Differences among brain tumor stem cell types and fetal neural stem cells in focal regions of histone modifications and DNA methylation, broad regions of modifications, and bivalent promoters

BMC Genomics

Mark C Bieda¹  Sally Yoo¹ 

[1]Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada

关键词: Bivalent promoters;    Histone modifications;    Chromatin immunoprecipitation;    Epigenetics;    Cancer stem cells;   

Others  :  1141188
DOI  :  10.1186/1471-2164-15-724

 received in 2014-02-27, accepted in 2014-08-04,  发布年份 2014

【 摘 要 】

Background

Aberrational epigenetic marks are believed to play a major role in establishing the abnormal features of cancer cells. Rational use and development of drugs aimed at epigenetic processes requires an understanding of the range, extent, and roles of epigenetic reprogramming in cancer cells. Using ChIP-chip and MeDIP-chip approaches, we localized well-established and prevalent epigenetic marks (H3K27me3, H3K4me3, H3K9me3, DNA methylation) on a genome scale in several lines of putative glioma stem cells (brain tumor stem cells, BTSCs) and, for comparison, normal human fetal neural stem cells (fNSCs).

Results

We determined a substantial “core” set of promoters possessing each mark in every surveyed BTSC cell type, which largely overlapped the corresponding fNSC sets. However, there was substantial diversity among cell types in mark localization. We observed large differences among cell types in total number of H3K9me3+ positive promoters and peaks and in broad modifications (defined as >50 kb peak length) for H3K27me3 and, to a lesser extent, H3K9me3. We verified that a change in a broad modification affected gene expression of CACNG7. We detected large numbers of bivalent promoters, but most bivalent promoters did not display direct overlap of contrasting epigenetic marks, but rather occupied nearby regions of the proximal promoter. There were significant differences in the sets of promoters bearing bivalent marks in the different cell types and few consistent differences between fNSCs and BTSCs.

Conclusions

Overall, our “core set” data establishes sets of potential therapeutic targets, but the diversity in sets of sites and broad modifications among cell types underscores the need to carefully consider BTSC subtype variation in epigenetic therapy. Our results point toward substantial differences among cell types in the activity of the production/maintenance systems for H3K9me3 and for broad regions of modification (H3K27me3 or H3K9me3). Finally, the unexpected diversity in bivalent promoter sets among these multipotent cells indicates that bivalent promoters may play complex roles in the overall biology of these cells. These results provide key information for forming the basis for future rational drug therapy aimed at epigenetic processes in these cells.

【 授权许可】

   
2014 Yoo and Bieda; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

Figure 3.

Figure 4.

Figure 5.

Figure 6.

【 参考文献 】

• [1]Feinberg AP, Vogelstein B: Hypomethylation distinguishes genes of some human cancers from their normal counterparts. Nature 1983, 301:89-92.
• [2]Greger V, Passarge E, Höpping W, Messmer E, Horsthemke B: Epigenetic changes may contribute to the formation and spontaneous regression of retinoblastoma. Hum Genet 1989, 83:155-158.
• [3]Dawson MA, Kouzarides T: Cancer Epigenetics: From Mechanism to Therapy. Cell 2012, 150:12-27.
• [4]Mund C, Hackanson B, Stresemann C, Lübbert M, Lyko F: Characterization of DNA demethylation effects induced by 5-Aza-2’-deoxycytidine in patients with myelodysplastic syndrome. Cancer Res 2005, 65:7086-7090.
• [5]Cancer Genome Atlas Research Network: Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 2008, 455:1061-1068.
• [6]Sanai N, Alvarez-Buylla A, Berger MS: Neural stem cells and the origin of gliomas. N Engl J Med 2005, 353:811-822.
• [7]Stiles CD, Rowitch DH: Glioma stem cells: a midterm exam. Neuron 2008, 58:832-846.
• [8]Lewandowska J, Bartoszek A: DNA methylation in cancer development, diagnosis and therapy—multiple opportunities for genotoxic agents to act as methylome disruptors or remediators. Mutagenesis 2011, 26:475-487.
• [9]Takizawa T, Nakashima K, Namihira M, Ochiai W, Uemura A, Yanagisawa M, Fujita N, Nakao M, Taga T: DNA methylation is a critical cell-intrinsic determinant of astrocyte differentiation in the fetal brain. Dev Cell 2001, 1:749-758.
• [10]Lee J, Son MJ, Woolard K, Donin NM, Li A, Cheng CH, Kotliarova S, Kotliarov Y, Walling J, Ahn S, Kim M, Totonchy M, Cusack T, Ene C, Ma H, Su Q, Zenklusen JC, Zhang W, Maric D, Fine HA: Epigenetic-mediated dysfunction of the bone morphogenetic protein pathway inhibits differentiation of glioblastoma-initiating cells. Cancer Cell 2008, 13:69-80.
• [11]Van Haaften G, Dalgliesh GL, Davies H, Chen L, Bignell G, Greenman C, Edkins S, Hardy C, O’Meara S, Teague J, Butler A, Hinton J, Latimer C, Andrews J, Barthorpe S, Beare D, Buck G, Campbell PJ, Cole J, Forbes S, Jia M, Jones D, Kok CY, Leroy C, Lin M-L, McBride DJ, Maddison M, Maquire S, McLay K, Menzies A, et al.: Somatic mutations of the histone H3K27 demethylase gene UTX in human cancer. Nat Genet 2009, 41:521-523.
• [12]Jepsen K, Solum D, Zhou T, McEvilly RJ, Kim H-J, Glass CK, Hermanson O, Rosenfeld MG: SMRT-mediated repression of an H3K27 demethylase in progression from neural stem cell to neuron. Nature 2007, 450:415-419.
• [13]Abdouh M, Facchino S, Chatoo W, Balasingam V, Ferreira J, Bernier G: BMI1 sustains human glioblastoma multiforme stem cell renewal. J Neurosci Off J Soc Neurosci 2009, 29:8884-8896.
• [14]Kim TH, Barrera LO, Zheng M, Qu C, Singer MA, Richmond TA, Wu Y, Green RD, Ren B: A high-resolution map of active promoters in the human genome. Nature 2005, 436:876-880.
• [15]Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim T-K, Koche RP, Lee W, Mendenhall E, O’Donovan A, Presser A, Russ C, Xie X, Meissner A, Wernig M, Jaenisch R, Nusbaum C, Lander ES, Bernstein BE: Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 2007, 448:553-560.
• [16]Barski A, Cuddapah S, Cui K, Roh T-Y, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K: High-resolution profiling of histone methylations in the human genome. Cell 2007, 129:823-837.
• [17]Beisel C, Paro R: Silencing chromatin: comparing modes and mechanisms. Nat Rev Genet 2011, 12:123-135.
• [18]Kelly JJP, Stechishin O, Chojnacki A, Lun X, Sun B, Senger DL, Forsyth P, Auer RN, Dunn JF, Cairncross JG, Parney IF, Weiss S: Proliferation of human glioblastoma stem cells occurs independently of exogenous mitogens. Stem Cells 2009, 27:1722-1733.
• [19]Chen J, Li Y, Yu T-S, McKay RM, Burns DK, Kernie SG, Parada LF: A restricted cell population propagates glioblastoma growth after chemotherapy. Nature 2012, 488:522-526.
• [20]Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J, Fry B, Meissner A, Wernig M, Plath K, Jaenisch R, Wagschal A, Feil R, Schreiber SL, Lander ES: A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 2006, 125:315-326.
• [21]Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M, ENCODE Project Consortium: An integrated encyclopedia of DNA elements in the human genome. Nature 2012, 489:57-74.
• [22]Talbert PB, Henikoff S: Spreading of silent chromatin: inaction at a distance. Nat Rev Genet 2006, 7:793-803.
• [23]Acevedo LG, Bieda M, Green R, Farnham PJ: Analysis of the mechanisms mediating tumor-specific changes in gene expression in human liver tumors. Cancer Res 2008, 68:2641-2651.
• [24]O’Geen H, Squazzo SL, Iyengar S, Blahnik K, Rinn JL, Chang HY, Green R, Farnham PJ: Genome-wide analysis of KAP1 binding suggests autoregulation of KRAB-ZNFs. PLoS Genet 2007, 3:e89.
• [25]Komashko VM, Acevedo LG, Squazzo SL, Iyengar SS, Rabinovich A, O’Geen H, Green R, Farnham PJ: Using ChIP-chip technology to reveal common principles of transcriptional repression in normal and cancer cells. Genome Res 2008, 18:521-532.
• [26]Huang DW, Sherman BT, Lempicki RA: Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2008, 4:44-57.
• [27]Lee Y, Scheck AC, Cloughesy TF, Lai A, Dong J, Farooqi HK, Liau LM, Horvath S, Mischel PS, Nelson SF: Gene expression analysis of glioblastomas identifies the major molecular basis for the prognostic benefit of younger age. BMC Med Genomics 2008, 1:52.
• [28]Vastenhouw NL, Schier AF: Bivalent histone modifications in early embryogenesis. Curr Opin Cell Biol 2012, 24:374-386.
• [29]Rada-Iglesias A, Wysocka J: Epigenomics of human embryonic stem cells and induced pluripotent stem cells: insights into pluripotency and implications for disease. Genome Med 2011, 3:36.
• [30]Hirabayashi Y, Gotoh Y: Epigenetic control of neural precursor cell fate during development. Nat Rev Neurosci 2010, 11:377-388.
• [31]Krebs J: Lewin’s GENES X. Sudbury: Jones & Bartlett Learning; 2011.
• [32]Li A, Walling J, Kotliarov Y, Center A, Steed ME, Ahn SJ, Rosenblum M, Mikkelsen T, Zenklusen JC, Fine HA: Genomic changes and gene expression profiles reveal that established glioma cell lines are poorly representative of primary human gliomas. Mol Cancer Res 2008, 6:21-30.
• [33]Verhaak RGW, Hoadley KA, Purdom E, Wang V, Qi Y, Wilkerson MD, Miller CR, Ding L, Golub T, Mesirov JP, Alexe G, Lawrence M, O’Kelly M, Tamayo P, Weir BA, Gabriel S, Winckler W, Gupta S, Jakkula L, Feiler HS, Hodgson JG, James CD, Sarkaria JN, Brennan C, Kahn A, Spellman PT, Wilson RK, Speed TP, Gray JW, Meyerson M, et al.: Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell 2010, 17:98-110.
• [34]Engström PG, Tommei D, Stricker SH, Ender C, Pollard SM, Bertone P: Digital transcriptome profiling of normal and glioblastoma-derived neural stem cells identifies genes associated with patient survival. Genome Med 2012, 4:76.
• [35]Beier D, Hau P, Proescholdt M, Lohmeier A, Wischhusen J, Oefner PJ, Aigner L, Brawanski A, Bogdahn U, Beier CP: CD133(+) and CD133(-) glioblastoma-derived cancer stem cells show differential growth characteristics and molecular profiles. Cancer Res 2007, 67:4010-4015.
• [36]Li Q, Jedlicka A, Ahuja N, Gibbons MC, Baylin SB, Burger PC, Issa JP: Concordant methylation of the ER and N33 genes in glioblastoma multiforme. Oncogene 1998, 16:3197-3202.
• [37]Mueller W, Nutt CL, Ehrich M, Riemenschneider MJ, von Deimling A, van den Boom D, Louis DN: Downregulation of RUNX3 and TES by hypermethylation in glioblastoma. Oncogene 2007, 26:583-593.
• [38]Suganuma T, Workman JL: Signals and combinatorial functions of histone modifications. Annu Rev Biochem 2011, 80:473-499.
• [39]Probst AV, Dunleavy E, Almouzni G: Epigenetic inheritance during the cell cycle. Nat Rev Mol Cell Biol 2009, 10:192-206.
• [40]Marks H, Kalkan T, Menafra R, Denissov S, Jones K, Hofemeister H, Nichols J, Kranz A, Stewart AF, Smith A, Stunnenberg HG: The transcriptional and epigenomic foundations of ground state pluripotency. Cell 2012, 149:590-604.
• [41]Marks H, Chow JC, Denissov S, Françoijs K-J, Brockdorff N, Heard E, Stunnenberg HG: High-resolution analysis of epigenetic changes associated with X inactivation. Genome Res 2009, 19:1361-1373.
• [42]Stropp T, McPhillips T, Ludäscher B, Bieda M: Workflows for microarray data processing in the Kepler environment. BMC Bioinformatics 2012, 13:102.
• [43]Krig SR, Jin VX, Bieda MC, O’Geen H, Yaswen P, Green R, Farnham PJ: Identification of genes directly regulated by the oncogene ZNF217 using chromatin immunoprecipitation (ChIP)-chip assays. J Biol Chem 2007, 282:9703-9712.
• [44]Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, et al.: Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007, 447:799-816.
• [45]VanGuilder HD, Vrana KE, Freeman WM: Twenty-five years of quantitative PCR for gene expression analysis. Biotechniques 2008, 44:619-626.