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Fang D, Gan H, Cheng L, Lee JH, Zhou H, Sarkaria J, Daniels D, Zhang Z. GENE-10. H3K27ME3-MEDIATED SILENCING TUMOR SUPPRESSORS SUPPORTS THE PROLIFERATION OF PEDIATRIC BRAIN TUMOR CELLS HARBORING THE H3.3K27M MUTATION. Neuro Oncol 2017. [DOI: 10.1093/neuonc/nox083.081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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52
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Lassman A, Gan H, Robert-Rapp L, Ansell P, Merrell R, Kumthekar P, Gomez E, Holen K, Reardon D, van den Bent M. P09.25 Identifying the correct patient (pt) population for ABT414: biomarker assays for epidermal growth factor receptor (EGFR) in pts with glioblastoma (GBM). Neuro Oncol 2017. [DOI: 10.1093/neuonc/nox036.281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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53
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van den Bent M, Gan H, Lassman A, Kumthekar P, Butowski N, Nabors L, Simes J, Maag D, Reardon D. OS07.4 Efficacy of a novel antibody-drug conjugate (ADC), ABT-414, as monotherapy in epidermal growth factor receptor (EGFR) amplified (EGFRamp), recurrent glioblastoma (rGBM). Neuro Oncol 2017. [DOI: 10.1093/neuonc/nox036.045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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54
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Gopman DB, Dennis CL, McMichael RD, Hao X, Wang Z, Wang X, Gan H, Zhou Y, Zhang J, Huai Y. Enhanced ferromagnetic resonance linewidth of the free layer in perpendicular magnetic tunnel junctions. AIP ADVANCES 2017; 7:055932. [PMID: 28690916 PMCID: PMC5497521 DOI: 10.1063/1.4977969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 11/28/2016] [Indexed: 06/07/2023]
Abstract
We report the frequency dependence of the ferromagnetic resonance linewidth of the free layer in magnetic tunnel junctions with all perpendicular-to-the-plane magnetized layers. While the magnetic-field-swept linewidth nominally shows a linear growth with frequency in agreement with Gilbert damping, an additional frequency-dependent linewidth broadening occurs that shows a strong asymmetry between the absorption spectra for increasing- and decreasing external magnetic field. Inhomogeneous magnetic fields produced during reversal of the reference and pinned layer complex is demonstrated to be at the origin of the symmetry breaking and the linewidth enhancement. Consequentially, this linewidth enhancement provides indirect information on the magnetic coercivity of the reference and pinned layers. These results have important implications for the characterization of perpendicular magnetized magnetic random access memory bit cells.
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Wu R, Wang Z, Zhang H, Gan H, Zhang Z. H3K9me3 demethylase Kdm4d facilitates the formation of pre-initiative complex and regulates DNA replication. Nucleic Acids Res 2017; 45:169-180. [PMID: 27679476 PMCID: PMC5224507 DOI: 10.1093/nar/gkw848] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 09/13/2016] [Accepted: 09/14/2016] [Indexed: 11/30/2022] Open
Abstract
DNA replication is tightly regulated to occur once and only once per cell cycle. How chromatin, the physiological substrate of DNA replication machinery, regulates DNA replication remains largely unknown. Here we show that histone H3 lysine 9 demethylase Kdm4d regulates DNA replication in eukaryotic cells. Depletion of Kdm4d results in defects in DNA replication, which can be rescued by the expression of H3K9M, a histone H3 mutant transgene that reverses the effect of Kdm4d on H3K9 methylation. Kdm4d interacts with replication proteins, and its recruitment to DNA replication origins depends on the two pre-replicative complex components (origin recognition complex [ORC] and minichromosome maintenance [MCM] complex). Depletion of Kdm4d impairs the recruitment of Cdc45, proliferating cell nuclear antigen (PCNA), and polymerase δ, but not ORC and MCM proteins. These results demonstrate a novel mechanism by which Kdm4d regulates DNA replication by reducing the H3K9me3 level to facilitate formation of pre-initiative complex.
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56
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Qi W, Li H, Zhang H, Liu S, Wang Y, Gai D, Lu Q, Gan H, Shi Y. Rehabilitation effect of exercise with soft tissue manipulation in patients with lumbar muscle strain. Niger J Clin Pract 2017; 20:629-633. [DOI: 10.4103/njcp.njcp_126_16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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57
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van den Bent M, Gan H, Reardon DA, Papadopoulos KP, Merrell R, Kumthekar P, Roberts-Rapp L, Holen K, Ansell P, Lassman AB. P06.02 Transcriptional profiling to identify determinants associated with response to ABT-414 in patients with glioblastoma. Neuro Oncol 2016. [DOI: 10.1093/neuonc/now188.093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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58
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Fang D, Gan H, Lee JH, Han J, Wang Z, Riester SM, Jin L, Chen J, Zhou H, Wang J, Zhang H, Yang N, Bradley EW, Ho TH, Rubin BP, Bridge JA, Thibodeau SN, Ordog T, Chen Y, van Wijnen AJ, Oliveira AM, Xu RM, Westendorf JJ, Zhang Z. The histone H3.3K36M mutation reprograms the epigenome of chondroblastomas. Science 2016; 352:1344-8. [PMID: 27229140 PMCID: PMC5460624 DOI: 10.1126/science.aae0065] [Citation(s) in RCA: 194] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Accepted: 05/16/2016] [Indexed: 12/18/2022]
Abstract
More than 90% of chondroblastomas contain a heterozygous mutation replacing lysine-36 with methionine-36 (K36M) in the histone H3 variant H3.3. Here we show that H3K36 methylation is reduced globally in human chondroblastomas and in chondrocytes harboring the same genetic mutation, due to inhibition of at least two H3K36 methyltransferases, MMSET and SETD2, by the H3.3K36M mutant proteins. Genes with altered expression as well as H3K36 di- and trimethylation in H3.3K36M cells are enriched in cancer pathways. In addition, H3.3K36M chondrocytes exhibit several hallmarks of cancer cells, including increased ability to form colonies, resistance to apoptosis, and defects in differentiation. Thus, H3.3K36M proteins reprogram the H3K36 methylation landscape and contribute to tumorigenesis, in part through altering the expression of cancer-associated genes.
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59
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Ameratunga M, McArthur G, Gan H, Cher L. Prolonged disease control with MEK inhibitor in neurofibromatosis type I-associated glioblastoma. J Clin Pharm Ther 2016; 41:357-359. [DOI: 10.1111/jcpt.12378] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 02/12/2016] [Indexed: 01/16/2023]
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60
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de Guzman J, Gan H. Dural arteriovenous malformation at the right paramedian area of skull base in a 52year old male: a case report. J Neurol Sci 2015. [DOI: 10.1016/j.jns.2015.08.1328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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61
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Van den Bent M, Roberts-Rapp L, Ansell P, Kular R, Song M, Sokolova I, Gan H, Papadopoulos K, Lassman A, Merrell R, Kumthekar P, Scott A, Gomez E, Fischer J, Bhathena A, Holen K, Lai R, Reardon D. 2903 Identifying the correct patient (pt) population for ABT-414: Biomarker assays for epidermal growth factor receptor (EGFR) in pts with glioblastoma (GBM). Eur J Cancer 2015. [DOI: 10.1016/s0959-8049(16)31620-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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62
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Yu C, Gan H, Han J, Zhou ZX, Jia S, Chabes A, Farrugia G, Ordog T, Zhang Z. Strand-Specific Analysis Shows Protein Binding at Replication Forks and PCNA Unloading from Lagging Strands when Forks Stall. Mol Cell 2014. [DOI: 10.1016/j.molcel.2014.11.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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63
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Yu C, Gan H, Han J, Zhou ZX, Jia S, Chabes A, Farrugia G, Ordog T, Zhang Z. Strand-specific analysis shows protein binding at replication forks and PCNA unloading from lagging strands when forks stall. Mol Cell 2014; 56:551-63. [PMID: 25449133 DOI: 10.1016/j.molcel.2014.09.017] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 08/11/2014] [Accepted: 09/18/2014] [Indexed: 11/30/2022]
Abstract
In eukaryotic cells, DNA replication proceeds with continuous synthesis of leading-strand DNA and discontinuous synthesis of lagging-strand DNA. Here we describe a method, eSPAN (enrichment and sequencing of protein-associated nascent DNA), which reveals the genome-wide association of proteins with leading and lagging strands of DNA replication forks. Using this approach in budding yeast, we confirm the strand specificities of DNA polymerases delta and epsilon and show that the PCNA clamp is enriched at lagging strands compared with leading-strand replication. Surprisingly, at stalled forks, PCNA is unloaded specifically from lagging strands. PCNA unloading depends on the Elg1-containing alternative RFC complex, ubiquitination of PCNA, and the checkpoint kinases Mec1 and Rad53. Cells deficient in PCNA unloading exhibit increased chromosome breaks. Our studies provide a tool for studying replication-related processes and reveal a mechanism whereby checkpoint kinases regulate strand-specific unloading of PCNA from stalled replication forks to maintain genome stability.
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Anderson N, Jackson J, Khoo V, Schneider M, Rolfo M, Gan H, Kaegi K, Sneyd F, Lim Joon D, Wada M. Gross Tumor Volume Size and Oral Cavity Dose Drive Dysphagia in Definitive (Chemo) IMRT for Head and Neck Cancer. Int J Radiat Oncol Biol Phys 2014. [DOI: 10.1016/j.ijrobp.2014.05.1711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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65
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Gan H, Zheng D, Lei Y, Li S, Zhang Q, Zhou S, Li J, Lin C. Monte Carlo Dose Evaluation for Pancreatic Stereotactic Body Radiation Therapy. Int J Radiat Oncol Biol Phys 2014. [DOI: 10.1016/j.ijrobp.2014.05.1177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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66
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Zheng D, Gan H, Zhen W, Lin C, Driewer J, Wahl A, Zhou S. Is PTV Still Appropriate for Prescription Specification in Monte Carlo SBRT Lung Planning? Int J Radiat Oncol Biol Phys 2014. [DOI: 10.1016/j.ijrobp.2014.05.1910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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67
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Zheng S, Wang F, Gan H, Lu J, Jabbour S, Yue N, Zou W. Patient Treatment and Prognosis Information Extraction With Adaptive Self Learning Medical Form Generating System. Int J Radiat Oncol Biol Phys 2014. [DOI: 10.1016/j.ijrobp.2014.05.2360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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68
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Li J, Denniston K, Hussain S, Gan H, Lin C. Comparison of CT and MRI-Based Gross Tumor Volume and Organ at Risk Delineation for Pancreatic Cancer Patients Undergoing Neoadjuvant Stereotactic Body Radiation Therapy. Int J Radiat Oncol Biol Phys 2014. [DOI: 10.1016/j.ijrobp.2014.05.1158] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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69
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Zhang M, Zhang Q, Gan H, Li S, Zhou S. SU-E-T-360: Stereotactic Radiosurgery Plan Evaluation Using High Order Central Moments. Med Phys 2014. [DOI: 10.1118/1.4888693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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70
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Gan H, Wen L, Liao S, Lin X, Ma T, Liu J, Song CX, Wang M, He C, Han C, Tang F. Dynamics of 5-hydroxymethylcytosine during mouse spermatogenesis. Nat Commun 2013; 4:1995. [PMID: 23759713 DOI: 10.1038/ncomms2995] [Citation(s) in RCA: 154] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 05/09/2013] [Indexed: 01/02/2023] Open
Abstract
Little is known about how patterns of DNA methylation change during mammalian spermatogenesis. 5 hmC has been recognized as a stable intermediate of DNA demethylation with potential regulatory functions in the mammalian genome. However, its global pattern in germ cells has yet to be addressed. Here, we first conducted absolute quantification of 5 hmC in eight consecutive types of mouse spermatogenic cells using liquid chromatography-tandem mass spectrometry, and then mapped its distributions in various genomic regions using our chemical labeling and enrichment method coupled with deep sequencing. We found that 5 hmC mapped differentially to and changed dynamically in genomic regions related to expression regulation of protein-coding genes, piRNA precursor genes and repetitive elements. Moreover, 5 hmC content correlated with the levels of various transcripts quantified by RNA-seq. These results suggest that the highly ordered alterations of 5 hmC in the mouse genome are potentially crucial for the differentiation of spermatogenic cells.
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71
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Caretti V, Noll A, Woo P, Monje M, Cockle J, Bruning-Richardson A, Picton S, Levesley J, Ilett E, Short S, Melcher A, Lawler S, Garzia L, Dubuc A, Pitcher G, Northcott P, Mariampillai A, Mack S, Zayne K, Chan T, Skowron P, Wu X, Lionel A, Morrisy S, Hawkins C, Kongkham P, Rutka J, Huang A, Kenney A, Yang V, Salter M, Taylor M, Garzia L, Morrisy S, Skowron P, Jelveh S, Lindsay P, Largaespada D, Collier L, Dupuy A, Hill R, Taylor M, Hsieh TH, Wang HW, Cheng WC, Wong TT, Huang X, He Y, Dubuc A, Hashizume R, Zhang W, Stehbens S, Younger S, Barshow S, Zhu S, Wu X, Taylor M, Mueller S, Weiss W, James D, Shuman M, Jan YN, Jan L, Marigil M, Jauregi P, Idoate MA, Xipell E, Aldave G, Gonzalez-Huarriz M, Tejada-Solis S, Diez-Valle R, Montero-Carcaboso A, Mora J, Alonso MM, Taylor K, Mackay A, Truffaux N, Morozova O, Butterfield Y, Phillipe C, Vinci M, de Torres C, Cruz O, Mora J, Hargrave D, Monje M, Puget S, Yip S, Jones C, Grill J, Kaul A, Chen YH, Dahiya S, Emnett R, Gianino S, Gutmann D, Miwa T, Oi S, Nonaka Y, Sasaki H, Yoshida K, Lopez E, de Leon AP, Sepulveda C, Zarate L, Diego-Perez J, Pong W, Ding L, McLellan M, Hussain I, Emnett R, Gianino S, Higer S, Leonard J, Guha A, Mardis E, Gutmann D, Sarkar C, Pathak P, Jha P, Purkait S, Sharma V, Sharma MC, Suri V, Faruq M, Mukherjee M, Sivasankaran B, Velayutham RP, Fraschilla IR, Morris KJ, MacDonald TJ, Read TA, Sturm D, Northcott P, Jones D, Korshunov A, Picard D, Lichter P, Huang A, Pfister S, Kool M, Yao TW, Zhang J, Anna B, Brummer T, Gupta N, Nicolaides T, Chan KM, Fang D, Gan H, Hashizume R, Yu C, Schroeder M, Gupta N, Mueller S, James D, Jenkins R, Sarkaria J, Zhang Z. PEDIATRICS LABORATORY RESEARCH. Neuro Oncol 2013. [DOI: 10.1093/neuonc/not186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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72
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Anderson N, Jackson J, Wada M, Schneider-Kolsky M, Rolfo M, Gan H, Kaegi K, Sneyd F, Lim Joon D, Khoo V. Creating Guidelines for Reactive and Prophylactic Enteral Feeding in Definitive (Chemo) IMRT for Head-and-Neck Cancer. Int J Radiat Oncol Biol Phys 2013. [DOI: 10.1016/j.ijrobp.2013.06.1246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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73
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Han G, Liu D, Gan H, Li S, Wang Z, Tan W, Zhen W, Hu D. A Dosimetric Study of Intensity Modulated Radiation Therapy for Locally-Advanced Nasopharyngeal Carcinoma With or Without Hippocampal Sparing. Int J Radiat Oncol Biol Phys 2013. [DOI: 10.1016/j.ijrobp.2013.06.1846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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74
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Chan KM, Han J, Fang D, Gan H, Zhang Z. A lesson learned from the H3.3K27M mutation found in pediatric glioma: a new approach to the study of the function of histone modifications in vivo? Cell Cycle 2013; 12:2546-52. [PMID: 23907119 DOI: 10.4161/cc.25625] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Glioblastoma (GBM) is the most aggressive primary brain tumor in human. Recent studies on high-grade pediatric GBM have identified two recurrent mutations (K27M and G34R/V) in genes encoding histone H3 (H3F3A for H3.3 and HIST1H3B for H3.1). The two histone H3 mutations are mutually exclusive and give rise to tumors in different brain compartments. Recently, we and others have shown that the histone H3 K27M mutation specifically altered the di- and tri-methylation of endogenous histone H3 at Lys27. Genome-wide studies using ChIP-seq on H3.3K27M patient samples indicate a global reduction of H3K27me3 on chromatin. Remarkably, we also found a dramatic enrichment of H3K27me3 and EZH2 (the catalytic subunit H3K27 methyltransferase) at hundreds of gene loci in H3.3K27M patient cells. Here, we discuss potential mechanisms whereby H3K27me3 is enriched at chromatin loci in cells expressing the H3.3K27M mutation and report effects of Lys-to-Met mutations of other well-studied lysine residues of histone H3.1/H3.3 and H4 on the corresponding endogenous lysine methylation. We suggest that mutation(s) on histones may be found in a variety of human diseases, and the expression of mutant histones may help to address the function of histone lysine methylation and possibly other modifications in mammalian cells.
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75
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Chan KM, Fang D, Gan H, Hashizume R, Yu C, Schroeder M, Gupta N, Mueller S, James CD, Jenkins R, Sarkaria J, Zhang Z. The histone H3.3K27M mutation in pediatric glioma reprograms H3K27 methylation and gene expression. Genes Dev 2013; 27:985-90. [PMID: 23603901 DOI: 10.1101/gad.217778.113] [Citation(s) in RCA: 515] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Recent studies have identified a Lys 27-to-methionine (K27M) mutation at one allele of H3F3A, one of the two genes encoding histone H3 variant H3.3, in 60% of high-grade pediatric glioma cases. The median survival of this group of patients after diagnosis is ∼1 yr. Here we show that the levels of H3K27 di- and trimethylation (H3K27me2 and H3K27me3) are reduced globally in H3.3K27M patient samples due to the expression of the H3.3K27M mutant allele. Remarkably, we also observed that H3K27me3 and Ezh2 (the catalytic subunit of H3K27 methyltransferase) at chromatin are dramatically increased locally at hundreds of gene loci in H3.3K27M patient cells. Moreover, the gain of H3K27me3 and Ezh2 at gene promoters alters the expression of genes that are associated with various cancer pathways. These results indicate that H3.3K27M mutation reprograms epigenetic landscape and gene expression, which may drive tumorigenesis.
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