Molecular Diagnosis of Diffuse Gliomas Through Sequencing of Cell-Free Circulating Tumor DNA from Cerebrospinal Fluid
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The Landscape of Somatic Mutations in Epigenetic Regulators Across 1,000 Paediatric Cancer Genomes
ARTICLE Received 24 Sep 2013 | Accepted 12 Mar 2014 | Published 8 Apr 2014 DOI: 10.1038/ncomms4630 The landscape of somatic mutations in epigenetic regulators across 1,000 paediatric cancer genomes Robert Huether1,*, Li Dong2,*, Xiang Chen1, Gang Wu1, Matthew Parker1, Lei Wei1, Jing Ma2, Michael N. Edmonson1, Erin K. Hedlund1, Michael C. Rusch1, Sheila A. Shurtleff2, Heather L. Mulder3, Kristy Boggs3, Bhavin Vadordaria3, Jinjun Cheng2, Donald Yergeau3, Guangchun Song2, Jared Becksfort1, Gordon Lemmon1, Catherine Weber2, Zhongling Cai2, Jinjun Dang2, Michael Walsh4, Amanda L. Gedman2, Zachary Faber2, John Easton3, Tanja Gruber2,4, Richard W. Kriwacki5, Janet F. Partridge6, Li Ding7,8,9, Richard K. Wilson7,8,9, Elaine R. Mardis7,8,9, Charles G. Mullighan2, Richard J. Gilbertson10, Suzanne J. Baker10, Gerard Zambetti6, David W. Ellison2, Jinghui Zhang1 & James R. Downing2 Studies of paediatric cancers have shown a high frequency of mutation across epigenetic regulators. Here we sequence 633 genes, encoding the majority of known epigenetic regulatory proteins, in over 1,000 paediatric tumours to define the landscape of somatic mutations in epigenetic regulators in paediatric cancer. Our results demonstrate a marked variation in the frequency of gene mutations across 21 different paediatric cancer subtypes, with the highest frequency of mutations detected in high-grade gliomas, T-lineage acute lymphoblastic leukaemia and medulloblastoma, and a paucity of mutations in low-grade glioma and retinoblastoma. The most frequently mutated genes are H3F3A, PHF6, ATRX, KDM6A, SMARCA4, ASXL2, CREBBP, EZH2, MLL2, USP7, ASXL1, NSD2, SETD2, SMC1A and ZMYM3. We identify novel loss-of-function mutations in the ubiquitin-specific processing protease 7 (USP7) in paediatric leukaemia, which result in decreased deubiquitination activity. -
Histone H3.3 Maintains Genome Integrity During Mammalian Development
Downloaded from genesdev.cshlp.org on September 25, 2021 - Published by Cold Spring Harbor Laboratory Press Histone H3.3 maintains genome integrity during mammalian development Chuan-Wei Jang, Yoichiro Shibata, Joshua Starmer, Della Yee, and Terry Magnuson Department of Genetics, Carolina Center for Genome Sciences, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599-7264, USA Histone H3.3 is a highly conserved histone H3 replacement variant in metazoans and has been implicated in many important biological processes, including cell differentiation and reprogramming. Germline and somatic mutations in H3.3 genomic incorporation pathway components or in H3.3 encoding genes have been associated with human congenital diseases and cancers, respectively. However, the role of H3.3 in mammalian development remains un- clear. To address this question, we generated H3.3-null mouse models through classical genetic approaches. We found that H3.3 plays an essential role in mouse development. Complete depletion of H3.3 leads to developmental retardation and early embryonic lethality. At the cellular level, H3.3 loss triggers cell cycle suppression and cell death. Surprisingly, H3.3 depletion does not dramatically disrupt gene regulation in the developing embryo. Instead, H3.3 depletion causes dysfunction of heterochromatin structures at telomeres, centromeres, and pericentromeric regions of chromosomes, leading to mitotic defects. The resulting karyotypical abnormalities and DNA damage lead to p53 pathway activation. In summary, our results reveal that an important function of H3.3 is to support chro- mosomal heterochromatic structures, thus maintaining genome integrity during mammalian development. [Keywords: histone H3.3; genome integrity; transcriptional regulation; cell proliferation; apoptosis; mouse embryonic development] Supplemental material is available for this article. -
M2139: Molecular Analysis for Gliomas
Molecular Analysis for Gliomas Policy Number: AHS – M2139 – Molecular Analysis Prior Policy Name and Number, as applicable: for Gliomas • AHS – M2139 – Analysis of MGMT Promoter Methylation for Malignant Gliomas Initial Presentation Date: 06/16/2021 Revision Date: N/A I. Policy Description Glioma refers to tumors resulting from metaplastic transformation of glial tissue of the nervous system. Tumors have historically been classified by the retained histologic features of the three types of glial cells: astrocytes, oligodendrocytes, and ependymal cells. Tumors of each type can vary widely in aggressiveness, response to treatment, and prognosis (Louis, Schiff, & Batchelor, 2020). Molecular genetic features were added to histopathologic appearance in the current WHO classification to yield more biologically homogeneous and narrowly defined diagnostic entities for greater diagnostic accuracy, improved patient management, more accurate determinations of prognosis, and better treatment response (Louis et al., 2016). II. Related Policies Policy Number Policy Title AHS-M2109 Molecular Panel Testing of Cancers for Diagnosis, Prognosis, and Identification of Targeted Therapy III. Indications and/or Limitations of Coverage Application of coverage criteria is dependent upon an individual’s benefit coverage at the time of the request 1. MGMT promoter methylation testing IS MEDICALLY NECESSARY for prognosis of malignant gliomas. 2. IDH1 and IDH2 testing IS MEDICALLY NECESSARY for prognosis of malignant gliomas. M2139 Molecular Analysis for Gliomas Page 1 of 15 3. Testing for the co-deletion of 1p and 19q by either fluorescence in situ hybridization (FISH) or polymerase chain reaction (PCR) for the characterization of gliomas and/or to guide treatment decisions IS MEDICALLY NECESSARY. 4. ATRX mutation testing via EITHER immunohistochemistry OR gene sequencing IS MEDICALLY NECESSARY for the prognosis of malignant gliomas. -
Somatic Histone H3 Alterations in Pediatric Diffuse Intrinsic Pontine
BRIEF COMMUNICATIONS (c.83A>T) in H3F3A resulting in a substitution to methionine at lysine 27 Somatic histone H3 alterations in (p.Lys27Met) in the histone H3.3 protein (Supplementary Fig. 1). In the tumor from a fifth affected individual, an analogous adenine-to- pediatric diffuse intrinsic pontine thymine transversion (c.83A>T) encoding a p.Lys27Met alteration was gliomas and non-brainstem identified in the closely related HIST1H3B gene, which codes for the histone H3.1 isoform. glioblastomas To determine the frequency of mutations in the histone H3 gene family, we performed targeted sequencing of the exons encoding Lys27 in all 16 1,8 2,8 3,8 Gang Wu , Alberto Broniscer , Troy A McEachron , genes that code for histone H3 isoforms in a validation cohort comprising 4 3 5 5 Charles Lu , Barbara S Paugh , Jared Becksfort , Chunxu Qu , 43 DIPGs as well as 36 non-BS-PGs (see Supplementary Methods and 4 1 1 3 Li Ding , Robert Huether , Matthew Parker , Junyuan Zhang , Supplementary Tables 1 and 2). Including the original seven individuals 2 3 6 Amar Gajjar , Michael A Dyer , Charles G Mullighan , with DIPG analyzed by WGS, we found recurrent adenine-to-thymine 3 4 4 Richard J Gilbertson , Elaine R Mardis , Richard K Wilson , transversions encoding p.Lys27Met alterations in H3F3A or HIST1H3B in 6 6 1 James R Downing , David W Ellison , Jinghui Zhang & 78% of DIPGs and 22% of non-BS-PGs (Fig. 1 and Table 1). In addition, 3 Suzanne J Baker for the St. Jude Children’s Research Hospital– a new guanine-to-adenine transition resulting in a p.Gly34Arg alteration 7 Washington University Pediatric Cancer Genome Project in H3F3A was identified in 5 of 36 (14%) non-BS-PGs but not in any of the 50 DIPGs analyzed. -
Detection of H3K27M Mutation in Cases of Brain Stem Subependymoma
Human Pathology (2019) 84,262–269 www.elsevier.com/locate/humpath Original contribution Detection of H3K27M mutation in cases of brain stem subependymoma☆ Kun Yao MD a,1, Zejun Duan MS a,1, Yin Wang MD b, Mingshan Zhang MD c, Tao Fan MD c, Bin Wu BS c, Xueling Qi BS a,⁎ aDepartment of Pathology, San Bo Brain Hospital, Capital Medical University, Haidian District, Beijing, China bDepartment of Pathology, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, China cDepartment of Neurosurgery, San Bo Brain Hospital, Capital Medical University, Haidian District, Beijing, China Received 5 August 2018; revised 2 October 2018; accepted 11 October 2018 Keywords: Summary Subependymomas are rare, slow-growing, grade I glial tumors of the central nervous system. Re- H3K27M mutation; cently, diffuse midline gliomas with mutations in the H3.1 or H3.3 genes at the position of amino acid 27, Subependymoma; resulting in the replacement of lysine by methionine (K27M), were defined as the new grade IV entity. As Brain stem neoplasm; H3K27M mutations have been reported in midline gliomas, gangliogliomas, and pilocytic astrocytomas, Sanger sequencing whether they occur in midline subependymomas has been unclear. We determined whether any such muta- tions can be found in them and analyzed the prognostic relevance of any such mutations in subependymo- mas. Four subependymomas, all in the brain stem, harbored H3K27M mutations. No such mutation was found in any of the subependymomas from other locations. The mutations were identified by immunohisto- chemical stains and confirmed with Sanger sequencing. The median follow-up of the patients with the mutations in their tumors was 3.2 years, and 3 are still alive, having received no adjuvant therapy. -
Product Data Sheet
For research purposes only, not for human use Product Data Sheet Anti-Histone H3 (MonoMethyl K36) Antibody Catalog # Source Reactivity Applications CPA9358 Rabbit H, M, R WB, IH Description Rabbit polyclonal to Histone H3 (MonoMethyl K36) Immunogen KLH-conjugated synthetic peptide encompassing a sequence of human Histone H3. The exact sequence is proprietary. Purification The antibody was purified by affinity chromatography. Specificity Recognizes endogenous levels of Histone H3 (MonoMethyl K36) protein. Clonality Polyclonal Form Liquid in 0.42% Potassium phosphate, 0.87% Sodium chloride, pH 7.3, 30% glycerol, and 0.01% sodium azide. Dilution WB (1/200 - 1/500), IH (1/200 - 1/500) Gene Symbol HIST1H3A; HIST1H3B; HIST1H3C; HIST1H3D; HIST1H3E; HIST1H3F; HIST1H3G; HIST1H3H; HIST1H3I; HIST1H3J; HIST2H3A; HIST2H3C; HIST2H3D; H3F3A; H3F3B Alternative Names HIST1H3A; H3FA; HIST1H3B; H3FL; HIST1H3C; H3FC; HIST1H3D; H3FB; HIST1H3E; H3FD; HIST1H3F; H3FI; HIST1H3G; H3FH; HIST1H3H; H3FK; HIST1H3I; H3FF; HIST1H3J; H3FJ; Histone H3.1; Histone H3/a; Histone H3/b; Histone H3/c; Histone H3/d; Histone H3/f; Histone H3/ Entrez Gene 8350, 8351, 8352, 8353, 8354, 8355, 8356, 8357, 8358, 8968 (Human); 319152, 15077, 15078 (Mouse); 291159, 100361558 (Rat) SwissProt P68431, Q71DI3, P84243 (Human); P68433, P84228, P84244 (Mouse); Q6LED0, P84245 (Rat) Storage/Stability Shipped at 4°C. Upon delivery aliquot and store at -20°C for one year. Avoid freeze/thaw cycles. Application key: E- ELISA, WB- Western blot, IH- Immunohistochemistry, IF- Immunofluorescence, FC- -
Clinical and Genomic Characteristics of Adult Diffuse Midline Glioma
pISSN 1598-2998, eISSN 2005-9256 https://doi.org/10.4143/crt.2020.694 Cancer Res Treat. 2021;53(2):389-398 Original Article Clinical and Genomic Characteristics of Adult Diffuse Midline Glioma Changhee Park1, Tae Min Kim1,2, Jeong Mo Bae3, Hongseok Yun4, Jin Wook Kim5, Seung Hong Choi6, Soon-Tae Lee7, Joo Ho Lee8, Sung-Hye Park3, Chul-Kee Park5 1Department of Internal Medicine, Seoul National University Hospital, Seoul, 2Cancer Research Institute, Seoul National University, Seoul, 3Department of Pathology, Seoul National University Hospital, Seoul, 4Biomedical Research Institute, Seoul National University Hospital, Seoul, Departments of 5Neurosurgery, 6Radiology, 7Neurology, and 8Radiation Oncology, Seoul National University Hospital, Seoul, Korea Purpose The treatment outcomes and genomic profiles of diffuse midline glioma (DMG) in adult patients are rarely characterized. We performed a retrospective study to evaluate the clinicogenomic profiles of adult patients with brain DMG. Materials and Methods Patients aged ≥ 18 years diagnosed with brain DMG at Seoul National University Hospital were included. The clinicopathological parameters, treatment outcomes, survival, and genomic profiles using 82-gene targeted next-generation sequenc- ing (NGS) were analyzed. The 6-month progression-free survival (PFS6) after radiotherapy and overall survival (OS) were evaluated. Results Thirty-three patients with H3-mutant brain DMG were identified. The median OS from diagnosis was 21.8 months (95% confi- dence interval [CI], 13.2 to not available [NA]) and involvement of the ponto-medullary area tended to have poor OS (median OS, 20.4 months [95% CI, 9.3 to NA] vs. 43.6 months [95% CI, 18.2 to NA]; p=0.07). -
Histone H3.1 (Human) Cell-Based ELISA Kit
Histone H3.1 (Human) Cell-Based ELISA Kit Catalog # : KA2761 規格 : [ 1 Kit ] List All Specification Application Image Product Histone H3.1 (Human) Cell-Based ELISA Kit is an indirect enzyme-linked Qualitative Description: immunoassay for qualitative determination of Histone H3 expression in cultured cells. Reactivity: Human, Mouse, Rat Storage Store the kit at 4°C. Instruction: Protocol: Protocol Download Suitable Attached Cell, Loosely Attached Cell, Suspension Cell Sample: Label: HRP-conjugated Detection Colorimetric Method: Regulation For research use only (RUO) Status: Datasheet: Download Applications Qualitative HIST1H3A HIST1H3D HIST1H3C HIST1H3E HIST1H3I HIST1H3G HIST1H3J HIST1H3H HIST1H3B HIST1H3F Gene Information Entrez GeneID: 8350 Protein P68431 Accession#: Gene Name: HIST1H3A Gene Alias: H3/A,H3FA Gene histone cluster 1, H3a Description: Omim ID: 602810 Gene Ontology: Hyperlink Gene Summary: Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. This structure consists of approximately 146 bp of DNA wrapped around a Page 1 of 6 2021/6/18 nucleosome, an octamer composed of pairs of each of the four core histones (H2A, H2B, H3, and H4). The chromatin fiber is further compacted through the interaction of a linker histone, H1, with the DNA between the nucleosomes to form higher order chromatin structures. This gene is intronless and encodes a member of the histone H3 family. Transcripts from this gene lack polyA tails; instead, they contain a palindromic termination element. This gene is found in the large histone gene cluster on chromosome 6p22-p21.3. [provided by RefSeq Other H3 histone family, member A,histone 1, H3a Designations: Gene Information Entrez GeneID: 8351 Protein P68431 Accession#: Gene Name: HIST1H3D Gene Alias: H3/b,H3FB Gene histone cluster 1, H3d Description: Omim ID: 602811 Gene Ontology: Hyperlink Gene Summary: Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. -
Identification of Prognostic Markers in Diffuse Midline Gliomas H3K27M
Brain Pathology ISSN 1015-6305 RESEARCH ARTICLE Identification of prognostic markers in diffuse midline gliomas H3K27M-mutant Charlotte Dufour1 ; Romain Perbet1,2; Pierre Leblond3; Romain Vasseur2 ; Laurence Stechly4; Adeline Pierache5; Nicolas Reyns6; Gustavo Touzet6; Emilie Le Rhun7,8,9; Matthieu Vinchon10; Claude-Alain Maurage1,2; Fabienne Escande4; Florence Renaud1,2 1 Institute of Pathology, Centre de Biologie Pathologie, Lille University Hospital, Lille, F-59000, France. 2 Univ Lille, Inserm, UMR 1172 – JPARC – Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, Lille, F-59000, France. 3 Department of Paediatric Oncology, Centre Oscar Lambret, Lille, F-59000, France. 4 Department of Biochemistry and Molecular Biology, Centre de Biologie Pathologie, Lille University Hospital, Lille, F-59000, France. 5 Department of Biostatistics and Data Management, Lille University Hospital, Lille, F-59000, France. 6 Department of Stereotactic Neurosurgery, Lille University Hospital, Lille, F-59000, France. 7 Univ Lille, Inserm, U-1192, Lille, F-59000, France. 8 Department of Neuro-Oncology and Neurosurgery, Lille University Hospital, Lille, F-59000, France. 9 Department of Neurology, Breast Cancer, Centre Oscar Lambret, Lille, F-59000, France. 10 Department of Paediatric Neurosurgery, Lille University Hospital, Lille, F-59000, France. Keywords Abstract chomosomal profile, diffuse midline gliomas, H3K27M-mutant, molecular Pediatric diffuse midline gliomas are devastating diseases. Among them, diffuse alterations, prognostic markers, translational midline gliomas H3K27M-mutant are associated with worse prognosis. However, study. recent studies have highlighted significant differences in clinical behavior and bio- logical alterations within this specific subgroup. In this context, simple markers are Abbreviations needed to refine the prognosis of diffuse midline gliomas H3K27M-mutant and aCGH, comparative genomic hybridization guide the clinical management of patients. -
"The Genecards Suite: from Gene Data Mining to Disease Genome Sequence Analyses". In: Current Protocols in Bioinformat
The GeneCards Suite: From Gene Data UNIT 1.30 Mining to Disease Genome Sequence Analyses Gil Stelzer,1,5 Naomi Rosen,1,5 Inbar Plaschkes,1,2 Shahar Zimmerman,1 Michal Twik,1 Simon Fishilevich,1 Tsippi Iny Stein,1 Ron Nudel,1 Iris Lieder,2 Yaron Mazor,2 Sergey Kaplan,2 Dvir Dahary,2,4 David Warshawsky,3 Yaron Guan-Golan,3 Asher Kohn,3 Noa Rappaport,1 Marilyn Safran,1 and Doron Lancet1,6 1Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel 2LifeMap Sciences Ltd., Tel Aviv, Israel 3LifeMap Sciences Inc., Marshfield, Massachusetts 4Toldot Genetics Ltd., Hod Hasharon, Israel 5These authors contributed equally to the paper 6Corresponding author GeneCards, the human gene compendium, enables researchers to effectively navigate and inter-relate the wide universe of human genes, diseases, variants, proteins, cells, and biological pathways. Our recently launched Version 4 has a revamped infrastructure facilitating faster data updates, better-targeted data queries, and friendlier user experience. It also provides a stronger foundation for the GeneCards suite of companion databases and analysis tools. Improved data unification includes gene-disease links via MalaCards and merged biological pathways via PathCards, as well as drug information and proteome expression. VarElect, another suite member, is a phenotype prioritizer for next-generation sequencing, leveraging the GeneCards and MalaCards knowledgebase. It au- tomatically infers direct and indirect scored associations between hundreds or even thousands of variant-containing genes and disease phenotype terms. Var- Elect’s capabilities, either independently or within TGex, our comprehensive variant analysis pipeline, help prepare for the challenge of clinical projects that involve thousands of exome/genome NGS analyses. -
Effects of H3.3G34V Mutation on Genomic H3K36 and H3K27 Methylation Patterns in Isogenic Pediatric Glioma Cells
Huang et al. acta neuropathol commun (2020) 8:219 https://doi.org/10.1186/s40478-020-01092-4 RESEARCH Open Access Efects of H3.3G34V mutation on genomic H3K36 and H3K27 methylation patterns in isogenic pediatric glioma cells Tina Yi‑Ting Huang1, Andrea Piunti2, Jin Qi1, Marc Morgan2, Elizabeth Bartom2, Ali Shilatifard2 and Amanda M. Saratsis1,2,3* Abstract Histone H3.3 mutation (H3F3A) occurs in 50% of cortical pediatric high‑grade gliomas. This mutation replaces glycine 34 with arginine or valine (G34R/V), impairing SETD2 activity (H3K36‑specifc trimethyltransferase). Consequently, reduced H3K36me3 is observed on H3.3G34V nucleosomes relative to wild‑type, contributing to genomic instabil‑ ity and driving a distinct gene expression signature associated with tumorigenesis. However, it is not known if this diferential H3K36me3 enrichment is due to H3.3G34V mutant protein alone. Therefore, we set to elucidate the efect of H3.3G34V mutant protein in pediatric glioma on H3K36me3, H3K27me3 and H3.3 enrichment in vitro. We found that the doxycycline‑inducible shRNA knockdown of mutant H3F3A encoding the H3.3G34V protein resulted in loss of H3.3G34V enrichment and increased H3K36me3 enrichment throughout the genome. After knockdown, H3.3G34V enrichment was preserved at loci observed to have the greatest H3.3G34V and H3K36me3 enrichment prior to knockdown. Induced expression of mutant H3.3G34V protein in vitro was insufcient to induce genomic H3K36me3 enrichment patterns observed in H3.3G34V mutant glioma cells. We also observed strong co‑enrichment of H3.3G34V and wild‑type H3.3 protein, as well as greater H3K27me3 enrichment, in cells expressing H3.3G34V. -
Histone H3F3A and HIST1H3B K27M Mutations Define Two Subgroups of Diffuse Intrinsic Pontine Gliomas with Different Prognosis and Phenotypes
Acta Neuropathol (2015) 130:815–827 DOI 10.1007/s00401-015-1478-0 ORIGINAL PAPER Histone H3F3A and HIST1H3B K27M mutations define two subgroups of diffuse intrinsic pontine gliomas with different prognosis and phenotypes David Castel1,2 · Cathy Philippe1 · Raphaël Calmon3 · Ludivine Le Dret1 · Nathalène Truffaux1 · Nathalie Boddaert3 · Mélanie Pagès7 · Kathryn R. Taylor4 · Patrick Saulnier5 · Ludovic Lacroix5 · Alan Mackay4 · Chris Jones4 · Christian Sainte‑Rose6 · Thomas Blauwblomme6 · Felipe Andreiuolo7 · Stephanie Puget6 · Jacques Grill1,2 · Pascale Varlet7 · Marie‑Anne Debily1,8 Received: 24 June 2015 / Revised: 8 September 2015 / Accepted: 10 September 2015 / Published online: 23 September 2015 © The Author(s) 2015. This article is published with open access at Springerlink.com Abstract Diffuse intrinsic pontine glioma (DIPG) is the a systematic stereotactic biopsy and were included in most severe paediatric solid tumour, with no significant this observational retrospective study. Histone H3 genes therapeutic progress made in the past 50 years. Recent mutations were assessed by immunochemistry and direct studies suggest that diffuse midline glioma, H3-K27M sequencing, whilst global gene expression profiling and mutant, may comprise more than one biological entity. chromosomal imbalances were determined by microar- The aim of the study was to determine the clinical and bio- rays. A full description of the MRI findings at diagnosis logical variables that most impact their prognosis. Ninety- and at relapse was integrated with the molecular profiling one patients with classically defined DIPG underwent data and clinical outcome. All DIPG but one were found to harbour either a somatic H3-K27M mutation and/or loss of H3K27 trimethylation. We also discovered a novel K27M This work was presented at the International Symposium mutation in HIST2H3C, and a lysine-to-isoleucine substitu- of Pediatric Neuro-Oncology meeting held in June 2014 in tion (K27I) in H3F3A, also creating a loss of trimethyla- Singapore.