Histone Mark Profiling in Pediatric Astrocytomas Reveals Prognostic Significance of H3K9 Trimethylation and Histone Methyltransferase SUV39H1.
Adolescent
Astrocytoma
/ diagnosis
Brain Neoplasms
/ diagnosis
Cell Line, Tumor
Child
Child, Preschool
Cohort Studies
Female
Gene Expression Profiling
/ methods
Histone Code
/ physiology
Histone-Lysine N-Methyltransferase
/ biosynthesis
Humans
Infant
Male
Methylation
Methyltransferases
/ biosynthesis
Prognosis
Repressor Proteins
/ biosynthesis
H3K9me3
Histone methylation
Pediatric astrocytomas
SUV39H1
Survival
Journal
Neurotherapeutics : the journal of the American Society for Experimental NeuroTherapeutics
ISSN: 1878-7479
Titre abrégé: Neurotherapeutics
Pays: United States
ID NLM: 101290381
Informations de publication
Date de publication:
07 2021
07 2021
Historique:
accepted:
07
07
2021
pubmed:
24
7
2021
medline:
4
3
2022
entrez:
23
7
2021
Statut:
ppublish
Résumé
Alterations in global histone methylation regulate gene expression and participate in cancer onset and progression. The profile of histone methylation marks in pediatric astrocytomas is currently understudied with limited data on their distribution among grades. The global expression patterns of repressive histone marks H3K9me3, H3K27me3, and H4K20me3 and active H3K4me3 and H3K36me3 along with their writers SUV39H1, SETDB1, EZH2, MLL2, and SETD2 were investigated in 46 pediatric astrocytomas and normal brain tissues. Associations between histone marks and modifying enzymes with clinicopathological characteristics and disease-specific survival were studied along with their functional impact in proliferation and migration of pediatric astrocytoma cell lines using selective inhibitors in vitro. Upregulation of histone methyltransferase gene expression and deregulation of histone code were detected in astrocytomas compared to normal brain tissues, with higher levels of SUV39H1, SETDB1, and SETD2 as well as H4K20me3 and H3K4me3 histone marks. Pilocytic astrocytomas exhibited lower MLL2 levels compared to diffusely infiltrating tumors indicating a differential pattern of epigenetic regulator expression between the two types of astrocytic neoplasms. Moreover, higher H3K9me3, H3K36me3, and SETDB1 expression was detected in grade IIΙ/IV compared to grade II astrocytomas. In univariate analysis, elevated H3K9me3 and MLL2 and diminished SUV39H1 expression adversely affected survival. Upon multivariate survival analysis, only SUV39H1 expression was revealed as an independent prognostic factor of adverse significance. Treatment of pediatric astrocytoma cell lines with SUV39H1 inhibitor reduced proliferation and cell migration. Our data implicate H3K9me3 and SUV39H1 in the pathobiology of pediatric astrocytomas, with SUV39H1 yielding prognostic information independent of other clinicopathologic variables.
Identifiants
pubmed: 34296393
doi: 10.1007/s13311-021-01090-x
pii: 10.1007/s13311-021-01090-x
pmc: PMC8609021
doi:
Substances chimiques
Repressor Proteins
0
SUV39H1 protein, human
EC 2.1.1.
Methyltransferases
EC 2.1.1.-
Histone-Lysine N-Methyltransferase
EC 2.1.1.43
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
2073-2090Informations de copyright
© 2021. The American Society for Experimental NeuroTherapeutics, Inc.
Références
Izycka-Swieszewska E, Bien E, Stefanowicz J, et al. Malignant gliomas as second neoplasms in pediatric cancer survivors: Neuropathological study. Biomed Res Int 2018:4596812. https://doi.org/10.1155/2018/4596812
Louis DN, Perry A, Reifenberger G, et al. The 2016 World Health Organization Classification of Tumors of the Central Nervous System: a summary. Acta Neuropathol 2016; 131: 803–820 https://doi.org/10.1007/s00401-016-1545-1 .
doi: 10.1007/s00401-016-1545-1
pubmed: 27157931
Collins VP, Jones DTW, Giannini C. Pilocytic astrocytoma: pathology, molecular mechanisms and markers. Acta Neuropathol 2015; 129: 775–788 https://doi.org/10.1007/s00401-015-1410-7
doi: 10.1007/s00401-015-1410-7
pubmed: 25792358
pmcid: 4436848
Klonou A, Spiliotakopoulou D, Themistocleous MS, Piperi C, Papavassiliou AG. Chromatin remodeling defects in pediatric brain tumors. Ann Transl Med 2018; 6: 248–248. https://doi.org/10.21037/atm.2018.04.08
doi: 10.21037/atm.2018.04.08
pubmed: 30069450
pmcid: 6046298
Gonçalves FG, Alves CAPF, Vossough A. Updates in pediatric malignant gliomas. Top Magn Reson Imaging 2020; 29: 83–94 https://doi.org/10.1097/RMR.0000000000000235 .
doi: 10.1097/RMR.0000000000000235
pubmed: 32271285
Zhao Z, Shilatifard A. Epigenetic modifications of histones in cancer. Genome Biol 2019; 20:245. https://doi.org/10.1186/s13059-019-1870-5
doi: 10.1186/s13059-019-1870-5
pubmed: 31747960
pmcid: 6868810
Miller JL, Grant PA. The role of DNA methylation and histone modifications in transcriptional regulation in humans. Subcell Biochem 2013; 61: 289–317. https://doi.org/10.1007/978-94-007-4525-4_13
doi: 10.1007/978-94-007-4525-4_13
pubmed: 23150256
pmcid: 6611551
Bapat SA, Jin V, Berry N, et al. Multivalent epigenetic marks confer microenvironment-responsive epigenetic plasticity to ovarian cancer cells. Epigenetics 2010; 5: 717–730. https://doi.org/10.4161/epi.5.8.13014
doi: 10.4161/epi.5.8.13014
Schotta G, Lachner M, Sarma K, et al. A silencing pathway to induce H3-K9 and H4-K20 trimethylation at constitutive heterochromatin. Genes Dev 2004; 18: 1251–1262. https://doi.org/10.1101/gad.300704
doi: 10.1101/gad.300704
pubmed: 15145825
pmcid: 420351
Becker JS, Nicetto D, Zaret KS. H3K9me3-Dependent Heterochromatin: Barrier to Cell Fate Changes. Trends Genet 2016; 32: 29–41 https://doi.org/10.1016/j.tig.2015.11.001
doi: 10.1016/j.tig.2015.11.001
pubmed: 26675384
Zhou M, Li Y, Lin S, et al. H3K9me3, H3K36me3 , and H4K20me3 Expression Correlates with Patient Outcome in Esophageal Squamous Cell Carcinoma as Epigenetic Markers. Dig Dis Sci 2019; 64: 2147–2157. https://doi.org/10.1007/s10620-019-05529-2
doi: 10.1007/s10620-019-05529-2
pubmed: 30788686
Spyropoulou A, Gargalionis A, Dalagiorgou G, et al. Role of histone lysine methyltransferases SUV39H1 and SETDB1 in gliomagenesis: Modulation of cell proliferation, migration, and colony formation. NeuroMolecular Med 2014; 16: 70–82. https://doi.org/10.1007/s12017-013-8254-x
doi: 10.1007/s12017-013-8254-x
pubmed: 23943221
Sepsa A, Levidou G, Gargalionis A, et al. Emerging role of linker histone variant H1x as a biomarker with prognostic value in astrocytic gliomas. A multivariate analysis including trimethylation of H3K9 and H4K20. PLoS One 2015; 10: e0115101. https://doi.org/10.1371/journal.pone.0115101
Loyola A, Tagami H, Bonaldi T, et al. The HP1α-CAF1-SetDB1-containing complex provides H3K9me1 for Suv39-mediated K9me3 in pericentric heterochromatin. EMBO Rep 2009; 10: 769–775. https://doi.org/10.1038/embor.2009.90
doi: 10.1038/embor.2009.90
pubmed: 19498464
pmcid: 2727428
Kleer CG, Cao Q, Varambally S, et al. EZH2 is a marker of aggressive breast cancer and promotes neoplastic transformation of breast epithelial cells. Proc Natl Acad Sci USA 2003; 100: 11606–11611. https://doi.org/10.1073/pnas.1933744100
doi: 10.1073/pnas.1933744100
pubmed: 14500907
pmcid: 208805
Chen YN, Hou SQ, Jiang R, Sun JL, Cheng CD, Qian ZR. EZH2 is a potential prognostic predictor of glioma. J Cell Mol Med 2020; 25: 925–936. https://doi.org/10.1111/jcmm.16149
doi: 10.1111/jcmm.16149
pubmed: 33277782
pmcid: 7812280
Bracken AP, Pasini D, Capra M, Prosperini E, Colli E, Helin K. EZH2 is downstream of the pRB-E2F pathway, essential for proliferation and amplified in cancer. EMBO J 2003; 22: 5323–5335. https://doi.org/10.1093/emboj/cdg542
doi: 10.1093/emboj/cdg542
pubmed: 14532106
pmcid: 213796
Bernstein BE, Humphrey EL, Erlich RL, et al. Methylation of histone H3 Lys 4 in coding regions of active genes. Proc Natl Acad Sci USA 2002; 99: 8695–8700. https://doi.org/10.1073/pnas.082249499
doi: 10.1073/pnas.082249499
pubmed: 12060701
pmcid: 124361
Chen K, Chen Z, Wu D, et al. Broad H3K4me3 is associated with increased transcription elongation and enhancer activity at tumor-suppressor genes. Nat Genet 2015; 47: 1149–1157. https://doi.org/10.1038/ng.3385
doi: 10.1038/ng.3385
pubmed: 26301496
pmcid: 4780747
Bogeas A, Morvan-Dubois G, El-Habr EA, Lejeune FX, Defrance M, Narayanan A, Kuranda K, Burel-Vandenbos F, Sayd S, Delaunay V, Dubois LG, Parrinello H, Rialle S, Fabrega S, Idbaih A, Haiech J, Bièche I, Virolle T, Goodhardt M, Chneiweiss H, Junier MP. Changes in chromatin state reveal ARNT2 at a node of a tumorigenic transcription factor signature driving glioblastoma cell aggressiveness. Acta Neuropathol. 2018; 135(2): 267-283. https://doi.org/10.1007/s00401-017-1783-x .
doi: 10.1007/s00401-017-1783-x
pubmed: 29149419
Ellinger J, Kahl P, Mertens C, et al. Prognostic relevance of global histone H3 lysine 4 (H3K4) methylation in renal cell carcinoma. Int J Cancer 2010; 127: 2360–2366. https://doi.org/10.1002/ijc.25250
doi: 10.1002/ijc.25250
pubmed: 20162570
Wen H, Li Y, Xi Y, et al. ZMYND11 links histone H3.3K36me3 to transcription elongation and tumour suppression. Nature 2014; 508: 263–268. https://doi.org/10.1038/nature13045
Li M, Cheng J, Ma Y, et al. The histone demethylase JMJD2A promotes glioma cell growth via targeting Akt-mTOR signaling. Cancer Cell Int 2020; 20:101. https://doi.org/10.1186/s12935-020-01177-z
doi: 10.1186/s12935-020-01177-z
pubmed: 32256210
pmcid: 7106579
Viaene AN, Santi M, Rosenbaum J, Li MM, Surrey LF, Nasrallah MP. SETD2 mutations in primary central nervous system tumors. Acta Neuropathol Commun 2018; 6: 123. https://doi.org/10.1186/s40478-018-0623-0
doi: 10.1186/s40478-018-0623-0
pubmed: 30419952
pmcid: 6231273
Zaravinos A, Bizakis J, Spandidos DA. RKIP and BRAF aberrations in human nasal polyps and the adjacent turbinate mucosae. Cancer Lett 2008; 264: 288–298. https://doi.org/10.1016/j.canlet.2008.01.046
doi: 10.1016/j.canlet.2008.01.046
pubmed: 18329792
Theodoropoulos G, Papaconstantinou I, Felekouras E, et al. Relation between common polymorphisms in genes related to inflammatory response and colarectal cancer. World J Gastroenterol 2006; 12: 5037–5043. https://doi.org/10.3748/wjg.v12.i31.5037
doi: 10.3748/wjg.v12.i31.5037
pubmed: 16937502
pmcid: 4087409
Griesinger AM, Birks DK, Donson AM, et al. Characterization of Distinct Immunophenotypes across Pediatric Brain Tumor Types. J Immunol 2013; 191: 4880–4888. https://doi.org/10.4049/jimmunol.1301966
doi: 10.4049/jimmunol.1301966
pubmed: 24078694
Klaus B, Reisenauer S. An end to end workflow for differential gene expression using Affymetrix microarrays [version 2]. F1000Research 2018; 5:1384. https://doi.org/10.12688/f1000research.8967.2
Vandel J, Gheeraert C, Staels B, Eeckhoute J, Lefebvre P, Dubois-Chevalier J. GIANT: galaxy-based tool for interactive analysis of transcriptomic data. Sci Rep 2020; 10:19835. https://doi.org/10.1038/s41598-020-76769-w
doi: 10.1038/s41598-020-76769-w
pubmed: 33199699
pmcid: 7670435
Huber W, Carey VJ, Gentleman R, et al. Orchestrating high-throughput genomic analysis with Bioconductor. Nat Methods 2015; 12: 115–121. https://doi.org/10.1038/nmeth.3252
doi: 10.1038/nmeth.3252
pubmed: 25633503
pmcid: 4509590
Koster J, Volckmann R, Zwijnenburg D, Molenaar P, Versteeg R. R2: Genomics analysis and visualization platform Cancer Res 2019; 79:2490. Abstract.
Huang T, Garcia R, Qi J, Lulla R, Horbinski C. 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 https://doi.org/10.18632/oncotarget.26430
doi: 10.18632/oncotarget.26430
pubmed: 30647848
pmcid: 6324678
Chan KM, Fang D, Gan H, et al. The histone H3.3K27M mutation in pediatric glioma reprograms H3K27 methylation and gene expression. Genes Dev 2013; 27: 985–990. https://doi.org/10.1101/gad.217778.113
Lee CH, Yu JR, Granat J, Saldaña-Meyer R, et al. Automethylation of PRC2 promotes H3K27 methylation and is impaired in H3K27M pediatric glioma. Genes Dev 2019; 33: 1428–1440. https://doi.org/10.1101/gad.328773.119
doi: 10.1101/gad.328773.119
pubmed: 31488577
pmcid: 6771381
Pathak P, Jha P, Purkait S, et al. Altered global histone-trimethylation code and H3F3A-ATRX mutation in pediatric GBM. J Neurooncol 2015; 121: 489–497. https://doi.org/10.1007/s11060-014-1675-z
doi: 10.1007/s11060-014-1675-z
pubmed: 25479829
Bender S, Tang Y, Lindroth AM, et al. Reduced H3K27me3 and DNA hypomethylation are major drivers of gene expression in K27M mutant pediatric high-grade gliomas. Cancer Cell 2013; 24: 660–672. https://doi.org/10.1016/j.ccr.2013.10.006
doi: 10.1016/j.ccr.2013.10.006
pubmed: 24183680
Mohammad, F, Weissmann, S, Leblanc, B, et al. EZH2 is a potential therapeutic target for H3K27M-mutant pediatric gliomas. Nat Med 2017; 23, 483–492. https://doi.org/10.1038/nm.4293 .
doi: 10.1038/nm.4293
pubmed: 28263309
Ahsan S, Raabe EH, Haffner MC, et al. Increased 5-hydroxymethylcytosine and decreased 5-methylcytosine are indicators of global epigenetic dysregulation in diffuse intrinsic pontine glioma. Acta Neuropathol Commun 2014; 2: 59. https://doi.org/10.1186/2051-5960-2-59
doi: 10.1186/2051-5960-2-59
pubmed: 24894482
pmcid: 4229804
Venneti S, Felicella MM, Coyne T, et al. Histone 3 lysine 9 trimethylation is differentially associated with isocitrate dehydrogenase mutations in oligodendrogliomas and high-grade astrocytomas. J Neuropathol Exp Neurol 2013; 72: 298–306. https://doi.org/10.1097/NEN.0b013e3182898113
doi: 10.1097/NEN.0b013e3182898113
pubmed: 23481705
Yoshimoto K, Hatae R, Sangatsuda Y, Suzuki SO. Prevalence and clinicopathological features of H3.3 G34-mutant high-grade gliomas : a retrospective study of 411 consecutive glioma cases in a single institution. Brain Tumor Pathol 2017; 34: 103–112. https://doi.org/10.1007/s10014-017-0287-7
Deng H, Zeng J, Zhang T, et al. Histone H3.3K27M mobilizes multiple cancer/testis (CT) antigens in pediatric glioma. Mol Cancer Res 2018; 16: 623–633. https://doi.org/10.1158/1541-7786.MCR-17-0460
Matsumura Y, Nakaki R, Inagaki T, et al. H3K4/H3K9me3 Bivalent Chromatin Domains Targeted by Lineage-Specific DNA Methylation Pauses Adipocyte Differentiation. Mol Cell 2015; 60: 584–596. https://doi.org/10.1016/j.molcel.2015.10.025
doi: 10.1016/j.molcel.2015.10.025
pubmed: 26590716
Mauser R, Kungulovski G, Keup C, Reinhardt R, Jeltsch A. Application of dual reading domains as novel reagents in chromatin biology reveals a new H3K9me3 and H3K36me2/3 bivalent chromatin state. Epigenetics and Chromatin 2017; 10: 45. https://doi.org/10.1186/s13072-017-0153-1
doi: 10.1186/s13072-017-0153-1
pubmed: 28946896
pmcid: 5613355
Tan S-L, Nishi M, Ohtsuka T, et al. Essential roles of the histone methyltransferase ESET in the epigenetic control of neural progenitor cells during development. Development 2012; 139: 3806– 3816. https://doi.org/10.1242/dev.082198
doi: 10.1242/dev.082198
pubmed: 22991445