101
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Histone H3 tail binds a unique sensing pocket in EZH2 to activate the PRC2 methyltransferase. Proc Natl Acad Sci U S A 2019; 116:8295-8300. [PMID: 30967505 DOI: 10.1073/pnas.1819029116] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Enhancer of Zeste Homolog 2 (EZH2) is the catalytic subunit of Polycomb Repressor Complex 2 (PRC2), the enzyme that catalyzes monomethylation, dimethylation, and trimethylation of lysine 27 on histone H3 (H3K27). Trimethylation at H3K27 (H3K27me3) is associated with transcriptional silencing of developmentally important genes. Intriguingly, H3K27me3 is mutually exclusive with H3K36 trimethylation on the same histone tail. Disruptions in this cross-talk result in aberrant H3K27/H3K36 methylation patterns and altered transcriptional profiles that have been implicated in tumorigenesis and other disease states. Despite their importance, the molecular details of how PRC2 "senses" H3K36 methylation are unclear. We demonstrate that PRC2 is activated in cis by the unmodified side chain of H3K36, and that this activation results in a fivefold increase in the k cat of its enzymatic activity catalyzing H3K27 methylation compared with activity on a substrate methylated at H3K36. Using a photo-cross-linking MS strategy and histone methyltransferase activity assays on PRC2 mutants, we find that EZH2 contains a specific sensing pocket for the H3K36 methylation state that allows the complex to distinguish between modified and unmodified H3K36 residues, altering enzymatic activity accordingly to preferentially methylate the unmodified nucleosome substrate. We also present evidence that this process may be disrupted in some cases of Weaver syndrome.
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102
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Review of ependymomas: assessment of consensus in pathological diagnosis and correlations with genetic profiles and outcome. Brain Tumor Pathol 2019; 36:92-101. [PMID: 30929114 DOI: 10.1007/s10014-019-00338-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 03/17/2019] [Indexed: 12/30/2022]
Abstract
We focused on histological and immunohistochemical characteristics of ependymoma (EPN) with molecular profiles to develop more reproducible criteria of the diagnosis. Three expert neuropathologists reviewed the pathology of 130 samples from the Japan Pediatric Molecular Neuro-Oncology Group study. Confirmed cases were assessed for histology, surrogate markers, molecular subgrouping, and survival data. We reached a consensus regarding the diagnosis of EPNs in 100% of spinal cord tumors and 93% of posterior fossa (PF) tumors that had been diagnosed as EPNs by local pathologists, whereas we reached a consensus regarding only 77% of the local diagnosis of supratentorial (ST) EPNs. Among the PF-EPNs, most of anaplastic ependymomas (AEPNs) were defined as EPN-A by methylation profiling, which was significantly correlated with the subgroup assignment. Regarding prognosis, the overall survival of patients with PF-EPN was significantly better than that of patients with PF AEPN (p = 0.01). Histologically, all ependymoma, RELA fusion-positive (EPN-RELA) qualified as Grade III. Both L1 cell adhesion molecule and nuclear factor kappaB p65 antibodies showed good sensitivity for detecting EPN-RELA. This study indicated that the expert consensus pathological diagnosis could correlate well with the molecular classifications in EPNs. ST EPNs should be diagnosed more carefully by histological and molecular analyses.
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103
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Filbin M, Monje M. Developmental origins and emerging therapeutic opportunities for childhood cancer. Nat Med 2019; 25:367-376. [PMID: 30842674 DOI: 10.1038/s41591-019-0383-9] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 02/01/2019] [Indexed: 02/07/2023]
Abstract
Cancer is the leading disease-related cause of death in children in developed countries. Arising in the context of actively growing tissues, childhood cancers are fundamentally diseases of dysregulated development. Childhood cancers exhibit a lower overall mutational burden than adult cancers, and recent sequencing studies have revealed that the genomic events central to childhood oncogenesis include mutations resulting in broad epigenetic changes or translocations that result in fusion oncoproteins. Here, we will review the developmental origins of childhood cancers, epigenetic dysregulation in tissue stem/precursor cells in numerous examples of childhood cancer oncogenesis and emerging therapeutic opportunities aimed at both cell-intrinsic and microenvironmental targets together with new insights into the mechanisms underlying long-term sequelae of childhood cancer therapy.
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Affiliation(s)
- Mariella Filbin
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorder Center and Harvard Medical School, Boston, MA, USA
| | - Michelle Monje
- Department of Neurology, Stanford University, Stanford, CA, USA.
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104
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Scheie D, Kufaishi HHA, Broholm H, Lund EL, de Stricker K, Melchior LC, Grauslund M. Biomarkers in tumors of the central nervous system - a review. APMIS 2019; 127:265-287. [PMID: 30740783 DOI: 10.1111/apm.12916] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 12/07/2018] [Indexed: 12/21/2022]
Abstract
Until recently, diagnostics of brain tumors were almost solely based on morphology and immunohistochemical stainings for relatively unspecific lineage markers. Although certain molecular markers have been known for longer than a decade (combined loss of chromosome 1p and 19q in oligodendrogliomas), molecular biomarkers were not included in the WHO scheme until 2016. Now, the classification of diffuse gliomas rests on an integration of morphology and molecular results. Also, for many other central nervous system tumor entities, specific diagnostic, prognostic and predictive biomarkers have been detected and continue to emerge. Previously, we considered brain tumors with similar histology to represent a single disease entity. We now realize that histologically identical tumors might show alterations in different molecular pathways, and often represent separate diseases with different natural history and response to treatment. Hence, knowledge about specific biomarkers is of great importance for individualized treatment and follow-up. In this paper we review the biomarkers that we currently use in the diagnostic work-up of brain tumors.
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Affiliation(s)
- David Scheie
- Department of Pathology, Rigshospitalet, Copenhagen, Denmark
| | | | - Helle Broholm
- Department of Pathology, Rigshospitalet, Copenhagen, Denmark
| | - Eva Løbner Lund
- Department of Pathology, Rigshospitalet, Copenhagen, Denmark
| | | | | | - Morten Grauslund
- Department of Genetics and Pathology, Laboratory Medicine, Lund, Sweden
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105
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Na K, Kim HS, Shim HS, Chang JH, Kang SG, Kim SH. Targeted next-generation sequencing panel (TruSight Tumor 170) in diffuse glioma: a single institutional experience of 135 cases. J Neurooncol 2019; 142:445-454. [PMID: 30710203 DOI: 10.1007/s11060-019-03114-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 01/29/2019] [Indexed: 12/17/2022]
Abstract
PURPOSE The TruSight Tumor 170 (TST-170) panel consists of a DNA workflow for the identification of single-nucleotide variants, small insertions and deletions, and copy number variation, as well as a panel of 55 genes for a RNA workflow for the identification of splice variants and gene fusions. To date, the application of TST-170 in diffuse gliomas (DGs) has not been described. METHODS We analyzed 135 samples of DG, which were diagnosed by WHO criteria based on histological features and conventional molecular tests including immunostaining, 1p/19q FISH, and analysis of MGMT methylation and TERT promoter mutation. RESULTS A total of 135 cases consisted of 38 IDH-mutant [17 astrocytoma (AC), 13 oligodendroglioma (OD) and eight glioblastoma (GBM)], 87 IDH-wildtype (six AC, three OD and 78 GBM), and 10 diffuse midline glioma, H3K27M-mutant. DNA analysis enabled the detection of all mutations identified in these samples by conventional techniques, and the results were highly comparable to the known mutations in each subtype. RNA analysis detected four fusion genes including PTPRZ1-MET, FGFR3-TACC3, FAM131B-BRAF, and RET-CCDC6 and one splicing variant (EGFR vIII mutant). Clustered copy number loss in 1p and 19q loci genes were detected in 1p/19q-codeleted OD. CONCLUSIONS The application of TST-170 panel based NGS in clinical and laboratory setting is expected to improve diagnostic accuracy and prognostication. Most benefits are expected in IDH-wildtype DG, a group of genetically heterogenous tumors harboring DNA sequence changes, copy number alterations, and fusions in a large number of oncogenes and tumor suppressor genes.
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Affiliation(s)
- Kiyong Na
- Department of Pathology, Kyung Hee University School of Medicine, Seoul, Republic of Korea.,Department of Pathology, Yonsei University College of Medicine, Severance Hospital, Seoul, Republic of Korea
| | - Hyun-Soo Kim
- Department of Pathology, Yonsei University College of Medicine, Severance Hospital, Seoul, Republic of Korea
| | - Hyo Sup Shim
- Department of Pathology, Yonsei University College of Medicine, Severance Hospital, Seoul, Republic of Korea
| | - Jong Hee Chang
- Department of Neurosurgery, Yonsei University College of Medicine, Severance Hospital, Seoul, Republic of Korea
| | - Seok-Gu Kang
- Department of Neurosurgery, Yonsei University College of Medicine, Severance Hospital, Seoul, Republic of Korea
| | - Se Hoon Kim
- Department of Pathology, Yonsei University College of Medicine, Severance Hospital, Seoul, Republic of Korea.
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106
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Larson JD, Kasper LH, Paugh BS, Jin H, Wu G, Kwon CH, Fan Y, Shaw TI, Silveira AB, Qu C, Xu R, Zhu X, Zhang J, Russell HR, Peters JL, Finkelstein D, Xu B, Lin T, Tinkle CL, Patay Z, Onar-Thomas A, Pounds SB, McKinnon PJ, Ellison DW, Zhang J, Baker SJ. Histone H3.3 K27M Accelerates Spontaneous Brainstem Glioma and Drives Restricted Changes in Bivalent Gene Expression. Cancer Cell 2019; 35:140-155.e7. [PMID: 30595505 PMCID: PMC6570409 DOI: 10.1016/j.ccell.2018.11.015] [Citation(s) in RCA: 180] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 10/13/2018] [Accepted: 11/23/2018] [Indexed: 12/31/2022]
Abstract
Diffuse intrinsic pontine gliomas (DIPGs) are incurable childhood brainstem tumors with frequent histone H3 K27M mutations and recurrent alterations in PDGFRA and TP53. We generated genetically engineered inducible mice and showed that H3.3 K27M enhanced neural stem cell self-renewal while preserving regional identity. Neonatal induction of H3.3 K27M cooperated with activating platelet-derived growth factor receptor α (PDGFRα) mutant and Trp53 loss to accelerate development of diffuse brainstem gliomas that recapitulated human DIPG gene expression signatures and showed global changes in H3K27 posttranslational modifications, but relatively restricted gene expression changes. Genes upregulated in H3.3 K27M tumors were enriched for those associated with neural development where H3K27me3 loss released the poised state of apparently bivalent promoters, whereas downregulated genes were enriched for those encoding homeodomain transcription factors.
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Affiliation(s)
- Jon D Larson
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Lawryn H Kasper
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Barbara S Paugh
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Hongjian Jin
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Gang Wu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Chang-Hyuk Kwon
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Yiping Fan
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Timothy I Shaw
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - André B Silveira
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Chunxu Qu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Raymond Xu
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Xiaoyan Zhu
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Junyuan Zhang
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Helen R Russell
- Department of Genetics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jennifer L Peters
- Cellular Imaging Shared Resource, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - David Finkelstein
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Beisi Xu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Tong Lin
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Christopher L Tinkle
- Department of Radiation Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Zoltan Patay
- Department of Diagnostic Imaging, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Arzu Onar-Thomas
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Stanley B Pounds
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Peter J McKinnon
- Department of Genetics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - David W Ellison
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Suzanne J Baker
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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107
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Fuller C. A little piece of mind: best practices for brain tumor intraoperative consultation. Mod Pathol 2019; 32:44-57. [PMID: 30600316 DOI: 10.1038/s41379-018-0147-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 07/31/2018] [Indexed: 01/01/2023]
Abstract
The workup of the vast majority of brain tumors is initiated at intraoperative consultation. These fresh tumor samples are often quite small and given the nature of the "prime real estate" being sampled, there is never a guarantee that additional tissue will be provided to the responsible pathologist upon request. The 2016 World Health Organization (WHO) Classification of Central Nervous System (CNS) Tumors introduced the concept of "integrative diagnoses," many diagnostic entities now requiring molecular testing in addition to the more routine pathologic workup. Molecular testing relative to targeted therapeutics may also be requested in many circumstances. That said, appropriate preparation for and handling of any potential brain tumor sample at intraoperative consultation is crucial to (1) provide diagnostic information to the operating neurosurgeon that can influence the course of the procedure, and (2) best allow for any necessary ancillary studies purposed for diagnosis and patient care. This review highlights best practices in handling brain tumor intraoperative consultations in this era of expanding required molecular testing. Included is a high-yield overview of ancillary/molecular testing commonly utilized in the workup of infiltrative gliomas, CNS embryonal tumors, and ependymomas, as well as molecular testing to aid in determination of targeted therapeutic options.
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Affiliation(s)
- Christine Fuller
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
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108
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Schloss KB, Gramazio CC, Silverman AT, Parker ML, Wang AS. Mapping Color to Meaning in Colormap Data Visualizations. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS 2019; 25:810-819. [PMID: 30188827 DOI: 10.1109/tvcg.2018.2865147] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
To interpret data visualizations, people must determine how visual features map onto concepts. For example, to interpret colormaps, people must determine how dimensions of color (e.g., lightness, hue) map onto quantities of a given measure (e.g., brain activity, correlation magnitude). This process is easier when the encoded mappings in the visualization match people's predictions of how visual features will map onto concepts, their inferred mappings. To harness this principle in visualization design, it is necessary to understand what factors determine people's inferred mappings. In this study, we investigated how inferred color-quantity mappings for colormap data visualizations were influenced by the background color. Prior literature presents seemingly conflicting accounts of how the background color affects inferred color-quantity mappings. The present results help resolve those conflicts, demonstrating that sometimes the background has an effect and sometimes it does not, depending on whether the colormap appears to vary in opacity. When there is no apparent variation in opacity, participants infer that darker colors map to larger quantities (dark-is-more bias). As apparent variation in opacity increases, participants become biased toward inferring that more opaque colors map to larger quantities (opaque-is-more bias). These biases work together on light backgrounds and conflict on dark backgrounds. Under such conflicts, the opaque-is-more bias can negate, or even supersede the dark-is-more bias. The results suggest that if a design goal is to produce colormaps that match people's inferred mappings and are robust to changes in background color, it is beneficial to use colormaps that will not appear to vary in opacity on any background color, and to encode larger quantities in darker colors.
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109
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Huang T, Garcia R, Qi J, Lulla R, Horbinski C, Behdad A, Wadhwani N, Shilatifard A, James C, Saratsis AM. Detection of histone H3 K27M mutation and post-translational modifications in pediatric diffuse midline glioma via tissue immunohistochemistry informs diagnosis and clinical outcomes. Oncotarget 2018; 9:37112-37124. [PMID: 30647848 PMCID: PMC6324678 DOI: 10.18632/oncotarget.26430] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 11/26/2018] [Indexed: 12/29/2022] Open
Abstract
Pediatric diffuse midline glioma is a highly morbid glial neoplasm that may arise in the thalamus or brainstem (also known as diffuse intrinsic pontine glioma or DIPG). Because tumor anatomic location precludes surgical resection, diagnosis and treatment is based on MR imaging and analysis of biopsy specimens. Up to 80% of pediatric diffuse midline gliomas harbor a histone H3 mutation resulting in the replacement of lysine 27 with methionine (K27M) in genes encoding histone H3 variant H3.3 (H3F3A) or H3.1 (HIST1H3B). H3K27M mutant glioma responds more poorly to treatment and is associated with worse clinical outcome than wild-type tumors, so mutation detection is now diagnostic for a new clinical entity, diffuse midline glioma H3K27M mutant, as defined in the most recent WHO classification system. We previously reported patterns of histone H3 trimethylation (H3K27me3) and acetylation (H3K27Ac) associated with H3K27M mutation that impact transcription regulation and contribute to tumorigenesis. Given the clinical implications of the H3K27M mutation and these associated H3 post-translational modifications (PTMs), we set to determine whether they can be characterized via immunohistochemistry (IHC) in a cohort of pediatric glioma (n = 69) and normal brain tissue (n = 4) specimens. We observed 100% concordance between tissue IHC and molecular sequencing for detecting H3K27M mutation. In turn, H3K37M and H3K27me3 results, but not H3K27Ac staining patterns, were predictive of clinical outcomes. Our results demonstrate H3K27M and H3K27me3 staining of pediatric glioma tissue may be useful for diagnosis, stratification to epigenetic targeted therapies, and longitudinal monitoring of treatment response.
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Affiliation(s)
- Tina Huang
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Roxanna Garcia
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Jin Qi
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Rishi Lulla
- Division of Pediatric Hematology/Oncology, Hasbro Children's Hospital, The Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Craig Horbinski
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Amir Behdad
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Nitin Wadhwani
- Department of Pathology, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Charles James
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Amanda M Saratsis
- Division of Pediatric Neurosurgery, Department of Surgery, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA.,Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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110
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Khatua S, Mangum R, Bertrand KC, Zaky W, McCall D, Mack SC. Pediatric ependymoma: current treatment and newer therapeutic insights. Future Oncol 2018; 14:3175-3186. [PMID: 30418040 DOI: 10.2217/fon-2018-0502] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Advances in genomic, transcriptomic and epigenomic profiling now identifies pediatric ependymoma as a defined biological entity. Molecular interrogation has segregated these tumors into distinct biological subtypes based on anatomical location, age and clinical outcome, which now defines the need to tailor therapy even for histologically similar tumors. These findings now provide reasons for a paradigm shift in therapy, which should profile future clinical trials focused on targeted therapeutic strategies and risk-based treatment. The need to diagnose and differentiate the aggressive variants, which include the posterior fossa group A and the supratentorial RELA fusion subtypes, is imperative to escalate therapy and improve survival.
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Affiliation(s)
- Soumen Khatua
- Department of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ross Mangum
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA.,Department of Pediatric Hematology & Oncology, Texas Children's Cancer & Hematology Centers, Houston, TX 77030, USA
| | - Kelsey C Bertrand
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA.,Department of Pediatric Hematology & Oncology, Texas Children's Cancer & Hematology Centers, Houston, TX 77030, USA
| | - Wafik Zaky
- Department of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - David McCall
- Department of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Stephen C Mack
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA.,Department of Pediatric Hematology & Oncology, Texas Children's Cancer & Hematology Centers, Houston, TX 77030, USA
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111
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Abstract
Childhood cancer is fundamentally a disease of dysregulated development. Why does it rarely occur during the fetal period, a time of enormous growth and development?
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Affiliation(s)
- Michelle Monje
- Departments of Neurology and Pediatrics, Stanford University, 265 Campus Drive, Stanford, CA, USA.
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112
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Testa U, Castelli G, Pelosi E. Genetic Abnormalities, Clonal Evolution, and Cancer Stem Cells of Brain Tumors. Med Sci (Basel) 2018; 6:E85. [PMID: 30279357 PMCID: PMC6313628 DOI: 10.3390/medsci6040085] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 09/19/2018] [Accepted: 09/25/2018] [Indexed: 02/06/2023] Open
Abstract
Brain tumors are highly heterogeneous and have been classified by the World Health Organization in various histological and molecular subtypes. Gliomas have been classified as ranging from low-grade astrocytomas and oligodendrogliomas to high-grade astrocytomas or glioblastomas. These tumors are characterized by a peculiar pattern of genetic alterations. Pediatric high-grade gliomas are histologically indistinguishable from adult glioblastomas, but they are considered distinct from adult glioblastomas because they possess a different spectrum of driver mutations (genes encoding histones H3.3 and H3.1). Medulloblastomas, the most frequent pediatric brain tumors, are considered to be of embryonic derivation and are currently subdivided into distinct subgroups depending on histological features and genetic profiling. There is emerging evidence that brain tumors are maintained by a special neural or glial stem cell-like population that self-renews and gives rise to differentiated progeny. In many instances, the prognosis of the majority of brain tumors remains negative and there is hope that the new acquisition of information on the molecular and cellular bases of these tumors will be translated in the development of new, more active treatments.
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Affiliation(s)
- Ugo Testa
- Department of Oncology, Istituto Superiore di Sanità, 00161 Rome, Italy.
| | - Germana Castelli
- Department of Oncology, Istituto Superiore di Sanità, 00161 Rome, Italy.
| | - Elvira Pelosi
- Department of Oncology, Istituto Superiore di Sanità, 00161 Rome, Italy.
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113
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Zhang RR, Kuo JS. Reduced H3K27me3 is a New Epigenetic Biomarker for Pediatric Posterior Fossa Ependymomas. Neurosurgery 2018; 81:N7-N8. [PMID: 28873995 DOI: 10.1093/neuros/nyx262] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
| | - John S Kuo
- University of Wisconsin Madison, Wisconsin
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114
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Pajtler KW, Wen J, Sill M, Lin T, Orisme W, Tang B, Hübner JM, Ramaswamy V, Jia S, Dalton JD, Haupfear K, Rogers HA, Punchihewa C, Lee R, Easton J, Wu G, Ritzmann TA, Chapman R, Chavez L, Boop FA, Klimo P, Sabin ND, Ogg R, Mack SC, Freibaum BD, Kim HJ, Witt H, Jones DTW, Vo B, Gajjar A, Pounds S, Onar-Thomas A, Roussel MF, Zhang J, Taylor JP, Merchant TE, Grundy R, Tatevossian RG, Taylor MD, Pfister SM, Korshunov A, Kool M, Ellison DW. Molecular heterogeneity and CXorf67 alterations in posterior fossa group A (PFA) ependymomas. Acta Neuropathol 2018; 136:211-226. [PMID: 29909548 DOI: 10.1007/s00401-018-1877-0] [Citation(s) in RCA: 186] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 06/10/2018] [Accepted: 06/10/2018] [Indexed: 12/21/2022]
Abstract
Of nine ependymoma molecular groups detected by DNA methylation profiling, the posterior fossa type A (PFA) is most prevalent. We used DNA methylation profiling to look for further molecular heterogeneity among 675 PFA ependymomas. Two major subgroups, PFA-1 and PFA-2, and nine minor subtypes were discovered. Transcriptome profiling suggested a distinct histogenesis for PFA-1 and PFA-2, but their clinical parameters were similar. In contrast, PFA subtypes differed with respect to age at diagnosis, gender ratio, outcome, and frequencies of genetic alterations. One subtype, PFA-1c, was enriched for 1q gain and had a relatively poor outcome, while patients with PFA-2c ependymomas showed an overall survival at 5 years of > 90%. Unlike other ependymomas, PFA-2c tumors express high levels of OTX2, a potential biomarker for this ependymoma subtype with a good prognosis. We also discovered recurrent mutations among PFA ependymomas. H3 K27M mutations were present in 4.2%, occurring only in PFA-1 tumors, and missense mutations in an uncharacterized gene, CXorf67, were found in 9.4% of PFA ependymomas, but not in other groups. We detected high levels of wildtype or mutant CXorf67 expression in all PFA subtypes except PFA-1f, which is enriched for H3 K27M mutations. PFA ependymomas are characterized by lack of H3 K27 trimethylation (H3 K27-me3), and we tested the hypothesis that CXorf67 binds to PRC2 and can modulate levels of H3 K27-me3. Immunoprecipitation/mass spectrometry detected EZH2, SUZ12, and EED, core components of the PRC2 complex, bound to CXorf67 in the Daoy cell line, which shows high levels of CXorf67 and no expression of H3 K27-me3. Enforced reduction of CXorf67 in Daoy cells restored H3 K27-me3 levels, while enforced expression of CXorf67 in HEK293T and neural stem cells reduced H3 K27-me3 levels. Our data suggest that heterogeneity among PFA ependymomas could have clinicopathologic utility and that CXorf67 may have a functional role in these tumors.
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Affiliation(s)
- Kristian W Pajtler
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), 69120, Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, University Hospital, 69120, Heidelberg, Germany
| | - Ji Wen
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Martin Sill
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), 69120, Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Tong Lin
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Wilda Orisme
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Bo Tang
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Jens-Martin Hübner
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), 69120, Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Vijay Ramaswamy
- Division of Hematology/Oncology, Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada
- Division of Neurosurgery, Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada
| | - Sujuan Jia
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - James D Dalton
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Kelly Haupfear
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Hazel A Rogers
- Children's Brain Tumour Research Centre, University of Nottingham, Nottingham, UK
| | | | - Ryan Lee
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - John Easton
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Gang Wu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Timothy A Ritzmann
- Children's Brain Tumour Research Centre, University of Nottingham, Nottingham, UK
| | - Rebecca Chapman
- Children's Brain Tumour Research Centre, University of Nottingham, Nottingham, UK
| | - Lukas Chavez
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), 69120, Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Fredrick A Boop
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Paul Klimo
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Noah D Sabin
- Department of Diagnostic Imaging, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Robert Ogg
- Department of Diagnostic Imaging, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Stephen C Mack
- Division of Neurosurgery, Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, Baylor College of Medicine, Houston, TX, USA
| | - Brian D Freibaum
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Hong Joo Kim
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Hendrik Witt
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), 69120, Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, University Hospital, 69120, Heidelberg, Germany
| | - David T W Jones
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), 69120, Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Baohan Vo
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Amar Gajjar
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Stan Pounds
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Arzu Onar-Thomas
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Martine F Roussel
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - J Paul Taylor
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Thomas E Merchant
- Department of Radiation Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Richard Grundy
- Children's Brain Tumour Research Centre, University of Nottingham, Nottingham, UK
| | - Ruth G Tatevossian
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Michael D Taylor
- Division of Neurosurgery, Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada
| | - Stefan M Pfister
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), 69120, Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, University Hospital, 69120, Heidelberg, Germany
| | - Andrey Korshunov
- Department of Neuropathology, University of Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marcel Kool
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), 69120, Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - David W Ellison
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
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115
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Klonou A, Spiliotakopoulou D, Themistocleous MS, Piperi C, Papavassiliou AG. Chromatin remodeling defects in pediatric brain tumors. ANNALS OF TRANSLATIONAL MEDICINE 2018; 6:248. [PMID: 30069450 DOI: 10.21037/atm.2018.04.08] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Brain tumors are regarded as the most prevalent solid neoplasms in children and the principal reason of death in this population. Even though surgical resection, radiotherapy and chemotherapy have improved outcome, a significant number of patients die in 6-12 months after diagnosis while those who survive, frequently experience side effects and relapses. Several studies suggest that many types of cancer including pediatric brain tumors are characterized by alterations in epigenetic profiles with deregulated chromatin remodeling and posttranslational covalent histone modifications playing a prominent role. Moreover, interplay of genetic and epigenetic changes has been associated to tumor growth and invasion as well as to modulation of patient's response to current treatment. Therefore, detection of tumor-specific histone changes and elucidation of the underlying gene defects will allow successful tailoring of personalized treatment. The goal of this review is to provide an update of genetic and epigenetic alterations that characterize pediatric brain tumors focusing on histone modifications, aiming at directing future molecular and epigenetic therapeutic targeting.
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Affiliation(s)
- Alexia Klonou
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Danai Spiliotakopoulou
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Christina Piperi
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Athanasios G Papavassiliou
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, Athens, Greece
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116
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Abstract
Recent advances in molecular pathology have reshaped the practice of brain tumor diagnostics. The classification of gliomas has been restructured with the discovery of isocitrate dehydrogenase (IDH) 1/2 mutations in the vast majority of lower grade infiltrating gliomas and secondary glioblastomas (GBM), with IDH-mutant astrocytomas further characterized by TP53 and ATRX mutations. Whole-arm 1p/19q codeletion in conjunction with IDH mutations now define oligodendrogliomas, which are also enriched for CIC, FUBP1, PI3K, NOTCH1, and TERT-p mutations. IDH-wild-type (wt) infiltrating astrocytomas are mostly primary GBMs and are characterized by EGFR, PTEN, TP53, NF1, RB1, PDGFRA, and CDKN2A/B alterations, TERT-p mutations, and characteristic copy number alterations including gains of chromosome 7 and losses of 10. Other clinically and genetically distinct infiltrating astrocytomas include the aggressive H3K27M-mutant midline gliomas, and smaller subsets that occur in the setting of NF1 or have BRAF V600E mutations. Low-grade pediatric gliomas are both genetically and biologically distinct from their adult counterparts and often harbor a single driver event often involving BRAF, FGFR1, or MYB/MYBL1 genes. Large scale genomic and epigenomic analyses have identified distinct subgroups of ependymomas tightly linked to tumor location and clinical behavior. The diagnosis of embryonal neoplasms also integrates molecular testing: (I) 4 molecularly defined, biologically distinct subtypes of medulloblastomas are now recognized; (II) 3 histologic entities have now been reclassified under a diagnosis of "embryonal tumor with multilayered rosettes (ETMR), C19MC-altered"; and (III) atypical teratoid/rhabdoid tumors (AT/RT) now require SMARCB1 (INI1) or SMARCA4 (BRG1) alterations for their diagnosis. We discuss the practical use of contemporary biomarkers for an integrative diagnosis of central nervous system neoplasia.
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117
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cIMPACT-NOW update 2: diagnostic clarifications for diffuse midline glioma, H3 K27M-mutant and diffuse astrocytoma/anaplastic astrocytoma, IDH-mutant. Acta Neuropathol 2018; 135:639-642. [PMID: 29497819 DOI: 10.1007/s00401-018-1826-y] [Citation(s) in RCA: 253] [Impact Index Per Article: 42.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 02/23/2018] [Indexed: 01/16/2023]
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118
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Rudà R, Reifenberger G, Frappaz D, Pfister SM, Laprie A, Santarius T, Roth P, Tonn JC, Soffietti R, Weller M, Moyal ECJ. EANO guidelines for the diagnosis and treatment of ependymal tumors. Neuro Oncol 2018; 20:445-456. [PMID: 29194500 PMCID: PMC5909649 DOI: 10.1093/neuonc/nox166] [Citation(s) in RCA: 155] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Ependymal tumors are rare CNS tumors and may occur at any age, but their proportion among primary brain tumors is highest in children and young adults. Thus, the level of evidence of diagnostic and therapeutic interventions is higher in the pediatric compared with the adult patient population.The diagnosis and disease staging is performed by craniospinal MRI. Tumor classification is achieved by histological and molecular diagnostic assessment of tissue specimens according to the World Health Organization (WHO) classification 2016. Surgery is the crucial initial treatment in both children and adults. In pediatric patients with intracranial ependymomas of WHO grades II or III, surgery is followed by local radiotherapy regardless of residual tumor volume. In adults, radiotherapy is employed in patients with anaplastic ependymoma WHO grade III, and in case of incomplete resection of WHO grade II ependymoma. Chemotherapy alone is reserved for young children <12 months and for adults with recurrent disease when further surgery and irradiation are no longer feasible. A gross total resection is the mainstay of treatment in spinal ependymomas, and radiotherapy is reserved for incompletely resected tumors. Nine subgroups of ependymal tumors across different anatomical compartments (supratentorial, posterior fossa, spinal) and patient ages have been identified with distinct genetic and epigenetic alterations, and with distinct outcomes. These findings may lead to more precise diagnostic and prognostic assessments, molecular subgroup-adapted therapies, and eventually new recommendations pending validation in prospective studies.
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Affiliation(s)
- Roberta Rudà
- Department of Neuro-Oncology, University of Turin and City of Health and Science University Hospital, Turin, Italy
| | - Guido Reifenberger
- Institute of Neuropathology, Medical Faculty, Heinrich Heine University Düsseldorf and German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany
| | - Didier Frappaz
- Département de Neuro-Oncologie, Centre Léon-Bérard, Institut d’Hématologie et Oncologie Pédiatrique et Adulte, Lyon, France
| | - Stefan M Pfister
- Division of Pediatric Neuro-oncology, German Cancer Research Center, DKTK, Heidelberg, Germany and Department of Pediatric Oncology, Hematology and Immunology, University Hospital Heidelberg, Heidelberg, Germany
| | - Anne Laprie
- Department of Radiation Oncology, Institut Universitaire du Cancer de Toulouse Oncopole, Toulouse, France
| | | | - Patrick Roth
- Department of Neurology and Brain Tumor Center, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Joerg Christian Tonn
- Department of Neurosurgery Ludwig-Maximilians-Universität and DKTK partner site, University of Munich, Munich, Germany
| | - Riccardo Soffietti
- Department of Neuro-Oncology, University of Turin and City of Health and Science University Hospital, Turin, Italy
| | - Michael Weller
- Department of Neurology and Brain Tumor Center, University Hospital Zurich and University of Zurich, Zurich, Switzerland
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119
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Yang A, Jiao Y, Yang S, Deng M, Yang X, Mao C, Sun Y, Ding N, Li N, Zhang M, Jin S, Zhang H, Jiang Y. Homocysteine activates autophagy by inhibition of CFTR expression via interaction between DNA methylation and H3K27me3 in mouse liver. Cell Death Dis 2018; 9:169. [PMID: 29415998 PMCID: PMC5833451 DOI: 10.1038/s41419-017-0216-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 11/11/2017] [Accepted: 12/13/2017] [Indexed: 12/12/2022]
Abstract
Elevated homocysteine (Hcy) levels have been reported to be involved in liver injury, and autophagy plays an important role in normal hepatic physiology and pathophysiology, but the mechanism underlying Hcy regulated autophagy is currently unknown. In this study, CBS+/- mice were fed with regular diet for 12 weeks to establish a hyperhomocysteinemia (HHcy) model and HL-7702 cells were treated with Hcy, we found that Hcy increases autophagy and aggravates liver injury by downregulation of cystic fibrosis transmembrane conductance regulator (CFTR) expression in vivo and in vitro. Overexpression of CFTR inhibited the formation of autophagosomes and the expression of autophagy-related proteins BECN1, LC3-II/I and Atg12, while the expression of p62 increased in Hcy-treated hepatocytes and CBS+/- mice injected with lentivirus expressing CFTR. Further study showed that CFTR expression is regulated by the interaction of DNA methyltransferase 1 (DNMT1) and enhancer of zeste homolog 2 (EZH2), which, respectively, regulate DNA methylation and histone H3 lysine 27 trimethylation (H3K27me3). In conclusion, our study showed that Hcy activates autophagy by inhibition of CFTR expression via interaction between H3K27me3 and DNA methylation in the mouse liver. These findings provide new insight into the mechanism of Hcy-induced autophagy in liver injury.
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Affiliation(s)
- Anning Yang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, 750004, China.,Ningxia Key Laboratory of Vascular Injury and Repair Research, Yinchuan, China
| | - Yun Jiao
- Ningxia Medical University General Hospital, Yinchuan, 750004, China
| | - Songhao Yang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, 750004, China.,Ningxia Key Laboratory of Vascular Injury and Repair Research, Yinchuan, China
| | - Mei Deng
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, 750004, China.,Ningxia Key Laboratory of Vascular Injury and Repair Research, Yinchuan, China
| | - Xiaoling Yang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, 750004, China.,Ningxia Key Laboratory of Vascular Injury and Repair Research, Yinchuan, China
| | - Caiyan Mao
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, 750004, China.,Ningxia Key Laboratory of Vascular Injury and Repair Research, Yinchuan, China
| | - Yue Sun
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, 750004, China.,Ningxia Key Laboratory of Vascular Injury and Repair Research, Yinchuan, China
| | - Ning Ding
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, 750004, China.,Ningxia Key Laboratory of Vascular Injury and Repair Research, Yinchuan, China
| | - Nan Li
- Pharmacy college, Ningxia Medical University, Yinchuan, 750004, China
| | - Minghao Zhang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, 750004, China.,Ningxia Key Laboratory of Vascular Injury and Repair Research, Yinchuan, China
| | - Shaoju Jin
- Pharmacy college, Ningxia Medical University, Yinchuan, 750004, China
| | - Huiping Zhang
- Ningxia Key Laboratory of Vascular Injury and Repair Research, Yinchuan, China. .,Ningxia Medical University General Hospital, Yinchuan, 750004, China.
| | - Yideng Jiang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, 750004, China. .,Ningxia Key Laboratory of Vascular Injury and Repair Research, Yinchuan, China.
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120
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Flavahan WA, Gaskell E, Bernstein BE. Epigenetic plasticity and the hallmarks of cancer. Science 2018; 357:357/6348/eaal2380. [PMID: 28729483 DOI: 10.1126/science.aal2380] [Citation(s) in RCA: 799] [Impact Index Per Article: 133.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Chromatin and associated epigenetic mechanisms stabilize gene expression and cellular states while also facilitating appropriate responses to developmental or environmental cues. Genetic, environmental, or metabolic insults can induce overly restrictive or overly permissive epigenetic landscapes that contribute to pathogenesis of cancer and other diseases. Restrictive chromatin states may prevent appropriate induction of tumor suppressor programs or block differentiation. By contrast, permissive or "plastic" states may allow stochastic oncogene activation or nonphysiologic cell fate transitions. Whereas many stochastic events will be inconsequential "passengers," some will confer a fitness advantage to a cell and be selected as "drivers." We review the broad roles played by epigenetic aberrations in tumor initiation and evolution and their potential to give rise to all classic hallmarks of cancer.
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Affiliation(s)
- William A Flavahan
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA, and Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Elizabeth Gaskell
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA, and Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Bradley E Bernstein
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA, and Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
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121
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Cieślik M, Chinnaiyan AM. Cancer transcriptome profiling at the juncture of clinical translation. Nat Rev Genet 2017; 19:93-109. [PMID: 29279605 DOI: 10.1038/nrg.2017.96] [Citation(s) in RCA: 156] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Methodological breakthroughs over the past four decades have repeatedly revolutionized transcriptome profiling. Using RNA sequencing (RNA-seq), it has now become possible to sequence and quantify the transcriptional outputs of individual cells or thousands of samples. These transcriptomes provide a link between cellular phenotypes and their molecular underpinnings, such as mutations. In the context of cancer, this link represents an opportunity to dissect the complexity and heterogeneity of tumours and to discover new biomarkers or therapeutic strategies. Here, we review the rationale, methodology and translational impact of transcriptome profiling in cancer.
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Affiliation(s)
- Marcin Cieślik
- Michigan Center for Translational Pathology, University of Michigan.,Department of Pathology, University of Michigan
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan.,Department of Pathology, University of Michigan.,Comprehensive Cancer Center, University of Michigan.,Department of Urology, University of Michigan.,Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan 48109, USA
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122
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Abstract
PURPOSE OF REVIEW To synthesize, integrate, and comment on recent research developments to our understanding of the molecular basis of ependymoma (EPN), and to place this in context with current treatment and research efforts. RECENT FINDINGS Our recent understanding of the histologically defined molecular entity EPN has rapidly advanced through genomic, transcriptomic, and epigenomic profiling studies. SUMMARY These advancements lay the groundwork for development of future EPN biomarkers, models, and therapeutics. Our review discusses these discoveries and their impact on our clinical understanding of this disease. Lastly, we offer insight into clinical and research areas requiring further validation, and open questions remaining in the field.
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123
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Significance of H3K27me3 loss in the diagnosis of malignant peripheral nerve sheath tumors. Mod Pathol 2017; 30:1710-1719. [PMID: 28776579 DOI: 10.1038/modpathol.2017.97] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 06/13/2017] [Accepted: 06/18/2017] [Indexed: 12/22/2022]
Abstract
The diagnosis of malignant peripheral nerve sheath tumors can be challenging and other spindle cell sarcomas commonly enter in the differential diagnosis. Loss of trimethylation at lysine 27 of histone-H3 (H3K27me3) by immunohistochemistry was recently described in malignant peripheral nerve sheath tumors. However, its specificity remains controversial. We therefore studied 82 synovial sarcomas, 39 malignant peripheral nerve sheath tumors, and 10 fibrosarcomatous dermatofibrosarcoma protuberans for H3K27me3 loss by immunohistochemistry. The diagnoses were based on morphology, immunophenotype, and genetics based on WHO classification. H3K27me3 immunohistochemistry was scored by two pathologists based on fraction of cells with nuclear staining (score 0 to 3+). Loss of H3K27me3 (score 0) was seen in 44% of malignant peripheral nerve sheath tumors and 9% of synovial sarcomas yielding positive and negative predictive values of 71% and 77%, respectively. Loss of H3K27me3 was seen in 10% of fibrosarcomatous dermatofibrosarcoma protuberans, yielding positive and negative predictive values of 94 and 29% in the differential diagnosis of malignant peripheral nerve sheath tumor versus fibrosarcomatous dermatofibrosarcoma protuberans. Partial loss (score 1-2) was common in all three tumor types. Among malignant peripheral nerve sheath tumors, there was no significant association between H3K27me3 loss and gender, tumor site, or size, and progression-free or overall survival. Patients with tumors with H3K27me3 loss were younger than those with tumors with retained H3K27me3 expression (P=0.011). H3K27me3 expression was lost in 50 and 31% of sporadic and Neurofibromatosis-associated malignant peripheral nerve sheath tumors, respectively (P=0.25).Complete H3K27me3 loss is a moderately sensitive and relatively specific marker for the diagnosis of malignant peripheral nerve sheath tumor when the differential diagnosis includes synovial sarcoma and fibrosarcomatous dermatofibrosarcoma protuberans. Partial loss has limited diagnostic utility. H3K27me3 status does not show significant association with clinical outcome in malignant peripheral nerve sheath tumors.
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124
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Panwalkar P, Clark J, Ramaswamy V, Hawes D, Yang F, Dunham C, Yip S, Hukin J, Sun Y, Schipper MJ, Chavez L, Margol A, Pekmezci M, Chung C, Banda A, Bayliss JM, Curry SJ, Santi M, Rodriguez FJ, Snuderl M, Karajannis MA, Saratsis AM, Horbinski CM, Carret AS, Wilson B, Johnston D, Lafay-Cousin L, Zelcer S, Eisenstat D, Silva M, Scheinemann K, Jabado N, McNeely PD, Kool M, Pfister SM, Taylor MD, Hawkins C, Korshunov A, Judkins AR, Venneti S. Immunohistochemical analysis of H3K27me3 demonstrates global reduction in group-A childhood posterior fossa ependymoma and is a powerful predictor of outcome. Acta Neuropathol 2017; 134:705-714. [PMID: 28733933 DOI: 10.1007/s00401-017-1752-4] [Citation(s) in RCA: 156] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 07/14/2017] [Accepted: 07/14/2017] [Indexed: 10/19/2022]
Abstract
Posterior fossa ependymomas (EPN_PF) in children comprise two morphologically identical, but biologically distinct tumor entities. Group-A (EPN_PFA) tumors have a poor prognosis and require intensive therapy. In contrast, group-B tumors (EPN_PFB) exhibit excellent prognosis and the current consensus opinion recommends future clinical trials to test the possibility of treatment de-escalation in these patients. Therefore, distinguishing these two tumor subtypes is critical. EPN_PFA and EPN_PFB can be distinguished based on DNA methylation signatures, but these assays are not routinely available. We have previously shown that a subset of poorly prognostic childhood EPN_PF exhibits global reduction in H3K27me3. Therefore, we set out to determine whether a simple immunohistochemical assay for H3K27me3 could be used to segregate EPN_PFA from EPN_PFB tumors. We assembled a cohort of 230 childhood ependymomas and H3K27me3 immunohistochemistry was assessed as positive or negative in a blinded manner. H3K27me3 staining results were compared with DNA methylation-based subgroup information available in 112 samples [EPN_PFA (n = 72) and EPN_PFB tumors (n = 40)]. H3K27me3 staining was globally reduced in EPN_PFA tumors and immunohistochemistry showed 99% sensitivity and 100% specificity in segregating EPN_PFA from EPN_PFB tumors. Moreover, H3K27me3 immunostaining was sufficient to delineate patients with worse prognosis in two independent, non-overlapping cohorts (n = 133 and n = 97). In conclusion, immunohistochemical evaluation of H3K27me3 global reduction is an economic, easily available and readily adaptable method for defining high-risk EPN_PFA from low-risk posterior fossa EPN_PFB tumors to inform prognosis and to enable the design of future clinical trials.
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125
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Rethinking childhood ependymoma: a retrospective, multi-center analysis reveals poor long-term overall survival. J Neurooncol 2017; 135:201-211. [PMID: 28733870 PMCID: PMC5658456 DOI: 10.1007/s11060-017-2568-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 07/13/2017] [Indexed: 11/24/2022]
Abstract
Ependymoma is the third most common brain tumor in children, but there is a paucity of large studies with more than 10 years of follow-up examining the long-term survival and recurrence patterns of this disease. We conducted a retrospective chart review of 103 pediatric patients with WHO Grades II/III intracranial ependymoma, who were treated at Dana-Farber/Boston Children’s Cancer and Blood Disorders Center and Chicago’s Ann & Robert H. Lurie Children’s Hospital between 1985 and 2008, and an additional 360 ependymoma patients identified from the Surveillance Epidemiology and End Results (SEER) database. For the institutional cohort, we evaluated clinical and histopathological prognostic factors of overall survival (OS) and progression-free survival (PFS) using the log-rank test, and univariate and multivariate Cox proportional-hazards models. Overall survival rates were compared to those of the SEER cohort. Median follow-up time was 11 years. Ten-year OS and PFS were 50 ± 5% and 29 ± 5%, respectively. Findings were validated in the independent SEER cohort, with 10-year OS rates of 52 ± 3%. GTR and grade II pathology were associated with significantly improved OS. However, GTR was not curative for all children. Ten-year OS for patients treated with a GTR was 61 ± 7% and PFS was 36 ± 6%. Pathological examination confirmed most recurrent tumors to be ependymoma, and 74% occurred at the primary tumor site. Current treatment paradigms are not sufficient to provide long-term cure for children with ependymoma. Our findings highlight the urgent need to develop novel treatment approaches for this devastating disease.
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Characterization of gliomas: from morphology to molecules. Virchows Arch 2017; 471:257-269. [DOI: 10.1007/s00428-017-2181-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 06/06/2017] [Accepted: 06/16/2017] [Indexed: 01/28/2023]
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127
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Ryall S, Guzman M, Elbabaa SK, Luu B, Mack SC, Zapotocky M, Taylor MD, Hawkins C, Ramaswamy V. H3 K27M mutations are extremely rare in posterior fossa group A ependymoma. Childs Nerv Syst 2017. [PMID: 28623522 DOI: 10.1007/s00381-017-3481-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Mutations in the tail of histone H3 (K27M) are frequently found in pediatric midline high-grade glioma's but have rarely been reported in other malignancies. Recently, recurrent somatic nucleotide variants in histone H3 (H3 K27M) have been reported in group A posterior fossa ependymoma (EPN_PFA), an entity previously described to have no recurrent mutations. However, the true incidence of H3 K27M mutations in EPN_PFA is unknown. METHODS In order to discern the frequency of K27M mutations in histone H3 in EPN_PFA, we analyzed 151 EPN_PFA previously profiled with genome-wide methylation arrays using a validated droplet digital PCR assay. RESULTS We identified only 1 case out of 151 EPN_PFA harboring the K27M mutation indicating that histone mutations are extremely rare in EPN_PFA. Morphologically, this single mutated case is clearly consistent with an ependymoma, and the presence of the K27M mutation was confirmed using immunohistochemistry. DISCUSSION K27M mutations are extremely rare in EPN_PFA. Routine evaluation of K27M mutations in EPN_PFA is of limited utility, and is unlikely to have any bearing on prognosis and/or future risk stratification.
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Affiliation(s)
- Scott Ryall
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Miguel Guzman
- Pathology and Laboratory Medicine, Cardinal Glennon Children's Hospital, Pathology Department, Saint Louis University, Saint Louis, MO, USA
| | - Samer K Elbabaa
- Department of Neurological Surgery, Saint Louis University School of Medicine, Saint Louis, MO, USA
| | - Betty Luu
- Program in Developmental and Stem Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON, Canada
| | | | - Michal Zapotocky
- Division of Haematology/Oncology, Hospital for Sick Children, University of Toronto, 555 University Ave, Toronto, ON, M5G 1X8, Canada
| | - Michael D Taylor
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Program in Developmental and Stem Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON, Canada
- Division of Neurosurgery, Hospital for Sick Children, Toronto, ON, Canada
| | - Cynthia Hawkins
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Program in Developmental and Stem Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON, Canada
- Department of Pediatric Laboratory Medicine, Hospital for Sick Children, Toronto, ON, Canada
| | - Vijay Ramaswamy
- Division of Haematology/Oncology, Hospital for Sick Children, University of Toronto, 555 University Ave, Toronto, ON, M5G 1X8, Canada.
- Program in Neuroscience and Mental Health, Arthur and Sonia Labatt Brain Tumour Reserch Centre, Hospital for Sick Children, Toronto, ON, Canada.
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128
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Fuller CE, Jones DTW, Kieran MW. New Classification for Central Nervous System Tumors: Implications for Diagnosis and Therapy. Am Soc Clin Oncol Educ Book 2017; 37:753-763. [PMID: 28561665 DOI: 10.1200/edbk_175088] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The 2016 World Health Organization Classification of Tumors of the Central Nervous System (WHO 2016) represents a noteworthy divergence from prior classification schemas. This new classification introduced the concept of "integrated diagnoses" based on a marriage of both phenotypic (microscopic) and genotypic parameters, with the intended goals of improving diagnostic accuracy and patient management. The result is a major restructuring in many of the brain tumor categories, with the codification of multiple new tumor entities and subgroups. It is therefore imperative that pathologists, clinicians, and neuro-oncology researchers alike rapidly become familiar with this new classification schema. Many of the diagnostic updates set forth in the WHO 2016 have impacted brain tumor types that commonly arise in the pediatric age group, particularly within the diffuse glioma, ependymoma, and embryonal tumor categories. This review gives a brief overview of (1) the WHO 2016 as it relates to pediatric central nervous system (CNS) tumors, with an emphasis on molecular diagnostic tools used in the clinical arena, (2) ongoing and developing approaches to the molecular and genomic classification of pediatric CNS tumors, and (3) the impact of this new classification schema on clinical trials in pediatric neuro-oncology.
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Affiliation(s)
- Christine E Fuller
- From the Cincinnati Children's Hospital Medical Center, Cincinnati, OH; German Cancer Research Center, Heidelberg, Germany; Dana-Farber Cancer Institute, Boston, MA
| | - David T W Jones
- From the Cincinnati Children's Hospital Medical Center, Cincinnati, OH; German Cancer Research Center, Heidelberg, Germany; Dana-Farber Cancer Institute, Boston, MA
| | - Mark W Kieran
- From the Cincinnati Children's Hospital Medical Center, Cincinnati, OH; German Cancer Research Center, Heidelberg, Germany; Dana-Farber Cancer Institute, Boston, MA
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Expression of long non-coding RNAs in autoimmunity and linkage to enhancer function and autoimmune disease risk genetic variants. J Autoimmun 2017; 81:99-109. [PMID: 28420548 DOI: 10.1016/j.jaut.2017.03.014] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 03/29/2017] [Accepted: 03/31/2017] [Indexed: 01/19/2023]
Abstract
Genome-wide association studies have identified numerous genetic variants conferring autoimmune disease risk. Most of these genetic variants lie outside protein-coding genes hampering mechanistic explorations. Numerous mRNAs are also differentially expressed in autoimmune disease but their regulation is also unclear. The majority of the human genome is transcribed yet its biologic significance is incompletely understood. We performed whole genome RNA-sequencing [RNA-seq] to categorize expression of mRNAs, known and novel long non-coding RNAs [lncRNAs] in leukocytes from subjects with autoimmune disease and identified annotated and novel lncRNAs differentially expressed across multiple disorders. We found that loci transcribing novel lncRNAs were not randomly distributed across the genome but co-localized with leukocyte transcriptional enhancers, especially super-enhancers, and near genetic variants associated with autoimmune disease risk. We propose that alterations in enhancer function, including lncRNA expression, produced by genetics and environment, change cellular phenotypes contributing to disease risk and pathogenesis and represent attractive therapeutic targets.
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