Diffuse midline gliomas (DMGs) bearing driver mutations of histone 3 lysine 27 (H3K27M) are incurable brain tumors with unique epigenomes. Here, we generated a syngeneic H3K27M mouse model to study the amino acid metabolic dependencies of these tumors. H3K27M mutant cells were highly dependent on methionine. Interrogating the methionine cycle dependency through a short-interfering RNA screen identified the enzyme methionine adenosyltransferase 2A (MAT2A) as a critical vulnerability in these tumors. This vulnerability was not mediated through the canonical mechanism of MTAP deletion; instead, DMG cells have lower levels of MAT2A protein, which is mediated by negative feedback induced by the metabolite decarboxylated S-adenosyl methionine. Depletion of residual MAT2A induces global depletion of H3K36me3, a chromatin mark of transcriptional elongation perturbing oncogenic and developmental transcriptional programs. Moreover, methionine-restricted diets extended survival in multiple models of DMG in vivo. Collectively, our results suggest that MAT2A presents an exploitable therapeutic vulnerability in H3K27M gliomas.

Baylor College of Medicine Texas Children's Cancer and Hematology Centers Dan L Duncan Cancer Center Houston TX USA

Department of Cell Biology School of Basic Medical Sciences Nanjing Medical University Nanjing China

Department of Developmental Biology University of Pittsburgh and Rangos Research Center Animal Imaging Core Pittsburgh PA USA

Department of Developmental Neurobiology St Jude Children's Research Hospital Memphis TN USA

Department of Human Genetics McGill University Montreal Quebec Canada

Department of Molecular and Integrative Physiology University of Michigan Medical School Ann Arbor MI USA

Department of Molecular Cell and Developmental Biology University of California Santa Cruz CA USA

Department of Molecular Genetics University of Toronto Toronto Ontario Canada

Department of Neurobiology University of Pittsburgh Pittsburgh PA USA

Department of Neurological Surgery University of Pittsburgh School of Medicine Pittsburgh PA USA

Department of Neurology Adult Neurooncology Program UPMC Hillman Cancer Center Pittsburgh PA USA

Department of Pediatric Hematology and Oncology 2nd Faculty of Medicine Charles University and University Hospital Motol Prague Czech Republic

Department of Pediatric Hematology and Oncology St Jude Children's Research Hospital Memphis TN USA

Department of Pediatrics McGill University The Research Institute of the McGill University Health Center Montreal Quebec Canada

Department of Pharmacology and Chemical Biology University of Pittsburgh Pittsburgh PA USA

Department of Pharmacy UPMC Shadyside Pittsburgh PA USA

Department of Radiology Children's Hospital of Pittsburgh Pittsburgh PA USA

John G Rangos Sr Research Center Children's Hospital of Pittsburgh Pittsburgh PA USA

Lady Davis Research Institute Jewish General Hospital Montreal Quebec Canada

Pediatric Neuro Oncology Program UPMC Children's Hospital of Pittsburgh Pittsburgh PA USA

Pediatrics Division of Hematology Oncology Program UPMC Children's Hospital of Pittsburgh Pittsburgh PA USA

State Key Laboratory of Veterinary Etiological Biology Lanzhou Veterinary Research Institute Chinese Academy of Agricultural Sciences Lanzhou PR China

University of California Santa Cruz Genomics Institute Santa Cruz CA USA

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Nat Cancer. 2022 Jul;3(7):899. doi: 10.1038/s43018-022-00407-9. PubMed

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Louis DN et al. The 2021 WHO classification of tumors of the central nervous system: a summary. Neuro-oncology 10.1093/neuonc/noab106 (2021). PubMed DOI PMC

Hoffman LM et al. Clinical, radiologic, pathologic, and molecular characteristics of long-term survivors of diffuse intrinsic pontine glioma (DIPG): a collaborative report from the International and European Society for Pediatric Oncology DIPG registries. J. Clin. Oncol 36, 1963–1972 (2018). PubMed PMC

Warren KE Diffuse intrinsic pontine glioma: poised for progress. Front. Oncol 2, 205 (2012). PubMed PMC

Sturm D et al. Hotspot mutations in H3F3A and IDH1 define distinct epigenetic and biological subgroups of glioblastoma. Cancer Cell 22, 425–437 (2012). PubMed

Ostrom QT et al. CBTRUS statistical report: primary brain and central nervous system tumors diagnosed in the United States in 2008–2012. Neuro-oncology 17, iv1–iv62 (2015). PubMed PMC

Jones C et al. Pediatric high-grade glioma: biologically and clinically in need of new thinking. Neuro-oncology 19, 153–161 (2017). PubMed PMC

Lewis PW et al. Inhibition of PRC2 activity by a gain-of-function H3 mutation found in pediatric glioblastoma. Science 340, 857–861 (2013). PubMed PMC

Nagaraja S et al. Transcriptional dependencies in diffuse intrinsic pontine glioma. Cancer Cell 31, 635–652 (2017). PubMed PMC

Silveira AB et al. H3.3 K27M depletion increases differentiation and extends latency of diffuse intrinsic pontine glioma growth in vivo. Acta neuropathologica 10.1007/s00401-019-01975-4 (2019). PubMed DOI PMC

Vinci M et al. Functional diversity and cooperativity between subclonal populations of pediatric glioblastoma and diffuse intrinsic pontine glioma cells. Nat. Med 10.1038/s41591-018-0086-7 (2018). PubMed DOI PMC

Koncar RF et al. Identification of novel RAS signaling therapeutic vulnerabilities in diffuse intrinsic pontine gliomas. Cancer Res. 79, 4026–4041 (2019). PubMed

Larson JD et al. Histone H3.3 K27M accelerates spontaneous brainstem glioma and drives restricted changes in bivalent gene expression. Cancer Cell 35, 140–155 (2019). PubMed PMC

Harutyunyan AS et al. H3K27M induces defective chromatin spread of PRC2-mediated repressive H3K27me2/me3 and is essential for glioma tumorigenesis. Nat. Commun 10, 1262 (2019). PubMed PMC

Krug B et al. Pervasive H3K27 acetylation leads to ERV expression and a therapeutic vulnerability in H3K27M gliomas. Cancer Cell 35, 782–797 (2019). PubMed PMC

Michealraj KA et al. Metabolic regulation of the epigenome drives lethal infantile ependymoma. Cell 10.1016/j.cell.2020.04.047 (2020). PubMed DOI PMC

Kaelin WG Jr. & McKnight SL Influence of metabolism on epigenetics and disease. Cell 153, 56–69 (2013). PubMed PMC

Dawson MA & Kouzarides T Cancer epigenetics: from mechanism to therapy. Cell 150, 12–27 (2012). PubMed

Lu C & Thompson CB Metabolic regulation of epigenetics. Cell Metab. 16, 9–17 (2012). PubMed PMC

Noushmehr H et al. Identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma. Cancer Cell 17, 510–522 (2010). PubMed PMC

Vander Heiden MG & DeBerardinis RJ Understanding the intersections between metabolism and cancer biology. Cell 168, 657–669 (2017). PubMed PMC

Gaude E & Frezza C Tissue-specific and convergent metabolic transformation of cancer correlates with metastatic potential and patient survival. Nat. Commun 7, 13041 (2016). PubMed PMC

Filbin MG et al. Developmental and oncogenic programs in H3K27M gliomas dissected by single-cell RNA-seq. Science 360, 331–335 (2018). PubMed PMC

Monje M et al. Hedgehog-responsive candidate cell of origin for diffuse intrinsic pontine glioma. PNAS 108, 4453–4458 (2011). PubMed PMC

Mackay A et al. Integrated molecular meta-analysis of 1,000 pediatric high-grade and diffuse intrinsic pontine glioma. Cancer Cell 32, 520–537 (2017). PubMed PMC

Kondo S et al. Simultaneous on/off regulation of transgenes located on a mammalian chromosome with Cre-expressing adenovirus and a mutant loxP. Nucleic Acids Res. 31, e76 (2003). PubMed PMC

Ahn JI et al. Comprehensive transcriptome analysis of differentiation of embryonic stem cells into midbrain and hindbrain neurons. Dev. Biol 265, 491–501 (2004). PubMed

Gao X et al. Dietary methionine influences therapy in mouse cancer models and alters human metabolism. Nature 572, 397–401 (2019). PubMed PMC

Sanderson SM, Gao X, Dai Z & Locasale JW Methionine metabolism in health and cancer: a nexus of diet and precision medicine. Nat. Rev. Cancer 19, 625–637 (2019). PubMed

Mavrakis KJ et al. Disordered methionine metabolism in MTAP/CDKN2A-deleted cancers leads to dependence on PRMT5. Science 351, 1208–1213 (2016). PubMed

Mohammad F et al. EZH2 is a potential therapeutic target for H3K27M-mutant pediatric gliomas. Nat. Med 23, 483–492 (2017). PubMed

Borrego SL et al. Metabolic changes associated with methionine stress sensitivity in MDA-MB-468 breast cancer cells. Cancer Metab. 4, 9 (2016). PubMed PMC

Chen Z et al. Mice deficient in methylenetetrahydrofolate reductase exhibit hyperhomocysteinemia and decreased methylation capacity, with neuropathology and aortic lipid deposition. Hum. Mol. Genet 10, 433–443 (2001). PubMed

Pendleton KE et al. The U6 snRNA m(6)A methyltransferase METTL16 regulates SAM synthetase intron retention. Cell 169, 824–835 (2017). PubMed PMC

Ohnuma M et al. N1-aminopropylagmatine, a new polyamine produced as a key intermediate in polyamine biosynthesis of an extreme thermophile, Thermus thermophilus. J. Biol. Chem 280, 30073–30082 (2005). PubMed

Regenass U et al. CGP 48664, a new S-adenosylmethionine decarboxylase inhibitor with broad spectrum antiproliferative and antitumor activity. Cancer Res. 54, 3210–3217 (1994). PubMed

Orlando DA et al. Quantitative ChIP-seq normalization reveals global modulation of the epigenome. Cell Rep. 9, 1163–1170 (2014). PubMed

Andersson R et al. An atlas of active enhancers across human cell types and tissues. Nature 507, 455–461 (2014). PubMed PMC

Jessa S et al. Stalled developmental programs at the root of pediatric brain tumors. Nat. Genet 51, 1702–1713 (2019). PubMed PMC

Pathania M et al. H3.3(K27M) cooperates with Trp53 loss and PDGFRA gain in mouse embryonic neural progenitor cells to induce invasive high-grade gliomas. Cancer Cell 32, 684–700 (2017). PubMed PMC

Schnütgen F et al. A directional strategy for monitoring Cre-mediated recombination at the cellular level in the mouse. Nat. Biotechnol 21, 562–565 (2003). PubMed

Orentreich N, Matias JR, DeFelice A & Zimmerman JA Low methionine ingestion by rats extends life span. J. Nutr 123, 269–274 (1993). PubMed

Lee BC et al. Methionine restriction extends lifespan of Drosophila melanogaster under conditions of low amino-acid status. Nat. Commun 5, 3592 (2014). PubMed PMC

Ser Z et al. Targeting one carbon metabolism with an antimetabolite disrupts pyrimidine homeostasis and induces nucleotide overflow. Cell Rep. 15, 2367–2376 (2016). PubMed PMC

Schmidt JA et al. Plasma concentrations and intakes of amino acids in male meat-eaters, fish-eaters, vegetarians and vegans: a cross-sectional analysis in the EPIC-Oxford cohort. Eur. J. Clin. Nutr 70, 306–312 (2016). PubMed PMC

Hu J & Cheung NK Methionine depletion with recombinant methioninase: in vitro and in vivo efficacy against neuroblastoma and its synergism with chemotherapeutic drugs. Int. J. Cancer 124, 1700–1706 (2009). PubMed PMC

Marjon K et al. MTAP deletions in cancer create vulnerability to targeting of the MAT2A/PRMT5/RIOK1 axis. Cell Rep. 15, 574–587 (2016). PubMed

Wang Z et al. Methionine is a metabolic dependency of tumor-initiating cells. Nat. Med 25, 825–837 (2019). PubMed

Quinlan CL et al. Targeting S-adenosylmethionine biosynthesis with a novel allosteric inhibitor of Mat2A. Nat. Chem. Biol 13, 785–792 (2017). PubMed

Strekalova E et al. S-adenosylmethionine biosynthesis is a targetable metabolic vulnerability of cancer stem cells. Breast Cancer Res. Treat 175, 39–50 (2019). PubMed PMC

Mahmood N et al. Methyl donor S-adenosylmethionine (SAM) supplementation attenuates breast cancer growth, invasion, and metastasis in vivo; therapeutic and chemopreventive applications. Oncotarget 9, 5169–5183 (2018). PubMed PMC

Hashizume R et al. Pharmacologic inhibition of histone demethylation as a therapy for pediatric brainstem glioma. Nat. Med 20, 1394–1396 (2014). PubMed PMC

Bender S et al. Reduced H3K27me3 and DNA hypomethylation are major drivers of gene expression in K27M mutant pediatric high-grade gliomas. Cancer Cell 24, 660–672 (2013). PubMed

Zhang D et al. AMD1 is essential for ESC self-renewal and is translationally down-regulated on differentiation to neural precursor cells. Genes Dev. 26, 461–473 (2012). PubMed PMC

Khan A et al. Dual targeting of polyamine synthesis and uptake in diffuse intrinsic pontine gliomas. Nat. Commun 12, 971 (2021). PubMed PMC

Guiraud SP et al. High-throughput and simultaneous quantitative analysis of homocysteine-methionine cycle metabolites and co-factors in blood plasma and cerebrospinal fluid by isotope dilution LC-MS/MS. Anal. Bioanal. Chem 409, 295–305 (2017). PubMed PMC

Chantalat S et al. Histone H3 trimethylation at lysine 36 is associated with constitutive and facultative heterochromatin. Genome Res. 21, 1426–1437 (2011). PubMed PMC

Chen CT, Gottlieb DI & Cohen BA Ultraconserved elements in the Olig2 promoter. PLoS ONE 3, e3946 (2008). PubMed PMC

Grasso CS et al. Functionally defined therapeutic targets in diffuse intrinsic pontine glioma. Nat. Med 21, 555–559 (2015). PubMed PMC

Langmead B, Trapnell C, Pop M & Salzberg SL Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009). PubMed PMC

Anders S & Huber W Differential expression analysis for sequence count data. Genome Biol. 11, R106 (2010). PubMed PMC

Love MI, Huber W & Anders S Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014). PubMed PMC

Kim SY & Volsky DJ PAGE: parametric analysis of gene set enrichment. BMC Bioinf. 6, 144 (2005). PubMed PMC

Raudvere U et al. g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update). Nucleic Acids Res. 47, W191–W198 (2019). PubMed PMC

Langmead B & Salzberg SL Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012). PubMed PMC

Stovner EB & Sætrom P epic2 efficiently finds diffuse domains in ChIP-seq data. Bioinformatics 35, 4392–4393 (2019). PubMed

Zang C et al. A clustering approach for identification of enriched domains from histone modification ChIP-seq data. Bioinformatics 25, 1952–1958 (2009). PubMed PMC

Yu G, Wang LG & He QY ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization. Bioinformatics 31, 2382–2383 (2015). PubMed

Brennan CW et al. The somatic genomic landscape of glioblastoma. Cell 155, 462–477 (2013). PubMed PMC

Cerami E et al. The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov. 2, 401–404 (2012). PubMed PMC

Gao J et al. Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Science Signal. 6, pl1 (2013). PubMed PMC