IDH1 mutation is sufficient to establish the glioma hypermethylator phenotype

Nature

Volumn 483, Issue 7390, 2012, Pages 479-483

  Turcan, Sevin ^a   Rohle, Daniel ^a,b   Goenka, Anuj ^a   Walsh, Logan A ^a   Fang, Fang ^a   Yilmaz, Emrullah ^a   Campos, Carl ^a   Fabius, Armida W M ^a   Lu, Chao ^a,c   Ward, Patrick S ^a,c   Thompson, Craig B ^a   Kaufman, Andrew ^a   Guryanova, Olga ^a   Levine, Ross ^a   Heguy, Adriana ^a   Viale, Agnes ^a   Morris, Luc G T ^a   Huse, Jason T ^a   Mellinghoff, Ingo K ^a,b   Chan, Timothy A ^a,b  

^a MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

^b WEILL CORNELL MEDICAL COLLEGE   (United States)

^c UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE; ISOCITRATE DEHYDROGENASE; ISOCITRATE DEHYDROGENASE 1; TRANSCRIPTOME; UNCLASSIFIED DRUG;

CANCER; CYTOLOGY; GENE EXPRESSION; GENOME; GENOMICS; MUTATION; PATHOGENICITY; PHENOTYPE; PROTEIN; PUBLIC HEALTH; SURVIVAL;

ARTICLE; ASTROCYTE; CARCINOGENESIS; CPG ISLAND; DNA METHYLATION; GENE EXPRESSION; GENE MUTATION; GLIOBLASTOMA; GLIOMA; GLIOMA CPG ISLAND METHYLATOR PHENOTYPE; HUMAN; HUMAN CELL; METHYLOME; PHENOTYPE; PRIORITY JOURNAL;

ASTROCYTES; CELL SURVIVAL; CELLS, CULTURED; CPG ISLANDS; DNA METHYLATION; EPIGENESIS, GENETIC; EPIGENOMICS; GENE EXPRESSION REGULATION; GLIOBLASTOMA; GLIOMA; HEK293 CELLS; HISTONES; HUMANS; ISOCITRATE DEHYDROGENASE; METABOLOME; MUTATION; PHENOTYPE; TUMOR CELLS, CULTURED;

EID: 84858796263     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature10866     Document Type: Article

References (42)

1. Noushmehr, H. et al. Identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma. Cancer Cell 17, 510-522 (2010).
2. Fang, F. et al. Breast cancer methylomes establish an epigenomic foundation for metastasis. Sci. Transl. Med. 3, 75ra25 (2011).
3. Toyota, M. et al. CpG island methylator phenotype in colorectal cancer. Proc. Natl Acad. Sci. USA 96, 8681-8686 (1999). (Pubitemid 29354851)
4. Yan, H. et al. IDH1 and IDH2 mutations in gliomas. N. Engl. J. Med. 360, 765-773 (2009).
5. Parsons, D. W. et al. An integrated genomic analysis of human glioblastoma multiforme. Science 321, 1807-1812 (2008).
6. Sjoblom, T. et al. The consensus coding sequences of human breast and colorectal cancers. Science 314, 268-274 (2006). (Pubitemid 44571966)
7. Mardis, E. R. et al. Recurring mutations found by sequencing an acute myeloid leukemia genome. N. Engl. J. Med. 361, 1058-1066 (2009).
8. Dang, L. et al. Cancer-associated IDH1 mutations produce 2-hydroxyglutarate. Nature 462, 739-744 (2009).
9. Figueroa, M. E. et al. Leukemic IDH1 and IDH2 mutations result in a hypermethylation phenotype, disrupt TET2 function, and impair hematopoietic differentiation. Cancer Cell 18, 553-567 (2010).
10. Ward, P. S. et al. The common feature of leukemia-associated IDH1 and IDH2 mutations is a neomorphic enzyme activity converting a-ketoglutarate to 2-hydroxyglutarate. Cancer Cell 17, 225-234 (2010).
11. Jones, P. A. & Baylin, S. B. The epigenomics of cancer. Cell 128, 683-692 (2007). (Pubitemid 46273572)
12. Ohm, J. E. et al. A stem cell-like chromatin pattern may predispose tumor suppressor genes toDNA hypermethylation and heritable silencing. Nature Genet. 39, 237-242 (2007). (Pubitemid 46184356)
13. Cheng, Y. W. et al. CpG island methylator phenotype associates with low-degree chromosomalabnormalities in colorectal cancer. Clin.Cancer Res.14, 6005-6013 (2008).
14. Sonoda, Y. et al. Formation of intracranial tumors by genetically modified human astrocytes defines four pathways critical in the development of human anaplastic astrocytoma. Cancer Res. 61, 4956-4960 (2001). (Pubitemid 32681517)
15. Vivanco, I. et al. Identification of the JNK signaling pathway as a functional target of the tumor suppressor PTEN. Cancer Cell 11, 555-569 (2007). (Pubitemid 46856910)
16. Sonoda, Y. et al. Akt pathway activation converts anaplastic astrocytoma to glioblastoma multiforme in a human astrocyte model of glioma. Cancer Res. 61, 6674-6678 (2001). (Pubitemid 32896484)
17. Pieper, R. O. Defined human cellular systems in the study of glioma development. Front. Biosci. 8, s19-s27 (2003). (Pubitemid 38925400)
18. Bibikova, M. et al. High density DNA methylation array with single CpG site resolution. Genomics 98, 288-295 (2011).
19. Sandoval, J. et al. Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome. Epigenetics 6, 692-702 (2011).
20. Mutskov, V. & Felsenfeld, G. Silencing of transgene transcription precedes methylationofpromoterDNAandhistoneH3lysine9.EMBOJ.23,138-149(2004). (Pubitemid 38165754)
21. Bracken, A. P. et al. Genome-wide mapping of Polycomb target genes unravels their roles in cell fate transitions. Genes Dev. 20, 1123-1136 (2006).
22. Furnari, F. B. et al. Malignant astrocytic glioma: genetics, biology, and paths to treatment. Genes Dev. 21, 2683-2710 (2007). (Pubitemid 350070717)
23. Docherty, S. J. et al. Bisulfite-based epityping on pooled genomicDNA provides an accurate estimate of average group DNA methylation. Epigenetics Chromatin 2, 3 (2009).
24. Hegi, M. E. et al. MGMT gene silencing and benefit from temozolomide in glioblastoma. N. Engl. J. Med. 352, 997-1003 (2005). (Pubitemid 40349502)
25. Solomon, D. A. et al. Identification of p18INK4c as a tumor suppressor gene in glioblastoma multiforme. Cancer Res. 68, 2564-2569 (2008). (Pubitemid 351556252)
26. Etcheverry, A. et al. DNA methylation in glioblastoma: impact on gene expression and clinical outcome. BMC Genomics 11, 701 (2010).
27. The Cancer Genome Atlas Network.Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455, 1061-1068 (2008).
28. Lendahl, U., Zimmerman, L. B.&McKay, R. D.CNS stemcells express a newclass of intermediate filament protein. Cell 60, 585-595 (1990).
29. Xu, W. et al. Oncometabolite 2-hydroxyglutarate is a competitive inhibitor of a-ketoglutarate-dependent dioxygenases. Cancer Cell 19, 17-30 (2011).
30. He, Y. F. et al. Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA. Science 333, 1303-1307 (2011).
31. Reich, M. et al. GenePattern 2.0. Nature Genet. 38, 500-501 (2006).
32. Verhaak, R. G. et al. Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell 17, 98-110 (2010).
33. Thomas, P. D. et al. PANTHER: a library of protein families and subfamilies indexed by function. Genome Res. 13, 2129-2141 (2003). (Pubitemid 37161770)
34. Rhodes, D. R. et al. Molecular concepts analysis links tumors, pathways, mechanisms, and drugs. Neoplasia 9, 443-454 (2007). (Pubitemid 46799988)
35. Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA 102, 15545-15550 (2005). (Pubitemid 41528093)
36. Vlassenbroeck, I. et al. Validation of real-time methylation-specific PCR to determine O6-methylguanine-DNA methyltransferase gene promoter methylation in glioma. J. Mol. Diagn. 10, 332-337 (2008). (Pubitemid 352019119)
37. Gordon, D., Abajian, C. & Green, P. Consed: a graphical tool for sequence finishing. Genome Res. 8, 195-202 (1998).
38. Nickerson, D. A., Tobe, V. O.&Taylor, S. L. PolyPhred: automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing. Nucleic Acids Res. 25, 2745-2751 (1997).
39. Chen, K. et al. PolyScan: an automatic indel and SNP detection approach to the analysis of human resequencing data. Genome Res. 17, 659-666 (2007). (Pubitemid 46715517)
40. Major, J. E. Genomic mutation consequence calculator. Bioinformatics 23, 3091-3092 (2007). (Pubitemid 350162876)
41. Galli, R. et al. Isolation and characterization of tumorigenic, stem-like neural precursors from human glioblastoma. Cancer Res. 64, 7011-7021 (2004). (Pubitemid 39331011)
42. De Filippis, L. et al. A novel, immortal, andmultipotent human neural stem cell line generating functional neurons and oligodendrocytes. Stem Cells 25, 2312-2321 (2007). (Pubitemid 47480490)