Childhood Brain Tumor Biology

Pediatric brain tumors are the most common solid cancers found in children. Many of these tumors, such as Diffuse Intrinsic Pontine Gliomas (DIPGs) and Ependymomas, are driven by changes in epigenetic factors, which influence how genes are expressed without altering the DNA sequence itself.

The posterior fossa—a region that includes the cerebellum, pons, and brain stem—is the most common location in the brain for these childhood cancers. Disruptions in the epigenetic pathways that regulate development in the growing brain may play a crucial role in the biology of these tumors.

Diffuse Intrinsic Pontine Gliomas (DIPGs)

DIPGs are devastating pediatric brain tumors that carry a dismal prognosis with more than 90% of patients passing away within 1.5 years of diagnosis. 

Genomic analyses of DIPG have shown recurrent mutations in genes encoding histone H3 at position 27 where the lysine residue is replaced by methionine (K27M). The K27M mutation is found in 60-80% of DIPG patients.

Because lysine residues on histone tails are subject to post-translational modifications, our group and others have shown that the H3K27M mutation results in a global reduction in repressive H3K27me3 (above figure). We study how these H3K27M mutations cause tumors with the goal to develop new treatments for DIPG patients.

Chung et al. Integrated Metabolic and Epigenomic Reprograming by H3K27M Mutations in Diffuse Intrinsic Pontine Gliomas. Cancer Cell. 2020 Jul 30:S1535-6108(20)30369-X. doi: 10.1016/j.ccell.2020.07.008. 

Pun et al. H3K27M-mutant diffuse midline glioma with extensive intratumoral microthrombi in a young adult with COVID-19-associated coagulopathy.,Acta Neuropathol. 2020 Aug;140(2):227-229. doi: 10.1007/s00401-020-02184-0.

Pratt et al. Circumscribed/non-diffuse histology confers a better prognosis in H3K27M-mutant gliomas. Acta Neuropathol. 2018 Feb;135(2):299-301.

Venneti et al. A sensitive and specific histopathologic prognostic marker for H3F3A K27M mutant pediatric glioblastomas. Acta Neuropathol. 2014 Nov;128(5):743-53. doi: 10.1007/s00401-014-1338-3. Epub 2014 Sep 9.

Venneti et al. Evaluation of H3K27me3 and EZH2 in pediatric glial and glioneuronal tumors shows decreased H3K27me3 in H3F3A K27M mutant glioblastomas. Brain Pathol. 2013 Sep;23(5):558-64. doi: 10.1111/bpa.12042. Epub 2013 Mar 6.

Koschmann et al. Multi-focal sequencing of a diffuse intrinsic pontine glioma establishes PTEN loss as an early event npj Precision Oncology 1, Article number: 32 (2017) doi:10.1038/s41698-017-0033-y

Childhood Ependymomas

Ependymomas in children are devastating tumors that most frequently arise in the developing posterior fossa. While childhood posterior fossa ependymomas do not bear recurrent mutations, they show profound epigenetic changes in DNA methylation and global reduction in H3K27me3. Comparison of DNA methylation and genome-wide H3K27me3 enrichment from both DIPGs and childhood ependymomas patient samples show extensive overlap and point to factors that regulate neuronal stem cells called radial glia during development.

Venneti S. Integrating ependymoma molecular subgroups into clinical trials.Neuro Oncol. 2019 Oct 9;21(10):1219-1220. doi: 10.1093/neuonc/noz132.

Ellison DW et al. cIMPACT-NOW update 7: advancing the molecular classification of ependymal tumors. Brain Pathol. 2020 Jun 5. doi: 10.1111/bpa.12866.

Pratt D et al. Diffuse intrinsic pontine glioma-like tumor with EZHIP expression and molecular features of PFA ependymoma. Acta Neuropathol Commun. 2020 Mar 20;8(1):37. doi: 10.1186/s40478-020-00905-w.

Panwalkar et al., Immunohistochemical analysis of H3K27me3 demonstrates global reduction in group-A childhood posterior fossa ependymoma and is a powerful predictor of outcome. Acta Neuropathol. 2017 Jul 21. doi: 10.1007/s00401-017-1752-4.

Bayliss et al. Lowered H3K27me3 and DNA hypomethylation define poorly prognostic pediatric posterior fossa ependymomas. Science Transnational Medicine. 2016 Nov 23 Nov 2016: Vol. 8, Issue 366, pp. 366ra161.

Metabolism and Epigenetics

We study the relationship between cancer metabolism and epigenetics in brain tumors. Oncogenes in primary brain tumors in adults and children reprogram uptake and metabolism of nutrients such as glucose and glutamine to modulate many cellular functions including epigenetics. We evaluate the effects of altered metabolism on histone and DNA methylation in brain tumors, such as gliomas with isocitrate dehydrogenase (IDH) 1/2 mutations, and diffuse intrinsic pontine gliomas (DIPG) with histone H3K27M mutations.

Chung et al. Integrated Metabolic and Epigenomic Reprograming by H3K27M Mutations in Diffuse Intrinsic Pontine Gliomas. Cancer Cell. 2020 Jul 30:S1535-6108(20)30369-X. doi: 10.1016/j.ccell.2020.07.008. 

Natarajan SK and Venneti S Glutamine Metabolism in Brain Tumors. Cancers (Basel). 2019 Oct 24;11(11):1628. doi: 10.3390/cancers11111628.

Venneti S, Thompson CB. Metabolic Reprogramming in Brain Tumors. Annu Rev Pathol. 2016 Dec 21.

Wahl DR and Venneti S. 2-Hydoxyglutarate: D/Riving Pathology in gLiomaS. Brain Pathology. 2015 Nov;25(6):760-8.

Intlekofer AM, Dematteo RG, Venneti S et al. Hypoxia Induces Production of L-2-Hydroxyglutarate. Cell Metabolism. 2015 Aug 4;22(2):304-11.

Lu C, Venneti et al. Induction of sarcomas by mutant IDH2. Genes Development. 2013 Sep 15;27(18):1986-98. doi: 10.1101/gad.226753.113.

Venneti et al. Histone 3 lysine 9 trimethylation is differentially associated with IDH mutations in oligodendrogliomas and high-grade astrocytomas.J Neuropathol Exp Neurol. 2013 Apr;72(4):298-306. doi: 10.1097/NEN.0b013e3182898113.

Venneti et al. Metabolic modulation of epigenetics in gliomas.Brain Pathol. 2013 Mar;23(2):217-21. doi: 10.1111/bpa.12022.

Glutamine-based PET imaging

Positron emission tomography (PET) imaging is a means to evaluate changes in metabolism in cancer and takes advantage of increased nutrient uptake in tumor cells. The two main nutrients that cancer cells utilize are glucose and glutamine. Using radiolabeled glucose (FDG) and glutamine (FGln), we can image metabolic nutrient uptake in tumors in animal models and living patients. Above are images from a glioma patient showing tumor glutamine uptake (red arrows) compared to minimal signal in the surrounding brain enabling clear tumor delineation.

Venneti et al. Glutamine-based PET imaging facilitates enhanced metabolic evaluation of gliomas in vivo. Science Translational Medicine. 2015 Feb 11;7(274):274ra17. doi: 10.1126/scitranslmed.aaa1009.

Kim et al. Non-invasive metabolic imaging of brain tumors in the era of precision medicine. Nature Reviews Clinical Oncology.  2016 Jul 19. doi: 10.1038/nrclinonc.2016.108.

Dunphy et al. In Vivo PET Assay of Tumor Glutamine Flux and Metabolism: In-Human Trial of 18F-(2S,4R )-4-Fluoroglutamine. Radiology. 2018 Jan 31:162610. doi: 10.1148/radiol.2017162610.