach to search for potential common cancer biomarkers. Using the TFactS web-tool with a catalogue of experimentally established gene regulations, we could predict transcription factors (TFs) regulated in 305 different human cancer cell lines covering a large panel of tumor types. We also identified chromosomal regions having significant copy number variation (CNV) in these cell lines. Within the scope of TFactS catalogue, 88 TFs whose activity status were explained by their gene expressions and CNVs were identified. Their minimal connected network (MCN) of protein-protein interactions forms a significant module within the human curated TF proteome. Functional analysis of the proteins included in this MCN revealed enrichment in cancer pathways as well as inflammation. The ten most central proteins in MCN are TFs that trans-regulate 157 known genes encoding secreted and transmembrane proteins. In publicly available collections of gene expression data from 8,525 patient tissues, 86 genes were differentially regulated in cancer compared to inflammatory diseases and controls. From TCGA cancer gene expression data sets, 50 genes were significantly associated to patient survival in at least one tumor type. Enrichment analysis shows that these genes mechanistically interact in common cancer pathways. Among these cancer biomarker candidates, TFRC, MET and VEGFA are commonly amplified genes in tumors and their encoded proteins stained positive in more than 80% of malignancies from public databases. They are linked to angiogenesis and hypoxia, which are common in cancer. They could be interesting for further investigations in cancer diagnostic strategies.
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Affiliation(s)
- Ahmed Essaghir
- de Duve institute, Université Catholique de Louvain, Brussels, Belgium.
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