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Nacev BA, Dabas Y, Paul MR, Pacheco C, Mitchener M, Perez Y, Fang Y, Soshnev AA, Barrows D, Carroll T, Socci ND, St Jean SC, Tiwari S, Gruss MJ, Monette S, Tap WD, Garcia BA, Muir T, Allis CD. Cancer-associated Histone H3 N-terminal arginine mutations disrupt PRC2 activity and impair differentiation. Nat Commun 2024; 15:5155. [PMID: 38886411 PMCID: PMC11183192 DOI: 10.1038/s41467-024-49486-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 06/06/2024] [Indexed: 06/20/2024] Open
Abstract
Dysregulated epigenetic states are a hallmark of cancer and often arise from genetic alterations in epigenetic regulators. This includes missense mutations in histones, which, together with associated DNA, form nucleosome core particles. However, the oncogenic mechanisms of most histone mutations are unknown. Here, we demonstrate that cancer-associated histone mutations at arginines in the histone H3 N-terminal tail disrupt repressive chromatin domains, alter gene regulation, and dysregulate differentiation. We find that histone H3R2C and R26C mutants reduce transcriptionally repressive H3K27me3. While H3K27me3 depletion in cells expressing these mutants is exclusively observed on the minor fraction of histone tails harboring the mutations, the same mutants recurrently disrupt broad H3K27me3 domains in the chromatin context, including near developmentally regulated promoters. H3K27me3 loss leads to de-repression of differentiation pathways, with concordant effects between H3R2 and H3R26 mutants despite different proximity to the PRC2 substrate, H3K27. Functionally, H3R26C-expressing mesenchymal progenitor cells and murine embryonic stem cell-derived teratomas demonstrate impaired differentiation. Collectively, these data show that cancer-associated H3 N-terminal arginine mutations reduce PRC2 activity and disrupt chromatin-dependent developmental functions, a cancer-relevant phenotype.
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Affiliation(s)
- Benjamin A Nacev
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA.
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA.
- UPMC Hillman Cancer Center, Pittsburgh, PA, 15213, USA.
| | - Yakshi Dabas
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, 10065, USA
| | - Matthew R Paul
- Bioinformatics Resource Center, The Rockefeller University, New York, NY, 10065, USA
| | - Christian Pacheco
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, 10065, USA
| | - Michelle Mitchener
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - Yekaterina Perez
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yan Fang
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, 10065, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Alexey A Soshnev
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, 10065, USA
- Department of Neuroscience, Developmental and Regenerative Biology, The University of Texas at San Antonio, San Antonio, TX, 78249, USA
| | - Douglas Barrows
- Bioinformatics Resource Center, The Rockefeller University, New York, NY, 10065, USA
| | - Thomas Carroll
- Bioinformatics Resource Center, The Rockefeller University, New York, NY, 10065, USA
| | - Nicholas D Socci
- Bioinformatics Core, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Samantha C St Jean
- Laboratory of Comparative Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Sagarika Tiwari
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA, 15213, USA
| | - Michael J Gruss
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA, 15213, USA
| | - Sebastien Monette
- Laboratory of Comparative Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - William D Tap
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Tom Muir
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - C David Allis
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, 10065, USA
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2
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Batsios G, Udutha S, Taglang C, Gillespie AM, Lau B, Ji S, Phoenix T, Mueller S, Venneti S, Koschmann C, Viswanath P. GABA production induced by imipridones is a targetable and imageable metabolic alteration in diffuse midline gliomas. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.07.597982. [PMID: 38915617 PMCID: PMC11195108 DOI: 10.1101/2024.06.07.597982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Diffuse midline gliomas (DMGs) are lethal primary brain tumors in children. The imipridones ONC201 and ONC206 induce mitochondrial dysfunction and have emerged as promising therapies for DMG patients. However, efficacy as monotherapy is limited, identifying a need for strategies that enhance response. Another hurdle is the lack of biomarkers that report on drug-target engagement at an early timepoint after treatment onset. Here, using 1 H-magnetic resonance spectroscopy, which is a non-invasive method of quantifying metabolite pool sizes, we show that accumulation of ψ-aminobutyric acid (GABA) is an early metabolic biomarker that can be detected within a week of ONC206 treatment, when anatomical alterations are absent, in mice bearing orthotopic xenografts. Mechanistically, imipridones activate the mitochondrial protease ClpP and upregulate the stress-responsive transcription factor ATF4. ATF4, in turn, upregulates glutamate decarboxylase, which synthesizes GABA, and downregulates ABAT , which degrades GABA, leading to GABA accumulation in DMG cells and tumors. Functionally, GABA secreted by imipridone-treated cells acts in an autocrine manner via the GABAB receptor to induce expression of superoxide dismutase (SOD1), which mitigates imipridone-induced oxidative stress and, thereby, curbs apoptosis. Importantly, blocking autocrine GABA signaling using the clinical stage GABAB receptor antagonist SGS-742 exacerbates oxidative stress and synergistically induces apoptosis in combination with imipridones in DMG cells and orthotopic tumor xenografts. Collectively, we identify GABA as a unique metabolic adaptation to imipridones that can be leveraged for non-invasive assessment of drug-target engagement and therapy. Clinical translation of our studies has the potential to enable precision metabolic therapy and imaging for DMG patients. One Sentence Summary Imipridones induce GABA accumulation in diffuse midline gliomas, an effect that can be leveraged for therapy and non-invasive imaging.
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Furst LM, Roussel EM, Leung RF, George AM, Best SA, Whittle JR, Firestein R, Faux MC, Eisenstat DD. The Landscape of Pediatric High-Grade Gliomas: The Virtues and Pitfalls of Pre-Clinical Models. BIOLOGY 2024; 13:424. [PMID: 38927304 PMCID: PMC11200883 DOI: 10.3390/biology13060424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 05/31/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024]
Abstract
Pediatric high-grade gliomas (pHGG) are malignant and usually fatal central nervous system (CNS) WHO Grade 4 tumors. The majority of pHGG consist of diffuse midline gliomas (DMG), H3.3 or H3.1 K27 altered, or diffuse hemispheric gliomas (DHG) (H3.3 G34-mutant). Due to diffuse tumor infiltration of eloquent brain areas, especially for DMG, surgery has often been limited and chemotherapy has not been effective, leaving fractionated radiation to the involved field as the current standard of care. pHGG has only been classified as molecularly distinct from adult HGG since 2012 through Next-Generation sequencing approaches, which have shown pHGG to be epigenetically regulated and specific tumor sub-types to be representative of dysregulated differentiating cells. To translate discovery research into novel therapies, improved pre-clinical models that more adequately represent the tumor biology of pHGG are required. This review will summarize the molecular characteristics of different pHGG sub-types, with a specific focus on histone K27M mutations and the dysregulated gene expression profiles arising from these mutations. Current and emerging pre-clinical models for pHGG will be discussed, including commonly used patient-derived cell lines and in vivo modeling techniques, encompassing patient-derived xenograft murine models and genetically engineered mouse models (GEMMs). Lastly, emerging techniques to model CNS tumors within a human brain environment using brain organoids through co-culture will be explored. As models that more reliably represent pHGG continue to be developed, targetable biological and genetic vulnerabilities in the disease will be more rapidly identified, leading to better treatments and improved clinical outcomes.
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Affiliation(s)
- Liam M. Furst
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3052, Australia; (L.M.F.); (E.M.R.); (R.F.L.); (M.C.F.)
- Stem Cell Medicine, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia;
| | - Enola M. Roussel
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3052, Australia; (L.M.F.); (E.M.R.); (R.F.L.); (M.C.F.)
- Stem Cell Medicine, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia;
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia;
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
| | - Ryan F. Leung
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3052, Australia; (L.M.F.); (E.M.R.); (R.F.L.); (M.C.F.)
- Stem Cell Medicine, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia;
| | - Ankita M. George
- Stem Cell Medicine, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia;
| | - Sarah A. Best
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3010, Australia;
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - James R. Whittle
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia;
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3010, Australia;
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Ron Firestein
- Department of Molecular and Translational Science, Monash University, Clayton, VIC 3168, Australia;
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia
| | - Maree C. Faux
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3052, Australia; (L.M.F.); (E.M.R.); (R.F.L.); (M.C.F.)
- Stem Cell Medicine, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia;
- Department of Surgery, University of Melbourne, Parkville, VIC 3010, Australia
| | - David D. Eisenstat
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3052, Australia; (L.M.F.); (E.M.R.); (R.F.L.); (M.C.F.)
- Stem Cell Medicine, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia;
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia
- Children’s Cancer Centre, The Royal Children’s Hospital Melbourne, 50 Flemington Road, Parkville, VIC 3052, Australia
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Weisbrod LJ, Thiraviyam A, Vengoji R, Shonka N, Jain M, Ho W, Batra SK, Salehi A. Diffuse intrinsic pontine glioma (DIPG): A review of current and emerging treatment strategies. Cancer Lett 2024; 590:216876. [PMID: 38609002 PMCID: PMC11231989 DOI: 10.1016/j.canlet.2024.216876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 04/14/2024]
Abstract
Diffuse intrinsic pontine glioma (DIPG) is a childhood malignancy of the brainstem with a dismal prognosis. Despite recent advances in its understanding at the molecular level, the prognosis of DIPG has remained unchanged. This article aims to review the current understanding of the genetic pathophysiology of DIPG and to highlight promising therapeutic targets. Various DIPG treatment strategies have been investigated in pre-clinical studies, several of which have shown promise and have been subsequently translated into ongoing clinical trials. Ultimately, a multifaceted therapeutic approach that targets cell-intrinsic alterations, the micro-environment, and augments the immune system will likely be necessary to eradicate DIPG.
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Affiliation(s)
- Luke J Weisbrod
- Department of Neurosurgery, University of Nebraska Medical Center, Omaha, NE, 68198-5870, USA
| | - Anand Thiraviyam
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68198-5870, USA
| | - Raghupathy Vengoji
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68198-5870, USA
| | - Nicole Shonka
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198-5870, USA; Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, 68198-5870, USA
| | - Maneesh Jain
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68198-5870, USA; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198-5870, USA; Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, 68198-5870, USA
| | - Winson Ho
- Department of Neurosurgery, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Surinder K Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68198-5870, USA; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198-5870, USA; Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, 68198-5870, USA
| | - Afshin Salehi
- Department of Neurosurgery, University of Nebraska Medical Center, Omaha, NE, 68198-5870, USA; Division of Pediatric Neurosurgery, Children's Nebraska, Omaha, NE, 68114, USA.
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5
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Saratsis AM, Knowles T, Petrovic A, Nazarian J. H3K27M mutant glioma: Disease definition and biological underpinnings. Neuro Oncol 2024; 26:S92-S100. [PMID: 37818718 PMCID: PMC11066930 DOI: 10.1093/neuonc/noad164] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Indexed: 10/12/2023] Open
Abstract
High-grade glioma (HGG) is the most common cause of cancer death in children and the most common primary central nervous system tumor in adults. While pediatric HGG was once thought to be biologically similar to the adult form of disease, research has shown these malignancies to be significantly molecularly distinct, necessitating distinct approaches to their clinical management. However, emerging data have shown shared molecular events in pediatric and adult HGG including the histone H3K27M mutation. This somatic missense mutation occurs in genes encoding one of two isoforms of the Histone H3 protein, H3F3A (H3.3), or HIST1H3B (H3.1), and is detected in up to 80% of pediatric diffuse midline gliomas and in up to 60% of adult diffuse gliomas. Importantly, the H3K27M mutation is associated with poorer overall survival and response to therapy compared to patients with H3 wild-type tumors. Here, we review the clinical features and biological underpinnings of pediatric and adult H3K27M mutant glioma, offering a groundwork for understanding current research and clinical approaches for the care of patients suffering with this challenging disease.
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Affiliation(s)
| | | | - Antonela Petrovic
- DMG Research Center, Department of Oncology, University Children’s Hospital, University of Zürich, Zürich, Switzerland
| | - Javad Nazarian
- Research Center for Genetic Medicine, Children’s National Health System, Washington, District of Columbia, USA
- Brain Tumor Institute, Children’s National Health System, Washington, District of Columbia, USA
- DMG Research Center, Department of Pediatrics, University Children’s Hospital, University of Zurich, Zürich, Switzerland
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6
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Mueller S, Kline C, Franson A, van der Lugt J, Prados M, Waszak SM, Plasschaert SLA, Molinaro AM, Koschmann C, Nazarian J. Rational combination platform trial design for children and young adults with diffuse midline glioma: A report from PNOC. Neuro Oncol 2024; 26:S125-S135. [PMID: 38124481 PMCID: PMC11066905 DOI: 10.1093/neuonc/noad181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Indexed: 12/23/2023] Open
Abstract
Background Diffuse midline glioma (DMG) is a devastating pediatric brain tumor unresponsive to hundreds of clinical trials. Approximately 80% of DMGs harbor H3K27M oncohistones, which reprogram the epigenome to increase the metabolic profile of the tumor cells. Methods We have previously shown preclinical efficacy of targeting both oxidative phosphorylation and glycolysis through treatment with ONC201, which activates the mitochondrial protease ClpP, and paxalisib, which inhibits PI3K/mTOR, respectively. Results ONC201 and paxalisib combination treatment aimed at inducing metabolic distress led to the design of the first DMG-specific platform trial PNOC022 (NCT05009992). Conclusions Here, we expand on the PNOC022 rationale and discuss various considerations, including liquid biome, microbiome, and genomic biomarkers, quality-of-life endpoints, and novel imaging modalities, such that we offer direction on future clinical trials in DMG.
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Affiliation(s)
- Sabine Mueller
- Department of Neurology, Neurosurgery and Pediatrics, University of California, San Francisco, California, USA
| | - Cassie Kline
- Division of Oncology, Department of Pediatrics, Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Andrea Franson
- Department of Pediatrics, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Michael Prados
- Department of Neurosurgery and Pediatrics, University of California, San Francisco, San Francisco, California, USA
| | - Sebastian M Waszak
- Department of Neurology, University of California, San Francisco, San Francisco, California, USA
- Laboratory of Computational Neuro-Oncology, Swiss Institute for Experimental Cancer Research, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | | | - Annette M Molinaro
- Division of Biomedical Statistics and Informatics, Department of Neurosurgery, University of California, San Francisco, San Francisco, California, USA
| | - Carl Koschmann
- Department of Pediatrics, University of Michigan, Ann Arbor, Michigan, USA
| | - Javad Nazarian
- Research Center for Genetic Medicine, Children’s National Health System, Washington, District of Columbia, USA
- Brain Tumor Institute, Children’s National Health System, Washington, District of Columbia, USA
- DMG Research Center, Department of Pediatrics, University Children’s Hospital, University of Zurich, Zürich, Switzerland
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7
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Romero P, Richart L, Aflaki S, Petitalot A, Burton M, Michaud A, Masliah-Planchon J, Kuhnowski F, Le Cam S, Baliñas-Gavira C, Méaudre C, Luscan A, Hamza A, Legoix P, Vincent-Salomon A, Wassef M, Holoch D, Margueron R. EZH2 mutations in follicular lymphoma distort H3K27me3 profiles and alter transcriptional responses to PRC2 inhibition. Nat Commun 2024; 15:3452. [PMID: 38658543 PMCID: PMC11043461 DOI: 10.1038/s41467-024-47701-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 04/08/2024] [Indexed: 04/26/2024] Open
Abstract
Mutations in chromatin regulators are widespread in cancer. Among them, the histone H3 lysine 27 methyltransferase Polycomb Repressive Complex 2 (PRC2) shows distinct alterations according to tumor type. This specificity is poorly understood. Here, we model several PRC2 alterations in one isogenic system to reveal their comparative effects. Focusing then on lymphoma-associated EZH2 mutations, we show that Ezh2Y641F induces aberrant H3K27 methylation patterns even without wild-type Ezh2, which are alleviated by partial PRC2 inhibition. Remarkably, Ezh2Y641F rewires the response to PRC2 inhibition, leading to induction of antigen presentation genes. Using a unique longitudinal follicular lymphoma cohort, we further link EZH2 status to abnormal H3K27 methylation. We also uncover unexpected variability in the mutational landscape of successive biopsies, pointing to frequent co-existence of different clones and cautioning against stratifying patients based on single sampling. Our results clarify how oncogenic PRC2 mutations disrupt chromatin and transcription, and the therapeutic vulnerabilities this creates.
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Affiliation(s)
- Pierre Romero
- Institut Curie, INSERM U934/CNRS UMR 3215, Paris Sciences et Lettres Research University, Sorbonne University, Paris, France
- Institut Curie, Department of Pathology, Paris Sciences et Lettres Research University, Paris, France
| | - Laia Richart
- Institut Curie, INSERM U934/CNRS UMR 3215, Paris Sciences et Lettres Research University, Sorbonne University, Paris, France
| | - Setareh Aflaki
- Institut Curie, INSERM U934/CNRS UMR 3215, Paris Sciences et Lettres Research University, Sorbonne University, Paris, France
| | - Ambre Petitalot
- Institut Curie, INSERM U934/CNRS UMR 3215, Paris Sciences et Lettres Research University, Sorbonne University, Paris, France
| | - Megan Burton
- Institut Curie, INSERM U934/CNRS UMR 3215, Paris Sciences et Lettres Research University, Sorbonne University, Paris, France
| | - Audrey Michaud
- Institut Curie, INSERM U934/CNRS UMR 3215, Paris Sciences et Lettres Research University, Sorbonne University, Paris, France
| | - Julien Masliah-Planchon
- Institut Curie, Pharmacogenetics Unit, Department of Genetics, Paris Sciences et Lettres Research University, Paris, France
| | - Frédérique Kuhnowski
- Institut Curie, Department of Clinical Hematology, Paris Sciences et Lettres Research University, Paris, France
| | - Samuel Le Cam
- Institut Curie, INSERM U934/CNRS UMR 3215, Paris Sciences et Lettres Research University, Sorbonne University, Paris, France
| | - Carlos Baliñas-Gavira
- Institut Curie, INSERM U934/CNRS UMR 3215, Paris Sciences et Lettres Research University, Sorbonne University, Paris, France
| | - Céline Méaudre
- Institut Curie, Department of Pathology, Paris Sciences et Lettres Research University, Paris, France
| | - Armelle Luscan
- Institut Curie, INSERM U934/CNRS UMR 3215, Paris Sciences et Lettres Research University, Sorbonne University, Paris, France
| | - Abderaouf Hamza
- Institut Curie, Pharmacogenetics Unit, Department of Genetics, Paris Sciences et Lettres Research University, Paris, France
| | - Patricia Legoix
- Institut Curie, Genomics of Excellence (ICGex) Platform, Paris Sciences et Lettres Research University, Paris, France
| | - Anne Vincent-Salomon
- Institut Curie, Department of Pathology, Paris Sciences et Lettres Research University, Paris, France
| | - Michel Wassef
- Institut Curie, INSERM U934/CNRS UMR 3215, Paris Sciences et Lettres Research University, Sorbonne University, Paris, France
| | - Daniel Holoch
- Institut Curie, INSERM U934/CNRS UMR 3215, Paris Sciences et Lettres Research University, Sorbonne University, Paris, France.
| | - Raphaël Margueron
- Institut Curie, INSERM U934/CNRS UMR 3215, Paris Sciences et Lettres Research University, Sorbonne University, Paris, France.
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8
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Peterson ER, Sajjakulnukit P, Scott AJ, Heaslip C, Andren A, Wilder-Romans K, Zhou W, Palavalasa S, Korimerla N, Lin A, O'Brien A, Kothari A, Zhao Z, Zhang L, Morgan MA, Venneti S, Koschmann C, Jabado N, Lyssiotis CA, Castro MG, Wahl DR. Purine salvage promotes treatment resistance in H3K27M-mutant diffuse midline glioma. Cancer Metab 2024; 12:11. [PMID: 38594734 PMCID: PMC11003124 DOI: 10.1186/s40170-024-00341-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 03/21/2024] [Indexed: 04/11/2024] Open
Abstract
BACKGROUND Diffuse midline gliomas (DMG), including diffuse intrinsic pontine gliomas (DIPGs), are a fatal form of brain cancer. These tumors often carry a driver mutation on histone H3 converting lysine 27 to methionine (H3K27M). DMG-H3K27M are characterized by altered metabolism and resistance to standard of care radiation (RT) but how the H3K27M mediates the metabolic response to radiation and consequent treatment resistance is uncertain. METHODS We performed metabolomics on irradiated and untreated H3K27M isogenic DMG cell lines and observed an H3K27M-specific enrichment for purine synthesis pathways. We profiled the expression of purine synthesis enzymes in publicly available patient data and our models, quantified purine synthesis using stable isotope tracing, and characterized the in vitro and in vivo response to de novo and salvage purine synthesis inhibition in combination with RT. RESULTS DMG-H3K27M cells activate purine metabolism in an H3K27M-specific fashion. In the absence of genotoxic treatment, H3K27M-expressing cells have higher relative activity of de novo synthesis and apparent lower activity of purine salvage demonstrated via stable isotope tracing of key metabolites in purine synthesis and by lower expression of hypoxanthine-guanine phosphoribosyltransferase (HGPRT), the rate-limiting enzyme of purine salvage into IMP and GMP. Inhibition of de novo guanylate synthesis radiosensitized DMG-H3K27M cells in vitro and in vivo. Irradiated H3K27M cells upregulated HGPRT expression and hypoxanthine-derived guanylate salvage but maintained high levels of guanine-derived salvage. Exogenous guanine supplementation decreased radiosensitization in cells treated with combination RT and de novo purine synthesis inhibition. Silencing HGPRT combined with RT markedly suppressed DMG-H3K27M tumor growth in vivo. CONCLUSIONS Our results indicate that DMG-H3K27M cells rely on highly active purine synthesis, both from the de novo and salvage synthesis pathways. However, highly active salvage of free purine bases into mature guanylates can bypass inhibition of the de novo synthetic pathway. We conclude that inhibiting purine salvage may be a promising strategy to overcome treatment resistance in DMG-H3K27M tumors.
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Affiliation(s)
- Erik R Peterson
- Doctoral Program in Cancer Biology, University of Michigan, Ann Arbor, MI, USA
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Peter Sajjakulnukit
- Doctoral Program in Cancer Biology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Andrew J Scott
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Caleb Heaslip
- Massachusetts College of Pharmacy and Health Sciences, Boston, MA, USA
| | - Anthony Andren
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Kari Wilder-Romans
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Weihua Zhou
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Sravya Palavalasa
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Navyateja Korimerla
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Angelica Lin
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Alexandra O'Brien
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Ayesha Kothari
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Zitong Zhao
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Li Zhang
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Meredith A Morgan
- Doctoral Program in Cancer Biology, University of Michigan, Ann Arbor, MI, USA
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Sriram Venneti
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
- Department of Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Carl Koschmann
- Doctoral Program in Cancer Biology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
| | - Nada Jabado
- Department of Pediatrics, McGill University, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Costas A Lyssiotis
- Doctoral Program in Cancer Biology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Maria G Castro
- Doctoral Program in Cancer Biology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
- Department of Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI, USA
- Department of Neurosurgery, University of Michigan, Ann Arbor, MI, USA
| | - Daniel R Wahl
- Doctoral Program in Cancer Biology, University of Michigan, Ann Arbor, MI, USA.
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA.
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.
- Medical Science Unit I, 1301 Catherine Street, Rm 4433, Ann Arbor, MI, 48109, USA.
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9
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Tibben BM, Rothbart SB. Mechanisms of DNA Methylation Regulatory Function and Crosstalk with Histone Lysine Methylation. J Mol Biol 2024; 436:168394. [PMID: 38092287 PMCID: PMC10957332 DOI: 10.1016/j.jmb.2023.168394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/06/2023] [Accepted: 12/06/2023] [Indexed: 12/20/2023]
Abstract
DNA methylation is a well-studied epigenetic modification that has key roles in regulating gene expression, maintaining genome integrity, and determining cell fate. Precisely how DNA methylation patterns are established and maintained in specific cell types at key developmental stages is still being elucidated. However, research over the last two decades has contributed to our understanding of DNA methylation regulation by other epigenetic processes. Specifically, lysine methylation on key residues of histone proteins has been shown to contribute to the allosteric regulation of DNA methyltransferase (DNMT) activities. In this review, we discuss the dynamic interplay between DNA methylation and histone lysine methylation as epigenetic regulators of genome function by synthesizing key recent studies in the field. With a focus on DNMT3 enzymes, we discuss mechanisms of DNA methylation and histone lysine methylation crosstalk in the regulation of gene expression and the maintenance of genome integrity. Further, we discuss how alterations to the balance of various sites of histone lysine methylation and DNA methylation contribute to human developmental disorders and cancers. Finally, we provide perspectives on the current direction of the field and highlight areas for continued research and development.
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Affiliation(s)
- Bailey M Tibben
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Scott B Rothbart
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA.
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10
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Sun Y, Sun J, Ying K, Chen J, Chen T, Tao L, Bian W, Qiu L. EP300 regulates the SLC16A1-AS1-AS1/TCF3 axis to promote lung cancer malignancies through the Wnt signaling pathway. Heliyon 2024; 10:e27727. [PMID: 38515708 PMCID: PMC10955305 DOI: 10.1016/j.heliyon.2024.e27727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 03/03/2024] [Accepted: 03/06/2024] [Indexed: 03/23/2024] Open
Abstract
Objective To investigate the regulatory mechanism of EP300 in the interaction between SLC16A1-AS1 and TCF3 to activate the Wnt pathway, thereby promoting malignant progression in lung cancer. Methods In lung cancer cell lines, SLC16A1-AS1 was knocked down, and the impact of this knockdown on the malignant progression of lung cancer cells was assessed through clonogenic assays, Transwell assays, and apoptosis experiments. The regulatory relationship between EP300 and SLC16A1-AS1 was investigated through bioinformatic analysis and ChIP experiments. The expression of SLC16A1-AS1 and TCF3 in 56 paired lung cancer tissues was examined using RT-qPCR, and their correlation was analyzed. The interaction between TCF3 and SLC16A1-AS1 was explored through bioinformatic analysis and CoIP experiments. Activation of the Wnt/β-catenin pathway was assessed by detecting the accumulation of β-catenin in the nucleus through Western blotting. The role of EP300 in regulating the effect of SLC16A1-AS1/TCF3-mediated Wnt/β-catenin signaling on lung cancer malignant progression was validated through in vitro and in vivo experiments. Results SLC16A1-AS1 is highly expressed in lung cancer and regulates its malignant progression. EP300 mediates histone modifications on the SLC16A1-AS1 promoter, thus controlling its expression. SLC16A1-AS1 exhibits specific interactions with TCF3, and the SLC16A1-AS1/TCF3 complex activates the Wnt/β-catenin pathway. EP300 plays a critical role in regulating the impact of SLC16A1-AS1/TCF3-mediated Wnt/β-catenin signaling on lung cancer malignant progression. Conclusion EP300 regulates the SLC16A1-AS1/TCF3-mediated Wnt/β-catenin signaling pathway, influencing the malignant progression of lung cancer.
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Affiliation(s)
- Yunhao Sun
- Department of Thoracic Surgery, The First People's Hospital of Yancheng City, The Yancheng Clinical College of Xuzhou Medical University, Yancheng, Jiangsu, 224005, PR China
| | - Jian Sun
- Department of Thoracic Surgery, The First People's Hospital of Yancheng City, The Yancheng Clinical College of Xuzhou Medical University, Yancheng, Jiangsu, 224005, PR China
| | - Kaijun Ying
- Department of Thoracic Surgery, The First People's Hospital of Yancheng City, The Yancheng Clinical College of Xuzhou Medical University, Yancheng, Jiangsu, 224005, PR China
| | - Jinjin Chen
- Oncology Department, The First People's Hospital of Yancheng City, The Yancheng Clinical College of Xuzhou Medical University, Yancheng, Jiangsu, 224005, PR China
| | - Tingting Chen
- Department of Emergency, The First People's Hospital of Yancheng City, The Yancheng Clinical College of Xuzhou Medical University, Yancheng, Jiangsu, 224005, PR China
| | - Leilei Tao
- Oncology Department, The First People's Hospital of Yancheng City, The Yancheng Clinical College of Xuzhou Medical University, Yancheng, Jiangsu, 224005, PR China
| | - Weigang Bian
- Oncology Department, The First People's Hospital of Yancheng City, The Yancheng Clinical College of Xuzhou Medical University, Yancheng, Jiangsu, 224005, PR China
| | - Limin Qiu
- Department of Thoracic Surgery, The First People's Hospital of Yancheng City, The Yancheng Clinical College of Xuzhou Medical University, Yancheng, Jiangsu, 224005, PR China
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11
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Kim H, Lebeau B, Papadopoli D, Jovanovic P, Russo M, Avizonis D, Morita M, Afzali F, Ursini-Siegel J, Postovit LM, Witcher M, Topisirovic I. MTOR modulation induces selective perturbations in histone methylation which influence the anti-proliferative effects of mTOR inhibitors. iScience 2024; 27:109188. [PMID: 38433910 PMCID: PMC10904987 DOI: 10.1016/j.isci.2024.109188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 01/11/2024] [Accepted: 02/06/2024] [Indexed: 03/05/2024] Open
Abstract
Emerging data suggest a significant cross-talk between metabolic and epigenetic programs. However, the relationship between the mechanistic target of rapamycin (mTOR), which is a pivotal metabolic regulator, and epigenetic modifications remains poorly understood. Our results show that mTORC1 activation caused by the abrogation of its negative regulator tuberous sclerosis complex 2 (TSC2) coincides with increased levels of the histone modification H3K27me3 but not H3K4me3 or H3K9me3. This selective H3K27me3 induction was mediated via 4E-BP-dependent increase in EZH2 protein levels. Surprisingly, mTOR inhibition also selectively induced H3K27me3. This was independent of TSC2, and was paralleled by reduced EZH2 and increased EZH1 protein levels. Notably, the ability of mTOR inhibitors to induce H3K27me3 levels was positively correlated with their anti-proliferative effects. Collectively, our findings demonstrate that both activation and inhibition of mTOR selectively increase H3K27me3 by distinct mechanisms, whereby the induction of H3K27me3 may potentiate the anti-proliferative effects of mTOR inhibitors.
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Affiliation(s)
- HaEun Kim
- Department of Experimental Medicine, McGill University, Montreal, QC H3A 0G4, Canada
- Lady Davis Institute, SMBD JGH, McGill University, Montreal, QC H3T 1E2, Canada
| | - Benjamin Lebeau
- Department of Experimental Medicine, McGill University, Montreal, QC H3A 0G4, Canada
- Lady Davis Institute, SMBD JGH, McGill University, Montreal, QC H3T 1E2, Canada
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - David Papadopoli
- Lady Davis Institute, SMBD JGH, McGill University, Montreal, QC H3T 1E2, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H3A 0G4, Canada
| | - Predrag Jovanovic
- Department of Experimental Medicine, McGill University, Montreal, QC H3A 0G4, Canada
- Lady Davis Institute, SMBD JGH, McGill University, Montreal, QC H3T 1E2, Canada
| | - Mariana Russo
- Goodman Cancer Research Centre, Montréal, QC H3A 1A3, Canada
| | - Daina Avizonis
- Goodman Cancer Research Centre, Montréal, QC H3A 1A3, Canada
| | - Masahiro Morita
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Farzaneh Afzali
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON K7L 3N6, Canada
| | - Josie Ursini-Siegel
- Department of Experimental Medicine, McGill University, Montreal, QC H3A 0G4, Canada
- Lady Davis Institute, SMBD JGH, McGill University, Montreal, QC H3T 1E2, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H3A 0G4, Canada
- Department of Biochemistry, McGill University, Montreal, QC H3A 0G4, Canada
| | - Lynne-Marie Postovit
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON K7L 3N6, Canada
| | - Michael Witcher
- Department of Experimental Medicine, McGill University, Montreal, QC H3A 0G4, Canada
- Lady Davis Institute, SMBD JGH, McGill University, Montreal, QC H3T 1E2, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H3A 0G4, Canada
| | - Ivan Topisirovic
- Department of Experimental Medicine, McGill University, Montreal, QC H3A 0G4, Canada
- Lady Davis Institute, SMBD JGH, McGill University, Montreal, QC H3T 1E2, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H3A 0G4, Canada
- Department of Biochemistry, McGill University, Montreal, QC H3A 0G4, Canada
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12
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Fernando D, Ahmed AU, Williams BRG. Therapeutically targeting the unique disease landscape of pediatric high-grade gliomas. Front Oncol 2024; 14:1347694. [PMID: 38525424 PMCID: PMC10957575 DOI: 10.3389/fonc.2024.1347694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/19/2024] [Indexed: 03/26/2024] Open
Abstract
Pediatric high-grade gliomas (pHGG) are a rare yet devastating malignancy of the central nervous system's glial support cells, affecting children, adolescents, and young adults. Tumors of the central nervous system account for the leading cause of pediatric mortality of which high-grade gliomas present a significantly grim prognosis. While the past few decades have seen many pediatric cancers experiencing significant improvements in overall survival, the prospect of survival for patients diagnosed with pHGGs has conversely remained unchanged. This can be attributed in part to tumor heterogeneity and the existence of the blood-brain barrier. Advances in discovery research have substantiated the existence of unique subgroups of pHGGs displaying alternate responses to different therapeutics and varying degrees of overall survival. This highlights a necessity to approach discovery research and clinical management of the disease in an alternative subtype-dependent manner. This review covers traditional approaches to the therapeutic management of pHGGs, limitations of such methods and emerging alternatives. Novel mutations which predominate the pHGG landscape are highlighted and the therapeutic potential of targeting them in a subtype specific manner discussed. Collectively, this provides an insight into issues in need of transformative progress which arise during the management of pHGGs.
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Affiliation(s)
- Dasun Fernando
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC, Australia
- Department of Molecular and Translational Sciences, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
| | - Afsar U. Ahmed
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC, Australia
- Department of Molecular and Translational Sciences, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
| | - Bryan R. G. Williams
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC, Australia
- Department of Molecular and Translational Sciences, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
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13
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Hosseini A, Lindholm HT, Chen R, Mehdipour P, Marhon SA, Ishak CA, Moore PC, Classon M, Di Gioacchino A, Greenbaum B, De Carvalho DD. Retroelement decay by the exonuclease XRN1 is a viral mimicry dependency in cancer. Cell Rep 2024; 43:113684. [PMID: 38261511 DOI: 10.1016/j.celrep.2024.113684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 10/31/2023] [Accepted: 01/03/2024] [Indexed: 01/25/2024] Open
Abstract
Viral mimicry describes the immune response induced by endogenous stimuli such as double-stranded RNA (dsRNA) from endogenous retroelements. Activation of viral mimicry has the potential to kill cancer cells or augment anti-tumor immune responses. Here, we systematically identify mechanisms of viral mimicry adaptation associated with cancer cell dependencies. Among the top hits is the RNA decay protein XRN1 as an essential gene for the survival of a subset of cancer cell lines. XRN1 dependency is mediated by mitochondrial antiviral signaling protein and protein kinase R activation and is associated with higher levels of cytosolic dsRNA, higher levels of a subset of Alus capable of forming dsRNA, and higher interferon-stimulated gene expression, indicating that cells die due to induction of viral mimicry. Furthermore, dsRNA-inducing drugs such as 5-aza-2'-deoxycytidine and palbociclib can generate a synthetic dependency on XRN1 in cells initially resistant to XRN1 knockout. These results indicate that XRN1 is a promising target for future cancer therapeutics.
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Affiliation(s)
- Amir Hosseini
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Håvard T Lindholm
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Pathology, Oslo University Hospital-Rikshospitalet, 0372 Oslo, Norway
| | - Raymond Chen
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Parinaz Mehdipour
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Sajid A Marhon
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Charles A Ishak
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Paul C Moore
- Pfizer Centers for Therapeutic Innovation, South San Francisco, CA 94080, USA
| | - Marie Classon
- Pfizer Centers for Therapeutic Innovation, South San Francisco, CA 94080, USA
| | - Andrea Di Gioacchino
- Laboratoire de Physique de l'Ecole Normale Supérieure, PSL & CNRS UMR8063, Sorbonne Université, Université de Paris, Paris, France
| | - Benjamin Greenbaum
- Physiology, Biophysics & Systems Biology, Weill Cornell Medicine, Weill Cornell Medical College, New York, NY 10065, USA; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Daniel D De Carvalho
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada.
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14
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Leszczynska KB, Freitas-Huhtamäki A, Jayaprakash C, Dzwigonska M, Vitorino FNL, Horth C, Wojnicki K, Gielniewski B, Szadkowska P, Kaza B, Nazarian J, Ciolkowski MK, Trubicka J, Grajkowska W, Garcia BA, Majewski J, Kaminska B, Mieczkowski J. H2A.Z histone variants facilitate HDACi-dependent removal of H3.3K27M mutant protein in pediatric high-grade glioma cells. Cell Rep 2024; 43:113707. [PMID: 38306270 PMCID: PMC11026119 DOI: 10.1016/j.celrep.2024.113707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 10/22/2023] [Accepted: 01/11/2024] [Indexed: 02/04/2024] Open
Abstract
Diffuse intrinsic pontine gliomas (DIPGs) are deadly pediatric brain tumors, non-resectable due to brainstem localization and diffusive growth. Over 80% of DIPGs harbor a mutation in histone 3 (H3.3 or H3.1) resulting in a lysine-to-methionine substitution (H3K27M). Patients with DIPG have a dismal prognosis with no effective therapy. We show that histone deacetylase (HDAC) inhibitors lead to a significant reduction in the H3.3K27M protein (up to 80%) in multiple glioma cell lines. We discover that the SB939-mediated H3.3K27M loss is partially blocked by a lysosomal inhibitor, chloroquine. The H3.3K27M loss is facilitated by co-occurrence of H2A.Z, as evidenced by the knockdown of H2A.Z isoforms. Chromatin immunoprecipitation sequencing (ChIP-seq) analysis confirms the occupancy of H3.3K27M and H2A.Z at the same SB939-inducible genes. We discover a mechanism showing that HDAC inhibition in DIPG leads to pharmacological modulation of the oncogenic H3.3K27M protein levels. These findings show the possibility of directly targeting the H3.3K27M oncohistone.
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Affiliation(s)
- Katarzyna B Leszczynska
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland.
| | | | - Chinchu Jayaprakash
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Monika Dzwigonska
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Francisca N L Vitorino
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Cynthia Horth
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Kamil Wojnicki
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Bartlomiej Gielniewski
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Paulina Szadkowska
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Beata Kaza
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Javad Nazarian
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, USA; Department of Pediatrics, University Children's Hospital Zürich, Zürich, Switzerland
| | | | | | | | - Benjamin A Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Jacek Majewski
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Bozena Kaminska
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Jakub Mieczkowski
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland; 3P-Medicine Laboratory, Medical University of Gdansk, Gdansk, Poland.
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15
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Verma A, Chi YY, Malvar J, Lamble A, Chaudhury S, Agarwal A, Li HT, Liang G, Leong R, Brown PA, Kaplan J, Schafer ES, Slone T, Pauly M, Chang BH, Stieglitz E, Wayne AS, Hijiya N, Bhojwani D. Nivolumab Plus 5-Azacitidine in Pediatric Relapsed/Refractory Acute Myeloid Leukemia (AML): Phase I/II Trial Results from the Therapeutic Advances in Childhood Leukemia and Lymphoma (TACL) Consortium. Cancers (Basel) 2024; 16:496. [PMID: 38339248 PMCID: PMC10854518 DOI: 10.3390/cancers16030496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/11/2024] [Accepted: 01/19/2024] [Indexed: 02/12/2024] Open
Abstract
Improvements in survival have been made over the past two decades for childhood acute myeloid leukemia (AML), but the approximately 40% of patients who relapse continue to have poor outcomes. A combination of checkpoint-inhibitor nivolumab and azacitidine has demonstrated improvements in median survival in adults with AML. This phase I/II study with nivolumab and azacitidine in children with relapsed/refractory AML (NCT03825367) was conducted through the Therapeutic Advances in Childhood Leukemia & Lymphoma consortium. Thirteen patients, median age 13.7 years, were enrolled. Patients had refractory disease with multiple reinduction attempts. Twelve evaluable patients were treated at the recommended phase II dose (established at dose level 1, 3 mg/kg/dose). Four patients (33%) maintained stable disease. This combination was well tolerated, with no dose-limiting toxicities observed. Grade 3-4 adverse events (AEs) were primarily hematological. Febrile neutropenia was the most common AE ≥ grade 3. A trend to improved quality of life was noted. Increases in CD8+ T cells and reductions in CD4+/CD8+ T cells and demethylation were observed. The combination was well tolerated and had an acceptable safety profile in pediatric patients with relapsed/refractory AML. Future studies might explore this combination for the maintenance of remission in children with AML at high risk of relapse.
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Affiliation(s)
- Anupam Verma
- Center for Cancer and Blood Disorders, Pediatric Hematology Oncology Branch, Children’s National Hospital, Washington, DC 20010, USA
- Division of Pediatric Hematology Oncology, Primary Children’s Hospital, University of Utah, Salt Lake City, UT 84113, USA
| | - Yueh-Yun Chi
- Division of Hematology-Oncology, Cancer and Blood Disease Institute, Children’s Hospital Los Angeles, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90027, USA; (Y.-Y.C.); (A.S.W.); (D.B.)
| | - Jemily Malvar
- Division of Hematology-Oncology, Cancer and Blood Disease Institute, Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA; (J.M.)
| | - Adam Lamble
- Department of Pediatric Hematology Oncology, Seattle Children’s Hospital, Seattle, WA 98105, USA;
| | - Sonali Chaudhury
- Department of Pediatric Hematology Oncology, Ann and Robert Lurie Children’s Hospital of Chicago, Chicago, IL 60611, USA;
| | - Archana Agarwal
- Department of Pathology, University of Utah and ARUP Laboratories, Salt Lake City, UT 84108, USA;
| | - Hong-Tao Li
- Department of Urology, University of Southern California, Los Angeles, CA 90033, USA; (H.-T.L.); (G.L.)
| | - Gangning Liang
- Department of Urology, University of Southern California, Los Angeles, CA 90033, USA; (H.-T.L.); (G.L.)
| | - Roy Leong
- Division of Hematology-Oncology, Cancer and Blood Disease Institute, Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA; (J.M.)
| | | | - Joel Kaplan
- Department of Pediatric Hematology Oncology, Atrium Health Levine Children’s Hospital, Wake Forrest University, Charlotte, NC 28203, USA;
| | - Eric S. Schafer
- Division of Pediatric Hematology/Oncology, Baylor College of Medicine, Texas Children’s Cancer and Hematology Center, Houston, TX 77030, USA;
| | - Tamra Slone
- Department of Pediatric Hematology Oncology, UT Southwestern, Dallas, TX 75235, USA;
| | - Melinda Pauly
- Department of Pediatric Hematology Oncology, Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA;
| | - Bill H. Chang
- Division of Pediatric Hematology Oncology, Oregon Health and Science University, Portland, OR 97239, USA;
| | - Elliot Stieglitz
- Department of Pediatric Oncology, University of California, San Francisco Benioff Children’s Hospitals, San Francisco, CA 94158, USA;
| | - Alan S. Wayne
- Division of Hematology-Oncology, Cancer and Blood Disease Institute, Children’s Hospital Los Angeles, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90027, USA; (Y.-Y.C.); (A.S.W.); (D.B.)
| | - Nobuko Hijiya
- Division of Pediatric Hematology Oncology and Stem Cell Transplant, Columbia University Medical Center, New York, NY 10032, USA;
| | - Deepa Bhojwani
- Division of Hematology-Oncology, Cancer and Blood Disease Institute, Children’s Hospital Los Angeles, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90027, USA; (Y.-Y.C.); (A.S.W.); (D.B.)
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16
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Casillo SM, Gatesman TA, Chilukuri A, Varadharajan S, Johnson BJ, David Premkumar DR, Jane EP, Plute TJ, Koncar RF, Stanton ACJ, Biagi-Junior CAO, Barber CS, Halbert ME, Golbourn BJ, Halligan K, Cruz AF, Mansi NM, Cheney A, Mullett SJ, Land CV, Perez JL, Myers MI, Agrawal N, Michel JJ, Chang YF, Vaske OM, MichaelRaj A, Lieberman FS, Felker J, Shiva S, Bertrand KC, Amankulor N, Hadjipanayis CG, Abdullah KG, Zinn PO, Friedlander RM, Abel TJ, Nazarian J, Venneti S, Filbin MG, Gelhaus SL, Mack SC, Pollack IF, Agnihotri S. An ERK5-PFKFB3 axis regulates glycolysis and represents a therapeutic vulnerability in pediatric diffuse midline glioma. Cell Rep 2024; 43:113557. [PMID: 38113141 DOI: 10.1016/j.celrep.2023.113557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 07/28/2023] [Accepted: 11/22/2023] [Indexed: 12/21/2023] Open
Abstract
Metabolic reprogramming in pediatric diffuse midline glioma is driven by gene expression changes induced by the hallmark histone mutation H3K27M, which results in aberrantly permissive activation of oncogenic signaling pathways. Previous studies of diffuse midline glioma with altered H3K27 (DMG-H3K27a) have shown that the RAS pathway, specifically through its downstream kinase, extracellular-signal-related kinase 5 (ERK5), is critical for tumor growth. Further downstream effectors of ERK5 and their role in DMG-H3K27a metabolic reprogramming have not been explored. We establish that ERK5 is a critical regulator of cell proliferation and glycolysis in DMG-H3K27a. We demonstrate that ERK5 mediates glycolysis through activation of transcription factor MEF2A, which subsequently modulates expression of glycolytic enzyme PFKFB3. We show that in vitro and mouse models of DMG-H3K27a are sensitive to the loss of PFKFB3. Multi-targeted drug therapy against the ERK5-PFKFB3 axis, such as with small-molecule inhibitors, may represent a promising therapeutic approach in patients with pediatric diffuse midline glioma.
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Affiliation(s)
- Stephanie M Casillo
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Taylor A Gatesman
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Akanksha Chilukuri
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Srinidhi Varadharajan
- Department of Pediatric Hematology and Oncology, St Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Brenden J Johnson
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Daniel R David Premkumar
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Esther P Jane
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Tritan J Plute
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Robert F Koncar
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Ann-Catherine J Stanton
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Carlos A O Biagi-Junior
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Callie S Barber
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Matthew E Halbert
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Brian J Golbourn
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Katharine Halligan
- Division of Hematology Oncology, University of Pittsburgh School of Medicine, Pittsburgh, Pittsburgh, PA 15261, USA; Division of Hematology Oncology, Department of Pediatrics, Albany Medical College, Albany, NY 12208, USA
| | - Andrea F Cruz
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Neveen M Mansi
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Allison Cheney
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; University of California, Santa Cruz Genomics Institute, Santa Cruz, CA 95064, USA
| | - Steven J Mullett
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Clinton Van't Land
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA 15261, USA; Rangos Metabolic Core Facility, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Jennifer L Perez
- Department of Neurological Surgery, Mayo Clinic Alix School of Medicine, Rochester, MN 55905, USA
| | - Max I Myers
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Nishant Agrawal
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Joshua J Michel
- Rangos Flow Cytometry Core Laboratory, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Yue-Fang Chang
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Olena M Vaske
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; University of California, Santa Cruz Genomics Institute, Santa Cruz, CA 95064, USA
| | - Antony MichaelRaj
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Frank S Lieberman
- Adult Neuro-Oncology Program, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - James Felker
- Pediatric Neuro-Oncology Program, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Sruti Shiva
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA; Heart, Lung, Blood, and Vascular Medicine Institute, Department of Internal Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Kelsey C Bertrand
- Department of Pediatric Hematology and Oncology, St Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Nduka Amankulor
- Department of Neurosurgery, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Costas G Hadjipanayis
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Kalil G Abdullah
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Pascal O Zinn
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Robert M Friedlander
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Taylor J Abel
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Javad Nazarian
- Brain Tumor Institute, Children's National Hospital, Washington, DC 20010, USA
| | - Sriram Venneti
- Laboratory of Brain Tumor Metabolism and Epigenetics, Department of Pathology, University of Michigan Medical School, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mariella G Filbin
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Stacy L Gelhaus
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA; Health Sciences Mass Spectrometry Core, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Stephen C Mack
- Department of Pediatric Hematology and Oncology, St Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ian F Pollack
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Sameer Agnihotri
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA; Pediatric Neuro-Oncology Program, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA.
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17
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Tetens AR, Martin AM, Arnold A, Novak OV, Idrizi A, Tryggvadottir R, Craig-Schwartz J, Liapodimitri A, Lunsford K, Barbato MI, Eberhart CG, Resnick AC, Raabe EH, Koldobskiy MA. DNA methylation landscapes in DIPG reveal methylome variability that can be modified pharmacologically. Neurooncol Adv 2024; 6:vdae023. [PMID: 38468866 PMCID: PMC10926944 DOI: 10.1093/noajnl/vdae023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024] Open
Abstract
Background Diffuse intrinsic pontine glioma (DIPG) is a uniformly lethal brainstem tumor of childhood, driven by histone H3 K27M mutation and resultant epigenetic dysregulation. Epigenomic analyses of DIPG have shown global loss of repressive chromatin marks accompanied by DNA hypomethylation. However, studies providing a static view of the epigenome do not adequately capture the regulatory underpinnings of DIPG cellular heterogeneity and plasticity. Methods To address this, we performed whole-genome bisulfite sequencing on a large panel of primary DIPG specimens and applied a novel framework for analysis of DNA methylation variability, permitting the derivation of comprehensive genome-wide DNA methylation potential energy landscapes that capture intrinsic epigenetic variation. Results We show that DIPG has a markedly disordered epigenome with increasingly stochastic DNA methylation at genes regulating pluripotency and developmental identity, potentially enabling cells to sample diverse transcriptional programs and differentiation states. The DIPG epigenetic landscape was responsive to treatment with the hypomethylating agent decitabine, which produced genome-wide demethylation and reduced the stochasticity of DNA methylation at active enhancers and bivalent promoters. Decitabine treatment elicited changes in gene expression, including upregulation of immune signaling such as the interferon response, STING, and MHC class I expression, and sensitized cells to the effects of histone deacetylase inhibition. Conclusions This study provides a resource for understanding the epigenetic instability that underlies DIPG heterogeneity. It suggests the application of epigenetic therapies to constrain the range of epigenetic states available to DIPG cells, as well as the use of decitabine in priming for immune-based therapies.
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Affiliation(s)
- Ashley R Tetens
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Allison M Martin
- Pediatric Hematology-Oncology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Antje Arnold
- Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Orlandi V Novak
- Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Adrian Idrizi
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Rakel Tryggvadottir
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jordyn Craig-Schwartz
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Athanasia Liapodimitri
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Kayleigh Lunsford
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Michael I Barbato
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Charles G Eberhart
- Neuropathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Adam C Resnick
- Center for Data-Driven Discovery in Biomedicine, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Division of Neurosurgery, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Eric H Raabe
- Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Neuropathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Michael A Koldobskiy
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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18
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Ramsoomair CK, Ceccarelli M, Heiss JD, Shah AH. The epitranscriptome of high-grade gliomas: a promising therapeutic target with implications from the tumor microenvironment to endogenous retroviruses. J Transl Med 2023; 21:893. [PMID: 38071304 PMCID: PMC10709919 DOI: 10.1186/s12967-023-04725-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 11/13/2023] [Indexed: 12/18/2023] Open
Abstract
Glioblastoma (GBM) comprises 45.6% of all primary malignant brain cancers and is one of the most common and aggressive intracranial tumors in adults. Intratumoral heterogeneity with a wide range of proteomic, genetic, and epigenetic dysregulation contributes to treatment resistance and poor prognosis, thus demanding novel therapeutic approaches. To date, numerous clinical trials have been developed to target the proteome and epigenome of high-grade gliomas with promising results. However, studying RNA modifications, or RNA epitranscriptomics, is a new frontier within neuro-oncology. RNA epitranscriptomics was discovered in the 1970s, but in the last decade, the extent of modification of mRNA and various non-coding RNAs has emerged and been implicated in transposable element activation and many other oncogenic processes within the tumor microenvironment. This review provides background information and discusses the therapeutic potential of agents modulating epitranscriptomics in high-grade gliomas. A particular emphasis will be placed on how combination therapies that include immune agents targeting hERV-mediated viral mimicry could improve the treatment of GBM.
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Affiliation(s)
- Christian K Ramsoomair
- Section of Virology and Immunotherapy, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, 1095 NW 14Th Terrace, Miami, FL, 33136, USA.
- Medical Scientist Training Program, University of Miami Miller School of Medicine, 1095 NW 14Th Terrace, Miami, FL, 33136, USA.
| | - Michele Ceccarelli
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, 1550 N.W. 10Th Avenue, Miami, FL, 33136, USA
| | - John D Heiss
- Surgical Neurology Branch, Disorders and Stroke, National Institute of Neurological, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ashish H Shah
- Section of Virology and Immunotherapy, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, 1095 NW 14Th Terrace, Miami, FL, 33136, USA.
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19
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Voon HPJ, Hii L, Garvie A, Udugama M, Krug B, Russo C, Chüeh AC, Daly RJ, Morey A, Bell TDM, Turner SJ, Rosenbluh J, Daniel P, Firestein R, Mann JR, Collas P, Jabado N, Wong LH. Pediatric glioma histone H3.3 K27M/G34R mutations drive abnormalities in PML nuclear bodies. Genome Biol 2023; 24:284. [PMID: 38066546 PMCID: PMC10704828 DOI: 10.1186/s13059-023-03122-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Point mutations in histone variant H3.3 (H3.3K27M, H3.3G34R) and the H3.3-specific ATRX/DAXX chaperone complex are frequent events in pediatric gliomas. These H3.3 point mutations affect many chromatin modifications but the exact oncogenic mechanisms are currently unclear. Histone H3.3 is known to localize to nuclear compartments known as promyelocytic leukemia (PML) nuclear bodies, which are frequently mutated and confirmed as oncogenic drivers in acute promyelocytic leukemia. RESULTS We find that the pediatric glioma-associated H3.3 point mutations disrupt the formation of PML nuclear bodies and this prevents differentiation down glial lineages. Similar to leukemias driven by PML mutations, H3.3-mutated glioma cells are sensitive to drugs that target PML bodies. We also find that point mutations in IDH1/2-which are common events in adult gliomas and myeloid leukemias-also disrupt the formation of PML bodies. CONCLUSIONS We identify PML as a contributor to oncogenesis in a subset of gliomas and show that targeting PML bodies is effective in treating these H3.3-mutated pediatric gliomas.
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Affiliation(s)
- Hsiao P J Voon
- Cancer Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Linda Hii
- Cancer Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Andrew Garvie
- Cancer Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Maheshi Udugama
- Cancer Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Brian Krug
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Caterina Russo
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Anderly C Chüeh
- Cancer Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Roger J Daly
- Cancer Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Alison Morey
- Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Toby D M Bell
- School of Chemistry, Monash University, Clayton, VIC, Australia
| | - Stephen J Turner
- Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Joseph Rosenbluh
- Cancer Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Paul Daniel
- Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
| | - Ron Firestein
- Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
| | - Jeffrey R Mann
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia
| | - Philippe Collas
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0317, Oslo, Norway
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, 0424, Oslo, Norway
| | - Nada Jabado
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada
- Department of Paediatrics, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Lee H Wong
- Cancer Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Australia.
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20
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Krug B, Hu B, Chen H, Ptack A, Chen X, Gretarsson KH, Deshmukh S, Kabir N, Andrade AF, Jabbour E, Harutyunyan AS, Lee JJY, Hulswit M, Faury D, Russo C, Xu X, Johnston MJ, Baguette A, Dahl NA, Weil AG, Ellezam B, Dali R, Blanchette M, Wilson K, Garcia BA, Soni RK, Gallo M, Taylor MD, Kleinman CL, Majewski J, Jabado N, Lu C. H3K27me3 spreading organizes canonical PRC1 chromatin architecture to regulate developmental programs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.28.567931. [PMID: 38116029 PMCID: PMC10729739 DOI: 10.1101/2023.11.28.567931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Polycomb Repressive Complex 2 (PRC2)-mediated histone H3K27 tri-methylation (H3K27me3) recruits canonical PRC1 (cPRC1) to maintain heterochromatin. In early development, polycomb-regulated genes are connected through long-range 3D interactions which resolve upon differentiation. Here, we report that polycomb looping is controlled by H3K27me3 spreading and regulates target gene silencing and cell fate specification. Using glioma-derived H3 Lys-27-Met (H3K27M) mutations as tools to restrict H3K27me3 deposition, we show that H3K27me3 confinement concentrates the chromatin pool of cPRC1, resulting in heightened 3D interactions mirroring chromatin architecture of pluripotency, and stringent gene repression that maintains cells in progenitor states to facilitate tumor development. Conversely, H3K27me3 spread in pluripotent stem cells, following neural differentiation or loss of the H3K36 methyltransferase NSD1, dilutes cPRC1 concentration and dissolves polycomb loops. These results identify the regulatory principles and disease implications of polycomb looping and nominate histone modification-guided distribution of reader complexes as an important mechanism for nuclear compartment organization. Highlights The confinement of H3K27me3 at PRC2 nucleation sites without its spreading correlates with increased 3D chromatin interactions.The H3K27M oncohistone concentrates canonical PRC1 that anchors chromatin loop interactions in gliomas, silencing developmental programs.Stem and progenitor cells require factors promoting H3K27me3 confinement, including H3K36me2, to maintain cPRC1 loop architecture.The cPRC1-H3K27me3 interaction is a targetable driver of aberrant self-renewal in tumor cells.
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21
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Venneti S, Kawakibi AR, Ji S, Waszak SM, Sweha SR, Mota M, Pun M, Deogharkar A, Chung C, Tarapore RS, Ramage S, Chi A, Wen PY, Arrillaga-Romany I, Batchelor TT, Butowski NA, Sumrall A, Shonka N, Harrison RA, de Groot J, Mehta M, Hall MD, Daghistani D, Cloughesy TF, Ellingson BM, Beccaria K, Varlet P, Kim MM, Umemura Y, Garton H, Franson A, Schwartz J, Jain R, Kachman M, Baum H, Burant CF, Mottl SL, Cartaxo RT, John V, Messinger D, Qin T, Peterson E, Sajjakulnukit P, Ravi K, Waugh A, Walling D, Ding Y, Xia Z, Schwendeman A, Hawes D, Yang F, Judkins AR, Wahl D, Lyssiotis CA, de la Nava D, Alonso MM, Eze A, Spitzer J, Schmidt SV, Duchatel RJ, Dun MD, Cain JE, Jiang L, Stopka SA, Baquer G, Regan MS, Filbin MG, Agar NY, Zhao L, Kumar-Sinha C, Mody R, Chinnaiyan A, Kurokawa R, Pratt D, Yadav VN, Grill J, Kline C, Mueller S, Resnick A, Nazarian J, Allen JE, Odia Y, Gardner SL, Koschmann C. Clinical Efficacy of ONC201 in H3K27M-Mutant Diffuse Midline Gliomas Is Driven by Disruption of Integrated Metabolic and Epigenetic Pathways. Cancer Discov 2023; 13:2370-2393. [PMID: 37584601 PMCID: PMC10618742 DOI: 10.1158/2159-8290.cd-23-0131] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 05/30/2023] [Accepted: 08/10/2023] [Indexed: 08/17/2023]
Abstract
Patients with H3K27M-mutant diffuse midline glioma (DMG) have no proven effective therapies. ONC201 has recently demonstrated efficacy in these patients, but the mechanism behind this finding remains unknown. We assessed clinical outcomes, tumor sequencing, and tissue/cerebrospinal fluid (CSF) correlate samples from patients treated in two completed multisite clinical studies. Patients treated with ONC201 following initial radiation but prior to recurrence demonstrated a median overall survival of 21.7 months, whereas those treated after recurrence had a median overall survival of 9.3 months. Radiographic response was associated with increased expression of key tricarboxylic acid cycle-related genes in baseline tumor sequencing. ONC201 treatment increased 2-hydroxyglutarate levels in cultured H3K27M-DMG cells and patient CSF samples. This corresponded with increases in repressive H3K27me3 in vitro and in human tumors accompanied by epigenetic downregulation of cell cycle regulation and neuroglial differentiation genes. Overall, ONC201 demonstrates efficacy in H3K27M-DMG by disrupting integrated metabolic and epigenetic pathways and reversing pathognomonic H3K27me3 reduction. SIGNIFICANCE The clinical, radiographic, and molecular analyses included in this study demonstrate the efficacy of ONC201 in H3K27M-mutant DMG and support ONC201 as the first monotherapy to improve outcomes in H3K27M-mutant DMG beyond radiation. Mechanistically, ONC201 disrupts integrated metabolic and epigenetic pathways and reverses pathognomonic H3K27me3 reduction. This article is featured in Selected Articles from This Issue, p. 2293.
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Affiliation(s)
| | | | - Sunjong Ji
- University of Michigan, Ann Arbor, Michigan
| | - Sebastian M. Waszak
- University of California, San Francisco, San Francisco, California
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo, Norway
- Laboratory of Computational Neuro-Oncology, Swiss Institute for Experimental Cancer Research, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Stefan R. Sweha
- University of Michigan, Ann Arbor, Michigan
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | | | | | - Chan Chung
- University of Michigan, Ann Arbor, Michigan
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Republic of Korea
| | | | | | | | - Patrick Y. Wen
- Center for Neuro-Oncology, Dana-Farber/Brigham and Women's Cancer Center, Boston, Massachusetts
| | | | | | | | | | | | | | - John de Groot
- University of California, San Francisco, San Francisco, California
| | | | | | | | | | | | - Kevin Beccaria
- Department of Neurosurgery, Necker Sick Children's University Hospital and Paris Descartes University, Paris, France
| | - Pascale Varlet
- Department of Neuropathology, Sainte-Anne Hospital and Paris Descartes University, Paris, France
| | | | | | | | | | | | | | | | - Heidi Baum
- University of Michigan, Ann Arbor, Michigan
| | | | - Sophie L. Mottl
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo, Norway
| | | | | | | | | | | | | | | | | | | | - Yujie Ding
- University of Michigan, Ann Arbor, Michigan
| | - Ziyun Xia
- University of Michigan, Ann Arbor, Michigan
| | | | - Debra Hawes
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Fusheng Yang
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Alexander R. Judkins
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, California
| | | | | | - Daniel de la Nava
- Health Research Institute of Navarra (IdiSNA), Pamplona, Spain
- Solid Tumor Program, Cima Universidad de Navarra, Pamplona, Spain
- Department of Pediatrics, Clínica Universidad de Navarra, Pamplona, Spain
| | - Marta M. Alonso
- Health Research Institute of Navarra (IdiSNA), Pamplona, Spain
- Solid Tumor Program, Cima Universidad de Navarra, Pamplona, Spain
- Department of Pediatrics, Clínica Universidad de Navarra, Pamplona, Spain
| | - Augustine Eze
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC
| | - Jasper Spitzer
- Institute of Innate Immunity, AG Immunogenomics, University Hospital Bonn, Bonn, Germany
- Institute of Clinical Chemistry and Clinical Pharmacology, AG Immunmonitoring and Genomics, University Hospital Bonn, Bonn, Germany
| | - Susanne V. Schmidt
- Institute of Innate Immunity, AG Immunogenomics, University Hospital Bonn, Bonn, Germany
- Institute of Clinical Chemistry and Clinical Pharmacology, AG Immunmonitoring and Genomics, University Hospital Bonn, Bonn, Germany
| | - Ryan J. Duchatel
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, Callaghan, NSW, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
- Paediatric Program, Mark Hughes Foundation Centre for Brain Cancer Research, College of Health, Medicine, and Wellbeing, Callaghan, NSW, Australia
| | - Matthew D. Dun
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, Callaghan, NSW, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
- Paediatric Program, Mark Hughes Foundation Centre for Brain Cancer Research, College of Health, Medicine, and Wellbeing, Callaghan, NSW, Australia
| | - Jason E. Cain
- Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia
| | - Li Jiang
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorder Center, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Sylwia A. Stopka
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Gerard Baquer
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Michael S. Regan
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Mariella G. Filbin
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorder Center, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Nathalie Y.R. Agar
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Lili Zhao
- University of Michigan, Ann Arbor, Michigan
| | | | - Rajen Mody
- University of Michigan, Ann Arbor, Michigan
| | | | - Ryo Kurokawa
- University of Michigan, Ann Arbor, Michigan
- The University of Tokyo, Tokyo, Japan
| | - Drew Pratt
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Viveka N. Yadav
- Department of Pediatrics at Children's Mercy Research Institute, Kansas City, Missouri
| | - Jacques Grill
- Department of Pediatric and Adolescent Oncology and INSERM Unit 981, Gustave Roussy and University Paris-Saclay, Villejuif, France
| | - Cassie Kline
- Division of Oncology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Sabine Mueller
- University of California, San Francisco, San Francisco, California
- Department of Oncology, Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Adam Resnick
- Division of Oncology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Javad Nazarian
- Department of Pediatrics, Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
- Research Center for Genetic Medicine, Children's National Hospital, Washington, DC
- George Washington University School of Medicine and Health Sciences, Washington, DC
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22
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Salomoni P, Flanagan AM, Cottone L. (B)On(e)-cohistones and the epigenetic alterations at the root of bone cancer. Cell Death Differ 2023:10.1038/s41418-023-01227-9. [PMID: 37828086 DOI: 10.1038/s41418-023-01227-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 09/20/2023] [Accepted: 09/27/2023] [Indexed: 10/14/2023] Open
Abstract
Identification of mutations in histones in a number of human neoplasms and developmental syndromes represents the most compelling evidence to date for a causal role of epigenetic perturbations in human disease. In most cases, these mutations have gain of function properties that cause deviation from normal developmental processes leading to embryo defects and/or neoplastic transformation. These exciting discoveries represent a step-change in our understanding of the role of chromatin (dys)regulation in development and disease. However, the mechanisms of action of oncogenic histone mutations (oncohistones) remain only partially understood. Here, we critically assess existing literature on oncohistones focussing mainly on bone neoplasms. We show how it is possible to draw parallels with some of the cell-autonomous mechanisms of action described in paediatric brain cancer, although the functions of oncohistones in bone tumours remain under-investigated. In this respect, it is becoming clear that histone mutations targeting the same residues display, at least in part, tissue-specific oncogenic mechanisms. Furthermore, it is emerging that cancer cells carrying oncohistones can modify the surrounding microenvironment to support growth and/or alter differentiation trajectories. A better understanding of oncohistone function in different neoplasms provide potential for identification of signalling that could be targeted therapeutically. Finally, we discuss some of the main concepts and future directions in this research area, while also drawing possible connections and parallels with other cancer epigenetic mechanisms.
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Affiliation(s)
- Paolo Salomoni
- Nuclear Function Group, German Center for Neurodegenerative Diseases (DZNE), 53127, Bonn, Germany.
| | - Adrienne M Flanagan
- Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, Middlesex, HA7 4LP, UK
- Department of Pathology, UCL Cancer Institute, University College London, London, WC1E 6BT, UK
| | - Lucia Cottone
- Department of Pathology, UCL Cancer Institute, University College London, London, WC1E 6BT, UK.
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23
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Al Sharie S, Abu Laban D, Al-Hussaini M. Decoding Diffuse Midline Gliomas: A Comprehensive Review of Pathogenesis, Diagnosis and Treatment. Cancers (Basel) 2023; 15:4869. [PMID: 37835563 PMCID: PMC10571999 DOI: 10.3390/cancers15194869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 09/27/2023] [Accepted: 10/03/2023] [Indexed: 10/15/2023] Open
Abstract
Diffuse midline gliomas (DMGs) are a group of aggressive CNS tumors, primarily affecting children and young adults, which have historically been associated with dismal outcomes. As the name implies, they arise in midline structures in the CNS, primarily in the thalamus, brainstem, and spinal cord. In more recent years, significant advances have been made in our understanding of DMGs, including molecular features, with the identification of potential therapeutic targets. We aim to provide an overview of the most recent updates in the field of DMGs, including classification, molecular subtypes, diagnostic techniques, and emerging therapeutic strategies including a review of the ongoing clinical trials, thus providing the treating multidisciplinary team with a comprehensive understanding of the current landscape and potential therapeutic strategies for this devastating group of tumors.
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Affiliation(s)
- Sarah Al Sharie
- Faculty of Medicine, Yarmouk University, Irbid 21163, Jordan;
| | - Dima Abu Laban
- Department of Radiology, King Hussein Cancer Center, Amman 11941, Jordan;
| | - Maysa Al-Hussaini
- Department of Pathology and Laboratory Medicine, King Hussein Cancer Center, Amman 11941, Jordan
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24
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Sharma M, Barravecchia I, Magnuson B, Ferris SF, Apfelbaum A, Mbah NE, Cruz J, Krishnamoorthy V, Teis R, Kauss M, Koschmann C, Lyssiotis CA, Ljungman M, Galban S. Histone H3 K27M-mediated regulation of cancer cell stemness and differentiation in diffuse midline glioma. Neoplasia 2023; 44:100931. [PMID: 37647805 PMCID: PMC10474232 DOI: 10.1016/j.neo.2023.100931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 08/22/2023] [Accepted: 08/22/2023] [Indexed: 09/01/2023]
Abstract
Therapeutic resistance remains a major obstacle to preventing progression of H3K27M-altered Diffuse Midline Glioma (DMG). Resistance is driven in part by ALDH-positive cancer stem cells (CSC), with high ALDH1A3 expression observed in H3K27M-mutant DMG biopsies. We hypothesized that ALDH-mediated stemness and resistance may in part be driven by the oncohistone itself. Upon deletion of H3K27M, ALDH1A3 expression decreased dramatically and was accompanied by a gain in astrocytic marker expression and a loss of neurosphere forming potential, indicative of differentiation. Here we show that the oncohistone regulates histone acetylation through ALDH1A3 in a Wnt-dependent manner and that loss of H3K27M expression results in sensitization of DMGs to radiotherapy. The observed elevated Wnt signaling in H3K27M-altered DMG likely stems from a dramatic suppression of mRNA and protein expression of the Wnt inhibitor EYA4 driven by the oncohistone. Thus, our findings identify EYA4 as a bona fide tumor suppressor in DMG that upon suppression, results in aberrant Wnt signaling to orchestrate stemness and differentiation. Future studies will explore whether overexpression of EYA4 in DMG can impede growth and invasion. In summary, we have gained mechanistic insight into H3K27M-mediated regulation of cancer stemness and differentiation, which provides rationale for exploring new therapeutic targets for DMG.
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Affiliation(s)
- Monika Sharma
- Center for Molecular Imaging, The University of Michigan Medical School, Ann Arbor, MI 48109, United States; Department of Radiology, The University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Ivana Barravecchia
- Center for Molecular Imaging, The University of Michigan Medical School, Ann Arbor, MI 48109, United States; Department of Radiology, The University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Brian Magnuson
- Rogel Cancer Center, The University of Michigan Medical School, Ann Arbor, MI 48109, United States; Department of Biostatistics, School of Public Health, The University of Michigan, Ann Arbor, MI 48109, United States
| | - Sarah F Ferris
- Center for Molecular Imaging, The University of Michigan Medical School, Ann Arbor, MI 48109, United States; Department of Radiology, The University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - April Apfelbaum
- Center for Molecular Imaging, The University of Michigan Medical School, Ann Arbor, MI 48109, United States; Department of Radiology, The University of Michigan Medical School, Ann Arbor, MI 48109, United States; Rogel Cancer Center, The University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Nneka E Mbah
- Department of Molecular & Integrative Physiology, The University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Jeanette Cruz
- Center for Molecular Imaging, The University of Michigan Medical School, Ann Arbor, MI 48109, United States; Department of Radiology, The University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Varunkumar Krishnamoorthy
- Center for Molecular Imaging, The University of Michigan Medical School, Ann Arbor, MI 48109, United States; Department of Radiology, The University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Robert Teis
- Center for Molecular Imaging, The University of Michigan Medical School, Ann Arbor, MI 48109, United States; Department of Radiology, The University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - McKenzie Kauss
- Center for Molecular Imaging, The University of Michigan Medical School, Ann Arbor, MI 48109, United States; Department of Radiology, The University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Carl Koschmann
- Department of Pediatrics, The University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Costas A Lyssiotis
- Rogel Cancer Center, The University of Michigan Medical School, Ann Arbor, MI 48109, United States; Department of Molecular & Integrative Physiology, The University of Michigan Medical School, Ann Arbor, MI 48109, United States; Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Mats Ljungman
- Rogel Cancer Center, The University of Michigan Medical School, Ann Arbor, MI 48109, United States; Department of Radiation Oncology, The University of Michigan Medical School, Ann Arbor, MI 48109, United States; Center for RNA Biomedicine, The University of Michigan, Ann Arbor, MI 48109, United States
| | - Stefanie Galban
- Center for Molecular Imaging, The University of Michigan Medical School, Ann Arbor, MI 48109, United States; Department of Radiology, The University of Michigan Medical School, Ann Arbor, MI 48109, United States; Rogel Cancer Center, The University of Michigan Medical School, Ann Arbor, MI 48109, United States.
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25
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Peterson ER, Sajjakulnukit P, Scott AJ, Heaslip C, Andren A, Wilder-Romans K, Zhou W, Palavalasa S, Korimerla N, Lin A, Obrien A, Kothari A, Zhao Z, Zhang L, Morgan MA, Venneti S, Koschmann C, Jabado N, Lyssiotis CA, Castro MG, Wahl DR. Adaptive rewiring of purine metabolism promotes treatment resistance in H3K27M-mutant diffuse midline glioma. RESEARCH SQUARE 2023:rs.3.rs-3317816. [PMID: 37790517 PMCID: PMC10543500 DOI: 10.21203/rs.3.rs-3317816/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Background Diffuse midline gliomas (DMG), including diffuse intrinsic pontine gliomas (DIPGs), are a fatal form of brain cancer. These tumors often carry a driver mutation on histone H3 converting lysine 27 to methionine (H3K27M). DMG-H3K27M are characterized by altered metabolism and resistance to standard of care radiation (RT), but how the H3K27M mediates the metabolic response to radiation and consequent treatment resistance is uncertain. Methods We performed metabolomics on irradiated and untreated H3K27M isogenic DMG cell lines and observed an H3K27M-specific enrichment for purine synthesis pathways. We profiled the expression of purine synthesis enzymes in publicly available patient data and in our models, quantified purine synthetic flux using stable isotope tracing, and characterized the in vitro and in vivo response to de novo and salvage purine synthesis inhibition in combination with RT. Results DMG-H3K27M cells activate purine metabolism in an H3K27M-specific fashion. In the absence of genotoxic treatment, H3K27M-expressing cells have higher relative activity of de novosynthesis and lower activity of purine salvage due to decreased expression of the purine salvage enzymes. Inhibition of de novo synthesis radiosensitized DMG-H3K27M cells in vitro and in vivo. Irradiated H3K27M cells adaptively upregulate purine salvage enzyme expression and pathway activity. Silencing the rate limiting enzyme in purine salvage, hypoxanthine guanine phosphoribosyl transferase (HGPRT) when combined with radiation markedly suppressed DMG-H3K27M tumor growth in vivo. Conclusions H3K27M expressing cells rely on de novo purine synthesis but adaptively upregulate purine salvage in response to RT. Inhibiting purine salvage may help overcome treatment resistance in DMG-H3K27M tumors.
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Affiliation(s)
| | | | | | - Caleb Heaslip
- Massachusetts College of Pharmacy and Health Sciences
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26
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Garrett MC, Albano R, Carnwath T, Elahi L, Behrmann CA, Pemberton M, Woo D, O'Brien E, VanCauwenbergh B, Perentesis J, Shah S, Hagan M, Kendler A, Zhao C, Paranjpe A, Roskin K, Kornblum H, Plas DR, Lu QR. HDAC1 and HDAC6 are essential for driving growth in IDH1 mutant glioma. Sci Rep 2023; 13:12433. [PMID: 37528157 PMCID: PMC10394035 DOI: 10.1038/s41598-023-33889-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 04/20/2023] [Indexed: 08/03/2023] Open
Abstract
Low-grade and secondary high-grade gliomas frequently contain mutations in the IDH1 or IDH2 metabolic enzymes that are hypothesized to drive tumorigenesis by inhibiting many of the chromatin-regulating enzymes that regulate DNA structure. Histone deacetylase inhibitors are promising anti-cancer agents and have already been used in clinical trials. However, a clear understanding of their mechanism or gene targets is lacking. In this study, the authors genetically dissect patient-derived IDH1 mutant cultures to determine which HDAC enzymes drive growth in IDH1 mutant gliomas. A panel of patient-derived gliomasphere cell lines (2 IDH1 mutant lines, 3 IDH1 wildtype lines) were subjected to a drug-screen of epigenetic modifying drugs from different epigenetic classes. The effect of LBH (panobinostat) on gene expression and chromatin structure was tested on patient-derived IDH1 mutant lines. The role of each of the highly expressed HDAC enzymes was molecularly dissected using lentiviral RNA interference knock-down vectors and a patient-derived IDH1 mutant in vitro model of glioblastoma (HK252). These results were then confirmed in an in vivo xenotransplant model (BT-142). The IDH1 mutation leads to gene down-regulation, DNA hypermethylation, increased DNA accessibility and H3K27 hypo-acetylation in two distinct IDH1 mutant over-expression models. The drug screen identified histone deacetylase inhibitors (HDACi) and panobinostat (LBH) more specifically as the most selective compounds to inhibit growth in IDH1 mutant glioma lines. Of the eleven annotated HDAC enzymes (HDAC1-11) only six are expressed in IDH1 mutant glioma tissue samples and patient-derived gliomasphere lines (HDAC1-4, HDAC6, and HDAC9). Lentiviral knock-down experiments revealed that HDAC1 and HDAC6 are the most consistently essential for growth both in vitro and in vivo and target very different gene modules. Knock-down of HDAC1 or HDAC6 in vivo led to a more circumscribed less invasive tumor. The gene dysregulation induced by the IDH1 mutation is wide-spread and only partially reversible by direct IDH1 inhibition. This study identifies HDAC1 and HDAC6 as important and drug-targetable enzymes that are necessary for growth and invasiveness in IDH1 mutant gliomas.
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Affiliation(s)
- Matthew C Garrett
- Department of Neurosurgery, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA.
| | - Rebecca Albano
- Department of Neurosurgery, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Troy Carnwath
- University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Lubayna Elahi
- Department of Molecular Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Catherine A Behrmann
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH, 45267, USA
| | - Merissa Pemberton
- University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Daniel Woo
- Department of Neurology, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Eric O'Brien
- Division of Experimental Hematology and Cancer Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Brett VanCauwenbergh
- Division of Experimental Hematology and Cancer Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - John Perentesis
- Division of Experimental Hematology and Cancer Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Sanjit Shah
- Department of Neurosurgery, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Matthew Hagan
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Ady Kendler
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Chuntao Zhao
- Division of Experimental Hematology and Cancer Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Aditi Paranjpe
- Bioinformatics Collaborative Services, Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Krishna Roskin
- Bioinformatics Collaborative Services, Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Harley Kornblum
- Department of Molecular Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - David R Plas
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH, 45267, USA
| | - Q Richard Lu
- Division of Experimental Hematology and Cancer Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
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27
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Knowles T, Huang T, Qi J, An S, Burket N, Cooper S, Nazarian J, Saratsis AM. LIN28B and Let-7 in Diffuse Midline Glioma: A Review. Cancers (Basel) 2023; 15:3241. [PMID: 37370851 DOI: 10.3390/cancers15123241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/12/2023] [Accepted: 06/17/2023] [Indexed: 06/29/2023] Open
Abstract
Diffuse midline glioma (DMG) is the most lethal of all childhood cancers. DMGs are driven by histone-tail-mutation-mediated epigenetic dysregulation and partner mutations in genes controlling proliferation and migration. One result of this epigenetic and genetic landscape is the overexpression of LIN28B RNA binding protein. In other systems, LIN28B has been shown to prevent let-7 microRNA biogenesis; however, let-7, when available, faithfully suppresses tumorigenic pathways and induces cellular maturation by preventing the translation of numerous oncogenes. Here, we review the current literature on LIN28A/B and the let-7 family and describe their role in gliomagenesis. Future research is then recommended, with a focus on the mechanisms of LIN28B overexpression and localization in DMG.
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Affiliation(s)
- Truman Knowles
- W.M. Keck Science Department, Scripps, Pitzer, and Claremont McKenna Colleges, Claremont, CA 91711, USA
| | - Tina Huang
- Department of Neurosurgery, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Jin Qi
- Department of Neurosurgery, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Shejuan An
- Department of Neurosurgery, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Noah Burket
- Department of Neurosurgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Scott Cooper
- Department of Neurosurgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Javad Nazarian
- Department of Pediatrics, Children's National Hospital, Washington, DC 20010, USA
- Department of Pediatrics, Zurich Children's Hospital, 8032 Zurich, Switzerland
| | - Amanda M Saratsis
- Department of Neurosurgery, Lutheran General Hospital, Park Ridge, IL 60068, USA
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28
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Diffuse intrinsic pontine glioma: Insights into oncogenesis and opportunities for targeted therapy. PEDIATRIC HEMATOLOGY ONCOLOGY JOURNAL 2023. [DOI: 10.1016/j.phoj.2023.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023] Open
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29
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Ocasio JK, Budd KM, Roach JT, Andrews JM, Baker SJ. Oncohistones and disrupted development in pediatric-type diffuse high-grade glioma. Cancer Metastasis Rev 2023; 42:367-388. [PMID: 37119408 PMCID: PMC10441521 DOI: 10.1007/s10555-023-10105-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 04/05/2023] [Indexed: 05/01/2023]
Abstract
Recurrent, clonal somatic mutations in histone H3 are molecular hallmarks that distinguish the genetic mechanisms underlying pediatric and adult high-grade glioma (HGG), define biological subgroups of diffuse glioma, and highlight connections between cancer, development, and epigenetics. These oncogenic mutations in histones, now termed "oncohistones", were discovered through genome-wide sequencing of pediatric diffuse high-grade glioma. Up to 80% of diffuse midline glioma (DMG), including diffuse intrinsic pontine glioma (DIPG) and diffuse glioma arising in other midline structures including thalamus or spinal cord, contain histone H3 lysine 27 to methionine (K27M) mutations or, rarely, other alterations that result in a depletion of H3K27me3 similar to that induced by H3 K27M. This subgroup of glioma is now defined as diffuse midline glioma, H3K27-altered. In contrast, histone H3 Gly34Arg/Val (G34R/V) mutations are found in approximately 30% of diffuse glioma arising in the cerebral hemispheres of older adolescents and young adults, now classified as diffuse hemispheric glioma, H3G34-mutant. Here, we review how oncohistones modulate the epigenome and discuss the mutational landscape and invasive properties of histone mutant HGGs of childhood. The distinct mechanisms through which oncohistones and other mutations rewrite the epigenetic landscape provide novel insights into development and tumorigenesis and may present unique vulnerabilities for pHGGs. Lessons learned from these rare incurable brain tumors of childhood may have broader implications for cancer, as additional high- and low-frequency oncohistone mutations have been identified in other tumor types.
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Affiliation(s)
- Jennifer K Ocasio
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kaitlin M Budd
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
- St. Jude Graduate School of Biomedical Sciences, Memphis, TN, USA
| | - Jordan T Roach
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
- St. Jude Graduate School of Biomedical Sciences, Memphis, TN, USA
- College of Medicine, University of Tennessee Health Sciences Center, Memphis, TN, USA
| | - Jared M Andrews
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Suzanne J Baker
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA.
- St. Jude Graduate School of Biomedical Sciences, Memphis, TN, USA.
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30
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Nikolic A, Maule F, Bobyn A, Ellestad K, Paik S, Marhon SA, Mehdipour P, Lun X, Chen HM, Mallard C, Hay AJ, Johnston MJ, Gafuik CJ, Zemp FJ, Shen Y, Ninkovic N, Osz K, Labit E, Berger ND, Brownsey DK, Kelly JJ, Biernaskie J, Dirks PB, Derksen DJ, Jones SJM, Senger DL, Chan JA, Mahoney DJ, De Carvalho DD, Gallo M. macroH2A2 antagonizes epigenetic programs of stemness in glioblastoma. Nat Commun 2023; 14:3062. [PMID: 37244935 DOI: 10.1038/s41467-023-38919-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 05/22/2023] [Indexed: 05/29/2023] Open
Abstract
Self-renewal is a crucial property of glioblastoma cells that is enabled by the choreographed functions of chromatin regulators and transcription factors. Identifying targetable epigenetic mechanisms of self-renewal could therefore represent an important step toward developing effective treatments for this universally lethal cancer. Here we uncover an epigenetic axis of self-renewal mediated by the histone variant macroH2A2. With omics and functional assays deploying patient-derived in vitro and in vivo models, we show that macroH2A2 shapes chromatin accessibility at enhancer elements to antagonize transcriptional programs of self-renewal. macroH2A2 also sensitizes cells to small molecule-mediated cell death via activation of a viral mimicry response. Consistent with these results, our analyses of clinical cohorts indicate that high transcriptional levels of this histone variant are associated with better prognosis of high-grade glioma patients. Our results reveal a targetable epigenetic mechanism of self-renewal controlled by macroH2A2 and suggest additional treatment approaches for glioblastoma patients.
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Affiliation(s)
- Ana Nikolic
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Francesca Maule
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Anna Bobyn
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, AB, Canada
| | - Katrina Ellestad
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Seungil Paik
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | | | - Parinaz Mehdipour
- Princess Margaret Cancer Centre, Toronto, ON, Canada
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | - Xueqing Lun
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Huey-Miin Chen
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Claire Mallard
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Alexander J Hay
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Michael J Johnston
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Christopher J Gafuik
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Franz J Zemp
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Yaoqing Shen
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Nicoletta Ninkovic
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Katalin Osz
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Oncology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Elodie Labit
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Compararive Biology and Experimental Medicine, Faculty of Veterinary Medicine, and Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - N Daniel Berger
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Duncan K Brownsey
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Chemistry, Faculty of Science, University of Calgary, Calgary, AB, Canada
| | - John J Kelly
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Clinical Neurosciences, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Jeff Biernaskie
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Compararive Biology and Experimental Medicine, Faculty of Veterinary Medicine, and Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Peter B Dirks
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Darren J Derksen
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Chemistry, Faculty of Science, University of Calgary, Calgary, AB, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Donna L Senger
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Oncology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Jennifer A Chan
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Oncology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Douglas J Mahoney
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Daniel D De Carvalho
- Princess Margaret Cancer Centre, Toronto, ON, Canada
- Department of Medical Biophysics, Faculty of Science, University of Toronto, Toronto, ON, Canada
| | - Marco Gallo
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
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31
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Goldstein M. Targeting H3K27me3 loss in pediatric brain tumors - a perspective on epigenetically guided cancer therapy. Oncotarget 2023; 14:444-447. [PMID: 37171381 PMCID: PMC10178451 DOI: 10.18632/oncotarget.28427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Indexed: 05/13/2023] Open
Affiliation(s)
- Michael Goldstein
- Correspondence to:Michael Goldstein, Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA email
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32
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Mota M, Sweha S, Pun M, Natarajan S, Ding Y, Chung C, Hawes D, Yang F, Judkins A, Samajdar S, Cao X, Xiao L, Parolia A, Chinnaiyan A, Venneti S. Targeting SWI/SNF ATPases in H3.3K27M diffuse intrinsic pontine gliomas. Proc Natl Acad Sci U S A 2023; 120:e2221175120. [PMID: 37094128 PMCID: PMC10161095 DOI: 10.1073/pnas.2221175120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 03/30/2023] [Indexed: 04/26/2023] Open
Abstract
Diffuse midline gliomas (DMGs) including diffuse intrinsic pontine gliomas (DIPGs) bearing lysine-to-methionine mutations in histone H3 at lysine 27 (H3K27M) are lethal childhood brain cancers. These tumors harbor a global reduction in the transcriptional repressive mark H3K27me3 accompanied by an increase in the transcriptional activation mark H3K27ac. We postulated that H3K27M mutations, in addition to altering H3K27 modifications, reprogram the master chromatin remodeling switch/sucrose nonfermentable (SWI/SNF) complex. The SWI/SNF complex can exist in two main forms termed BAF and PBAF that play central roles in neurodevelopment and cancer. Moreover, BAF antagonizes PRC2, the main enzyme catalyzing H3K27me3. We demonstrate that H3K27M gliomas show increased protein levels of the SWI/SNF complex ATPase subunits SMARCA4 and SMARCA2, and the PBAF component PBRM1. Additionally, knockdown of mutant H3K27M lowered SMARCA4 protein levels. The proteolysis targeting chimera (PROTAC) AU-15330 that simultaneously targets SMARCA4, SMARCA2, and PBRM1 for degradation exhibits cytotoxicity in H3.3K27M but not H3 wild-type cells. AU-15330 lowered chromatin accessibility measured by ATAC-Seq at nonpromoter regions and reduced global H3K27ac levels. Integrated analysis of gene expression, proteomics, and chromatin accessibility in AU-15330-treated cells demonstrated reduction in the levels of FOXO1, a key member of the forkhead family of transcription factors. Moreover, genetic or pharmacologic targeting of FOXO1 resulted in cell death in H3K27M cells. Overall, our results suggest that H3K27M up-regulates SMARCA4 levels and combined targeting of SWI/SNF ATPases in H3.3K27M can serve as a potent therapeutic strategy for these deadly childhood brain tumors.
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Affiliation(s)
- Mateus Mota
- Laboratory of Brain Tumor Metabolism and Epigenetics, Department of Pathology, University of Michigan, Ann Arbor, MI48109
- Chad Carr Pediatric Tumor Center, Department of Pediatrics, University of Michigan, Ann Arbor, MI48109
| | - Stefan R. Sweha
- Laboratory of Brain Tumor Metabolism and Epigenetics, Department of Pathology, University of Michigan, Ann Arbor, MI48109
- Chad Carr Pediatric Tumor Center, Department of Pediatrics, University of Michigan, Ann Arbor, MI48109
| | - Matt Pun
- Laboratory of Brain Tumor Metabolism and Epigenetics, Department of Pathology, University of Michigan, Ann Arbor, MI48109
- Chad Carr Pediatric Tumor Center, Department of Pediatrics, University of Michigan, Ann Arbor, MI48109
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI48109
- Medical Scientist Training Program, University of Michigan Medical School, Ann Arbor, MI48109
| | - Siva Kumar Natarajan
- Laboratory of Brain Tumor Metabolism and Epigenetics, Department of Pathology, University of Michigan, Ann Arbor, MI48109
- Chad Carr Pediatric Tumor Center, Department of Pediatrics, University of Michigan, Ann Arbor, MI48109
| | - Yujie Ding
- Laboratory of Brain Tumor Metabolism and Epigenetics, Department of Pathology, University of Michigan, Ann Arbor, MI48109
- Chad Carr Pediatric Tumor Center, Department of Pediatrics, University of Michigan, Ann Arbor, MI48109
| | - Chan Chung
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Daegu42988, Korea
| | - Debra Hawes
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Keck School of Medicine University of Southern California, Los Angeles, CA90027
| | - Fusheng Yang
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Keck School of Medicine University of Southern California, Los Angeles, CA90027
| | - Alexander R. Judkins
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Keck School of Medicine University of Southern California, Los Angeles, CA90027
| | - Susanta Samajdar
- Aurigene Discovery Technologies, Bengaluru, Karnataka560100, India
| | - Xuhong Cao
- Michigan Center for Translational Pathology, Department of Pathology, University of Michigan Medical School, Ann Arbor, MI48109
| | - Lanbo Xiao
- Michigan Center for Translational Pathology, Department of Pathology, University of Michigan Medical School, Ann Arbor, MI48109
| | - Abhijit Parolia
- Michigan Center for Translational Pathology, Department of Pathology, University of Michigan Medical School, Ann Arbor, MI48109
| | - Arul M. Chinnaiyan
- Michigan Center for Translational Pathology, Department of Pathology, University of Michigan Medical School, Ann Arbor, MI48109
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI48109
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI48109
- HHMI, University of Michigan Medical School, Ann Arbor, MI48109
| | - Sriram Venneti
- Laboratory of Brain Tumor Metabolism and Epigenetics, Department of Pathology, University of Michigan, Ann Arbor, MI48109
- Chad Carr Pediatric Tumor Center, Department of Pediatrics, University of Michigan, Ann Arbor, MI48109
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI48109
- Michigan Center for Translational Pathology, Department of Pathology, University of Michigan Medical School, Ann Arbor, MI48109
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI48109
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33
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Andrade AF, Chen CCL, Jabado N. Oncohistones in brain tumors: the soil and seed. Trends Cancer 2023; 9:444-455. [PMID: 36933956 PMCID: PMC11075889 DOI: 10.1016/j.trecan.2023.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/11/2023] [Accepted: 02/21/2023] [Indexed: 03/18/2023]
Abstract
Recurrent somatic mutations in histone 3 (H3) variants (termed 'oncohistones') have been identified in high-grade gliomas (HGGs) in children and young adults and induce tumorigenesis through disruption of chromatin states. Oncohistones occur with exquisite neuroanatomical specificity and are associated with specific age distribution and epigenome landscapes. Here, we review the known intrinsic ('seed') and the extrinsic ('soil') factors needed for their optimal oncogenic effect and highlight the many unresolved questions regarding their effects on development and crosstalk with the tumor microenvironment. The 'seed and soil' analogy, used to explain tumor metastatic niches, also applies to oncohistones, which mainly thrive and flourish in specific chromatin states during very narrow windows of development, creating exquisite vulnerabilities, which could provide effective therapies for these deadly cancers.
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Affiliation(s)
| | - Carol C L Chen
- Department of Human Genetics, McGill University, Montreal, QC, H3A 0C7, Canada
| | - Nada Jabado
- Department of Human Genetics, McGill University, Montreal, QC, H3A 0C7, Canada; Department of Pediatrics, McGill University, Montreal, QC, H3A 0C7, Canada; The Research Institute of the McGill University Health Centre, Montreal, QC, H4A 3J1, Canada.
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34
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Lovibond S, Gewirtz AN, Pasquini L, Krebs S, Graham MS. The promise of metabolic imaging in diffuse midline glioma. Neoplasia 2023; 39:100896. [PMID: 36944297 PMCID: PMC10036941 DOI: 10.1016/j.neo.2023.100896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 02/10/2023] [Accepted: 03/13/2023] [Indexed: 03/23/2023]
Abstract
Recent insights into histopathological and molecular subgroups of glioma have revolutionized the field of neuro-oncology by refining diagnostic categories. An emblematic example in pediatric neuro-oncology is the newly defined diffuse midline glioma (DMG), H3 K27-altered. DMG represents a rare tumor with a dismal prognosis. The diagnosis of DMG is largely based on clinical presentation and characteristic features on conventional magnetic resonance imaging (MRI), with biopsy limited by its delicate neuroanatomic location. Standard MRI remains limited in its ability to characterize tumor biology. Advanced MRI and positron emission tomography (PET) imaging offer additional value as they enable non-invasive evaluation of molecular and metabolic features of brain tumors. These techniques have been widely used for tumor detection, metabolic characterization and treatment response monitoring of brain tumors. However, their role in the realm of pediatric DMG is nascent. By summarizing DMG metabolic pathways in conjunction with their imaging surrogates, we aim to elucidate the untapped potential of such imaging techniques in this devastating disease.
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Affiliation(s)
- Samantha Lovibond
- Molecular Imaging and Therapy Service, Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexandra N Gewirtz
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Luca Pasquini
- Molecular Imaging and Therapy Service, Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Simone Krebs
- Molecular Imaging and Therapy Service, Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Radiochemistry and Imaging Sciences Service, Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Radiology, Weill Cornell Medical College, New York, NY 10065, USA
| | - Maya S Graham
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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35
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Abstract
Our defenses against infection rely on the ability of the immune system to distinguish invading pathogens from self. This task is exceptionally challenging, if not seemingly impossible, in the case of retroviruses that have integrated almost seamlessly into the host. This review examines the limits of innate and adaptive immune responses elicited by endogenous retroviruses and other retroelements, the targets of immune recognition, and the consequences for host health and disease. Contrary to theoretical expectation, endogenous retroelements retain substantial immunogenicity, which manifests most profoundly when their epigenetic repression is compromised, contributing to autoinflammatory and autoimmune disease and age-related inflammation. Nevertheless, recent evidence suggests that regulated immune reactivity to endogenous retroelements is integral to immune system development and function, underpinning cancer immunosurveillance, resistance to infection, and responses to the microbiota. Elucidation of the interaction points with endogenous retroelements will therefore deepen our understanding of immune system function and contribution to disease.
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Affiliation(s)
- George Kassiotis
- Retroviral Immunology Laboratory, The Francis Crick Institute, London, United Kingdom;
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
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36
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Park J, Chung C. Epigenetic and Metabolic Changes in Diffuse Intrinsic Pontine Glioma. Brain Tumor Res Treat 2023; 11:86-93. [PMID: 37151150 PMCID: PMC10172016 DOI: 10.14791/btrt.2023.0011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/07/2023] [Accepted: 04/13/2023] [Indexed: 05/09/2023] Open
Abstract
Diffuse midline glioma (DMG), hitherto known as diffuse intrinsic pontine glioma (DIPG), is a rare and aggressive form of brain cancer that primarily affects children. Although the exact cause of DMG/DIPG is not known, a large proportion of DMG/DIPG tumors harbor mutations in the gene encoding the histone H3 protein, specifically the H3K27M mutation. This mutation decreases the level of H3K27me3, a histone modification that plays a vital role in regulating gene expression through epigenetic regulation. The mutation also alters the function of polycomb repressive complex 2 (PRC2), thereby preventing the repression of genes associated with cancer development. The decrease in H3K27me3 caused by the histone H3 mutation is accompanied by an increase in the level of H3K27ac, a post-translational modification related to active transcription. Dysregulation of histone modification markedly affects gene expression, contributing to cancer development and progression by promoting uncontrolled cell proliferation, tumor growth, and metabolism. DMG/DIPG alters the metabolism of methionine and the tricarboxylic acid cycle, as well as glucose and glutamine uptake. The role of epigenetic and metabolic changes in the development of DMG/DIPG has been studied extensively, and understanding these changes is critical to developing therapies targeting these pathways. Studies are currently underway to identify new therapeutic targets for DMG/DIPG, which may lead to the development of effective treatments for this devastating disease.
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Affiliation(s)
- Jiyoon Park
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Korea
- New Biology Research Center (NBRC), Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Korea
| | - Chan Chung
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Korea
- New Biology Research Center (NBRC), Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Korea.
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37
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Cohen LRZ, Kaffe B, Deri E, Leibson C, Nissim-Rafinia M, Maman M, Harpaz N, Ron G, Shema E, Meshorer E. PRC2-independent actions of H3.3K27M in embryonic stem cell differentiation. Nucleic Acids Res 2023; 51:1662-1673. [PMID: 36156096 PMCID: PMC9976889 DOI: 10.1093/nar/gkac800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/28/2022] [Accepted: 09/06/2022] [Indexed: 01/11/2023] Open
Abstract
The histone H3 variant, H3.3, is localized at specific regions in the genome, especially promoters and active enhancers, and has been shown to play important roles in development. A lysine to methionine substitution in position 27 (H3.3K27M) is a main cause of Diffuse Intrinsic Pontine Glioma (specifically Diffuse Midline Glioma, K27M-mutant), a lethal type of pediatric cancer. H3.3K27M has a dominant-negative effect by inhibiting the Polycomb Repressor Complex 2 (PRC2) activity. Here, we studied the immediate, genome-wide, consequences of the H3.3K27M mutation independent of PRC2 activity. We developed Doxycycline (Dox)-inducible mouse embryonic stem cells (ESCs) carrying a single extra copy of WT-H3.3, H3.3K27M and H3.3K27L, all fused to HA. We performed RNA-Seq and ChIP-Seq at different times following Dox induction in undifferentiated and differentiated ESCs. We find increased binding of H3.3 around transcription start sites in cells expressing both H3.3K27M and H3.3K27L compared with WT, but not in cells treated with PRC2 inhibitors. Differentiated cells carrying either H3.3K27M or H3.3K27L retain expression of ESC-active genes, in expense of expression of genes related to neuronal differentiation. Taken together, our data suggest that a modifiable H3.3K27 is required for proper histone incorporation and cellular maturation, independent of PRC2 activity.
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Affiliation(s)
- Lea R Z Cohen
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel.,The Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Binyamin Kaffe
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Eden Deri
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel.,The Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Chen Leibson
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Malka Nissim-Rafinia
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Moria Maman
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Nofar Harpaz
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Guy Ron
- The Racah Institute of Physics, The Center for Nanoscience and Nanotechnology, The Hebrew University, Jerusalem 9190401, Israel
| | - Efrat Shema
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Eran Meshorer
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel.,The Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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38
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Costa PMDS, Sales SLA, Pinheiro DP, Pontes LQ, Maranhão SS, Pessoa CDÓ, Furtado GP, Furtado CLM. Epigenetic reprogramming in cancer: From diagnosis to treatment. Front Cell Dev Biol 2023; 11:1116805. [PMID: 36866275 PMCID: PMC9974167 DOI: 10.3389/fcell.2023.1116805] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 02/01/2023] [Indexed: 02/16/2023] Open
Abstract
Disruption of the epigenetic program of gene expression is a hallmark of cancer that initiates and propagates tumorigenesis. Altered DNA methylation, histone modifications and ncRNAs expression are a feature of cancer cells. The dynamic epigenetic changes during oncogenic transformation are related to tumor heterogeneity, unlimited self-renewal and multi-lineage differentiation. This stem cell-like state or the aberrant reprogramming of cancer stem cells is the major challenge in treatment and drug resistance. Given the reversible nature of epigenetic modifications, the ability to restore the cancer epigenome through the inhibition of the epigenetic modifiers is a promising therapy for cancer treatment, either as a monotherapy or in combination with other anticancer therapies, including immunotherapies. Herein, we highlighted the main epigenetic alterations, their potential as a biomarker for early diagnosis and the epigenetic therapies approved for cancer treatment.
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Affiliation(s)
- Pedro Mikael da Silva Costa
- Department of Physiology and Pharmacology, Drug Research and Development Center, Federal University of Ceará, Fortaleza, Ceará, Brazil,Postgraduation Program in Biotechnology Northeastern Network of Biotechnology, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Sarah Leyenne Alves Sales
- Department of Physiology and Pharmacology, Drug Research and Development Center, Federal University of Ceará, Fortaleza, Ceará, Brazil,Postgraduation Program in Pharmacology, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | | | - Larissa Queiroz Pontes
- Oswaldo Cruz Foundation, FIOCRUZ-Ceará, Sector of Biotechnology, Eusebio, Ceará, Brazil,Postgraduation Program in Biotechnology and Natural Resources, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Sarah Sant’Anna Maranhão
- Department of Physiology and Pharmacology, Drug Research and Development Center, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Claudia do Ó. Pessoa
- Department of Physiology and Pharmacology, Drug Research and Development Center, Federal University of Ceará, Fortaleza, Ceará, Brazil,Postgraduation Program in Biotechnology Northeastern Network of Biotechnology, Federal University of Ceará, Fortaleza, Ceará, Brazil,Postgraduation Program in Pharmacology, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Gilvan Pessoa Furtado
- Oswaldo Cruz Foundation, FIOCRUZ-Ceará, Sector of Biotechnology, Eusebio, Ceará, Brazil,Postgraduation Program in Biotechnology and Natural Resources, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Cristiana Libardi Miranda Furtado
- Drug Research and Development Center, Postgraduate Program in Translational Medicine, Federal University of Ceará, Fortaleza, Ceará, Brazil,Experimental Biology Center, University of Fortaleza, Fortaleza, Ceará, Brazil,*Correspondence: Cristiana Libardi Miranda Furtado,
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39
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Pun M, Pratt D, Nano PR, Joshi PK, Jiang L, Englinger B, Rao A, Cieslik M, Chinnaiyan AM, Aldape K, Pfister S, Filbin MG, Bhaduri A, Venneti S. Common molecular features of H3K27M DMGs and PFA ependymomas map to hindbrain developmental pathways. Acta Neuropathol Commun 2023; 11:25. [PMID: 36759899 PMCID: PMC9912509 DOI: 10.1186/s40478-023-01514-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/11/2023] [Indexed: 02/11/2023] Open
Abstract
Globally decreased histone 3, lysine 27 tri-methylation (H3K27me3) is a hallmark of H3K27-altered diffuse midline gliomas (DMGs) and group-A posterior fossa ependymomas (PFAs). H3K27-altered DMGs are largely characterized by lysine-to-methionine mutations in histone 3 at position 27 (H3K27M). Most PFAs overexpress EZH inhibitory protein (EZHIP), which possesses a region of similarity to the mutant H3K27M. Both H3K27M and EZHIP inhibit the function of the polycomb repressive complex 2 (PRC2) responsible for H3K27me3 deposition. These tumors often arise in neighboring regions of the brainstem and posterior fossa. In rare cases PFAs harbor H3K27M mutations, and DMGs overexpress EZHIP. These findings together raise the possibility that certain cell populations in the developing hindbrain/posterior fossa are especially sensitive to modulation of H3K27me3 states. We identified shared molecular features by comparing genomic, bulk transcriptomic, chromatin-based profiles, and single-cell RNA-sequencing (scRNA-seq) data from the two tumor classes. Our approach demonstrated that 1q gain, a key biomarker in PFAs, is prognostic in H3.1K27M, but not H3.3K27M gliomas. Conversely, Activin A Receptor Type 1 (ACVR1), which is associated with mutations in H3.1K27M gliomas, is overexpressed in a subset of PFAs with poor outcome. Despite diffuse H3K27me3 reduction, previous work shows that both tumors maintain genomic H3K27me3 deposition at select sites. We demonstrate heterogeneity in shared patterns of residual H3K27me3 for both tumors that largely segregated with inferred anatomic tumor origins and progenitor populations of tumor cells. In contrast, analysis of genes linked to H3K27 acetylation (H3K27ac)-marked enhancers showed higher expression in astrocytic-like tumor cells. Finally, common H3K27me3-marked genes mapped closely to expression patterns in the human developing hindbrain. Overall, our data demonstrate developmentally relevant molecular similarities between PFAs and H3K27M DMGs and support the overall hypothesis that deregulated mechanisms of hindbrain development are central to the biology of both tumors.
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Affiliation(s)
- Matthew Pun
- Laboratory of Brain Tumor Metabolism and Epigenetics, Department of Pathology, University of Michigan, 3520E MSRB 1, 1150 W. Medical Center, Ann Arbor, MI, 41804, USA
- Chad Carr Pediatric Tumor Center, Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Medical Scientist Training Program, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Drew Pratt
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Dr., Room 2S235, Bethesda, MD, 20892, USA
| | - Patricia R Nano
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Piyush K Joshi
- Hopp Children's Cancer Center (KiTZ) Heidelberg, Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Li Jiang
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02115, USA
| | - Bernhard Englinger
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Department of Urology, Comprehensive Cancer Center, Medical University of Vienna, 1090, Vienna, Austria
- Center for Cancer Research and Comprehensive Cancer Center, Medical University Vienna, 1090, Vienna, Austria
| | - Arvind Rao
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Marcin Cieslik
- Michigan Center for Translational Pathology, Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Howard Hughes Medical Institute, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Kenneth Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Dr., Room 2S235, Bethesda, MD, 20892, USA
| | - Stefan Pfister
- Hopp Children's Cancer Center (KiTZ) Heidelberg, Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120, Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, 69120, Heidelberg, Germany
| | - Mariella G Filbin
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Aparna Bhaduri
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Sriram Venneti
- Laboratory of Brain Tumor Metabolism and Epigenetics, Department of Pathology, University of Michigan, 3520E MSRB 1, 1150 W. Medical Center, Ann Arbor, MI, 41804, USA.
- Chad Carr Pediatric Tumor Center, Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA.
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
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40
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Endogenous retroelements as alarms for disruptions to cellular homeostasis. Trends Cancer 2023; 9:55-68. [PMID: 36216729 DOI: 10.1016/j.trecan.2022.09.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 08/28/2022] [Accepted: 09/07/2022] [Indexed: 11/05/2022]
Abstract
Endogenous retroelements are DNA sequences which can duplicate and move to new locations in the genome. Actively moving endogenous retroelements can be disruptive to the host, and their expression is therefore often repressed. Interestingly, drugs that disrupt the repression of endogenous retroelements show promise for treating cancer. Expressed endogenous retroelements can activate innate immune receptors that activate the antiviral response, potentially leading to the death of cancer cells. We discuss disruptions to cellular processes which can lead to activation of the antiviral state from endogenous retroelements, and present the 'fire alarm hypothesis', where we argue that endogenous retroelements act as alarms for disruptions to these cellular processes. Furthermore, we discuss the properties of endogenous retroelements which make them suitable as alarms.
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Rechberger JS, Power BT, Power EA, Nesvick CL, Daniels DJ. H3K27-altered diffuse midline glioma: a paradigm shifting opportunity in direct delivery of targeted therapeutics. Expert Opin Ther Targets 2023; 27:9-17. [PMID: 36744399 PMCID: PMC10165636 DOI: 10.1080/14728222.2023.2177531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Despite much progress, the prognosis for H3K27-altered diffuse midline glioma (DMG), previously known as diffuse intrinsic pontine glioma when located in the brainstem, remains dark and dismal. AREAS COVERED A wealth of research over the past decade has revolutionized our understanding of the molecular basis of DMG, revealing potential targetable vulnerabilities for treatment of this lethal childhood cancer. However, obstacles to successful clinical implementation of novel therapies remain, including effective delivery across the blood-brain barrier (BBB) to the tumor site. Here, we review relevant literature and clinical trials and discuss direct drug delivery via convection-enhanced delivery (CED) as a promising treatment modality for DMG. We outline a comprehensive molecular, pharmacological, and procedural approach that may offer hope for afflicted patients and their families. EXPERT OPINION Challenges remain in successful drug delivery to DMG. While CED and other techniques offer a chance to bypass the BBB, the variables influencing successful intratumoral targeting are numerous and complex. We discuss these variables and potential solutions that could lead to the successful clinical implementation of preclinically promising therapeutic agents.
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Affiliation(s)
- Julian S Rechberger
- Department of Neurologic Surgery, Mayo Clinic, Rochester, MN, USA.,Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic Graduate School of Biomedical Sciences, Rochester, MN, USA
| | - Blake T Power
- Department of Neurologic Surgery, Mayo Clinic, Rochester, MN, USA
| | - Erica A Power
- Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Cody L Nesvick
- Department of Neurologic Surgery, Mayo Clinic, Rochester, MN, USA
| | - David J Daniels
- Department of Neurologic Surgery, Mayo Clinic, Rochester, MN, USA.,Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic Graduate School of Biomedical Sciences, Rochester, MN, USA
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42
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Skouras P, Markouli M, Strepkos D, Piperi C. Advances on Epigenetic Drugs for Pediatric Brain Tumors. Curr Neuropharmacol 2023; 21:1519-1535. [PMID: 36154607 PMCID: PMC10472812 DOI: 10.2174/1570159x20666220922150456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 08/14/2022] [Accepted: 09/08/2022] [Indexed: 11/22/2022] Open
Abstract
Pediatric malignant brain tumors represent the most frequent cause of cancer-related deaths in childhood. The therapeutic scheme of surgery, radiotherapy and chemotherapy has improved patient management, but with minimal progress in patients' prognosis. Emerging molecular targets and mechanisms have revealed novel approaches for pediatric brain tumor therapy, enabling personalized medical treatment. Advances in the field of epigenetic research and their interplay with genetic changes have enriched our knowledge of the molecular heterogeneity of these neoplasms and have revealed important genes that affect crucial signaling pathways involved in tumor progression. The great potential of epigenetic therapy lies mainly in the widespread location and the reversibility of epigenetic alterations, proposing a wide range of targeting options, including the possible combination of chemoand immunotherapy, significantly increasing their efficacy. Epigenetic drugs, including inhibitors of DNA methyltransferases, histone deacetylases and demethylases, are currently being tested in clinical trials on pediatric brain tumors. Additional novel epigenetic drugs include protein and enzyme inhibitors that modulate epigenetic modification pathways, such as Bromodomain and Extraterminal (BET) proteins, Cyclin-Dependent Kinase 9 (CDK9), AXL, Facilitates Chromatin Transcription (FACT), BMI1, and CREB Binding Protein (CBP) inhibitors, which can be used either as standalone or in combination with current treatment approaches. In this review, we discuss recent progress on epigenetic drugs that could possibly be used against the most common malignant tumors of childhood, such as medulloblastomas, high-grade gliomas and ependymomas.
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Affiliation(s)
- Panagiotis Skouras
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Mariam Markouli
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Dimitrios Strepkos
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Christina Piperi
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
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Groves A, Cooney TM. Epigenetic programming of pediatric high-grade glioma: Pushing beyond proof of concept to clinical benefit. Front Cell Dev Biol 2022; 10:1089898. [PMID: 36589742 PMCID: PMC9795020 DOI: 10.3389/fcell.2022.1089898] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 12/05/2022] [Indexed: 12/15/2022] Open
Abstract
Pediatric high-grade gliomas (pHGG) are a molecularly diverse group of malignancies, each incredibly aggressive and in dire need of treatment advancements. Genomic analysis has revolutionized our understanding of these tumors, identifying biologically relevant subgroups with differing canonical mutational profiles that vary based on tumor location and age. In particular, the discovery of recurrent histone H3 mutations (H3K27M in diffuse midline glioma, H3G34R/V in hemispheric pediatric high-grade gliomas) as unique "oncohistone" drivers revealed epigenetic dysregulation as a hallmark of pediatric high-grade gliomas oncogenesis. While reversing this signature through epigenetic programming has proven effective in several pre-clinical survival models, early results from pediatric high-grade gliomas clinical trials suggest that epigenetic modifier monotherapy will likely not provide long-term disease control. In this review we summarize the genetic, epigenetic, and cellular heterogeneity of pediatric high-grade gliomas, and highlight potential paths forward for epigenetic programming in this devastating disease.
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Affiliation(s)
- Andrew Groves
- Division of Hematology/Oncology, University of Iowa Stead Family Children’s Hospital, Iowa City, IA, United States,*Correspondence: Andrew Groves,
| | - Tabitha M. Cooney
- Dana Farber/Boston Children’s Cancer and Blood Disorder Center, Boston, MA, United States
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44
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K27M in canonical and noncanonical H3 variants occurs in distinct oligodendroglial cell lineages in brain midline gliomas. Nat Genet 2022; 54:1865-1880. [PMID: 36471070 PMCID: PMC9742294 DOI: 10.1038/s41588-022-01205-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 09/16/2022] [Indexed: 12/12/2022]
Abstract
Canonical (H3.1/H3.2) and noncanonical (H3.3) histone 3 K27M-mutant gliomas have unique spatiotemporal distributions, partner alterations and molecular profiles. The contribution of the cell of origin to these differences has been challenging to uncouple from the oncogenic reprogramming induced by the mutation. Here, we perform an integrated analysis of 116 tumors, including single-cell transcriptome and chromatin accessibility, 3D chromatin architecture and epigenomic profiles, and show that K27M-mutant gliomas faithfully maintain chromatin configuration at developmental genes consistent with anatomically distinct oligodendrocyte precursor cells (OPCs). H3.3K27M thalamic gliomas map to prosomere 2-derived lineages. In turn, H3.1K27M ACVR1-mutant pontine gliomas uniformly mirror early ventral NKX6-1+/SHH-dependent brainstem OPCs, whereas H3.3K27M gliomas frequently resemble dorsal PAX3+/BMP-dependent progenitors. Our data suggest a context-specific vulnerability in H3.1K27M-mutant SHH-dependent ventral OPCs, which rely on acquisition of ACVR1 mutations to drive aberrant BMP signaling required for oncogenesis. The unifying action of K27M mutations is to restrict H3K27me3 at PRC2 landing sites, whereas other epigenetic changes are mainly contingent on the cell of origin chromatin state and cycling rate.
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Cottone L, Ligammari L, Lee HM, Knowles HJ, Henderson S, Bianco S, Davies C, Strauss S, Amary F, Leite AP, Tirabosco R, Haendler K, Schultze JL, Herrero J, O’Donnell P, Grigoriadis AE, Salomoni P, Flanagan AM. Aberrant paracrine signalling for bone remodelling underlies the mutant histone-driven giant cell tumour of bone. Cell Death Differ 2022; 29:2459-2471. [PMID: 36138226 PMCID: PMC9750984 DOI: 10.1038/s41418-022-01031-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/09/2022] [Accepted: 06/10/2022] [Indexed: 01/31/2023] Open
Abstract
Oncohistones represent compelling evidence for a causative role of epigenetic perturbations in cancer. Giant cell tumours of bone (GCTs) are characterised by a mutated histone H3.3 as the sole genetic driver present in bone-forming osteoprogenitor cells but absent from abnormally large bone-resorbing osteoclasts which represent the hallmark of these neoplasms. While these striking features imply a pathogenic interaction between mesenchymal and myelomonocytic lineages during GCT development, the underlying mechanisms remain unknown. We show that the changes in the transcriptome and epigenome in the mesenchymal cells caused by the H3.3-G34W mutation contribute to increase osteoclast recruitment in part via reduced expression of the TGFβ-like soluble factor, SCUBE3. Transcriptional changes in SCUBE3 are associated with altered histone marks and H3.3G34W enrichment at its enhancer regions. In turn, osteoclasts secrete unregulated amounts of SEMA4D which enhances proliferation of mutated osteoprogenitors arresting their maturation. These findings provide a mechanism by which GCTs undergo differentiation in response to denosumab, a drug that depletes the tumour of osteoclasts. In contrast, hTERT alterations, commonly found in malignant GCT, result in the histone-mutated neoplastic cells being independent of osteoclasts for their proliferation, predicting unresponsiveness to denosumab. We provide a mechanism for the initiation of GCT, the basis of which is dysfunctional cross-talk between bone-forming and bone-resorbing cells. The findings highlight the role of tumour/microenvironment bidirectional interactions in tumorigenesis and how this is exploited in the treatment of GCT.
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Affiliation(s)
- Lucia Cottone
- grid.83440.3b0000000121901201Department of Pathology, UCL Cancer Institute, University College London, London, WC1E 6BT UK
| | - Lorena Ligammari
- grid.83440.3b0000000121901201Department of Pathology, UCL Cancer Institute, University College London, London, WC1E 6BT UK
| | - Hang-Mao Lee
- grid.424247.30000 0004 0438 0426German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
| | - Helen J. Knowles
- grid.4991.50000 0004 1936 8948Botnar Institute for Musculoskeletal Sciences, Nuffield Department of Orthopaedics Rheumatology & Musculoskeletal Sciences, University of Oxford, Oxford, OX3 7LD UK
| | - Stephen Henderson
- grid.83440.3b0000000121901201Bill Lyons Informatics Centre (BLIC), UCL Cancer Institute, University College London, London, WC1E 6BT UK
| | - Sara Bianco
- grid.83440.3b0000000121901201Department of Pathology, UCL Cancer Institute, University College London, London, WC1E 6BT UK ,grid.83440.3b0000000121901201Samantha Dickson Brain Cancer Unit, Department of Cancer Biology, UCL Cancer Institute, University College London, London, WC1E 6BT UK
| | - Christopher Davies
- grid.83440.3b0000000121901201Department of Pathology, UCL Cancer Institute, University College London, London, WC1E 6BT UK ,grid.416177.20000 0004 0417 7890Department of Histopathology, Royal National Orthopaedic Hospital, Middlesex, Stanmore, HA7 4LP UK
| | - Sandra Strauss
- grid.439749.40000 0004 0612 2754London Sarcoma Service, University College London Hospitals Foundation Trust, London, WC1E 6DD UK
| | - Fernanda Amary
- grid.416177.20000 0004 0417 7890Department of Histopathology, Royal National Orthopaedic Hospital, Middlesex, Stanmore, HA7 4LP UK
| | - Ana Paula Leite
- grid.83440.3b0000000121901201Department of Pathology, UCL Cancer Institute, University College London, London, WC1E 6BT UK ,grid.83440.3b0000000121901201Samantha Dickson Brain Cancer Unit, Department of Cancer Biology, UCL Cancer Institute, University College London, London, WC1E 6BT UK
| | - Roberto Tirabosco
- grid.416177.20000 0004 0417 7890Department of Histopathology, Royal National Orthopaedic Hospital, Middlesex, Stanmore, HA7 4LP UK
| | - Kristian Haendler
- grid.424247.30000 0004 0438 0426German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany ,grid.10388.320000 0001 2240 3300Platform for Single Cell Genomics and Epigenomics (PRECISE) at the DZNE and the University of Bonn, 53127 Bonn, Germany ,grid.4562.50000 0001 0057 2672Institute of Human Genetics, University of Lübeck, Lübeck, Germany
| | - Joachim L. Schultze
- grid.424247.30000 0004 0438 0426German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany ,grid.10388.320000 0001 2240 3300Platform for Single Cell Genomics and Epigenomics (PRECISE) at the DZNE and the University of Bonn, 53127 Bonn, Germany ,grid.10388.320000 0001 2240 3300Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, 53115 Bonn, Germany
| | - Javier Herrero
- grid.83440.3b0000000121901201Bill Lyons Informatics Centre (BLIC), UCL Cancer Institute, University College London, London, WC1E 6BT UK
| | - Paul O’Donnell
- grid.416177.20000 0004 0417 7890Department of Radiology, Royal National Orthopaedic Hospital, Middlesex, Stanmore, HA7 4LP UK
| | - Agamemnon E. Grigoriadis
- grid.239826.40000 0004 0391 895XCentre for Craniofacial and Regenerative Biology, King’s College London, Guy’s Hospital, London, SE1 9RT UK
| | - Paolo Salomoni
- grid.424247.30000 0004 0438 0426German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany ,grid.83440.3b0000000121901201Samantha Dickson Brain Cancer Unit, Department of Cancer Biology, UCL Cancer Institute, University College London, London, WC1E 6BT UK
| | - Adrienne M. Flanagan
- grid.83440.3b0000000121901201Department of Pathology, UCL Cancer Institute, University College London, London, WC1E 6BT UK ,grid.416177.20000 0004 0417 7890Department of Histopathology, Royal National Orthopaedic Hospital, Middlesex, Stanmore, HA7 4LP UK
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Pal S, Kaplan JP, Nguyen H, Stopka SA, Savani MR, Regan MS, Nguyen QD, Jones KL, Moreau LA, Peng J, Dipiazza MG, Perciaccante AJ, Zhu X, Hunsel BR, Liu KX, Alexandrescu S, Drissi R, Filbin MG, McBrayer SK, Agar NYR, Chowdhury D, Haas-Kogan DA. A druggable addiction to de novo pyrimidine biosynthesis in diffuse midline glioma. Cancer Cell 2022; 40:957-972.e10. [PMID: 35985342 PMCID: PMC9575661 DOI: 10.1016/j.ccell.2022.07.012] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 06/09/2022] [Accepted: 07/26/2022] [Indexed: 12/18/2022]
Abstract
Diffuse midline glioma (DMG) is a uniformly fatal pediatric cancer driven by oncohistones that do not readily lend themselves to drug development. To identify druggable targets for DMG, we conducted a genome-wide CRISPR screen that reveals a DMG selective dependency on the de novo pathway for pyrimidine biosynthesis. This metabolic vulnerability reflects an elevated rate of uridine/uracil degradation that depletes DMG cells of substrates for the alternate salvage pyrimidine biosynthesis pathway. A clinical stage inhibitor of DHODH (rate-limiting enzyme in the de novo pathway) diminishes uridine-5'-phosphate (UMP) pools, generates DNA damage, and induces apoptosis through suppression of replication forks-an "on-target" effect, as shown by uridine rescue. Matrix-assisted laser desorption/ionization (MALDI) mass spectroscopy imaging demonstrates that this DHODH inhibitor (BAY2402234) accumulates in the brain at therapeutically relevant concentrations, suppresses de novo pyrimidine biosynthesis in vivo, and prolongs survival of mice bearing intracranial DMG xenografts, highlighting BAY2402234 as a promising therapy against DMGs.
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Affiliation(s)
- Sharmistha Pal
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jakub P Kaplan
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Huy Nguyen
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Sylwia A Stopka
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA; Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Milan R Savani
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Michael S Regan
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Quang-De Nguyen
- Lurie Family Imaging Center, Center for Biomedical Imaging in Oncology, Dana-Farber Cancer Institute, Boston, MA 02210, USA
| | - Kristen L Jones
- Lurie Family Imaging Center, Center for Biomedical Imaging in Oncology, Dana-Farber Cancer Institute, Boston, MA 02210, USA
| | - Lisa A Moreau
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jingyu Peng
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Marina G Dipiazza
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Andrew J Perciaccante
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Xiaoting Zhu
- Center for Childhood Cancer and Blood Diseases, Nationwide Children's Hospital, Columbus, OH 43205, USA; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Bradley R Hunsel
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Kevin X Liu
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Radiation Oncology, Brigham and Women's Hospital, Boston Children's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Sanda Alexandrescu
- Department of Pathology, Harvard Medical School Boston, Boston Children's Hospital, 300 Longwood Avenue, Bader 104, Boston, MA 02115, USA
| | - Rachid Drissi
- Center for Childhood Cancer and Blood Diseases, Nationwide Children's Hospital, Columbus, OH 43205, USA; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Mariella G Filbin
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA 02115, USA
| | - Samuel K McBrayer
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Nathalie Y R Agar
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA; Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Dipanjan Chowdhury
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Daphne A Haas-Kogan
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Radiation Oncology, Brigham and Women's Hospital, Boston Children's Hospital, Harvard Medical School, Boston, MA 02215, USA.
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Karami Fath M, Babakhaniyan K, Anjomrooz M, Jalalifar M, Alizadeh SD, Pourghasem Z, Abbasi Oshagh P, Azargoonjahromi A, Almasi F, Manzoor HZ, Khalesi B, Pourzardosht N, Khalili S, Payandeh Z. Recent Advances in Glioma Cancer Treatment: Conventional and Epigenetic Realms. Vaccines (Basel) 2022; 10:vaccines10091448. [PMID: 36146527 PMCID: PMC9501259 DOI: 10.3390/vaccines10091448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/14/2022] [Accepted: 08/27/2022] [Indexed: 11/29/2022] Open
Abstract
Glioblastoma (GBM) is the most typical and aggressive form of primary brain tumor in adults, with a poor prognosis. Successful glioma treatment is hampered by ineffective medication distribution across the blood-brain barrier (BBB) and the emergence of drug resistance. Although a few FDA-approved multimodal treatments are available for glioblastoma, most patients still have poor prognoses. Targeting epigenetic variables, immunotherapy, gene therapy, and different vaccine- and peptide-based treatments are some innovative approaches to improve anti-glioma treatment efficacy. Following the identification of lymphatics in the central nervous system, immunotherapy offers a potential method with the potency to permeate the blood-brain barrier. This review will discuss the rationale, tactics, benefits, and drawbacks of current glioma therapy options in clinical and preclinical investigations.
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Affiliation(s)
- Mohsen Karami Fath
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran 1571914911, Iran
| | - Kimiya Babakhaniyan
- Department of Medical Surgical Nursing, School of Nursing and Midwifery, Iran University of Medical Sciences, Tehran 1996713883, Iran
| | - Mehran Anjomrooz
- Department of Radiology, Shariati Hospital, Tehran University of Medical Sciences, Tehran 1411713135, Iran
| | | | | | - Zeinab Pourghasem
- Department of Microbiology, Islamic Azad University of Lahijan, Gilan 4416939515, Iran
| | - Parisa Abbasi Oshagh
- Department of Biology, Faculty of Basic Sciences, Malayer University, Malayer 6571995863, Iran
| | - Ali Azargoonjahromi
- Department of Nursing, School of Nursing and Midwifery, Shiraz University of Medical Sciences, Shiraz 7417773539, Iran
| | - Faezeh Almasi
- Pharmaceutical Biotechnology Lab, Department of Microbial Biotechnology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran 1411734115, Iran
| | - Hafza Zahira Manzoor
- Experimental and Translational Medicine, University of Insubria, Via jean Henry Dunant 3, 21100 Varese, Italy
| | - Bahman Khalesi
- Department of Research and Production of Poultry Viral Vaccine, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization, Karaj 3197619751, Iran
| | - Navid Pourzardosht
- Cellular and Molecular Research Center, Faculty of Medicine, Guilan University of Medical Sciences, Rasht 4193713111, Iran
| | - Saeed Khalili
- Department of Biology Sciences, Shahid Rajaee Teacher Training University, Tehran 1678815811, Iran
- Correspondence: (S.K.); (Z.P.)
| | - Zahra Payandeh
- Department of Medical Biochemistry and Biophysics, Division Medical Inflammation Research, Karolinska Institute, SE-17177 Stockholm, Sweden
- Correspondence: (S.K.); (Z.P.)
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48
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Doyle EJ, Morey L, Conway E. Know when to fold 'em: Polycomb complexes in oncogenic 3D genome regulation. Front Cell Dev Biol 2022; 10:986319. [PMID: 36105358 PMCID: PMC9464936 DOI: 10.3389/fcell.2022.986319] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 08/04/2022] [Indexed: 11/13/2022] Open
Abstract
Chromatin is spatially and temporally regulated through a series of orchestrated processes resulting in the formation of 3D chromatin structures such as topologically associating domains (TADs), loops and Polycomb Bodies. These structures are closely linked to transcriptional regulation, with loss of control of these processes a frequent feature of cancer and developmental syndromes. One such oncogenic disruption of the 3D genome is through recurrent dysregulation of Polycomb Group Complex (PcG) functions either through genetic mutations, amplification or deletion of genes that encode for PcG proteins. PcG complexes are evolutionarily conserved epigenetic complexes. They are key for early development and are essential transcriptional repressors. PcG complexes include PRC1, PRC2 and PR-DUB which are responsible for the control of the histone modifications H2AK119ub1 and H3K27me3. The spatial distribution of the complexes within the nuclear environment, and their associated modifications have profound effects on the regulation of gene transcription and the 3D genome. Nevertheless, how PcG complexes regulate 3D chromatin organization is still poorly understood. Here we glean insights into the role of PcG complexes in 3D genome regulation and compaction, how these processes go awry during tumorigenesis and the therapeutic implications that result from our insights into these mechanisms.
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Affiliation(s)
- Emma J. Doyle
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin, Ireland
| | - Lluis Morey
- Sylvester Comprehensive Cancer Centre, Miami, FL, United States
- Department of Human Genetics, Biomedical Research Building, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Eric Conway
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin, Ireland
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
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Deng J, Hua L, Bian L, Chen H, Chen L, Cheng H, Dou C, Geng D, Hong T, Ji H, Jiang Y, Lan Q, Li G, Liu Z, Qi S, Qu Y, Shi S, Sun X, Wang H, You Y, Yu H, Yue S, Zhang J, Zhang X, Wang S, Mao Y, Zhong P, Gong Y. Molecular diagnosis and treatment of meningiomas: an expert consensus (2022). Chin Med J (Engl) 2022; 135:1894-1912. [PMID: 36179152 PMCID: PMC9746788 DOI: 10.1097/cm9.0000000000002391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Indexed: 11/27/2022] Open
Abstract
ABSTRACT Meningiomas are the most common primary intracranial neoplasm with diverse pathological types and complicated clinical manifestations. The fifth edition of the WHO Classification of Tumors of the Central Nervous System (WHO CNS5), published in 2021, introduces major changes that advance the role of molecular diagnostics in meningiomas. To follow the revision of WHO CNS5, this expert consensus statement was formed jointly by the Group of Neuro-Oncology, Society of Neurosurgery, Chinese Medical Association together with neuropathologists and evidence-based experts. The consensus provides reference points to integrate key biomarkers into stratification and clinical decision making for meningioma patients. REGISTRATION Practice guideline REgistration for transPAREncy (PREPARE), IPGRP-2022CN234.
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Affiliation(s)
- Jiaojiao Deng
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai 200040, China
- National Center for Neurological Disorders, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Lingyang Hua
- Shanghai Key Laboratory of Brain Function and Restoration and Neural Regeneration, Shanghai 200040, China
- Neurosurgical Institute of Fudan University, Shanghai 200040, China
- Shanghai Clinical Medical Center of Neurosurgery, Shanghai 200040, China
| | - Liuguan Bian
- Department of Neurosurgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Hong Chen
- Department of Pathology, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Ligang Chen
- Department of Neurosurgery, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Hongwei Cheng
- Department of Neurosurgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, China
| | - Changwu Dou
- Department of Neurosurgery, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia 750306, China
| | - Dangmurenjiapu Geng
- Department of Neurosurgery, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830011, China
| | - Tao Hong
- Department of Neurosurgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China
| | - Hongming Ji
- Department of Neurosurgery, Shanxi Medical University Shanxi Provincial People's Hospital, Taiyuan, Shanxi 030012, China
| | - Yugang Jiang
- Department of Neurosurgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Qing Lan
- Department of Neurosurgery, The Second Affiliated Hospital of Soochow University, Soochow, Jiangsu 215004, China
| | - Gang Li
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, Shandong 250063, China
| | - Zhixiong Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Songtao Qi
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Yan Qu
- Department of Neurosurgery, Tangdu Hospital, The Fourth Military Medical University, Xi’an, Shaanxi 710038, China
| | - Songsheng Shi
- Department of Neurosurgery, Fujian Medical University Affiliated Union Hospital, Fuzhou, Fujian 350001, China
| | - Xiaochuan Sun
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400042, China
| | - Haijun Wang
- Department of Neurosurgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510080, China
| | - Yongping You
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Hualin Yu
- Department of Neurosurgery, Kunming Medical University First Affiliated Hospital, Kunming, Yunnan 650032, China
| | - Shuyuan Yue
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Jianming Zhang
- Department of Neurosurgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China
| | - Xiaohua Zhang
- Department of Neurosurgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Shuo Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, China
| | - Ying Mao
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Ping Zhong
- Shanghai Key Laboratory of Brain Function and Restoration and Neural Regeneration, Shanghai 200040, China
- Neurosurgical Institute of Fudan University, Shanghai 200040, China
- Shanghai Clinical Medical Center of Neurosurgery, Shanghai 200040, China
| | - Ye Gong
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai 200040, China
- National Center for Neurological Disorders, Huashan Hospital, Fudan University, Shanghai 200040, China
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50
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Dubois FPB, Shapira O, Greenwald NF, Zack T, Wala J, Tsai JW, Crane A, Baguette A, Hadjadj D, Harutyunyan AS, Kumar KH, Blattner-Johnson M, Vogelzang J, Sousa C, Kang KS, Sinai C, Wang DK, Khadka P, Lewis K, Nguyen L, Malkin H, Ho P, O'Rourke R, Zhang S, Gold R, Deng D, Serrano J, Snuderl M, Jones C, Wright KD, Chi SN, Grill J, Kleinman CL, Goumnerova LC, Jabado N, Jones DTW, Kieran MW, Ligon KL, Beroukhim R, Bandopadhayay P. Structural variants shape driver combinations and outcomes in pediatric high-grade glioma. NATURE CANCER 2022; 3:994-1011. [PMID: 35788723 PMCID: PMC10365847 DOI: 10.1038/s43018-022-00403-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 05/23/2022] [Indexed: 12/13/2022]
Abstract
We analyzed the contributions of structural variants (SVs) to gliomagenesis across 179 pediatric high-grade gliomas (pHGGs). The most recurrent SVs targeted MYC isoforms and receptor tyrosine kinases (RTKs), including an SV amplifying a MYC enhancer in 12% of diffuse midline gliomas (DMG), indicating an underappreciated role for MYC in pHGG. SV signature analysis revealed that tumors with simple signatures were TP53 wild type (TP53WT) but showed alterations in TP53 pathway members PPM1D and MDM4. Complex signatures were associated with direct aberrations in TP53, CDKN2A and RB1 early in tumor evolution and with later-occurring extrachromosomal amplicons. All pHGGs exhibited at least one simple-SV signature, but complex-SV signatures were primarily restricted to subsets of H3.3K27M DMGs and hemispheric pHGGs. Importantly, DMGs with complex-SV signatures were associated with shorter overall survival independent of histone mutation and TP53 status. These data provide insight into the impact of SVs on gliomagenesis and the mechanisms that shape them.
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Affiliation(s)
- Frank P B Dubois
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ofer Shapira
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Noah F Greenwald
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Travis Zack
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jeremiah Wala
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jessica W Tsai
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Alexander Crane
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Audrey Baguette
- Quantitative Life Sciences, McGill University, Montreal, QC, Canada
| | - Djihad Hadjadj
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | | | - Kiran H Kumar
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mirjam Blattner-Johnson
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jayne Vogelzang
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Cecilia Sousa
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Kyung Shin Kang
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Claire Sinai
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Dayle K Wang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Prasidda Khadka
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Lan Nguyen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hayley Malkin
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Patricia Ho
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ryan O'Rourke
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Shu Zhang
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rose Gold
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Davy Deng
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Chris Jones
- Division of Cancer Therapeutics and Department of Molecular Pathology, Institute of Cancer Research 15 Cotswold Road, Sutton, London, UK
| | - Karen D Wright
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Susan N Chi
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Jacques Grill
- Department of Pediatric and Adolescent Oncology and INSERM Unit 981, Gustave Roussy Institute and University of Paris Saclay, Villejuif, France
| | - Claudia L Kleinman
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Lady Davis Research Institute, Jewish General Hospital, Montreal, QC, Canada
| | - Liliana C Goumnerova
- Department of Neurosurgery, Boston Children's Hospital; Dana Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- LCG: Tromboprotea, MWK: Day One Biopharmaceuticals, San Francisco, CA, USA
| | - Nada Jabado
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Division of Experimental Medicine, Department of Medicine and Department of Pediatrics, McGill University, and The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - David T W Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mark W Kieran
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- LCG: Tromboprotea, MWK: Day One Biopharmaceuticals, San Francisco, CA, USA
| | - Keith L Ligon
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
- Department of Pathology, Brigham & Women's Hospital and Boston Children's Hospital, Boston, USA.
- Center for Patient Derived Models, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Rameen Beroukhim
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.
| | - Pratiti Bandopadhayay
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA.
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