Identification of Global DNA Methylation Signatures in Glioblastoma-Derived Cancer Stem Cells

Eun-Joon Lee; Prakash Rath; Jimei Liu; Dungsung Ryu; Lirong Pei; Satish K. Noonepalle; Austin Y. Shull; Qi Feng; N. Scott Litofsky; Douglas C. Miller; Douglas C. Anthony; Mark D. Kirk; John Laterra; Libin Deng; Hong-Bo Xin; Xinguo Wang; Jeong-Hyeon Choi; Huidong Shi

doi:10.1016/j.jgg.2015.06.003

Volume 42 Issue 7

Jul. 2015

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Article Navigation > Journal of Genetics and Genomics > 2015 > 42(7): 355-371

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Identification of Global DNA Methylation Signatures in Glioblastoma-Derived Cancer Stem Cells

doi: 10.1016/j.jgg.2015.06.003

a
GRU Cancer Center, Georgia Regents University, Augusta, GA 30912, USA
b
Department of Biology, College of Art and Sciences, University of Missouri, Columbia, MO 65211, USA
c
Department of Biochemistry and Molecular Biology, Georgia Regents University, Augusta, GA 30912, USA
d
Division of Neurological Surgery, University of Missouri School of Medicine, Columbia, MO 65211, USA
e
Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine, Columbia, MO 65211, USA
f
Department of Pathology and Laboratory Medicine, Brown University and Lifespan Academic Medical Center, Providence, RI 02903, USA
g
Department of Neurology, The Hugo W. Moser Research Institute at Kennedy Krieger Inc. and The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
h
Institute of Translational Medicine, Nanchang University, Nanchang 330031, China
i
David H. Murdock Research Institute, Kannapolis, NC 28081, USA
j
Department of Biostatistics and Epidemiology, Georgia Regents University, Augusta, GA 30912, USA

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Corresponding author: E-mail address: jechoi@gru.edu (Jeong-Hyeon Choi); E-mail address: hshi@gru.edu (Huidong Shi)
Received Date: 2015-01-22
Accepted Date: 2015-06-17
Rev Recd Date: 2015-06-17

Available Online: 2015-06-24

Publish Date: 2015-07-20

Abstract

Abstract

Glioblastoma (GBM) is the most common and most aggressive primary brain tumor in adults. The existence of a small population of stem-like tumor cells that efficiently propagate tumors and resist cytotoxic therapy is one proposed mechanism leading to the resilient behavior of tumor cells and poor prognosis. In this study, we performed an in-depth analysis of the DNA methylation landscape in GBM-derived cancer stem cells (GSCs). Parallel comparisons of primary tumors and GSC lines derived from these tumors with normal controls (a neural stem cell (NSC) line and normal brain tissue) identified groups of hyper- and hypomethylated genes that display a trend of either increasing or decreasing methylation levels in the order of controls, primary GBMs, and their counterpart GSC lines, respectively. Interestingly, concurrent promoter hypermethylation and gene body hypomethylation were observed in a subset of genes including MGMT, AJAP1 and PTPRN2. These unique DNA methylation signatures were also found in primary GBM-derived xenograft tumors indicating that they are not tissue culture-related epigenetic changes. Integration of GSC-specific epigenetic signatures with gene expression analysis further identified candidate tumor suppressor genes that are frequently down-regulated in GBMs such asSPINT2, NEFM and PENK. Forced re-expression of SPINT2 reduced glioma cell proliferative capacity, anchorage independent growth, cell motility, and tumor sphere formation in vitro. The results from this study demonstrate that GSCs possess unique epigenetic signatures that may play important roles in the pathogenesis of GBM.
- Glioblastoma,
- Cancer stem cells,
- DNA methylation,
- SPINT2

These authors contributed equally to this work.

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References(59)

References

[1]	Abate-Shen, C. Deregulated homeobox gene expression in cancer: cause or consequence? Nat. Rev. Cancer, 2 (2002),pp. 777-785
[2]	Abdel-Fattah, R., Xiao, A., Bomgardner, D. et al. J. Pathol., 209 (2006),pp. 15-24
[3]	Abdouh, M., Facchino, S., Chatoo, W. et al. BMI1 sustains human glioblastoma multiforme stem cell renewal J. Neurosci., 29 (2009),pp. 8884-8896
[4]	Bao, S., Wu, Q., McLendon, R.E. et al. Glioma stem cells promote radioresistance by preferential activation of the DNA damage response Nature, 444 (2006),pp. 756-760
[5]	Baylin, S.B. DNA methylation and gene silencing in cancer Nat. Clin. Pract. Oncol., 2 (2005),pp. S4-S11
[6]	Baysan, M., Woolard, K., Bozdag, S. et al. Micro-environment causes reversible changes in DNA methylation and mRNA expression profiles in patient-derived glioma stem cells PLoS One, 9 (2014),p. e94045
[7]	Bleau, A.M., Howard, B.M., Taylor, L.A. et al. New strategy for the analysis of phenotypic marker antigens in brain tumor-derived neurospheres in mice and humans Neurosurg. Focus, 24 (2008),p. E28
[8]	Bredel, M., Scholtens, D.M., Harsh, G.R. et al. A network model of a cooperative genetic landscape in brain tumors JAMA, 302 (2009),pp. 261-275
[9]	Cadieux, B., Ching, T.-T., VandenBerg, S.R. et al. Genome-wide hypomethylation in human glioblastomas associated with specific copy number alteration, methylenetetrahydrofolate reductase allele status, and increased proliferation Cancer Res., 66 (2006),pp. 8469-8476
[10]	Carlson, B.L., Pokorny, J.L., Schroeder, M.A. et al. Curr. Protoc. Pharmacol., 52 (2011),pp. 1-14
[11]	Cillo, C., Cantile, M., Mortarini, R. et al. Int. J. Cancer, 66 (1996),pp. 692-697
[12]	De Bacco, F., Casanova, E., Medico, E. et al. Cancer Res., 72 (2012),pp. 4537-4550
[13]	Dirks, P.B. Brain tumor stem cells: bringing order to the chaos of brain cancer J. Clin. Oncol., 26 (2008),pp. 2916-2924
[14]	Dong, W.J., Chen, X.B., Xie, J. et al. Epigenetic inactivation and tumor suppressor activity of HAI-2/SPINT2 in gastric cancer Int. J. Cancer, 127 (2010),pp. 1526-1534
[15]	Engstrom, P.G., Tommei, D., Stricker, S.H. et al. Digital transcriptome profiling of normal and glioblastoma-derived neural stem cells identifies genes associated with patient survival Genome Med., 4 (2012),p. 76
[16]	Eramo, A., Ricci-Vitiani, L., Zeuner, A. et al. Chemotherapy resistance of glioblastoma stem cells Cell Death Differ., 13 (2006),pp. 1238-1241
[17]	Galli, R., Binda, E., Orfanelli, U. et al. Isolation and characterization of tumorigenic, stem-like neural precursors from human glioblastoma Cancer Res., 64 (2004),pp. 7011-7021
[18]	Gravendeel, L.A.M., Kouwenhoven, M.C.M., Gevaert, O. et al. Intrinsic gene expression profiles of gliomas are a better predictor of survival than histology Cancer Res., 69 (2009),pp. 9065-9072
[19]	Hamasuna, R., Kataoka, H., Meng, J.Y. et al. Reduced expression of hepatocyte growth factor activator inhibitor type-2/placental bikunin (HAI-2/PB) in human glioblastomas: implication for anti-invasive role of HAI-2/PB in glioblastoma cells Int. J. Cancer, 93 (2001),pp. 339-345
[20]	Hansen, K.D., Timp, W., Bravo, H.C. et al. Increased methylation variation in epigenetic domains across cancer types Nat. Genet., 43 (2011),pp. 768-775
[21]	Hegi, M.E., Diserens, A.C., Gorlia, T. et al. N. Engl. J. Med., 352 (2005),pp. 997-1003
[22]	Higgins, D.M., Wang, R., Milligan, B. et al. Brain tumor stem cell multipotency correlates with nanog expression and extent of passaging in human glioblastoma xenografts Oncotarget, 4 (2013),pp. 792-801
[23]	Inagaki, A., Soeda, A., Oka, N. et al. Long-term maintenance of brain tumor stem cell properties under at non-adherent and adherent culture conditions Biochem. Biophys. Res. Commun., 361 (2007),pp. 586-592
[24]	Johnson, D., O'Neill, B. Glioblastoma survival in the United States before and during the temozolomide era J. Neurooncol., 107 (2012),pp. 359-364
[25]	Jones, P.A., Baylin, S.B. The fundamental role of epigenetic events in cancer Nat. Rev. Genet., 3 (2002),pp. 415-428
[26]	Jones, P.A., Baylin, S.B. The epigenomics of cancer Cell, 128 (2007),pp. 683-692
[27]	Joo, K.M., Jin, J., Kim, E. et al. MET signaling regulates glioblastoma stem cells Cancer Res., 72 (2012),pp. 3828-3838
[28]	Kamnasaran, D., Qian, B., Hawkins, C. et al. GATA6 is an astrocytoma tumor suppressor gene identified by gene trapping of mouse glioma model Proc. Natl. Acad. Sci. USA, 104 (2007),pp. 8053-8058
[29]	Kongkham, P.N., Northcott, P.A., Ra, Y.S. et al. Cancer Res., 68 (2008),pp. 9945-9953
[30]	Langmead, B., Trapnell, C., Pop, M. et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome Genome Biol., 10 (2009),p. R25
[31]	Lee, J., Kotliarova, S., Kotliarov, Y. et al. Tumor stem cells derived from glioblastomas cultured in bFGF and EGF more closely mirror the phenotype and genotype of primary tumors than do serum-cultured cell lines Cancer Cell, 9 (2006),pp. 391-403
[32]	Lee, T.I., Jenner, R.G., Boyer, L.A. et al. Control of developmental regulators by Polycomb in human embryonic stem cells Cell, 125 (2006),pp. 301-313
[33]	Li, Y., Li, A., Glas, M. et al. c-Met signaling induces a reprogramming network and supports the glioblastoma stem-like phenotype Proc. Natl. Acad. Sci. USA, 108 (2011),pp. 9951-9956
[34]	Lin, N., Di, C., Bortoff, K. et al. Mol. Cancer Res., 10 (2012),pp. 208-217
[35]	Martinez, R., Martin-Subero, J.I., Rohde, V. et al. A microarray-based DNA methylation study of glioblastoma multiforme Epigenetics, 4 (2009),pp. 255-264
[36]	McTavish, N., Copeland, L.A., Saville, M.K. et al. Proenkephalin assists stress-activated apoptosis through transcriptional repression of NF-κB- and p53-regulated gene targets Cell Death Differ., 14 (2007),pp. 1700-1710
[37]	Meissner, A., Mikkelsen, T.S., Gu, H. et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells Nature, 454 (2008),pp. 766-770
[38]	Morris, M.R., Gentle, D., Abdulrahman, M. et al. Tumor suppressor activity and epigenetic inactivation of hepatocyte growth factor activator inhibitor type 2/SPINT2 in papillary and clear cell renal cell carcinoma Cancer Res., 65 (2005),pp. 4598-4606
[39]	Munoz, P., Iliou, M.S., Esteller, M. Epigenetic alterations involved in cancer stem cell reprogramming Mol. Oncol., 6 (2012),pp. 620-636
[40]	Murat, A., Migliavacca, E., Gorlia, T. et al. Stem cell-related “self-renewal” signature and high epidermal growth factor receptor expression associated with resistance to concomitant chemoradiotherapy in glioblastoma J. Clin. Oncol., 26 (2008),pp. 3015-3024
[41]	Natsume, A., Ito, M., Katsushima, K. et al. Chromatin regulator PRC2 is a key regulator of epigenetic plasticity in glioblastoma Cancer Res., 73 (2013),pp. 4559-4570
[42]	Noushmehr, H., Weisenberger, D.J., Diefes, K. et al. Identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma Cancer Cell, 17 (2010),pp. 510-522
[43]	Ohm, J.E., McGarvey, K.M., Yu, X. et al. A stem cell-like chromatin pattern may predispose tumor suppressor genes to DNA hypermethylation and heritable silencing Nat. Genet., 39 (2007),pp. 237-242
[44]	Parr, C., Watkins, G., Mansel, R.E. et al. The hepatocyte growth factor regulatory factors in human breast cancer Clin. Cancer Res., 10 (2004),pp. 202-211
[45]	Pei, L., Choi, J.H., Liu, J. et al. Genome-wide DNA methylation analysis reveals novel epigenetic changes in chronic lymphocytic leukemia Epigenetics, 7 (2012),pp. 567-578
[46]	Rath, P., Lal, B., Ajala, O. et al. In vivo c-met pathway inhibition depletes human glioma xenografts of tumor-propagating stem-like cells Transl. Oncol., 6 (2013),pp. 104-111
[47]	Sarkaria, J.N., Carlson, B.L., Schroeder, M.A. et al. Use of an orthotopic xenograft model for assessing the effect of epidermal growth factor receptor amplification on glioblastoma radiation response Clin. Cancer Res., 12 (2006),pp. 2264-2271
[48]	Selamat, S.A., Galler, J.S., Joshi, A.D. et al. PLoS One, 6 (2011),p. e21443
[49]	Singh, S.K., Hawkins, C., Clarke, I.D. et al. Identification of human brain tumour initiating cells Nature, 432 (2004),pp. 396-401
[50]	Stricker, S.H., Feber, A., Engstrom, P.G. et al. Widespread resetting of DNA methylation in glioblastoma-initiating cells suppresses malignant cellular behavior in a lineage-dependent manner Genes Dev., 27 (2013),pp. 654-659
[51]	TCGA Comprehensive genomic characterization defines human glioblastoma genes and core pathways Nature, 455 (2008),pp. 1061-1068
[52]	Uhlmann, K., Rohde, K., Zeller, C. et al. Distinct methylation profiles of glioma subtypes Int. J. Cancer, 106 (2003),pp. 52-59
[53]	Varley, K.E., Gertz, J., Bowling, K.M. et al. Dynamic DNA methylation across diverse human cell lines and tissues Genome Res., 23 (2013),pp. 555-567
[54]	Vescovi, A.L., Galli, R., Reynolds, B.A. Brain tumour stem cells Nat. Rev. Cancer, 6 (2006),pp. 425-436
[55]	Ward, R.J., Dirks, P.B. Cancer stem cells: at the headwaters of tumor development Annu. Rev. Pathol., 2 (2007),pp. 175-189
[56]	Widschwendter, M., Fiegl, H., Egle, D. et al. Epigenetic stem cell signature in cancer Nat. Genet., 39 (2007),pp. 157-158
[57]	Wild, L., Flanagan, J.M. Genome-wide hypomethylation in cancer may be a passive consequence of transformation Biochim. Biophys. Acta, 1806 (2010),pp. 50-57
[58]	Wu, X., Rauch, T.A., Zhong, X. et al. CpG island hypermethylation in human astrocytomas Cancer Res., 70 (2010),pp. 2718-2727
[59]	Wurdak, H., Zhu, S., Romero, A. et al. An RNAi screen identifies TRRAP as a regulator of brain tumor-initiating cell differentiation Cell Stem Cell, 6 (2010),pp. 37-47