A systems approach identifies Enhancer of Zeste Homolog 2 (EZH2) as a protective factor in epilepsy
Autoři:
Nadia Khan aff001; Barry Schoenike aff002; Trina Basu aff002; Heidi Grabenstatter aff004; Genesis Rodriguez aff005; Caleb Sindic aff005; Margaret Johnson aff002; Eli Wallace aff006; Rama Maganti aff007; Raymond Dingledine aff008; Avtar Roopra aff002
Působiště autorů:
Cellular and Molecular Biology Graduate Program, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
aff001; Department of Neuroscience, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
aff002; Neuroscience Training Program, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
aff003; Department of Integrative Physiology, University of Colorado-Boulder, Boulder, Colorado, United States of America
aff004; College of Letters and Science, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
aff005; Cellular and Molecular Pathology Graduate Program, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
aff006; Department of Neurology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
aff007; Department of Pharmacology and Chemical Biology, Emory University, Atlanta, GA, United States of America
aff008
Vyšlo v časopise:
PLoS ONE 14(12)
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pone.0226733
Souhrn
Complex neurological conditions can give rise to large scale transcriptomic changes that drive disease progression. It is likely that alterations in one or a few transcription factors or cofactors underlie these transcriptomic alterations. Identifying the driving transcription factors/cofactors is a non-trivial problem and a limiting step in the understanding of neurological disorders. Epilepsy has a prevalence of 1% and is the fourth most common neurological disorder. While a number of anti-seizure drugs exist to treat seizures symptomatically, none is curative or preventive. This reflects a lack of understanding of disease progression. We used a novel systems approach to mine transcriptome profiles of rodent and human epileptic brain samples to identify regulators of transcriptional networks in the epileptic brain. We find that Enhancer of Zeste Homolog 2 (EZH2) regulates differentially expressed genes in epilepsy across multiple rodent models of acquired epilepsy. EZH2 undergoes a prolonged upregulation in the epileptic brain. A transient inhibition of EZH2 immediately after status epilepticus (SE) robustly increases spontaneous seizure burden weeks later. This suggests that EZH2 upregulation is a protective. These findings are the first to characterize a role for EZH2 in opposing epileptogenesis and debut a bioinformatic approach to identify nuclear drivers of complex transcriptional changes in disease.
Klíčová slova:
Gene expression – Gene regulation – Transcription factors – Mouse models – Mice – Factor analysis – Transcriptome analysis – Epilepsy
Zdroje
1. Hirtz D, Thurman DJ, Gwinn-Hardy K, Mohamed M, Chaudhuri AR, Zalutsky R. How common are the "common" neurologic disorders? Neurology. 2007;68(5):326–37. Epub 2007/01/31. doi: 10.1212/01.wnl.0000252807.38124.a3 17261678.
2. Temkin NR. Preventing and treating posttraumatic seizures: the human experience. Epilepsia. 2009;50 Suppl 2:10–3. doi: 10.1111/j.1528-1167.2008.02005.x 19187289.
3. Temkin NR, Jarell AD, Anderson GD. Antiepileptogenic agents: how close are we? Drugs. 2001;61(8):1045–55. doi: 10.2165/00003495-200161080-00002 11465868.
4. French JA, Williamson PD, Thadani VM, Darcey TM, Mattson RH, Spencer SS, et al. Characteristics of medial temporal lobe epilepsy: I. Results of history and physical examination. Ann Neurol. 1993;34(6):774–80. doi: 10.1002/ana.410340604 8250525.
5. Hesdorffer DC, Logroscino G, Cascino G, Annegers JF, Hauser WA. Risk of unprovoked seizure after acute symptomatic seizure: effect of status epilepticus. Ann Neurol. 1998;44(6):908–12. doi: 10.1002/ana.410440609 9851435.
6. Trinka E, Cock H, Hesdorffer D, Rossetti AO, Scheffer IE, Shinnar S, et al. A definition and classification of status epilepticus—Report of the ILAE Task Force on Classification of Status Epilepticus. Epilepsia. 2015;56(10):1515–23. Epub 2015/09/05. doi: 10.1111/epi.13121 26336950.
7. Garriga-Canut M, Schoenike B, Qazi R, Bergendahl K, Daley TJ, Pfender RM, et al. 2-Deoxy-D-glucose reduces epilepsy progression by NRSF-CtBP-dependent metabolic regulation of chromatin structure. Nat Neurosci. 2006;9(11):1382–7. doi: 10.1038/nn1791 17041593.
8. Vezzani A, Friedman A, Dingledine RJ. The role of inflammation in epileptogenesis. Neuropharmacology. 2013;69:16–24. Epub 2012/04/24. doi: 10.1016/j.neuropharm.2012.04.004 22521336; PubMed Central PMCID: PMC3447120.
9. Williams-Karnesky RL, Sandau US, Lusardi TA, Lytle NK, Farrell JM, Pritchard EM, et al. Epigenetic changes induced by adenosine augmentation therapy prevent epileptogenesis. J Clin Invest. 2013;123(8):3552–63. Epub 2013/07/19. doi: 10.1172/JCI65636 23863710; PubMed Central PMCID: PMC3726154.
10. Liu G, Gu B, He XP, Joshi RB, Wackerle HD, Rodriguiz RM, et al. Transient inhibition of TrkB kinase after status epilepticus prevents development of temporal lobe epilepsy. Neuron. 2013;79(1):31–8. doi: 10.1016/j.neuron.2013.04.027 23790754; PubMed Central PMCID: PMC3744583.
11. Becker AJ, Chen J, Zien A, Sochivko D, Normann S, Schramm J, et al. Correlated stage- and subfield-associated hippocampal gene expression patterns in experimental and human temporal lobe epilepsy. Eur J Neurosci. 2003;18(10):2792–802. Epub 2003/12/06. doi: 10.1111/j.1460-9568.2003.02993.x 14656328.
12. Borges K, Shaw R, Dingledine R. Gene expression changes after seizure preconditioning in the three major hippocampal cell layers. Neurobiol Dis. 2007;26(1):66–77. Epub 2007/01/24. doi: 10.1016/j.nbd.2006.12.001 17239605; PubMed Central PMCID: PMC2295285.
13. Hansen KF, Sakamoto K, Pelz C, Impey S, Obrietan K. Profiling status epilepticus-induced changes in hippocampal RNA expression using high-throughput RNA sequencing. Sci Rep. 2014;4:6930. Epub 2014/11/07. doi: 10.1038/srep06930 25373493; PubMed Central PMCID: PMC4894418.
14. McClelland S, Brennan GP, Dube C, Rajpara S, Iyer S, Richichi C, et al. The transcription factor NRSF contributes to epileptogenesis by selective repression of a subset of target genes. Elife. 2014;3:e01267. Epub 2014/08/15. doi: 10.7554/eLife.01267 25117540; PubMed Central PMCID: PMC4129437.
15. Johnson MR, Behmoaras J, Bottolo L, Krishnan ML, Pernhorst K, Santoscoy PLM, et al. Systems genetics identifies Sestrin 3 as a regulator of a proconvulsant gene network in human epileptic hippocampus. Nat Commun. 2015;6:6031. Epub 2015/01/24. doi: 10.1038/ncomms7031 25615886; PubMed Central PMCID: PMC4627576.
16. Dingledine R, Coulter DA, Fritsch B, Gorter JA, Lelutiu N, McNamara J, et al. Transcriptional profile of hippocampal dentate granule cells in four rat epilepsy models. Sci Data. 2017;4:170061. doi: 10.1038/sdata.2017.61 28485718; PubMed Central PMCID: PMC5423390.
17. Spitz F, Furlong EE. Transcription factors: from enhancer binding to developmental control. Nat Rev Genet. 2012;13(9):613–26. Epub 2012/08/08. doi: 10.1038/nrg3207 22868264.
18. Consortium EP. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science. 2004;306(5696):636–40. doi: 10.1126/science.1105136 15499007.
19. Yu H, Lee H, Herrmann A, Buettner R, Jove R. Revisiting STAT3 signalling in cancer: new and unexpected biological functions. Nat Rev Cancer. 2014;14(11):736–46. Epub 2014/10/25. doi: 10.1038/nrc3818 25342631.
20. Cao R, Wang L, Wang H, Xia L, Erdjument-Bromage H, Tempst P, et al. Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science. 2002;298(5595):1039–43. doi: 10.1126/science.1076997 12351676.
21. Schuettengruber B, Martinez AM, Iovino N, Cavalli G. Trithorax group proteins: switching genes on and keeping them active. Nat Rev Mol Cell Biol. 2011;12(12):799–814. doi: 10.1038/nrm3230 22108599.
22. Steffen PA, Ringrose L. What are memories made of? How Polycomb and Trithorax proteins mediate epigenetic memory. Nat Rev Mol Cell Biol. 2014;15(5):340–56. doi: 10.1038/nrm3789 24755934.
23. Subramanian A, Kuehn H, Gould J, Tamayo P, Mesirov JP. GSEA-P: a desktop application for Gene Set Enrichment Analysis. Bioinformatics. 2007;23(23):3251–3. Epub 2007/07/24. doi: 10.1093/bioinformatics/btm369 17644558.
24. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 2005;102(43):15545–50. Epub 2005/10/04. doi: 10.1073/pnas.0506580102 16199517; PubMed Central PMCID: PMC1239896.
25. Margueron R, Reinberg D. The Polycomb complex PRC2 and its mark in life. Nature. 2011;469(7330):343–9. Epub 2011/01/21. doi: 10.1038/nature09784 21248841; PubMed Central PMCID: PMC3760771.
26. Cao R, Zhang Y. SUZ12 is required for both the histone methyltransferase activity and the silencing function of the EED-EZH2 complex. Mol Cell. 2004;15(1):57–67. doi: 10.1016/j.molcel.2004.06.020 15225548.
27. Peters JM, Tedeschi A, Schmitz J. The cohesin complex and its roles in chromosome biology. Genes Dev. 2008;22(22):3089–114. Epub 2008/12/06. doi: 10.1101/gad.1724308 19056890.
28. Na J, Plews J, Li J, Wongtrakoongate P, Tuuri T, Feki A, et al. Molecular mechanisms of pluripotency and reprogramming. Stem Cell Res Ther. 2010;1(4):33. Epub 2010/10/27. doi: 10.1186/scrt33 20974014; PubMed Central PMCID: PMC2983446.
29. Fabregat A, Jupe S, Matthews L, Sidiropoulos K, Gillespie M, Garapati P, et al. The Reactome Pathway Knowledgebase. Nucleic Acids Res. 2018;46(D1):D649–D55. Epub 2017/11/18. doi: 10.1093/nar/gkx1132 29145629; PubMed Central PMCID: PMC5753187.
30. Li JZ, Bunney BG, Meng F, Hagenauer MH, Walsh DM, Vawter MP, et al. Circadian patterns of gene expression in the human brain and disruption in major depressive disorder. Proc Natl Acad Sci U S A. 2013;110(24):9950–5. Epub 2013/05/15. doi: 10.1073/pnas.1305814110 23671070; PubMed Central PMCID: PMC3683716.
31. Rakhade SN, Jensen FE. Epileptogenesis in the immature brain: emerging mechanisms. Nat Rev Neurol. 2009;5(7):380–91. Epub 2009/07/07. doi: 10.1038/nrneurol.2009.80 19578345; PubMed Central PMCID: PMC2822660.
32. Pasini D, Bracken AP, Jensen MR, Lazzerini Denchi E, Helin K. Suz12 is essential for mouse development and for EZH2 histone methyltransferase activity. EMBO J. 2004;23(20):4061–71. Epub 2004/09/24. doi: 10.1038/sj.emboj.7600402 15385962; PubMed Central PMCID: PMC524339.
33. Carvill GL, McMahon JM, Schneider A, Zemel M, Myers CT, Saykally J, et al. Mutations in the GABA Transporter SLC6A1 Cause Epilepsy with Myoclonic-Atonic Seizures. Am J Hum Genet. 2015;96(5):808–15. Epub 2015/04/14. doi: 10.1016/j.ajhg.2015.02.016 25865495; PubMed Central PMCID: PMC4570550.
34. Noebels JL, Avoli M, Rogawski M, Olsen R, Delgado-Escueta AV. "Jasper's Basic Mechanisms of the Epilepsies" Workshop. Epilepsia. 2010;51 Suppl 5:1–5. Epub 2011/01/25. doi: 10.1111/j.1528-1167.2010.02792.x 21208201; PubMed Central PMCID: PMC4651849.
35. Blumcke I, Beck H, Lie AA, Wiestler OD. Molecular neuropathology of human mesial temporal lobe epilepsy. Epilepsy Res. 1999;36(2–3):205–23. Epub 1999/10/09. doi: 10.1016/s0920-1211(99)00052-2 10515166.
36. Nadkarni S, LaJoie J, Devinsky O. Current treatments of epilepsy. Neurology. 2005;64(12 Suppl 3):S2–11. Epub 2005/07/05. doi: 10.1212/wnl.64.12_suppl_3.s2 15994220.
37. Stafstrom CE, Carmant L. Seizures and epilepsy: an overview for neuroscientists. Cold Spring Harb Perspect Med. 2015;5(6). Epub 2015/06/03. doi: 10.1101/cshperspect.a022426 26033084; PubMed Central PMCID: PMC4448698.
38. Staley K. Molecular mechanisms of epilepsy. Nat Neurosci. 2015;18(3):367–72. Epub 2015/02/25. doi: 10.1038/nn.3947 25710839; PubMed Central PMCID: PMC4409128.
39. Konze KD, Ma A, Li F, Barsyte-Lovejoy D, Parton T, Macnevin CJ, et al. An orally bioavailable chemical probe of the Lysine Methyltransferases EZH2 and EZH1. ACS Chem Biol. 2013;8(6):1324–34. Epub 2013/04/26. doi: 10.1021/cb400133j 23614352; PubMed Central PMCID: PMC3773059.
40. Racine RJ. Modification of seizure activity by electrical stimulation. II. Motor seizure. Electroencephalogr Clin Neurophysiol. 1972;32(3):281–94. Epub 1972/03/01. doi: 10.1016/0013-4694(72)90177-0 4110397.
41. Landis SC, Amara SG, Asadullah K, Austin CP, Blumenstein R, Bradley EW, et al. A call for transparent reporting to optimize the predictive value of preclinical research. Nature. 2012;490(7419):187–91. Epub 2012/10/13. doi: 10.1038/nature11556 23060188; PubMed Central PMCID: PMC3511845.
42. Kwon AT, Arenillas DJ, Worsley Hunt R, Wasserman WW. oPOSSUM-3: advanced analysis of regulatory motif over-representation across genes or ChIP-Seq datasets. G3 (Bethesda). 2012;2(9):987–1002. Epub 2012/09/14. doi: 10.1534/g3.112.003202 22973536; PubMed Central PMCID: PMC3429929.
43. Lambert SA, Jolma A, Campitelli LF, Das PK, Yin Y, Albu M, et al. The Human Transcription Factors. Cell. 2018;172(4):650–65. Epub 2018/02/10. doi: 10.1016/j.cell.2018.01.029 29425488.
44. Grabenstatter HL, Del Angel YC, Carlsen J, Wempe MF, White AM, Cogswell M, et al. The effect of STAT3 inhibition on status epilepticus and subsequent spontaneous seizures in the pilocarpine model of acquired epilepsy. Neurobiol Dis. 2014;62:73–85. Epub 2013/09/21. doi: 10.1016/j.nbd.2013.09.003 24051278; PubMed Central PMCID: PMC3908775.
45. Lund IV, Hu Y, Raol YH, Benham RS, Faris R, Russek SJ, et al. BDNF selectively regulates GABAA receptor transcription by activation of the JAK/STAT pathway. Sci Signal. 2008;1(41):ra9. Epub 2008/10/17. doi: 10.1126/scisignal.1162396 18922788; PubMed Central PMCID: PMC2651003.
46. Raible DJ, Frey LC, Del Angel YC, Carlsen J, Hund D, Russek SJ, et al. JAK/STAT pathway regulation of GABAA receptor expression after differing severities of experimental TBI. Exp Neurol. 2015;271:445–56. Epub 2015/07/15. doi: 10.1016/j.expneurol.2015.07.001 26172316; PubMed Central PMCID: PMC5969808.
47. Dasgupta M, Dermawan JK, Willard B, Stark GR. STAT3-driven transcription depends upon the dimethylation of K49 by EZH2. Proc Natl Acad Sci U S A. 2015;112(13):3985–90. Epub 2015/03/15. doi: 10.1073/pnas.1503152112 25767098; PubMed Central PMCID: PMC4386339.
48. Kim E, Kim M, Woo DH, Shin Y, Shin J, Chang N, et al. Phosphorylation of EZH2 activates STAT3 signaling via STAT3 methylation and promotes tumorigenicity of glioblastoma stem-like cells. Cancer Cell. 2013;23(6):839–52. Epub 2013/05/21. doi: 10.1016/j.ccr.2013.04.008 23684459; PubMed Central PMCID: PMC4109796.
49. Xu K, Wu ZJ, Groner AC, He HH, Cai C, Lis RT, et al. EZH2 oncogenic activity in castration-resistant prostate cancer cells is Polycomb-independent. Science. 2012;338(6113):1465–9. Epub 2012/12/15. doi: 10.1126/science.1227604 23239736; PubMed Central PMCID: PMC3625962.
50. Stapels M, Piper C, Yang T, Li M, Stowell C, Xiong ZG, et al. Polycomb group proteins as epigenetic mediators of neuroprotection in ischemic tolerance. Sci Signal. 2010;3(111):ra15. doi: 10.1126/scisignal.2000502 20197544; PubMed Central PMCID: PMC3878609.
51. Tatton-Brown K, Murray A, Hanks S, Douglas J, Armstrong R, Banka S, et al. Weaver syndrome and EZH2 mutations: Clarifying the clinical phenotype. Am J Med Genet A. 2013;161A(12):2972–80. Epub 2013/11/12. doi: 10.1002/ajmg.a.36229 24214728.
52. Cohen AS, Yap DB, Lewis ME, Chijiwa C, Ramos-Arroyo MA, Tkachenko N, et al. Weaver Syndrome-Associated EZH2 Protein Variants Show Impaired Histone Methyltransferase Function In Vitro. Hum Mutat. 2016;37(3):301–7. Epub 2015/12/24. doi: 10.1002/humu.22946 26694085; PubMed Central PMCID: PMC4832389.
53. Gibson WT, Hood RL, Zhan SH, Bulman DE, Fejes AP, Moore R, et al. Mutations in EZH2 cause Weaver syndrome. Am J Hum Genet. 2012;90(1):110–8. Epub 2011/12/20. doi: 10.1016/j.ajhg.2011.11.018 22177091; PubMed Central PMCID: PMC3257956.
54. Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics. 2003;19(2):185–93. Epub 2003/01/23. doi: 10.1093/bioinformatics/19.2.185 12538238.
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