IDH mutation impairs histone demethylation and results in a block to cell differentiation

Abstract

Recurrent mutations in isocitrate dehydrogenase 1 (IDH1) and IDH2 have been identified in gliomas, acute myeloid leukaemias (AML) and chondrosarcomas, and share a novel enzymatic property of producing 2-hydroxyglutarate (2HG) from α-ketoglutarate1,2,3,4,5,6. Here we report that 2HG-producing IDH mutants can prevent the histone demethylation that is required for lineage-specific progenitor cells to differentiate into terminally differentiated cells. In tumour samples from glioma patients, IDH mutations were associated with a distinct gene expression profile enriched for genes expressed in neural progenitor cells, and this was associated with increased histone methylation. To test whether the ability of IDH mutants to promote histone methylation contributes to a block in cell differentiation in non-transformed cells, we tested the effect of neomorphic IDH mutants on adipocyte differentiation in vitro. Introduction of either mutant IDH or cell-permeable 2HG was associated with repression of the inducible expression of lineage-specific differentiation genes and a block to differentiation. This correlated with a significant increase in repressive histone methylation marks without observable changes in promoter DNA methylation. Gliomas were found to have elevated levels of similar histone repressive marks. Stable transfection of a 2HG-producing mutant IDH into immortalized astrocytes resulted in progressive accumulation of histone methylation. Of the marks examined, increased H3K9 methylation reproducibly preceded a rise in DNA methylation as cells were passaged in culture. Furthermore, we found that the 2HG-inhibitable H3K9 demethylase KDM4C was induced during adipocyte differentiation, and that RNA-interference suppression of KDM4C was sufficient to block differentiation. Together these data demonstrate that 2HG can inhibit histone demethylation and that inhibition of histone demethylation can be sufficient to block the differentiation of non-transformed cells.

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Figure 1: IDH mutations are associated with dysregulation of glial differentiation and global histone methylation.
Figure 2: Differentiation arrest induced by mutant IDH or 2HG is associated with increased global and promoter-specific H3K9 and H3K27 methylation.
Figure 3: IDH mutation induces histone methylation increase in CNS-derived cells and can alter cell lineage gene expression.
Figure 4: 2HG-inhibitable H3K9 demethylase KDM4C is required for cell differentiation.

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Microarray data have been deposited with the ArrayExpress database under accession code E-MEXP-3239. Reprints and permissions information is available at www.nature.com/reprints.

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Acknowledgements

We thank members of the Thompson laboratory for technical help and critical reading of the manuscript. We thank T. A. Gocke and the genomic core of University of Pennsylvania for their assistance with the microarray study; the molecular cytology core facility of Memorial Sloan-Kettering Cancer Center (MSKCC) for technical help with the immunohistochemistry study; and O. Ouerfelli and M. K. Spassova at the organic synthesis core of MSKCC for the synthesis of octyl-2HG. This work was supported by grants from the National Cancer Institute and National Institutes of Health. R.L.L. is an Early Career Award recipient of the Howard Hughes Medical Institute and the Geoffrey Beene Junior Chair at MSKCC. D.M.O’R. is supported by the Betsy Cohen Fund of the Abramson Cancer Center at University of Pennsylvania. I.K.M. is supported by NCI-U54CA143798, the Doris Duke Charitable Foundation, and an Advanced Clinical Research Award in Glioma from the American Society of Clinical Oncology.

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C.L., P.S.W. and C.B.T. designed the study. C.L., P.S.W., G.S.K., D.R. and M.E.F. performed research; S.T., D.R., T.A.C. and I.K.M. contributed research material; C.L., P.S.W., G.S.K., O.A.-W., C.R.E., R.K., M.E.F., A.M., K.E.W., D.M.O’R., S.L.B., R.L.L. and C.B.T. contributed to data analysis and interpretation; C.L., P.S.W. and C.B.T. wrote the manuscript.

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Correspondence to Craig B. Thompson.

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C.B.T. is a consultant of Agios Pharmaceuticals and has a financial interest in Agios.

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Lu, C., Ward, P., Kapoor, G. et al. IDH mutation impairs histone demethylation and results in a block to cell differentiation. Nature 483, 474–478 (2012). https://doi.org/10.1038/nature10860

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