1
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Bruschi M, Midjek L, Ajlil Y, Vairy S, Lancien M, Ghermaoui S, Kergrohen T, Verreault M, Idbaih A, de Biagi CAO, Liu I, Filbin MG, Beccaria K, Blauwblomme T, Puget S, Tauziede-Espariat A, Varlet P, Dangouloff-Ros V, Boddaert N, Le Teuff G, Grill J, Montagnac G, Elkhatib N, Debily MA, Castel D. Diffuse midline glioma invasion and metastasis rely on cell-autonomous signaling. Neuro Oncol 2024; 26:553-568. [PMID: 37702430 PMCID: PMC10912010 DOI: 10.1093/neuonc/noad161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Indexed: 09/14/2023] Open
Abstract
BACKGROUND Diffuse midline gliomas (DMG) are pediatric tumors with negligible 2-year survival after diagnosis characterized by their ability to infiltrate the central nervous system. In the hope of controlling the local growth and slowing the disease, all patients receive radiotherapy. However, distant progression occurs frequently in DMG patients. Current clues as to what causes tumor infiltration circle mainly around the tumor microenvironment, but there are currently no known determinants to predict the degree of invasiveness. METHODS In this study, we use patient-derived glioma stem cells (GSCs) to create patient-specific 3D avatars to model interindividual invasion and elucidate the cellular supporting mechanisms. RESULTS We show that GSC models in 3D mirror the invasive behavior of the parental tumors, thus proving the ability of DMG to infiltrate as an autonomous characteristic of tumor cells. Furthermore, we distinguished 2 modes of migration, mesenchymal and ameboid-like, and associated the ameboid-like modality with GSCs derived from the most invasive tumors. Using transcriptomics of both organoids and primary tumors, we further characterized the invasive ameboid-like tumors as oligodendrocyte progenitor-like, with highly contractile cytoskeleton and reduced adhesion ability driven by crucial over-expression of bone morphogenetic pathway 7 (BMP7). Finally, we deciphered MEK, ERK, and Rho/ROCK kinases activated downstream of the BMP7 stimulation as actionable targets controlling tumor cell motility. CONCLUSIONS Our findings identify 2 new therapeutic avenues. First, patient-derived GSCs represent a predictive tool for patient stratification in order to adapt irradiation strategies. Second, autocrine and short-range BMP7-related signaling becomes a druggable target to prevent DMG spread and metastasis.
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Affiliation(s)
- Marco Bruschi
- Inserm U981, Molecular Predictors and New Targets in Oncology, Team Genomics and Oncogenesis of Pediatric Brain Tumors, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Lilia Midjek
- Inserm U1279, Gustave Roussy Institute, Université Paris-Saclay, Villejuif, France
| | - Yassine Ajlil
- Inserm U981, Molecular Predictors and New Targets in Oncology, Team Genomics and Oncogenesis of Pediatric Brain Tumors, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Stephanie Vairy
- Inserm U981, Molecular Predictors and New Targets in Oncology, Team Genomics and Oncogenesis of Pediatric Brain Tumors, Gustave Roussy, Université Paris-Saclay, Villejuif, France
- Département de Cancérologie de l’Enfant et de l’Adolescent, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Manon Lancien
- Inserm U981, Molecular Predictors and New Targets in Oncology, Team Genomics and Oncogenesis of Pediatric Brain Tumors, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Samia Ghermaoui
- Inserm U981, Molecular Predictors and New Targets in Oncology, Team Genomics and Oncogenesis of Pediatric Brain Tumors, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Thomas Kergrohen
- Inserm U981, Molecular Predictors and New Targets in Oncology, Team Genomics and Oncogenesis of Pediatric Brain Tumors, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Maite Verreault
- Sorbonne Université, AP-HP, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, DMU Neurosciences, Service de Neurologie 2-Mazarin, Paris, France
| | - Ahmed Idbaih
- Sorbonne Université, AP-HP, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, DMU Neurosciences, Service de Neurologie 2-Mazarin, Paris, France
| | - Carlos Alberto Oliveira de Biagi
- Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Ilon Liu
- Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Mariella G Filbin
- Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Kevin Beccaria
- Inserm U981, Molecular Predictors and New Targets in Oncology, Team Genomics and Oncogenesis of Pediatric Brain Tumors, Gustave Roussy, Université Paris-Saclay, Villejuif, France
- Department of Pediatric Neurosurgery, Necker Enfants Malades Hospital, APHP, Université Paris Cité, Paris, France
| | - Thomas Blauwblomme
- Department of Pediatric Neurosurgery, Necker Enfants Malades Hospital, APHP, Université Paris Cité, Paris, France
| | - Stephanie Puget
- Department of Pediatric Neurosurgery, Necker Enfants Malades Hospital, APHP, Université Paris Cité, Paris, France
| | - Arnault Tauziede-Espariat
- Department of Neuropathology, GHU Paris-Psychiatrie et Neurosciences, Sainte-Anne Hospital, ParisFrance
- Institut de Psychiatrie et Neurosciences de Paris (IPNP), UMR 1266, INSERM, IMA-BRAIN, Université de Paris, Paris, France
| | - Pascale Varlet
- Department of Neuropathology, GHU Paris-Psychiatrie et Neurosciences, Sainte-Anne Hospital, ParisFrance
- Institut de Psychiatrie et Neurosciences de Paris (IPNP), UMR 1266, INSERM, IMA-BRAIN, Université de Paris, Paris, France
| | - Volodia Dangouloff-Ros
- Paediatric Radiology Department, AP-HP, Hôpital Necker Enfants Malades, Université Paris Cité, Institut Imagine INSERM U1163, ParisFrance
| | - Nathalie Boddaert
- Paediatric Radiology Department, AP-HP, Hôpital Necker Enfants Malades, Université Paris Cité, Institut Imagine INSERM U1163, ParisFrance
| | - Gwenael Le Teuff
- Department of Biostatistics and Epidemiology, Gustave Roussy and Paris-Saclay University, Villejuif, France
| | - Jacques Grill
- Inserm U981, Molecular Predictors and New Targets in Oncology, Team Genomics and Oncogenesis of Pediatric Brain Tumors, Gustave Roussy, Université Paris-Saclay, Villejuif, France
- Département de Cancérologie de l’Enfant et de l’Adolescent, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Guillaume Montagnac
- Inserm U1279, Gustave Roussy Institute, Université Paris-Saclay, Villejuif, France
| | - Nadia Elkhatib
- Inserm U1279, Gustave Roussy Institute, Université Paris-Saclay, Villejuif, France
| | - Marie-Anne Debily
- Inserm U981, Molecular Predictors and New Targets in Oncology, Team Genomics and Oncogenesis of Pediatric Brain Tumors, Gustave Roussy, Université Paris-Saclay, Villejuif, France
- Département de Biologie, Université Evry Paris-Saclay, Evry, France
| | - David Castel
- Inserm U981, Molecular Predictors and New Targets in Oncology, Team Genomics and Oncogenesis of Pediatric Brain Tumors, Gustave Roussy, Université Paris-Saclay, Villejuif, France
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2
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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3
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Ausejo-Mauleon I, Labiano S, de la Nava D, Laspidea V, Zalacain M, Marrodán L, García-Moure M, González-Huarriz M, Hervás-Corpión I, Dhandapani L, Vicent S, Collantes M, Peñuelas I, Becher OJ, Filbin MG, Jiang L, Labelle J, de Biagi-Junior CAO, Nazarian J, Laternser S, Phoenix TN, van der Lugt J, Kranendonk M, Hoogendijk R, Mueller S, De Andrea C, Anderson AC, Guruceaga E, Koschmann C, Yadav VN, Gállego Pérez-Larraya J, Patiño-García A, Pastor F, Alonso MM. TIM-3 blockade in diffuse intrinsic pontine glioma models promotes tumor regression and antitumor immune memory. Cancer Cell 2023; 41:1911-1926.e8. [PMID: 37802053 PMCID: PMC10644900 DOI: 10.1016/j.ccell.2023.09.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 06/16/2023] [Accepted: 09/05/2023] [Indexed: 10/08/2023]
Abstract
Diffuse intrinsic pontine glioma (DIPG) is an aggressive brain stem tumor and the leading cause of pediatric cancer-related death. To date, these tumors remain incurable, underscoring the need for efficacious therapies. In this study, we demonstrate that the immune checkpoint TIM-3 (HAVCR2) is highly expressed in both tumor cells and microenvironmental cells, mainly microglia and macrophages, in DIPG. We show that inhibition of TIM-3 in syngeneic models of DIPG prolongs survival and produces long-term survivors free of disease that harbor immune memory. This antitumor effect is driven by the direct effect of TIM-3 inhibition in tumor cells, the coordinated action of several immune cell populations, and the secretion of chemokines/cytokines that create a proinflammatory tumor microenvironment favoring a potent antitumor immune response. This work uncovers TIM-3 as a bona fide target in DIPG and supports its clinical translation.
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Affiliation(s)
- Iker Ausejo-Mauleon
- 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
| | - Sara Labiano
- 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
| | - 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
| | - Virginia Laspidea
- 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 Zalacain
- 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
| | - Lucía Marrodán
- 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
| | - Marc García-Moure
- 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
| | - Marisol González-Huarriz
- 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
| | - Irati Hervás-Corpión
- 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
| | - Laasya Dhandapani
- 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
| | - Silvestre Vicent
- Health Research Institute of Navarra (IdiSNA), Pamplona, Spain; Solid Tumor Program, CIMA-Universidad de Navarra, Pamplona, Spain
| | - Maria Collantes
- Radiopharmacy Unit, Clínica Universidad de Navarra, Pamplona, Spain; Translational Molecular Imaging Unit, Clínica Universidad de Navarra, Pamplona, Spain
| | - Iván Peñuelas
- Health Research Institute of Navarra (IdiSNA), Pamplona, Spain; Radiopharmacy Unit, Clínica Universidad de Navarra, Pamplona, Spain; Translational Molecular Imaging Unit, Clínica Universidad de Navarra, Pamplona, Spain
| | - Oren J Becher
- Jack Martin Fund Division of Pediatric Hematology-oncology, Mount Sinai, New York, NY, USA
| | - Mariella G Filbin
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Li Jiang
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jenna Labelle
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Carlos A O de Biagi-Junior
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Javad Nazarian
- Children's National Health System, Center for Genetic Medicine Research, Washington, DC, USA; Virginia Tech University, Washington, DC, USA; Division of Oncology and Children's Research Center, DIPG/DMG Research Center Zurich, University Children's Hospital Zurich, Zurich, Switzerland
| | - Sandra Laternser
- Division of Oncology and Children's Research Center, DIPG/DMG Research Center Zurich, University Children's Hospital Zurich, Zurich, Switzerland
| | - Timothy N Phoenix
- Division of Pharmaceutical Sciences, James L. Winkle College of Pharmacy, University of Cincinnati, Cincinnati, OH, USA
| | | | | | - Raoull Hoogendijk
- Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Sabine Mueller
- University of California, San Francisco, San Francisco, CA, USA
| | - Carlos De Andrea
- Health Research Institute of Navarra (IdiSNA), Pamplona, Spain; Department of Pathology, Clínica Universidad de Navarra, Pamplona, Spain
| | - Ana C Anderson
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Elizabeth Guruceaga
- Health Research Institute of Navarra (IdiSNA), Pamplona, Spain; Bioinformatics Platform, CIMA-Universidad de Navarra, Pamplona, Spain
| | - Carl Koschmann
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
| | - Viveka Nand Yadav
- Department of Pediatrics, University of Missouri Kansas City School of Medicine, Kansas City, KS, USA; Department of Pediatrics, Children's Mercy Research Institute (CMRI), Kansas City, KS, USA; Department of Cancer Biology, University of Kansas Cancer Center. Kansas City, KS, USA
| | - Jaime Gállego Pérez-Larraya
- Health Research Institute of Navarra (IdiSNA), Pamplona, Spain; Solid Tumor Program, CIMA-Universidad de Navarra, Pamplona, Spain; Department of Neurology, Clínica Universidad de Navarra, Pamplona, Spain
| | - Ana Patiño-García
- 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
| | - Fernando Pastor
- Health Research Institute of Navarra (IdiSNA), Pamplona, Spain; Molecular Therapeutics Program, CIMA-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.
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4
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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: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Okonechnikov K, Joshi P, Sepp M, Leiss K, Sarropoulos I, Murat F, Sill M, Beck P, Chan KCH, Korshunov A, Sah F, Deng MY, Sturm D, DeSisto J, Donson AM, Foreman NK, Green AL, Robinson G, Orr BA, Gao Q, Darrow E, Hadley JL, Northcott PA, Gojo J, Kawauchi D, Hovestadt V, Filbin MG, von Deimling A, Zuckermann M, Pajtler KW, Kool M, Jones DTW, Jäger N, Kutscher LM, Kaessmann H, Pfister SM. Mapping pediatric brain tumors to their origins in the developing cerebellum. Neuro Oncol 2023; 25:1895-1909. [PMID: 37534924 PMCID: PMC10547518 DOI: 10.1093/neuonc/noad124] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Indexed: 08/04/2023] Open
Abstract
BACKGROUND Distinguishing the cellular origins of childhood brain tumors is key for understanding tumor initiation and identifying lineage-restricted, tumor-specific therapeutic targets. Previous strategies to map the cell-of-origin typically involved comparing human tumors to murine embryonal tissues, which is potentially limited due to species-specific differences. The aim of this study was to unravel the cellular origins of the 3 most common pediatric brain tumors, ependymoma, pilocytic astrocytoma, and medulloblastoma, using a developing human cerebellar atlas. METHODS We used a single-nucleus atlas of the normal developing human cerebellum consisting of 176 645 cells as a reference for an in-depth comparison to 4416 bulk and single-cell transcriptome tumor datasets, using gene set variation analysis, correlation, and single-cell matching techniques. RESULTS We find that the astroglial cerebellar lineage is potentially the origin for posterior fossa ependymomas. We propose that infratentorial pilocytic astrocytomas originate from the oligodendrocyte lineage and MHC II genes are specifically enriched in these tumors. We confirm that SHH and Group 3/4 medulloblastomas originate from the granule cell and unipolar brush cell lineages. Radiation-induced gliomas stem from cerebellar glial lineages and demonstrate distinct origins from the primary medulloblastoma. We identify tumor genes that are expressed in the cerebellar lineage of origin, and genes that are tumor specific; both gene sets represent promising therapeutic targets for future study. CONCLUSION Based on our results, individual cells within a tumor may resemble different cell types along a restricted developmental lineage. Therefore, we suggest that tumors can arise from multiple cellular states along the cerebellar "lineage of origin."
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Affiliation(s)
- Konstantin Okonechnikov
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Piyush Joshi
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Developmental Origins of Pediatric Cancer Junior Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mari Sepp
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Kevin Leiss
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Ioannis Sarropoulos
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Florent Murat
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
- INRAE, LPGP, Rennes, France
| | | | - Pengbo Beck
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Kenneth Chun-Ho Chan
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Andrey Korshunov
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Felix Sah
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Maximilian Y Deng
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dominik Sturm
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - John DeSisto
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, University of Colorado School of Medicine, Aurora, CO, USA
| | - Andrew M Donson
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, University of Colorado School of Medicine, Aurora, CO, USA
| | - Nicholas K Foreman
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, University of Colorado School of Medicine, Aurora, CO, USA
- Children’s Hospital Colorado, Aurora, CO, USA
| | - Adam L Green
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, University of Colorado School of Medicine, Aurora, CO, USA
- Children’s Hospital Colorado, Aurora, CO, USA
| | - Giles Robinson
- Department of Oncology, St Jude Children’s Research Hospital, Memphis, TN, USA
| | - Brent A Orr
- Department of Pathology, St Jude Children’s Research Hospital, Memphis, TN, USA
| | - Qingsong Gao
- Department of Pathology, St Jude Children’s Research Hospital, Memphis, TN, USA
- Department of Developmental Neurobiology, St Jude Children’s Research Hospital, Memphis, TN, USA
| | - Emily Darrow
- Department of Developmental Neurobiology, St Jude Children’s Research Hospital, Memphis, TN, USA
| | - Jennifer L Hadley
- Department of Developmental Neurobiology, St Jude Children’s Research Hospital, Memphis, TN, USA
| | - Paul A Northcott
- Department of Developmental Neurobiology, St Jude Children’s Research Hospital, Memphis, TN, USA
| | - Johannes Gojo
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics and Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
- Department of Neuropathology, NN Burdenko Neurosurgical Institute, Moscow, Russia
| | - Daisuke Kawauchi
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, Tokyo, Japan
| | - Volker Hovestadt
- Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of Harvard and MIT, Cambridge, USA
| | - Mariella G Filbin
- Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of Harvard and MIT, Cambridge, USA
| | - Andreas von Deimling
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Marc Zuckermann
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Kristian W Pajtler
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marcel Kool
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, the Netherlands
| | - David T W Jones
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Natalie Jäger
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Lena M Kutscher
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Developmental Origins of Pediatric Cancer Junior Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Henrik Kaessmann
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
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6
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Williams EA, Brastianos PK, Wakimoto H, Zolal A, Filbin MG, Cahill DP, Santagata S, Juratli TA. A comprehensive genomic study of 390 H3F3A-mutant pediatric and adult diffuse high-grade gliomas, CNS WHO grade 4. Acta Neuropathol 2023; 146:515-525. [PMID: 37524847 PMCID: PMC10412483 DOI: 10.1007/s00401-023-02609-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/30/2023] [Accepted: 06/26/2023] [Indexed: 08/02/2023]
Abstract
Malignant brain tumors, known as H3K27-altered diffuse midline glioma (DMG) and H3G34-mutant diffuse hemispheric glioma (DHG), can affect individuals of all ages and are classified as CNS WHO grade 4. We comprehensively characterized 390 H3F3A-mutant diffuse gliomas (201 females, 189 males) arising in pediatric patients (under 20 years old) and adults (20 years and older) evaluated by the CGP program at Foundation Medicine between 2013 and 2020. We assessed information from pathology reports, histopathology review, and clinical data. The cohort included 304 H3K27M-mutant DMG (156 females, 148 males) and 86 H3G34-mutant DHG (45 females, 41 males). Median patient age was 20 years (1-74 years). The frequency of H3K27M-mutant DMG was similar in both pediatric and adult patients in our cohort-48.6% of the patients were over 20 years old, 31.5% over 30, and 18% over 40 at initial diagnosis. FGFR1 hotspot point mutations (N546K and K656E) were exclusively identified in H3K27M-mutant DMG tumors (64/304, 21%; p = 0.0001); these tend to occur in older patients (median age: 32.5 years) and mainly arose in the diencephalon. H3K27M-mutant DMG had higher rates of mutations in NF1 (31.0 vs 8.1%; p = 0.0001) and PIK3CA/PIK3R1 (27.9% vs 15.1%; p = 0.016) compared to H3G34-mutant DHG. However, H3G34-mutant DHG had higher rates of targetable alterations in cell-cycle pathway genes (CDK4 and CDK6 amplification; CDKN2A/B deletion) (27.0 vs 9.0%). Potentially targetable PDGFRA alterations were identified in ~ 20% of both H3G34-mutant DHG and H3K27M-mutant DMG. Overall, in the present study H3K27M-mutant DMG occurred at similar rates in both adult and patient patients. Through our analysis, we were able to identify molecular features characteristic of DMG and DHG. By identifying the recurrent co-mutations including actionable FGFR1 point mutations found in nearly one-third of H3K27M-mutant DMG in young adults, our findings can inform clinical translational studies, patient diagnosis, and clinical trial design.
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Affiliation(s)
- Erik A Williams
- Department of Pathology and Laboratory Medicine, University of Miami, Sylvester Comprehensive Cancer Center, and Jackson Memorial Hospitals, Miami, USA
- Foundation Medicine Inc, Cambridge, USA
| | - Priscilla K Brastianos
- Department of Medicine, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, USA
| | - Hiroaki Wakimoto
- Department of Neurosurgery, Laboratory of Translational Neuro-Oncology, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, USA
| | - Amir Zolal
- Department of Neurosurgery, Division of Neuro-Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
| | - Mariella G Filbin
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniel P Cahill
- Department of Neurosurgery, Laboratory of Translational Neuro-Oncology, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, USA
| | - Sandro Santagata
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, USA
- Department of Systems Biology, Harvard Medical School, Boston, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, USA
| | - Tareq A Juratli
- Department of Neurosurgery, Laboratory of Translational Neuro-Oncology, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, USA.
- Department of Neurosurgery, Division of Neuro-Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany.
- National Center for Tumor Diseases (NCT), Partner Site Dresden, Dresden, Germany.
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7
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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. Abstract 3523: A systematic comparison of molecular features shared by H3K27-altered diffuse midline gliomas and posterior fossa A ependymomas. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-3523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
In children, brain tumors account for the highest mortality rates of all malignancies, and in contrast to adult brain cancers, pediatric tumors often arise in infratentorial regions. Two tumors in particular, H3K27-altered diffuse midline gliomas (DMGs) and group-A posterior fossa ependymomas (PFAs) arise from structures around the fourth ventricle, and strikingly, both tumors exhibit a global decrease in the histone mark histone 3, lysine 27 tri-methylation (H3K27me3) that is associated with transcriptional repression. H3K27-altered DMGs primarily are found primarily in the pons and exhibit by lysine-to-methionine mutations at H3K27 (H3K27M). This missense mutation results in inhibition of the catalytic activity of the polycomb repressive complex 2 (PRC2) which mediates H3K27me3 deposition. PFAs are found in the lateral recess of the fourth ventricle and the cerebellum and demonstrate overexpression of EZH inhibitory protein (EZHIP). EZHIP contains a domain with striking resemblance to the mutant H3K27M histone tail and similarly blocks PRC2 activity. Although H3K27me3 levels are dramatically reduced in both areas, select genes retain H3K27me3 in both tumor types. Increasingly, data have emerged demonstrating that cases of PFAs actually harbor H3K27M mutations and cases of H3-wildtype DMGs in fact overexpress EZHIP. The neighboring origins and overlapping recurrent H3K27me3-modulating alterations observed in these two pediatric brain tumors suggest certain populations of cells in the developing hindbrain may be particularly prone to malignant transformation in the setting of PRC2 inhibition. A systematic comparison of genomic, transcriptomic, and epigenomic datasets for both tumors identified key molecular similarities between subsets of DMGs and PFAs and highlighted how developmental signatures may be preserved in tumor expression profiles. Specifically, these analyses identify shared copy-number profiles between PFAs and different subtypes of DMGs and demonstrate that the Activin A Receptor Type 1 (ACVR1), a gene with recurrent activating mutations in H3K27-altered DMGs, is overexpressed in a subset PFAs with worse survival outcomes. Additionally, interrogation of the H3K27me3 and enhancer landscapes identified critical genes with similar chromatin profiles and revealed heterogeneity in repression of H3K27me3-marked genes that correlated with patterns of inferred anatomic origins for each tumor. Moreover, one of these genes, cellular retinoic acid binding partner 1 (CRABP1) showed enrichment in progenitor cell types in single-cell transcriptomic datasets. Together, these analyses characterize the common and unique molecular features of H3K27-altered DMGs and PFAs and shed light on the cellular contexts of the developing hindbrain that lead to development of each tumor.
Citation Format: Matthew Pun, Drew Pratt, Patricia R. Nano, Piyush K. Joshi, Li Jiang, Bernhard Englinger, Arvind Rao, Marcin Cieslik, Arul M. Chinnaiyan, Kenneth Aldape, Stefan Pfister, Mariella G. Filbin, Aparna Bhaduri, Sriram Venneti. A systematic comparison of molecular features shared by H3K27-altered diffuse midline gliomas and posterior fossa A ependymomas. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3523.
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Affiliation(s)
- Matthew Pun
- 1University of Michigan Medical School, Ann Arbor, MI
| | - Drew Pratt
- 2National Cancer Institute, Bethesda, MD
| | - Patricia R. Nano
- 3David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
| | - Piyush K. Joshi
- 4German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Li Jiang
- 5Dana Farber Cancer Institute, Boston, MA
| | | | - Arvind Rao
- 1University of Michigan Medical School, Ann Arbor, MI
| | | | | | | | - Stefan Pfister
- 4German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Aparna Bhaduri
- 3David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
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Hwang EI, Hanson D, Filbin MG, Mack SC. Why haven't we solved intracranial pediatric ependymoma? Current questions and barriers to treatment advances. Neoplasia 2023; 39:100895. [PMID: 36944298 PMCID: PMC10036929 DOI: 10.1016/j.neo.2023.100895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/20/2023] [Accepted: 02/28/2023] [Indexed: 03/22/2023]
Abstract
Pediatric intracranial ependymoma has seen a recent exponential expansion of biological findings, rapidly dividing the diagnosis into several subgroups, each with specific molecular and clinical characteristics. While such subdivision may complicate clinical conclusions from historical trials, this knowledge also provides an opportunity for interrogating the major clinical and biological questions preventing near-term translation into effective therapy for children with ependymoma. In this article, we briefly review some of the most critical clinical questions facing both patient management and the construct of future trials in childhood ependymoma, as well as explore some of the current barriers to efficient translation of preclinical discovery to the clinic.
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9
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Savchuk S, Gentry K, Wang W, Carleton E, Yalçın B, Liu Y, Pavarino EC, LaBelle J, Toland AM, Woo PJ, Qu F, Filbin MG, Krasnow MA, Sabatini BL, Sage J, Monje M, Venkatesh HS. Neuronal-Activity Dependent Mechanisms of Small Cell Lung Cancer Progression. bioRxiv 2023:2023.01.19.524430. [PMID: 36711554 PMCID: PMC9882339 DOI: 10.1101/2023.01.19.524430] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Neural activity is increasingly recognized as a critical regulator of cancer growth. In the brain, neuronal activity robustly influences glioma growth both through paracrine mechanisms and through electrochemical integration of malignant cells into neural circuitry via neuron-to-glioma synapses, while perisynaptic neurotransmitter signaling drives breast cancer brain metastasis growth. Outside of the CNS, innervation of tumors such as prostate, breast, pancreatic and gastrointestinal cancers by peripheral nerves similarly regulates cancer progression. However, the extent to which the nervous system regulates lung cancer progression, either in the lung or when metastatic to brain, is largely unexplored. Small cell lung cancer (SCLC) is a lethal high-grade neuroendocrine tumor that exhibits a strong propensity to metastasize to the brain. Here we demonstrate that, similar to glioma, metastatic SCLC cells in the brain co-opt neuronal activity-regulated mechanisms to stimulate growth and progression. Optogenetic stimulation of cortical neuronal activity drives proliferation and invasion of SCLC brain metastases. In the brain, SCLC cells exhibit electrical currents and consequent calcium transients in response to neuronal activity, and direct SCLC cell membrane depolarization is sufficient to promote the growth of SCLC tumors. In the lung, vagus nerve transection markedly inhibits primary lung tumor formation, progression and metastasis, highlighting a critical role for innervation in overall SCLC initiation and progression. Taken together, these studies illustrate that neuronal activity plays a crucial role in dictating SCLC pathogenesis in both primary and metastatic sites.
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11
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de Almeida Magalhães T, Alencastro Veiga Cruzeiro G, Ribeiro de Sousa G, Englinger B, Fernando Peinado Nagano L, Ancliffe M, Rodrigues da Silva K, Jiang L, Gojo J, Cherry Liu Y, Carline B, Kuchibhotla M, Pinto Saggioro F, Kazue Nagahashi Marie S, Mieko Oba-Shinjo S, Andres Yunes J, Gomes de Paula Queiroz R, Alberto Scrideli C, Endersby R, Filbin MG, Silva Borges K, Salic A, Gonzaga Tone L, Valera ET. Activation of Hedgehog signaling by the oncogenic RELA fusion reveals a primary cilia-dependent vulnerability in supratentorial ependymoma. Neuro Oncol 2023; 25:185-198. [PMID: 35640920 PMCID: PMC9825332 DOI: 10.1093/neuonc/noac147] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Supratentorial RELA fusion (ST-RELA) ependymomas (EPNs) are resistant tumors without an approved chemotherapeutic treatment. Unfortunately, the molecular mechanisms that lead to chemoresistance traits of ST-RELA remain elusive. The aim of this study was to assess RELA fusion-dependent signaling modules, specifically the role of the Hedgehog (Hh) pathway as a novel targetable vulnerability in ST-RELA. METHODS Gene expression was analyzed in EPN from patient cohorts, by microarray, RNA-seq, qRT-PCR, and scRNA-seq. Inhibitors against Smoothened (SMO) (Sonidegib) and Aurora kinase A (AURKA) (Alisertib) were evaluated. Protein expression, primary cilia formation, and drug effects were assessed by immunoblot, immunofluorescence, and immunohistochemistry. RESULTS Hh components were selectively overexpressed in EPNs induced by the RELA fusion. Single-cell analysis showed that the Hh signature was primarily confined to undifferentiated, stem-like cell subpopulations. Sonidegib exhibited potent growth-inhibitory effects on ST-RELA cells, suggesting a key role in active Hh signaling; importantly, the effect of Sonidegib was reversed by primary cilia loss. We, thus, tested the effect of AURKA inhibition by Alisertib, to induce cilia stabilization/reassembly. Strikingly, Alisertib rescued ciliogenesis and synergized with Sonidegib in killing ST-RELA cells. Using a xenograft model, we show that cilia loss is a mechanism for acquiring resistance to the inhibitory effect of Sonidegib. However, Alisertib fails to rescue cilia and highlights the need for other strategies to promote cilia reassembly, for treating ST-RELA tumors. CONCLUSION Our study reveals a crucial role for the Hh pathway in ST-RELA tumor growth, and suggests that rescue of primary cilia represents a vulnerability of the ST-RELA EPNs.
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Affiliation(s)
- Taciani de Almeida Magalhães
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Gustavo Alencastro Veiga Cruzeiro
- Department of Pediatrics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
- Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, Massachusetts, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Graziella Ribeiro de Sousa
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Bernhard Englinger
- Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, Massachusetts, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
- Department of Urology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Luis Fernando Peinado Nagano
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Mathew Ancliffe
- Brain Tumour Research Program, Telethon Kids Institute and the University of Western Australia, Nedlands, Western Australia, Australia
| | - Keteryne Rodrigues da Silva
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
- Brain Tumour Research Program, Telethon Kids Institute and the University of Western Australia, Nedlands, Western Australia, Australia
| | - Li Jiang
- Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, Massachusetts, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Johannes Gojo
- Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, Massachusetts, USA
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Yulu Cherry Liu
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Brooke Carline
- Brain Tumour Research Program, Telethon Kids Institute and the University of Western Australia, Nedlands, Western Australia, Australia
| | - Mani Kuchibhotla
- Brain Tumour Research Program, Telethon Kids Institute and the University of Western Australia, Nedlands, Western Australia, Australia
| | - Fabiano Pinto Saggioro
- Department of Pathology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Suely Kazue Nagahashi Marie
- Cellular and Molecular Biology Laboratory, Department of Neurology, Faculdade de Medicina (FMUSP), University of São Paulo, São Paulo, Brazil
| | - Sueli Mieko Oba-Shinjo
- Cellular and Molecular Biology Laboratory, Department of Neurology, Faculdade de Medicina (FMUSP), University of São Paulo, São Paulo, Brazil
| | - José Andres Yunes
- Molecular Biology Laboratory, Boldrini Children’s Center, Campinas, São Paulo, Brazil
| | | | - Carlos Alberto Scrideli
- Department of Pediatrics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Raelene Endersby
- Brain Tumour Research Program, Telethon Kids Institute and the University of Western Australia, Nedlands, Western Australia, Australia
| | - Mariella G Filbin
- Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, Massachusetts, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Kleiton Silva Borges
- Department of Pediatrics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
- Division of Endocrinology, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Adrian Salic
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Luiz Gonzaga Tone
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
- Department of Pediatrics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Elvis Terci Valera
- Department of Pediatrics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
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12
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Messinger D, Harris MK, Cummings JR, Thomas C, Yang T, Sweha SR, Woo R, Siddaway R, Burkert M, Stallard S, Qin T, Mullan B, Siada R, Ravindran R, Niculcea M, Dowling AR, Bradin J, Ginn KF, Gener MAH, Dorris K, Vitanza NA, Schmidt SV, Spitzer J, Li J, Filbin MG, Cao X, Castro MG, Lowenstein PR, Mody R, Chinnaiyan A, Desprez PY, McAllister S, Dun MD, Hawkins C, Waszak SM, Venneti S, Koschmann C, Yadav VN. Therapeutic targeting of prenatal pontine ID1 signaling in diffuse midline glioma. Neuro Oncol 2023; 25:54-67. [PMID: 35605606 PMCID: PMC9825316 DOI: 10.1093/neuonc/noac141] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Diffuse midline gliomas (DMG) are highly invasive brain tumors with rare survival beyond two years past diagnosis and limited understanding of the mechanism behind tumor invasion. Previous reports demonstrate upregulation of the protein ID1 with H3K27M and ACVR1 mutations in DMG, but this has not been confirmed in human tumors or therapeutically targeted. METHODS Whole exome, RNA, and ChIP-sequencing was performed on the ID1 locus in DMG tissue. Scratch-assay migration and transwell invasion assays of cultured cells were performed following shRNA-mediated ID1-knockdown. In vitro and in vivo genetic and pharmacologic [cannabidiol (CBD)] inhibition of ID1 on DMG tumor growth was assessed. Patient-reported CBD dosing information was collected. RESULTS Increased ID1 expression in human DMG and in utero electroporation (IUE) murine tumors is associated with H3K27M mutation and brainstem location. ChIP-sequencing indicates ID1 regulatory regions are epigenetically active in human H3K27M-DMG tumors and prenatal pontine cells. Higher ID1-expressing astrocyte-like DMG cells share a transcriptional program with oligo/astrocyte-precursor cells (OAPCs) from the developing human brain and demonstrate upregulation of the migration regulatory protein SPARCL1. Genetic and pharmacologic (CBD) suppression of ID1 decreases tumor cell invasion/migration and tumor growth in H3.3/H3.1K27M PPK-IUE and human DIPGXIIIP* in vivo models of pHGG. The effect of CBD on cell proliferation appears to be non-ID1 mediated. Finally, we collected patient-reported CBD treatment data, finding that a clinical trial to standardize dosing may be beneficial. CONCLUSIONS H3K27M-mediated re-activation of ID1 in DMG results in a SPARCL1+ migratory transcriptional program that is therapeutically targetable with CBD.
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Affiliation(s)
- Dana Messinger
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, University of Michigan Medical School (UMMS), Ann Arbor, Michigan, USA
| | - Micah K Harris
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, University of Michigan Medical School (UMMS), Ann Arbor, Michigan, USA
| | - Jessica R Cummings
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, University of Michigan Medical School (UMMS), Ann Arbor, Michigan, USA
| | - Chase Thomas
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, University of Michigan Medical School (UMMS), Ann Arbor, Michigan, USA
| | - Tao Yang
- Department of Neurology, University of Michigan Medical School (UMMS), Ann Arbor, Michigan, USA
| | - Stefan R Sweha
- Department of Pathology, University of Michigan Medical School (UMMS), Ann Arbor, Michigan, USA
| | - Rinette Woo
- Cancer Research, California Pacific Medical Center Research Institute; San Francisco, California, USA
| | - Robert Siddaway
- Arthur and Sonia Labatt Brain Tumour Research Centre and Division of Pathology, Hospital for Sick Children, Toronto, Canada
| | - Martin Burkert
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Stefanie Stallard
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, University of Michigan Medical School (UMMS), Ann Arbor, Michigan, USA
| | - Tingting Qin
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School (UMMS), Ann Arbor, Michigan, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, USA
| | - Brendan Mullan
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, University of Michigan Medical School (UMMS), Ann Arbor, Michigan, USA
| | - Ruby Siada
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, University of Michigan Medical School (UMMS), Ann Arbor, Michigan, USA
| | - Ramya Ravindran
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, University of Michigan Medical School (UMMS), Ann Arbor, Michigan, USA
| | - Michael Niculcea
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, University of Michigan Medical School (UMMS), Ann Arbor, Michigan, USA
| | - Abigail R Dowling
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, University of Michigan Medical School (UMMS), Ann Arbor, Michigan, USA
| | - Joshua Bradin
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, University of Michigan Medical School (UMMS), Ann Arbor, Michigan, USA
| | - Kevin F Ginn
- Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, Missouri, USA
| | - Melissa A H Gener
- Department of Pathology and Laboratory Medicine, Children’s Mercy Kansas City, Kansas City, Missouri, USA
| | - Kathleen Dorris
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | | | - Susanne V Schmidt
- Institute of Innate Immunity, AG Immunogenomics, University Bonn, Bonn, Germany
| | - Jasper Spitzer
- Institute of Innate Immunity, AG Immunogenomics, University Bonn, Bonn, Germany
| | - Jiang Li
- Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Department of Pediatric Oncology, Boston, Massachusetts, USA
| | - Mariella G Filbin
- Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Department of Pediatric Oncology, Boston, Massachusetts, USA
| | - Xuhong Cao
- Department of Pathology, University of Michigan Medical School (UMMS), Ann Arbor, Michigan, USA
| | - Maria G Castro
- Department of Neurosurgery, University of Michigan Medical School (UMMS), Ann Arbor, Michigan, USA
| | - Pedro R Lowenstein
- Department of Neurosurgery, University of Michigan Medical School (UMMS), Ann Arbor, Michigan, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School (UMMS), Ann Arbor, Michigan, USA
| | - Rajen Mody
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, University of Michigan Medical School (UMMS), Ann Arbor, Michigan, USA
| | - Arul Chinnaiyan
- Department of Pathology, University of Michigan Medical School (UMMS), Ann Arbor, Michigan, USA
| | - Pierre-Yves Desprez
- Cancer Research, California Pacific Medical Center Research Institute; San Francisco, California, USA
| | - Sean McAllister
- Cancer Research, California Pacific Medical Center Research Institute; San Francisco, California, USA
| | - Matthew D Dun
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan NSW, Australia
| | - Cynthia Hawkins
- Arthur and Sonia Labatt Brain Tumour Research Centre and Division of Pathology, Hospital for Sick Children, Toronto, Canada
| | - Sebastian M Waszak
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo, Norway
- Division of Pediatric and Adolescent Medicine, Department of Pediatric Research, Rikshospitalet, Oslo University Hospital, Oslo, Norway
| | - Sriram Venneti
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, University of Michigan Medical School (UMMS), Ann Arbor, Michigan, USA
| | - Carl Koschmann
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, University of Michigan Medical School (UMMS), Ann Arbor, Michigan, USA
| | - Viveka Nand Yadav
- Department of Pediatrics at Children’s Mercy Research Institute, Kansas City, Missouri, USA
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Panditharatna E, Marques JG, Wang T, Trissal MC, Liu I, Jiang L, Beck A, Groves A, Dharia NV, Li D, Hoffman SE, Kugener G, Shaw ML, Mire HM, Hack OA, Dempster JM, Lareau C, Dai L, Sigua LH, Quezada MA, Stanton ACJ, Wyatt M, Kalani Z, Goodale A, Vazquez F, Piccioni F, Doench JG, Root DE, Anastas JN, Jones KL, Conway AS, Stopka S, Regan MS, Liang Y, Seo HS, Song K, Bashyal P, Jerome WP, Mathewson ND, Dhe-Paganon S, Suvà ML, Carcaboso AM, Lavarino C, Mora J, Nguyen QD, Ligon KL, Shi Y, Agnihotri S, Agar NY, Stegmaier K, Stiles CD, Monje M, Golub TR, Qi J, Filbin MG. BAF Complex Maintains Glioma Stem Cells in Pediatric H3K27M Glioma. Cancer Discov 2022; 12:2880-2905. [PMID: 36305736 PMCID: PMC9716260 DOI: 10.1158/2159-8290.cd-21-1491] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 08/03/2022] [Accepted: 09/15/2022] [Indexed: 01/12/2023]
Abstract
Diffuse midline gliomas are uniformly fatal pediatric central nervous system cancers that are refractory to standard-of-care therapeutic modalities. The primary genetic drivers are a set of recurrent amino acid substitutions in genes encoding histone H3 (H3K27M), which are currently undruggable. These H3K27M oncohistones perturb normal chromatin architecture, resulting in an aberrant epigenetic landscape. To interrogate for epigenetic dependencies, we performed a CRISPR screen and show that patient-derived H3K27M-glioma neurospheres are dependent on core components of the mammalian BAF (SWI/SNF) chromatin remodeling complex. The BAF complex maintains glioma stem cells in a cycling, oligodendrocyte precursor cell-like state, in which genetic perturbation of the BAF catalytic subunit SMARCA4 (BRG1), as well as pharmacologic suppression, opposes proliferation, promotes progression of differentiation along the astrocytic lineage, and improves overall survival of patient-derived xenograft models. In summary, we demonstrate that therapeutic inhibition of the BAF complex has translational potential for children with H3K27M gliomas. SIGNIFICANCE Epigenetic dysregulation is at the core of H3K27M-glioma tumorigenesis. Here, we identify the BRG1-BAF complex as a critical regulator of enhancer and transcription factor landscapes, which maintain H3K27M glioma in their progenitor state, precluding glial differentiation, and establish pharmacologic targeting of the BAF complex as a novel treatment strategy for pediatric H3K27M glioma. See related commentary by Beytagh and Weiss, p. 2730. See related article by Mo et al., p. 2906.
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Affiliation(s)
- Eshini Panditharatna
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Joana G. Marques
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Tingjian Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Maria C. Trissal
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Ilon Liu
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Li Jiang
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Alexander Beck
- Center for Neuropathology, Ludwig Maximilian University of Munich, Munich, Germany
| | - Andrew Groves
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Neekesh V. Dharia
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Deyao Li
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Samantha E. Hoffman
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Guillaume Kugener
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - McKenzie L. Shaw
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
| | - Hafsa M. Mire
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Olivia A. Hack
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
| | - Joshua M. Dempster
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Caleb Lareau
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
- Department of Pathology, Stanford University, Stanford, California
| | - Lingling Dai
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Logan H. Sigua
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Michael A. Quezada
- Department of Neurology, Stanford University School of Medicine, Stanford, California
| | - Ann-Catherine J. Stanton
- Department of Neurosurgery, Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Meghan Wyatt
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Zohra Kalani
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Amy Goodale
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Francisca Vazquez
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Federica Piccioni
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
- Merck Research Laboratories, Cambridge, Massachusetts
| | - John G. Doench
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - David E. Root
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Jamie N. Anastas
- Division of Newborn Medicine and Epigenetics Program, Department of Medicine, Boston Children's Hospital, Boston, Massachusetts
- Department of Neurosurgery and Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Texas
| | - Kristen L. Jones
- Lurie Family Imaging Center, Center for Biomedical Imaging in Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Amy Saur Conway
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
| | - Sylwia 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
| | - Michael S. Regan
- 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
| | - Yu Liang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Hyuk-Soo Seo
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts
| | - Kijun Song
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Puspalata Bashyal
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - William P. Jerome
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
| | - Nathan D. Mathewson
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
- Department of Microbiology and Immunobiology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
- Department of Neurology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Sirano Dhe-Paganon
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts
| | - Mario L. Suvà
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
- Klarman Cell Observatory, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Angel M. Carcaboso
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Cinzia Lavarino
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Jaume Mora
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Quang-De Nguyen
- Lurie Family Imaging Center, Center for Biomedical Imaging in Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Keith L. Ligon
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
- Department of Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Pathology, Boston Children's Hospital, Boston, Massachusetts
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Yang Shi
- Division of Newborn Medicine and Epigenetics Program, Department of Medicine, Boston Children's Hospital, Boston, Massachusetts
- Ludwig Institute for Cancer Research, Oxford Branch, Oxford University, Oxford, United Kingdom
| | - Sameer Agnihotri
- Department of Neurosurgery, Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Nathalie Y.R. Agar
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- 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
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Charles D. Stiles
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Michelle Monje
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California
| | - Todd R. Golub
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Mariella G. Filbin
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
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14
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Liu I, Jiang L, Samuelsson ER, Marco Salas S, Beck A, Hack OA, Jeong D, Shaw ML, Englinger B, LaBelle J, Mire HM, Madlener S, Mayr L, Quezada MA, Trissal M, Panditharatna E, Ernst KJ, Vogelzang J, Gatesman TA, Halbert ME, Palova H, Pokorna P, Sterba J, Slaby O, Geyeregger R, Diaz A, Findlay IJ, Dun MD, Resnick A, Suvà ML, Jones DTW, Agnihotri S, Svedlund J, Koschmann C, Haberler C, Czech T, Slavc I, Cotter JA, Ligon KL, Alexandrescu S, Yung WKA, Arrillaga-Romany I, Gojo J, Monje M, Nilsson M, Filbin MG. The landscape of tumor cell states and spatial organization in H3-K27M mutant diffuse midline glioma across age and location. Nat Genet 2022; 54:1881-1894. [PMID: 36471067 PMCID: PMC9729116 DOI: 10.1038/s41588-022-01236-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 10/20/2022] [Indexed: 12/12/2022]
Abstract
Histone 3 lysine27-to-methionine (H3-K27M) mutations most frequently occur in diffuse midline gliomas (DMGs) of the childhood pons but are also increasingly recognized in adults. Their potential heterogeneity at different ages and midline locations is vastly understudied. Here, through dissecting the single-cell transcriptomic, epigenomic and spatial architectures of a comprehensive cohort of patient H3-K27M DMGs, we delineate how age and anatomical location shape glioma cell-intrinsic and -extrinsic features in light of the shared driver mutation. We show that stem-like oligodendroglial precursor-like cells, present across all clinico-anatomical groups, display varying levels of maturation dependent on location. We reveal a previously underappreciated relationship between mesenchymal cancer cell states and age, linked to age-dependent differences in the immune microenvironment. Further, we resolve the spatial organization of H3-K27M DMG cell populations and identify a mitotic oligodendroglial-lineage niche. Collectively, our study provides a powerful framework for rational modeling and therapeutic interventions.
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Affiliation(s)
- Ilon Liu
- grid.511177.4Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA USA ,grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Li Jiang
- grid.511177.4Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA USA ,grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Erik R. Samuelsson
- grid.10548.380000 0004 1936 9377Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Sergio Marco Salas
- grid.10548.380000 0004 1936 9377Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Alexander Beck
- grid.5252.00000 0004 1936 973XCenter for Neuropathology, Ludwig-Maximilians-University, Munich, Germany
| | - Olivia A. Hack
- grid.511177.4Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA USA ,grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Daeun Jeong
- grid.511177.4Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA USA ,grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - McKenzie L. Shaw
- grid.511177.4Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA USA ,grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Bernhard Englinger
- grid.511177.4Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA USA ,grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.22937.3d0000 0000 9259 8492Department of Urology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Jenna LaBelle
- grid.511177.4Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA USA ,grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Hafsa M. Mire
- grid.511177.4Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA USA ,grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Sibylle Madlener
- grid.22937.3d0000 0000 9259 8492Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Lisa Mayr
- grid.22937.3d0000 0000 9259 8492Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Michael A. Quezada
- grid.168010.e0000000419368956Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA USA
| | - Maria Trissal
- grid.511177.4Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA USA ,grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Eshini Panditharatna
- grid.511177.4Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA USA ,grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Kati J. Ernst
- grid.7497.d0000 0004 0492 0584Hopp Children’s Cancer Center Heidelberg (KiTZ), Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jayne Vogelzang
- grid.65499.370000 0001 2106 9910Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA USA
| | - Taylor A. Gatesman
- grid.21925.3d0000 0004 1936 9000Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA USA ,grid.239553.b0000 0000 9753 0008John G. Rangos Sr. Research Center, Children’s Hospital of Pittsburgh, Pittsburgh, PA USA
| | - Matthew E. Halbert
- grid.21925.3d0000 0004 1936 9000Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA USA ,grid.239553.b0000 0000 9753 0008John G. Rangos Sr. Research Center, Children’s Hospital of Pittsburgh, Pittsburgh, PA USA
| | - Hana Palova
- grid.10267.320000 0001 2194 0956Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Petra Pokorna
- grid.10267.320000 0001 2194 0956Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Jaroslav Sterba
- Pediatric Oncology Department, University Hospital Brno, Faculty of Medicine, Masaryk University, ICRC, Brno, Czech Republic
| | - Ondrej Slaby
- grid.10267.320000 0001 2194 0956Central European Institute of Technology, Masaryk University, Brno, Czech Republic ,grid.10267.320000 0001 2194 0956Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Rene Geyeregger
- grid.22937.3d0000 0000 9259 8492Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria ,grid.416346.2Department of Clinical Cell Biology and FACS Core Unit, St. Anna Children’s Cancer Research Institute (CCRI), Vienna, Austria
| | - Aaron Diaz
- grid.266102.10000 0001 2297 6811Department of Neurological Surgery, University of California San Francisco, San Francisco, CA USA
| | - Izac J. Findlay
- grid.266842.c0000 0000 8831 109XCancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales Australia ,grid.413648.cPrecision Medicine Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales Australia
| | - Matthew D. Dun
- grid.266842.c0000 0000 8831 109XCancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales Australia ,grid.413648.cPrecision Medicine Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales Australia
| | - Adam Resnick
- grid.239552.a0000 0001 0680 8770Center for Data Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA USA
| | - Mario L. Suvà
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.32224.350000 0004 0386 9924Department of Pathology, Center for Cancer Research, Massachusetts General Hospital, Boston, MA USA
| | - David T. W. Jones
- grid.7497.d0000 0004 0492 0584Hopp Children’s Cancer Center Heidelberg (KiTZ), Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sameer Agnihotri
- grid.21925.3d0000 0004 1936 9000Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA USA ,grid.239553.b0000 0000 9753 0008John G. Rangos Sr. Research Center, Children’s Hospital of Pittsburgh, Pittsburgh, PA USA
| | - Jessica Svedlund
- grid.10548.380000 0004 1936 9377Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Carl Koschmann
- grid.412590.b0000 0000 9081 2336Division of Pediatric Hematology/Oncology, Department of Pediatrics, Michigan Medicine, Ann Arbor, MI USA
| | - Christine Haberler
- grid.22937.3d0000 0000 9259 8492Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Thomas Czech
- grid.22937.3d0000 0000 9259 8492Department of Neurosurgery, Medical University of Vienna, Vienna, Austria
| | - Irene Slavc
- grid.22937.3d0000 0000 9259 8492Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Jennifer A. Cotter
- grid.239546.f0000 0001 2153 6013Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Keck School of Medicine of University of Southern California, Los Angeles, CA USA
| | - Keith L. Ligon
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.62560.370000 0004 0378 8294Department of Pathology, Brigham and Women’s Hospital, Boston, MA USA ,grid.2515.30000 0004 0378 8438Department of Pathology, Boston Children’s Hospital, Boston, MA USA
| | - Sanda Alexandrescu
- grid.2515.30000 0004 0378 8438Department of Pathology, Boston Children’s Hospital, Boston, MA USA
| | - W. K. Alfred Yung
- grid.240145.60000 0001 2291 4776Department of Neuro-Oncology, Brain Tumor Center, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Isabel Arrillaga-Romany
- grid.32224.350000 0004 0386 9924Massachusetts General Hospital, Cancer Center, Boston, MA USA
| | - Johannes Gojo
- grid.511177.4Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA USA ,grid.22937.3d0000 0000 9259 8492Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Michelle Monje
- grid.168010.e0000000419368956Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA USA ,grid.413575.10000 0001 2167 1581Howard Hughes Medical Institute, Stanford, CA USA
| | - Mats Nilsson
- grid.10548.380000 0004 1936 9377Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Mariella G. Filbin
- grid.511177.4Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA USA ,grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
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15
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So J, Mabe NW, Englinger B, Chow KH, Moyer SM, Yerrum S, Trissal MC, Marques JG, Kwon JJ, Shim B, Pal S, Panditharatna E, Quinn T, Schaefer DA, Jeong D, Mayhew DL, Hwang J, Beroukhim R, Ligon KL, Stegmaier K, Filbin MG, Hahn WC. VRK1 as a synthetic lethal target in VRK2 promoter-methylated cancers of the nervous system. JCI Insight 2022; 7:e158755. [PMID: 36040810 PMCID: PMC9675470 DOI: 10.1172/jci.insight.158755] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 08/24/2022] [Indexed: 11/17/2022] Open
Abstract
Collateral lethality occurs when loss of a gene/protein renders cancer cells dependent on its remaining paralog. Combining genome-scale CRISPR/Cas9 loss-of-function screens with RNA sequencing in over 900 cancer cell lines, we found that cancers of nervous system lineage, including adult and pediatric gliomas and neuroblastomas, required the nuclear kinase vaccinia-related kinase 1 (VRK1) for their survival in vivo. VRK1 dependency was inversely correlated with expression of its paralog VRK2. VRK2 knockout sensitized cells to VRK1 loss, and conversely, VRK2 overexpression increased cell fitness in the setting of VRK1 loss. DNA methylation of the VRK2 promoter was associated with low VRK2 expression in human neuroblastomas and adult and pediatric gliomas. Mechanistically, depletion of VRK1 reduced barrier-to-autointegration factor phosphorylation during mitosis, resulting in DNA damage and apoptosis. Together, these studies identify VRK1 as a synthetic lethal target in VRK2 promoter-methylated adult and pediatric gliomas and neuroblastomas.
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Affiliation(s)
- Jonathan So
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Nathaniel W Mabe
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorder Center and Harvard Medical School, Boston, Massachusetts, USA
| | - Bernhard Englinger
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorder Center and Harvard Medical School, Boston, Massachusetts, USA
- Department of Urology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Kin-Hoe Chow
- Department of Oncologic Pathology and
- Center for Patient Derived Models, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Sydney M Moyer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Smitha Yerrum
- Department of Oncologic Pathology and
- Center for Patient Derived Models, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Maria C Trissal
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorder Center and Harvard Medical School, Boston, Massachusetts, USA
| | - Joana G Marques
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorder Center and Harvard Medical School, Boston, Massachusetts, USA
| | - Jason J Kwon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Brian Shim
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Sangita Pal
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Eshini Panditharatna
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorder Center and Harvard Medical School, Boston, Massachusetts, USA
| | - Thomas Quinn
- Department of Oncologic Pathology and
- Center for Patient Derived Models, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Daniel A Schaefer
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorder Center and Harvard Medical School, Boston, Massachusetts, USA
| | - Daeun Jeong
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorder Center and Harvard Medical School, Boston, Massachusetts, USA
| | - David L Mayhew
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Radiation Oncology, Tufts Medical Center, Boston, Massachusetts, USA
| | - Justin Hwang
- Department of Medicine and
- Masonic Cancer Center, University of Minnesota-Twin Cities, Minneapolis, Minnesota, USA
| | - Rameen Beroukhim
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Keith L Ligon
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Urology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- Department of Oncologic Pathology and
| | - Kimberly Stegmaier
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorder Center and Harvard Medical School, Boston, Massachusetts, USA
| | - Mariella G Filbin
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorder Center and Harvard Medical School, Boston, Massachusetts, USA
| | - William C Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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16
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Bernstock JD, Hoffman SE, Kappel AD, Valdes PA, Essayed WI, Klinger NV, Kang KD, Totsch SK, Olsen HE, Schlappi CW, Filipski K, Gessler FA, Baird L, Filbin MG, Hashizume R, Becher OJ, Friedman GK. Immunotherapy approaches for the treatment of diffuse midline gliomas. Oncoimmunology 2022; 11:2124058. [PMID: 36185807 PMCID: PMC9519005 DOI: 10.1080/2162402x.2022.2124058] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Diffuse midline gliomas (DMG) are a highly aggressive and universally fatal subgroup of pediatric tumors responsible for the majority of childhood brain tumor deaths. Median overall survival is less than 12 months with a 90% mortality rate at 2 years from diagnosis. Research into the underlying tumor biology and numerous clinical trials have done little to change the invariably poor prognosis. Continued development of novel, efficacious therapeutic options for DMGs remains a critically important area of active investigation. Given that DMGs are not amenable to surgical resection, have only limited response to radiation, and are refractory to traditional chemotherapy, immunotherapy has emerged as a promising alternative treatment modality. This review summarizes the various immunotherapy-based treatments for DMG as well as their specific limitations. We explore the use of cell-based therapies, oncolytic virotherapy or immunovirotherapy, immune checkpoint inhibition, and immunomodulatory vaccination strategies, and highlight the recent clinical success of anti-GD2 CAR-T therapy in diffuse intrinsic pontine glioma (DIPG) patients. Finally, we address the challenges faced in translating preclinical and early phase clinical trial data into effective standardized treatment for DMG patients.
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Affiliation(s)
- Joshua D. Bernstock
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA,Department of Neurosurgery, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA,David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA,CONTACT Joshua D. Bernstock Department of Neurosurgery, Harvard Medical School, Brigham and Women’s Hospital, Boston Children’s Hospital, Hale Building, 60 Fenwood Road, Boston, MA02115, USA
| | - Samantha E. Hoffman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Children’s Hospital Cancer Center, Boston, MA, USA
| | - Ari D. Kappel
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA,Department of Neurosurgery, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Pablo A. Valdes
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA,Department of Neurosurgery, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Walid Ibn Essayed
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA,Department of Neurosurgery, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Neil V. Klinger
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA,Department of Neurosurgery, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Kyung-Don Kang
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Stacie K. Totsch
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Hannah E. Olsen
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Charles W. Schlappi
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Children’s Hospital Cancer Center, Boston, MA, USA
| | - Katharina Filipski
- Neurological Institute (Edinger Institute), University Hospital, Frankfurt Am Main, Germany,German Cancer Consortium (DKTK), Germany and German Cancer Research Center (DFKZ), Heidelberg, Germany,Frankfurt Cancer Institute (FCI), Frankfurt, Germany,University Cancer Center (UCT), Frankfurt, Germany
| | - Florian A. Gessler
- Department of Neurosurgery, University Medicine Rostock, Rostock, Germany
| | - Lissa Baird
- Department of Neurosurgery, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Mariella G. Filbin
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Children’s Hospital Cancer Center, Boston, MA, USA
| | - Rintaro Hashizume
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Oren J. Becher
- Department of Pediatrics, Division of Pediatric Hematology-Oncology, the Mount Sinai Hospital, NY, NY, USA
| | - Gregory K. Friedman
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL, USA,Department of Neurosurgery, University of Alabama at Birmingham, Birmingham, AL, USA,Gregory K. Friedman Division of Pediatric Hematology and Oncology, Department of Pediatrics, University of Alabama at Birmingham, 1600 7th Avenue South, Lowder 512, Birmingham, AL35233, USA
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17
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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: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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18
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Przystal JM, Cianciolo Cosentino C, Yadavilli S, Zhang J, Laternser S, Bonner ER, Prasad R, Dawood AA, Lobeto N, Chin Chong W, Biery MC, Myers C, Olson JM, Panditharatna E, Kritzer B, Mourabit S, Vitanza NA, Filbin MG, de Iuliis GN, Dun MD, Koschmann C, Cain JE, Grotzer MA, Waszak SM, Mueller S, Nazarian J. Imipridones affect tumor bioenergetics and promote cell lineage differentiation in diffuse midline gliomas. Neuro Oncol 2022; 24:1438-1451. [PMID: 35157764 PMCID: PMC9435508 DOI: 10.1093/neuonc/noac041] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Pediatric diffuse midline gliomas (DMGs) are incurable childhood cancers. The imipridone ONC201 has shown early clinical efficacy in a subset of DMGs. However, the anticancer mechanisms of ONC201 and its derivative ONC206 have not been fully described in DMGs. METHODS DMG models including primary human in vitro (n = 18) and in vivo (murine and zebrafish) models, and patient (n = 20) frozen and FFPE specimens were used. Drug-target engagement was evaluated using in silico ChemPLP and in vitro thermal shift assay. Drug toxicity and neurotoxicity were assessed in zebrafish models. Seahorse XF Cell Mito Stress Test, MitoSOX and TMRM assays, and electron microscopy imaging were used to assess metabolic signatures. Cell lineage differentiation and drug-altered pathways were defined using bulk and single-cell RNA-seq. RESULTS ONC201 and ONC206 reduce viability of DMG cells in nM concentrations and extend survival of DMG PDX models (ONC201: 117 days, P = .01; ONC206: 113 days, P = .001). ONC206 is 10X more potent than ONC201 in vitro and combination treatment was the most efficacious at prolonging survival in vivo (125 days, P = .02). Thermal shift assay confirmed that both drugs bind to ClpP, with ONC206 exhibiting a higher binding affinity as assessed by in silico ChemPLP. ClpP activation by both drugs results in impaired tumor cell metabolism, mitochondrial damage, ROS production, activation of integrative stress response (ISR), and apoptosis in vitro and in vivo. Strikingly, imipridone treatment triggered a lineage shift from a proliferative, oligodendrocyte precursor-like state to a mature, astrocyte-like state. CONCLUSION Targeting mitochondrial metabolism and ISR activation effectively impairs DMG tumorigenicity. These results supported the initiation of two pediatric clinical trials (NCT05009992, NCT04732065).
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Affiliation(s)
- Justyna M Przystal
- Department of Oncology, Children’s Research Center, University Children’s HospitalZurich, Zurich, Switzerland
| | - Chiara Cianciolo Cosentino
- Department of Oncology, Children’s Research Center, University Children’s HospitalZurich, Zurich, Switzerland
| | - Sridevi Yadavilli
- Department of Oncology, Children’s Research Center, University Children’s HospitalZurich, Zurich, Switzerland
- Research Center for Genetic Medicine, Children’s National Hospital, Washington, DC, USA
| | - Jie Zhang
- Department of Neurology, University of California, San Francisco, San Francisco, California, USA
| | - Sandra Laternser
- Department of Oncology, Children’s Research Center, University Children’s HospitalZurich, Zurich, Switzerland
| | - Erin R Bonner
- Research Center for Genetic Medicine, Children’s National Hospital, Washington, DC, USA
| | - Rachna Prasad
- Department of Oncology, Children’s Research Center, University Children’s HospitalZurich, Zurich, Switzerland
| | - Adam A Dawood
- Research Center for Genetic Medicine, Children’s National Hospital, Washington, DC, USA
| | - Nina Lobeto
- Department of Oncology, Children’s Research Center, University Children’s HospitalZurich, Zurich, Switzerland
| | - Wai Chin Chong
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Victoria, Australia and Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Matt C Biery
- The Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, Washington, USA
| | - Carrie Myers
- The Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, Washington, USA
| | - James M Olson
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Eshini Panditharatna
- Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, Massachusetts, USA
| | - Bettina Kritzer
- Department of Oncology, Children’s Research Center, University Children’s HospitalZurich, Zurich, Switzerland
| | - Sulayman Mourabit
- Department of Oncology, Children’s Research Center, University Children’s HospitalZurich, Zurich, Switzerland
| | - Nicholas A Vitanza
- The Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, Washington, USA
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Mariella G Filbin
- Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, Massachusetts, USA
| | - Geoffry N de Iuliis
- Reproductive Science Group, College of Engineering, Science and Environment, University of Newcastle, Callaghan, New South Wales, Australia
| | - Matthew D Dun
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, Hunter Medical Research Institute, University of Newcastle, Callaghan, New South Wales, Australia
| | - Carl Koschmann
- Department of Pediatrics, Michigan Medicine, Ann Arbor, Michigan, USA
| | - Jason E Cain
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Victoria, Australia and Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Michael A Grotzer
- Department of Oncology, Children’s Research Center, University Children’s HospitalZurich, Zurich, Switzerland
| | - Sebastian M Waszak
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway
| | - Sabine Mueller
- Department of Oncology, Children’s Research Center, University Children’s HospitalZurich, Zurich, Switzerland
- Department of Pediatrics and Neurosurgery, University of California, San Francisco, San Francisco, California, USA
- Department of Neurology, University of California, San Francisco, San Francisco, California, USA
| | - Javad Nazarian
- Department of Oncology, Children’s Research Center, University Children’s HospitalZurich, Zurich, Switzerland
- Research Center for Genetic Medicine, Children’s National Hospital, Washington, DC, USA
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19
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Ausejo-Mauleon I, Labiano S, De la Nava D, Garcia-Moure M, Laspidea V, Becher OJ, Jiang L, Filbin MG, Pastor F, Alonso MM. DIPG-22. Modifying the tumor microenvironment with a TIM-3 monoclonal antibody as a therapeutic strategy for DIPGs. Neuro Oncol 2022. [DOI: 10.1093/neuonc/noac079.079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Diffuse Midline Glioma, encompassing Diffuse Intrinsic Pontine Gliomas (DIPGs), are the most aggressive pediatric brain tumors. Their meager survival has not changed despite the combination of radiotherapy with targeted therapies emphasizing the urgent need for effective treatments. TIM-3 (HAVCR2) is a member of the T-cell immunoglobulin and mucin domain protein family. It is expressed on multiple immune cell types, including T cells, NK cells, myeloid populations, and microglia, regulating adaptive and innate immunity. In silico assessment of TIM-3 expression in DIPG datasets showed a robust expression of this gene. Single-cell sequencing analyses of DIPG biopsies uncover TIM-3 expression, especially in microglia. In vivo efficacy studies showed that treatment with AbTIM-3 significantly increased overall survival in two DIPG immunocompetent orthotopic models, led to long-term survivors (50%), and showed immune memory. TIM-3 treatment led to a significant increase in the tumor microenvironment of microglia, granulocytes, NK, and CD8+ cells and higher levels of IFNγ, GrzB and TNFα corresponding with an NK and T-cell activate phenotypes. Interestingly, there was a decrease in the Treg population which causes an increase in the pro-inflammatory CD8/Treg ratio. CD4, CD8 or NK cell depletion leads to a significant but not a total loss of treatment efficacy. CD4+ and CD8+ cells were aumented in treated draining lymph nodes and expressed higher amounts of pro-inflamattory cytokines than control-mice. Population analysis and depletion experiments demonstrated the relevance of NK, CD4, CD8 and myeloid populations in the response to anti-TIM-3 therapy. Interestingly, the depletion of the different immune populations combined or using immunodeficient Rag2 mice, did not completely abrogate the treatment efficacy. These results suggest the concurrence of an additional mechanism of action that together with the immune response leads to a robust anti-DIPG effect. In conclusion, these data demonstrate that TIM-3 is a potential target for the treatment of DIPG.
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Affiliation(s)
| | - Sara Labiano
- Department of Pediatrics, Clínica Universidad de Navarra , Pamplona , Spain
| | - Daniel De la Nava
- Department of Pediatrics, Clínica Universidad de Navarra , Pamplona , Spain
| | - Marc Garcia-Moure
- Department of Pediatrics, Clínica Universidad de Navarra , Pamplona , Spain
| | - Virginia Laspidea
- Department of Pediatrics, Clínica Universidad de Navarra , Pamplona , Spain
| | - Oren J Becher
- Division of Pediatric Hematology-Oncology, Mount Sinai Kravis Children’s Hospital , New York , USA
| | - Li Jiang
- Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center , Boston , USA
| | - Mariella G Filbin
- Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center , Boston , USA
| | - Fernando Pastor
- Aptamer Platform, Molecular Therapeutics Program CIMA Universidad de Navarra , Pamplona , Spain
| | - Marta M Alonso
- Department of Pediatrics, Clínica Universidad de Navarra , Pamplona , Spain
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20
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Federico A, Okonechnikov K, Carmona EB, Lammers JAS, Kranendonk MEG, Gojo J, Englinger B, Jiang L, Nierkens S, Calkoen FGJ, van der Lugt J, Filbin MG, Jäger N, Pfister SM, Kool M. EPEN-08. Single-cell transcriptome analysis defines a tumor-supportive microenvironment and tumor-stroma crosstalk in pediatric ependymoma and medulloblastoma. Neuro Oncol 2022. [DOI: 10.1093/neuonc/noac079.145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Brain tumors are the leading cause of disease-related death in childhood and strong efforts are required to develop innovative and efficient therapeutic strategies for patients with high-risk disease. Key critical factor of pediatric brain tumors is their molecular heterogeneity; one of the aspects that contributes to such heterogeneity is the intrinsic capacity of the tumor cells to organize, shape and exploit the surrounding brain tumor microenvironment (TME) to sustain tumor growth and malignant progression. TME was proved to play a crucial role in several malignancies, but in pediatric brain malignancies this has not been fully elucidated yet. Here, we aimed at characterizing the TME cell populations and their contributions in ependymoma and medulloblastoma, two of the most common pediatric brain tumor entities. Single-cell transcriptome analysis (n=65 ependymomas; n=39 medulloblastomas) of publicly available tumor datasets, as well as newly generated data of primary tumors and matching patient-derived tumor xenografts (PDX), showed an extensive heterogeneity of TME cell types with distinctive expression signatures. Amongst the identified TME populations, analysis revealed pro-inflammatory and proliferating myeloid cells, tumor-infiltrating lymphocytes, active regulatory T cells and vascular progenitor cells. Comparative analysis between primary and PDX tumors showed that tumor cells stimulated the host microenvironment, which in turn exhibited tumor-associated stromal signatures. Applying a deconvolution method, using our single cell data as reference, on a bulk tumor cohort including PFA ependymomas with different degree of immune infiltration, we observed an enrichment of polarized macrophages and microglia cells in tumor with high infiltration. Next, we identified TME markers involved in tumor-supportive functions, such as immune suppression (TIGIT, FOXP3, BCL2, CD19, ICAM2), pro-inflammatory stimuli (CCL3, CCL4, IL1B, GPNMB), extracellular matrix remodeling (COL4A1) and angiogenic processes (ANGPT2). TME markers with emerging role in ependymoma and medulloblastoma can be considered as possible targets for tailored and more effective anti-tumor therapeutic strategies.
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Affiliation(s)
- Aniello Federico
- Hopp Children’s Cancer Center , Heidelberg , Germany
- German Cancer Research Center , Heidelberg , Germany
| | - Konstantin Okonechnikov
- Hopp Children’s Cancer Center , Heidelberg , Germany
- German Cancer Research Center , Heidelberg , Germany
| | - Enrique Blanco Carmona
- Hopp Children’s Cancer Center , Heidelberg , Germany
- German Cancer Research Center , Heidelberg , Germany
| | | | | | - Johannes Gojo
- Hopp Children’s Cancer Center , Heidelberg , Germany
- Medical University of Vienna , Vienna , Austria
| | - Bernhard Englinger
- Dana-Farber Boston Children’s Cancer and Blood Disorders Center , Boston , USA
- Broad Institute of Harvard and MIT , Cambridge , USA
| | - Li Jiang
- Dana-Farber Boston Children’s Cancer and Blood Disorders Center , Boston , USA
- Broad Institute of Harvard and MIT , Cambridge , USA
| | | | | | | | - Mariella G Filbin
- Dana-Farber Boston Children’s Cancer and Blood Disorders Center , Boston , USA
- Broad Institute of Harvard and MIT , Cambridge , USA
| | - Natalie Jäger
- Hopp Children’s Cancer Center , Heidelberg , Germany
- German Cancer Research Center , Heidelberg , Germany
| | - Stefan M Pfister
- Hopp Children’s Cancer Center , Heidelberg , Germany
- German Cancer Research Center , Heidelberg , Germany
| | - Marcel Kool
- Hopp Children’s Cancer Center , Heidelberg , Germany
- German Cancer Research Center , Heidelberg , Germany
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21
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Gabler L, Gojo J, Smith KS, Bihannic L, Filbin MG, Northcott PA, Berger W, Hovestadt V. MEDB-82. Exploring cell-cell communication networks in medulloblastoma using single-cell genomics. Neuro Oncol 2022. [PMCID: PMC9164635 DOI: 10.1093/neuonc/noac079.456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Medulloblastoma is a high-risk embryonal brain tumor arising in the cerebellum. Genomic profiling has revealed a striking molecular heterogeneity between medulloblastoma patients, yet treatment regimens are mostly uniform. Many children with medulloblastoma die from their disease and surviving patients often face severe long-term side effects, highlighting an urgent need for more effective treatment options. We and others have recently identified pronounced intra-tumoral heterogeneity and defined cellular hierarchies within medulloblastoma tumors. The functional role of these cellular hierarchies remains unknown. We now hypothesize the existence of an inter-cellular communication network that is maintained by receptor/ligand interactions. To test our hypothesis, we use our medulloblastoma single-cell RNA sequencing dataset of 25 patients, as well as bulk RNA sequencing, DNA methylation array, and genome sequencing data across molecular subtypes. Single-cell RNA sequencing data are analyzed to dissect cell compartments characterized by high expression of potentially oncogenic receptors and their respective ligands. Consequently, cell type-specific roles in auto- or paracrine signal transduction within the cellular community are explored. We further investigate downstream oncogenic signaling pathways by approximating transcription factor activity and explore genetic and epigenetic activation mechanisms by matched genome sequencing and DNA methylation profiling, respectively. Our findings will be applied to deconvolute bulk RNA sequencing data, thus identifying therapeutically relevant signaling networks in larger cohorts of medulloblastoma patients. Eventually, candidate targets will be validated on patient-derived cell models and xenografts by overexpression and inhibition studies. Together, here we aim at identifying tumor-driving receptor/ligand interactions in medulloblastoma, with the goal to define targets susceptible to precision oncology approaches.
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Affiliation(s)
- Lisa Gabler
- Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center , Boston, MA , USA
- Broad Institute of Harvard and MIT , Cambridge, MA , USA
| | - Johannes Gojo
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna , Vienna , Austria
| | - Kyle S Smith
- Department of Developmental Neurobiology, St Jude Children’s Research Hospital , Memphis, TN , USA
| | - Laure Bihannic
- Department of Developmental Neurobiology, St Jude Children’s Research Hospital , Memphis, TN , USA
| | - Mariella G Filbin
- Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center , Boston, MA , USA
- Broad Institute of Harvard and MIT , Cambridge, MA , USA
| | - Paul A Northcott
- Department of Developmental Neurobiology, St Jude Children’s Research Hospital , Memphis, TN , USA
| | - Walter Berger
- Center for Cancer Research and Comprehensive Cancer Center, Medical University of Vienna , Vienna , Austria
| | - Volker Hovestadt
- Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center , Boston, MA , USA
- Broad Institute of Harvard and MIT , Boston, MA , USA
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22
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Klenner M, Freidel P, Filbin MG, Beck A. DIPG-39. New preclinical models for Diffuse Midline Glioma. Neuro Oncol 2022. [PMCID: PMC9164811 DOI: 10.1093/neuonc/noac079.096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Malignant brain tumors are the leading cause of childhood death in Germany, with Diffuse Midline Glioma (DMG) being the most lethal of all paediatric brain tumors. Current treatment strategies are limited to irradiation which prolongs survival only by a few months. Preclinical studies have identified effective drug candidates, but translation into the clinic remains a major obstacle. It is known that interactions between tumor cells and components of the TME (tumor microenvironment), such as cell to cell contacts between malignant and non-malignant cells or secreted factors, can increase therapy resistance and progression of brain tumors. However, these important factors are not present in most conventional cell culture models for drug testing. Consequently, there is a need for more realistic DMG models to improve the relevance and translational potential of current drug screening. Therefore, the goal of this study was to develop a new DMG model for drug testing, consisting of induced pluripotent stem cell (iPSC) derived human brain cells and patient derived DMG cells to better mimic the complex tumor microenvironment. We co-cultured three-dimensional cerebral organoids with DMG tumor spheres resulting in the formation of DMG-Brain-Organoids (DBO). Preliminary results show that co-culture induces distinct tumor cell subpopulations corresponding to those detected in DMG tumors by single cell RNA sequencing (Filbin et al., 2018). These subpopulations mainly differ in their proliferative capacity and their differential response to clinical interventions may be critical for therapeutic success. DBOs subjected to drug treatments (single or combination) were sectioned and individual therapy effects on tumor cell subpopulations and proliferative capacity were monitored using multiplexed immunofluorescence imaging. By observing drug effects in a realistic setup, we hope to improve the predictive power of our preclinical drug screens and to find new combination therapies for DMG.
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Affiliation(s)
- Marbod Klenner
- Ludwig-Maximilians-University , Munich, Bavaria , Germany
| | - Pia Freidel
- Ludwig-Maximilians-University , Munich, Bavaria , Germany
| | | | - Alexander Beck
- Ludwig-Maximilians-University , Munich, Bavaria , Germany
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23
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Gudenas B, Englinger B, Liu APY, Ahmad ST, Meredith D, Pfaff E, Paul L, Hadley J, Batts M, Klimo P, Boop FA, Gajjar A, Robinson G, Orr B, Lin H, Alexandrescu S, Jones DTW, Filbin MG, Northcott PA. ETMR-14. The single-cell landscape of pineoblastoma identifies developmental origins and exposes novel therapeutic vulnerabilities. Neuro Oncol 2022. [PMCID: PMC9165319 DOI: 10.1093/neuonc/noac079.192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Pineoblastoma (PB) is a rare and aggressive childhood brain tumor with highly variable age and treatment-associated outcomes. Our recent bulk tumor analyses of DNA methylation and mutational landscapes uncovered four discrete PB molecular subgroups (PB-miRNA1, PB-miRNA2, PB-MYC/FOXR2, and PB-RB), providing a major advance in our understanding of biological and clinical heterogeneity. However, developmental origins of PB subgroup heterogeneity and mechanisms governing how specific genetic alterations promote malignancy remain unknown. To resolve the cellular origins of PB, we assembled a large single-nucleus RNA-sequencing cohort (n=32) of primary PB tumors, including representatives from each subgroup. Transcriptomic analysis identified subgroup-specific gene expression programs driving intra-tumoral heterogeneity. In addition, we discovered substantial differences in the expression of miRNA biogenesis genes between the PB-miRNA1 and PB-miRNA2 subgroups, providing mechanistic support for their distinct subgroup identities despite overlapping driver events. The MYC/FOXR2 subgroup was characterized by over-expression of the FOXR2 proto-oncogene in bulk RNA-seq, which we validated in single-nuclei and identified co-expressed downstream target genes. To map PB subgroups to their putative developmental beginnings, we created a single-cell transcriptional atlas of the murine pineal gland across 11 developmental stages (E11-P21). Trajectory inference within the developing pineal gland revealed a differentiation continuum of early, mid, and mature alpha-/beta pinealocytes. Cross-species correlation and deconvolution identified significant associations between multiple PB subgroups and specific differentiation states of the pinealocyte lineage, suggestive of developmental origins. Characterization of pinealocyte development informed generation of biologically faithful disease models, including a novel genetically engineered mouse model of the PB-RB subgroup. PB-Rb1 mouse tumors were histologically and molecularly validated for their fidelity to human tumor counterparts, exhibiting up-regulation of key pinealocyte lineage markers that are diagnostic in patients. Finally, high-throughput drug screening identified several promising pharmacological candidates that may attenuate consequences of Rb1 deficiency in affected children.
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Affiliation(s)
- Brian Gudenas
- St. Jude Children’s Research Hospital , Memphis, TN , USA
| | | | - Anthony P Y Liu
- Li Ka Shing Faculty of Medicine, Hong Kong , SAR , China
- Hong Kong Children’s Hospital, Hong Kong , SAR , China
| | | | - David Meredith
- Brigham and Women’s Hospital and Harvard Medical School , Boston, MA , USA
| | - Elke Pfaff
- Hopp Children’s Cancer Center Heidelberg (KiTZ) , Heidelberg , Germany
- German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Leena Paul
- St. Jude Children’s Research Hospital , Memphis, TN , USA
| | | | - Melissa Batts
- St. Jude Children’s Research Hospital , Memphis, TN , USA
| | - Paul Klimo
- St. Jude Children’s Research Hospital , Memphis, TN , USA
- Le Bonheur Children’s Hospital , Memphis, TN , USA
| | - Frederick A Boop
- St. Jude Children’s Research Hospital , Memphis, TN , USA
- Le Bonheur Children’s Hospital , Memphis, TN , USA
| | - Amar Gajjar
- St. Jude Children’s Research Hospital , Memphis, TN , USA
| | - Giles Robinson
- St. Jude Children’s Research Hospital , Memphis, TN , USA
| | - Brent Orr
- St. Jude Children’s Research Hospital , Memphis, TN , USA
| | - Hong Lin
- St. Jude Children’s Research Hospital , Memphis, TN , USA
| | | | - David T W Jones
- Hopp Children’s Cancer Center Heidelberg (KiTZ) , Heidelberg , Germany
- German Cancer Research Center (DKFZ) , Heidelberg , Germany
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24
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Majzner RG, Ramakrishna S, Yeom KW, Patel S, Chinnasamy H, Schultz LM, Richards RM, Jiang L, Barsan V, Mancusi R, Geraghty AC, Good Z, Mochizuki AY, Gillespie SM, Toland AMS, Mahdi J, Reschke A, Nie EH, Chau IJ, Rotiroti MC, Mount CW, Baggott C, Mavroukakis S, Egeler E, Moon J, Erickson C, Green S, Kunicki M, Fujimoto M, Ehlinger Z, Reynolds W, Kurra S, Warren KE, Prabhu S, Vogel H, Rasmussen L, Cornell TT, Partap S, Fisher PG, Campen CJ, Filbin MG, Grant G, Sahaf B, Davis KL, Feldman SA, Mackall CL, Monje M. GD2-CAR T cell therapy for H3K27M-mutated diffuse midline gliomas. Nature 2022; 603:934-941. [PMID: 35130560 PMCID: PMC8967714 DOI: 10.1038/s41586-022-04489-4] [Citation(s) in RCA: 335] [Impact Index Per Article: 167.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 01/28/2022] [Indexed: 12/15/2022]
Abstract
Diffuse intrinsic pontine glioma (DIPG) and other H3K27M-mutated diffuse midline gliomas (DMGs) are universally lethal paediatric tumours of the central nervous system1. We have previously shown that the disialoganglioside GD2 is highly expressed on H3K27M-mutated glioma cells and have demonstrated promising preclinical efficacy of GD2-directed chimeric antigen receptor (CAR) T cells2, providing the rationale for a first-in-human phase I clinical trial (NCT04196413). Because CAR T cell-induced brainstem inflammation can result in obstructive hydrocephalus, increased intracranial pressure and dangerous tissue shifts, neurocritical care precautions were incorporated. Here we present the clinical experience from the first four patients with H3K27M-mutated DIPG or spinal cord DMG treated with GD2-CAR T cells at dose level 1 (1 × 106 GD2-CAR T cells per kg administered intravenously). Patients who exhibited clinical benefit were eligible for subsequent GD2-CAR T cell infusions administered intracerebroventricularly3. Toxicity was largely related to the location of the tumour and was reversible with intensive supportive care. On-target, off-tumour toxicity was not observed. Three of four patients exhibited clinical and radiographic improvement. Pro-inflammatory cytokine levels were increased in the plasma and cerebrospinal fluid. Transcriptomic analyses of 65,598 single cells from CAR T cell products and cerebrospinal fluid elucidate heterogeneity in response between participants and administration routes. These early results underscore the promise of this therapeutic approach for patients with H3K27M-mutated DIPG or spinal cord DMG.
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Affiliation(s)
- Robbie G Majzner
- Stanford Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA, USA.,Division of Pediatric Hematology, Oncology, Stem Cell Transplantation & Regenerative Medicine, Department of Pediatrics, Stanford University, Stanford, CA, USA.,Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Sneha Ramakrishna
- Stanford Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA, USA.,Division of Pediatric Hematology, Oncology, Stem Cell Transplantation & Regenerative Medicine, Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Kristen W Yeom
- Division of Neuroradiology, Department of Radiology, Stanford University, Stanford, CA, USA
| | - Shabnum Patel
- Stanford Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Harshini Chinnasamy
- Stanford Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Liora M Schultz
- Stanford Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA, USA.,Division of Pediatric Hematology, Oncology, Stem Cell Transplantation & Regenerative Medicine, Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Rebecca M Richards
- Stanford Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA, USA.,Division of Pediatric Hematology, Oncology, Stem Cell Transplantation & Regenerative Medicine, Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Li Jiang
- Division of Pediatric Neuro-Oncology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Valentin Barsan
- Stanford Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA, USA.,Division of Pediatric Hematology, Oncology, Stem Cell Transplantation & Regenerative Medicine, Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Rebecca Mancusi
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Anna C Geraghty
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Zinaida Good
- Stanford Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA, USA.,Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.,Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Aaron Y Mochizuki
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Shawn M Gillespie
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | | | - Jasia Mahdi
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Agnes Reschke
- Stanford Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA, USA.,Division of Pediatric Hematology, Oncology, Stem Cell Transplantation & Regenerative Medicine, Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Esther H Nie
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Isabelle J Chau
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Maria Caterina Rotiroti
- Division of Pediatric Hematology, Oncology, Stem Cell Transplantation & Regenerative Medicine, Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Christopher W Mount
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Christina Baggott
- Stanford Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Sharon Mavroukakis
- Stanford Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Emily Egeler
- Stanford Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Jennifer Moon
- Stanford Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Courtney Erickson
- Stanford Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Sean Green
- Division of Pediatric Hematology, Oncology, Stem Cell Transplantation & Regenerative Medicine, Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Michael Kunicki
- Stanford Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA, USA.,Division of Pediatric Hematology, Oncology, Stem Cell Transplantation & Regenerative Medicine, Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Michelle Fujimoto
- Stanford Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA, USA.,Division of Pediatric Hematology, Oncology, Stem Cell Transplantation & Regenerative Medicine, Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Zach Ehlinger
- Division of Pediatric Hematology, Oncology, Stem Cell Transplantation & Regenerative Medicine, Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Warren Reynolds
- Division of Pediatric Hematology, Oncology, Stem Cell Transplantation & Regenerative Medicine, Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Sreevidya Kurra
- Division of Pediatric Hematology, Oncology, Stem Cell Transplantation & Regenerative Medicine, Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Katherine E Warren
- Division of Pediatric Neuro-Oncology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Snehit Prabhu
- Stanford Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Hannes Vogel
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Lindsey Rasmussen
- Division of Critical Care Medicine, Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Timothy T Cornell
- Division of Critical Care Medicine, Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Sonia Partap
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Paul G Fisher
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Cynthia J Campen
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Mariella G Filbin
- Division of Pediatric Neuro-Oncology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Gerald Grant
- Department of Neurosurgery, Stanford University, Stanford, CA, USA
| | - Bita Sahaf
- Stanford Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA, USA.,Division of Pediatric Hematology, Oncology, Stem Cell Transplantation & Regenerative Medicine, Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Kara L Davis
- Stanford Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA, USA.,Division of Pediatric Hematology, Oncology, Stem Cell Transplantation & Regenerative Medicine, Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Steven A Feldman
- Stanford Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Crystal L Mackall
- Stanford Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA, USA. .,Division of Pediatric Hematology, Oncology, Stem Cell Transplantation & Regenerative Medicine, Department of Pediatrics, Stanford University, Stanford, CA, USA. .,Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA. .,Division of Stem Cell Transplantation and Cell Therapy, Department of Medicine, Stanford University, Stanford, CA, USA.
| | - Michelle Monje
- Stanford Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA, USA. .,Division of Pediatric Hematology, Oncology, Stem Cell Transplantation & Regenerative Medicine, Department of Pediatrics, Stanford University, Stanford, CA, USA. .,Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA. .,Department of Pathology, Stanford University, Stanford, CA, USA. .,Department of Neurosurgery, Stanford University, Stanford, CA, USA. .,Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
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25
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Zats LP, Ahmad L, Casden N, Lee MJ, Belzer V, Adato O, Bar Cohen S, Ko SHB, Filbin MG, Unger R, Lauffenburger DA, Segal RA, Behar O. An affinity for brainstem microglia in pediatric high-grade gliomas of brainstem origin. Neurooncol Adv 2022; 4:vdac117. [PMID: 35990702 PMCID: PMC9389428 DOI: 10.1093/noajnl/vdac117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Background High-grade gliomas (HGG) in children have a devastating prognosis and occur in a remarkable spatiotemporal pattern. Diffuse midline gliomas (DMG), including diffuse intrinsic pontine gliomas (DIPG), typically occur in mid-childhood, while cortical HGGs are more frequent in older children and adults. The mechanisms behind this pattern are not clear. Methods We used mouse organotypic slice cultures and glial cell cultures to test the impact of the microenvironment on human DIPG cells. Comparing the expression between brainstem and cortical microglia identified differentially expressed secreted proteins. The impact of some of these proteins on DIPGs was tested. Results DIPGs, pediatric HGGs of brainstem origin, survive and divide more in organotypic slice cultures originating in the brainstem as compared to the cortex. Moreover, brainstem microglia are better able to support tumors of brainstem origin. A comparison between the two microglial populations revealed differentially expressed genes. One such gene, interleukin-33 (IL33), is highly expressed in the pons of young mice and its DIPG receptor is upregulated in this context. Consistent with this observation, the expression levels of IL33 and its receptor, IL1RL1, are higher in DIPG biopsies compared to low-grade cortical gliomas. Furthermore, IL33 can enhance proliferation and clonability of HGGs of brainstem origin, while blocking IL33 in brainstem organotypic slice cultures reduced the proliferation of these tumor cells. Conclusions Crosstalk between DIPGs and the brainstem microenvironment, in particular microglia, through IL33 and other secreted factors, modulates spatiotemporal patterning of this HGG and could prove to be an important future therapeutic target.
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Affiliation(s)
- Liat Peretz Zats
- Department of Developmental Biology and Cancer Research, Faculty of Medicine, The Institute for Medical Research Israel-Canada, The Hebrew University , Jerusalem , Israel
| | - Labiba Ahmad
- Department of Developmental Biology and Cancer Research, Faculty of Medicine, The Institute for Medical Research Israel-Canada, The Hebrew University , Jerusalem , Israel
| | - Natania Casden
- Department of Developmental Biology and Cancer Research, Faculty of Medicine, The Institute for Medical Research Israel-Canada, The Hebrew University , Jerusalem , Israel
| | - Meelim J Lee
- Department of Biological Engineering, Massachusetts Institute of Technology , Cambridge, MA
| | - Vitali Belzer
- Department of Developmental Biology and Cancer Research, Faculty of Medicine, The Institute for Medical Research Israel-Canada, The Hebrew University , Jerusalem , Israel
| | - Orit Adato
- Faculty of Life Sciences, Bar Ilan University , Ramat Gan , Israel
| | - Shaked Bar Cohen
- Department of Developmental Biology and Cancer Research, Faculty of Medicine, The Institute for Medical Research Israel-Canada, The Hebrew University , Jerusalem , Israel
| | - Seung-Hyun B Ko
- Department of Biological Engineering, Massachusetts Institute of Technology , Cambridge, MA
| | - Mariella G Filbin
- Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center , Boston, MA
| | - Ron Unger
- Faculty of Life Sciences, Bar Ilan University , Ramat Gan , Israel
| | | | - Rosalind A Segal
- Department of Neurobiology, Harvard Medical School , Boston, MA , USA
- Departments of Cancer Biology and Pediatric Oncology, Dana-Farber Cancer Institute , Boston, MA
| | - Oded Behar
- Department of Developmental Biology and Cancer Research, Faculty of Medicine, The Institute for Medical Research Israel-Canada, The Hebrew University , Jerusalem , Israel
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26
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Liu I, Li J, Jeong D, Hack OA, Shaw M, Englinger B, Avihai B, Ernst K, Resnick A, Diaz A, Jones D, Koschmann C, Kleinman C, Jabado N, Cotter J, Ligon K, Alexandrescu S, Yung WKA, Czech T, Arrillaga-Romany I, Gojo J, Slavc I, Monje M, Filbin MG. EPCO-06. AGE- AND REGION-SPECIFIC MULTI-OMIC CHARACTERIZATION OF H3-K27M MUTANT DIFFUSE MIDLINE GLIOMA. Neuro Oncol 2021. [DOI: 10.1093/neuonc/noab196.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Diffuse midline gliomas driven by lysine27-to-methionine mutations in histone 3 (H3-K27M DMGs) are among the most fatal brain tumors. Molecular studies including single cell RNA-sequencing (scRNA-seq) of pediatric and predominantly pontine H3-K27M DMGs have shown that the H3-K27M oncohistone keeps glioma cells locked in a stem-like oligodendrocyte precursor cell (OPC) state that is capable of self-renewal and tumor-initiation. However, a comprehensive dissection of the cellular architecture of H3-K27M DMGs across different midline regions and age groups is required to better understand the cell-intrinsic and contextual regulation of H3-K27M DMG cell identities. In particular, the more recently described group of adult H3-K27M DMGs remains understudied. Here, we have collected and characterized 45 H3-K27M mutant patient tumors, spanning pontine (n=26), thalamic (n=17), and spinal (n=2) locations. Median age at surgery was 12 (2-68) years, encompassing 21 early childhood (0-10 years), 12 adolescent (11-20 years), and 12 adult (≥ 21 years) tumors. The majority of samples were obtained pre-treatment (n=28), as opposed to post-treatment or at autopsy (n=17). We profiled all 45 tumors by single cell/single nucleus RNA-seq and selected tumors were further characterized by the single cell assay for transposase-accessible chromatin (scATAC-seq). Our integrated analyses highlight the predominance of transcriptionally and epigenetically defined OPC-like tumor cells as the main cell population of H3-K27M DMGs across all age groups and locations. We further identify distinct age- and location-specific OPC-like cell subpopulations. Comparison of pediatric and adult tumors further demonstrates a significant increase of mesenchymal cell states in adult H3-K27M DMGs, which we link to differences in glioma-associated immune cell compartments between age groups. Together, this study sheds light on the effects of age- and region-dependent microenvironments in shaping cellular identities in H3-K27M DMGs.
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Affiliation(s)
- Ilon Liu
- Dana-Farber Cancer Institute, Boston, USA
| | - Jiang Li
- Dana-Farber Boston Children’s Cancer, Bostan, USA
| | - Daeun Jeong
- Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Olivia A Hack
- Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - McKenzie Shaw
- Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Bernhard Englinger
- Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Byron Avihai
- Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Kati Ernst
- Hopp Children’s Cancer Center Heidelberg (KiTZ) and Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Adam Resnick
- Center for Data Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, USA
| | - Aaron Diaz
- University of California, San Francisco, San Francisco, CA, USA
| | - David Jones
- Hopp Children’s Cancer Center Heidelberg (KiTZ) and Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Claudia Kleinman
- Department of Human Genetics, McGill University, Montreal, Canada
| | - Nada Jabado
- Department of Human Genetics, McGill University, Montreal, Canada
| | - Jennifer Cotter
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Keck School of Medicine of University of Southern California, Los Angeles, USA
| | | | | | - W K Alfred Yung
- University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - Thomas Czech
- Department of Neurosurgery, Medical University of Vienna, Vienna, Wien, Austria
| | | | - Johannes Gojo
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | - Irene Slavc
- Medical University of Vienna - Department of Pediatrics and Adolescent Medicine, Vienna, Austria
| | | | - Mariella G Filbin
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, USA
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27
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Yadav VN, Harris MK, Messinger D, Thomas C, Cummings JR, Yang T, Woo R, Siddaway R, Burkert M, Stallard S, Qin T, Mullan B, Siada R, Ravindran R, Niculcea M, Ginn KF, Gener MAH, Dorris K, Vitanza NA, Schmidt SV, Spitzer J, Li J, Filbin MG, Cao X, Castro MG, Lowenstein PR, Mody R, Chinnaiyan A, Desprez P, McAllister S, Hawkins C, Waszak SM, Venneti S, Koschmann C. TAMI-79. THERAPEUTIC REVERSAL OF PRENATAL PONTINE ID1 SIGNALING IN DIPG. Neuro Oncol 2021. [DOI: 10.1093/neuonc/noab196.861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Diffuse intrinsic pontine glioma (DIPG) is a highly aggressive pediatric brain tumor with rare survival beyond two years. This poor prognosis is largely due to the tumor's highly infiltrative and invasive nature. Nearly 80% of DMGs harbor K27M mutation in the genes encoding histone H3.1 (H3F3A) or H3.3 (HISTIH3B), often with concurrent ACVR1 mutation. Inhibitor of DNA-binding (ID) proteins are key transcriptional regulators of genes involved in lineage commitment and are associated with invasiveness and poor clinical outcomes in multiple human cancers. Introduction of H3K27M and ACVR1 mutations increase ID1 expression in cultured astrocytes, but this has not been confirmed in human tumors or targeted therapeutically. We developed an in-utero electroporation (IUE) murine H3K27M-driven tumor model, which demonstrates increased ID1 expression in H3K27M- and ACVR1-mutated tumor cells. Exome and transcriptome sequencing analysis of multi-focal DMG tumors (n=52) and normal brain tissue revealed that increased ID1 expression is associated with H3K27M/ACVR1-mutation and brainstem location, and correlates with poor survival in patients. ChIP-sequencing for H3K27ac and H3K27me3 in multiple DMG tumors (n=5) revealed that the ID1 gene is epigenetically active, which matches the epigenetic state of murine prenatal hindbrain cells. Higher ID1-expressing astrocyte-like DIPG cells share a similar transcriptional program with ID1+/SPARCL1+ positive oligo/astrocyte-precursor (OAPC) cells from the developing human brain and demonstrate upregulation of gene sets involved in regulation of cell migration. Both genetic and pharmacologic [cannabidiol (CBD)] suppression of ID1 result in decreased DIPG cell invasion/migration in vitro and invasion/tumor growth in multiple in vivo models. Mechanistically, CBD reduces proliferation through production of reactive oxygen species. Further, DIPG patients treated off-trial with CBD (n=15) displayed reduced ID1 tumor expression and improved overall survival. In summary, ID1 is upregulated in DIPG through K27M-mediated epigenetic reactivation of a developmental OAPC-like transcriptional state, and ID1-driven invasiveness of DIPG is therapeutically targetable with CBD.
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Affiliation(s)
| | | | | | | | | | - Tao Yang
- University of Michigan, Ann Arbor, MI, USA
| | - Rinette Woo
- CPMC Research Institute, San Francisco, CA, USA
| | | | | | | | | | | | - Ruby Siada
- University of Michigan, Ann Arbor, MI, USA
| | | | | | - Kevin F Ginn
- Department of Pediatrics, Children’s Mercy, Kansas City, MO, USA
| | - Melissa A H Gener
- Department of Pathology and Laboratory Medicine, Children’s, Kansas City, MO, USA
| | - Kathleen Dorris
- Department of Pediatrics, University of Colorado School, Aurora, CO, USA
| | | | | | | | - Jiang Li
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | | | - Xuhong Cao
- University of Michigan, Ann Arbor, MI, USA
| | | | | | - Rajen Mody
- University of Michigan, Ann Arbor, MI, USA
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28
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Hovestadt V, Beck A, Lambo S, Shaw M, Hack OA, Englinger B, Gojo J, Madlener S, Alexandrescu S, Pfister S, Kool M, Filbin MG. EPCO-27. SINGLE-CELL ANALYSIS OF ETMR PATIENT SAMPLES LINKS TRANSCRIPTIONAL PHENOTYPES TO GENETIC DRIVER ALTERATIONS AND INFORMS NOVEL THERAPEUTIC STRATEGIES. Neuro Oncol 2021. [DOI: 10.1093/neuonc/noab196.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
Embryonal tumor with multilayered rosettes (ETMR) is a malignant brain tumor that typically occurs in children under the age of three. Most patients die within two years of diagnosis, and more effective, targeted therapies are urgently needed. To better characterize the oncogenic mechanisms of key driver alterations and identify novel therapeutic targets, we studied the cellular heterogeneity of ETMR using single-cell RNA sequencing. Analyses conducted on >3,000 high-quality cells collected from ten primary and relapse specimens revealed a common cellular hierarchy across all tumors: A highly proliferative neural stem cell-like population (SOX2+) gives rise to intermediate progenitors (ASCL1+) and more differentiated neuron-like cells (STMN2/4+). These malignant populations closely match histological patterns of ETMR (i.e. rosettes, neuropil), as observed by immunofluorescence microscopy. Comparison to single-cell datasets from human embryos indicates resemblance to cell populations of the developing brain, but also reveals key ETMR-specific differences, including expression of the chromosome 19 miRNA cluster (C19MC, the presumed genetic driver of most ETMRs), which is restricted to the stem cell-like population. We next investigated if targeting C19MC is a viable strategy to disrupt the cellular hierarchy of ETMR. Silencing with antisense oligonucleotides shows pronounced reduction of cell line growth for a specific subset of the 46 members of C19MC. These miRNAs share seed sequences with evolutionary conserved miRNAs that have been shown to regulate pluripotency and self-renewal of embryonic stem cells. We hypothesize that select C19MC members play similar roles in ETMR and represent bona fide targets for therapeutic targeting using antisense technology.
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Affiliation(s)
- Volker Hovestadt
- Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Alexander Beck
- Center for Neuropathology and Prion Research, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Sander Lambo
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - McKenzie Shaw
- Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Olivia A Hack
- Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Bernhard Englinger
- Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Johannes Gojo
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | - Sibylle Madlener
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | | | - Stefan Pfister
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Marcel Kool
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Mariella G Filbin
- Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
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29
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Panwalkar P, Tamrazi B, Dang D, Chung C, Sweha S, Natarajan SK, Pun M, Bayliss J, Ogrodzinski MP, Pratt D, Mullan B, Hawes D, Yang F, Lu C, Sabari BR, Achreja A, Heon J, Animasahun O, Cieslik M, Dunham C, Yip S, Hukin J, Phillips JJ, Bornhorst M, Griesinger AM, Donson AM, Foreman NK, Garton HJ, Heth J, Muraszko K, Nazarian J, Koschmann C, Jiang L, Filbin MG, Nagrath D, Kool M, Korshunov A, Pfister SM, Gilbertson RJ, Allis CD, Chinnaiyan A, Lunt SY, Blüml S, Judkins AR, Venneti S. Targeting integrated epigenetic and metabolic pathways in lethal childhood PFA ependymomas. Sci Transl Med 2021; 13:eabc0497. [PMID: 34613815 PMCID: PMC8762577 DOI: 10.1126/scitranslmed.abc0497] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Childhood posterior fossa group A ependymomas (PFAs) have limited treatment options and bear dismal prognoses compared to group B ependymomas (PFBs). PFAs overexpress the oncohistone-like protein EZHIP (enhancer of Zeste homologs inhibitory protein), causing global reduction of repressive histone H3 lysine 27 trimethylation (H3K27me3), similar to the oncohistone H3K27M. Integrated metabolic analyses in patient-derived cells and tumors, single-cell RNA sequencing of tumors, and noninvasive metabolic imaging in patients demonstrated enhanced glycolysis and tricarboxylic acid (TCA) cycle metabolism in PFAs. Furthermore, high glycolytic gene expression in PFAs was associated with a poor outcome. PFAs demonstrated high EZHIP expression associated with poor prognosis and elevated activating mark histone H3 lysine 27 acetylation (H3K27ac). Genomic H3K27ac was enriched in PFAs at key glycolytic and TCA cycle–related genes including hexokinase-2 and pyruvate dehydrogenase. Similarly, mouse neuronal stem cells (NSCs) expressing wild-type EZHIP (EZHIP-WT) versus catalytically attenuated EZHIP-M406K demonstrated H3K27ac enrichment at hexokinase-2 and pyruvate dehydrogenase, accompanied by enhanced glycolysis and TCA cycle metabolism. AMPKα-2, a key component of the metabolic regulator AMP-activated protein kinase (AMPK), also showed H3K27ac enrichment in PFAs and EZHIP-WT NSCs. The AMPK activator metformin lowered EZHIP protein concentrations, increased H3K27me3, suppressed TCA cycle metabolism, and showed therapeutic efficacy in vitro and in vivo in patient-derived PFA xenografts in mice. Our data indicate that PFAs and EZHIP-WT–expressing NSCs are characterized by enhanced glycolysis and TCA cycle metabolism. Repurposing the antidiabetic drug metformin lowered pathogenic EZHIP, increased H3K27me3, and suppressed tumor growth, suggesting that targeting integrated metabolic/epigenetic pathways is a potential therapeutic strategy for treating childhood ependymomas.
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Affiliation(s)
- Pooja Panwalkar
- Laboratory of Brain Tumor Metabolism and Epigenetics, Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Benita Tamrazi
- Department of Radiology, Children’s Hospital Los Angeles, Keck School of Medicine University of Southern California, Los Angeles, CA, 90027, USA
| | - Derek Dang
- Laboratory of Brain Tumor Metabolism and Epigenetics, Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Chan Chung
- Laboratory of Brain Tumor Metabolism and Epigenetics, Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
- Current address- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea
| | - Stefan Sweha
- Laboratory of Brain Tumor Metabolism and Epigenetics, Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Siva Kumar Natarajan
- Laboratory of Brain Tumor Metabolism and Epigenetics, Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Matthew Pun
- Laboratory of Brain Tumor Metabolism and Epigenetics, Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jill Bayliss
- Laboratory of Brain Tumor Metabolism and Epigenetics, Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Martin P. Ogrodzinski
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48823, USA
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, 48823, USA
- Department of Physiology, Michigan State University, East Lansing, MI, 48823, USA
| | - Drew Pratt
- Laboratory of Brain Tumor Metabolism and Epigenetics, Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Brendan Mullan
- Department of Pediatrics, Michigan Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Debra Hawes
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Keck School of Medicine University of Southern California, Los Angeles, CA, 90027, USA
| | - Fusheng Yang
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Keck School of Medicine University of Southern California, Los Angeles, CA, 90027, USA
| | - Chao Lu
- Department of Genetics and Development and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Benjamin R. Sabari
- Laboratory of Chromatin Biology & Epigenetics, The Rockefeller University, New York, NY, 10065, USA
| | - Abhinav Achreja
- Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jin Heon
- Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Olamide Animasahun
- Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Marcin Cieslik
- Laboratory of Brain Tumor Metabolism and Epigenetics, Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Christopher Dunham
- Division of Anatomic Pathology, British Columbia Children's Hospital, Vancouver, British Columbia, V6H 3N1, Canada
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Stephen Yip
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Juliette Hukin
- Division of Hematology and Oncology, Children's and Women's Health Centre of B.C, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Joanna J. Phillips
- Department of Pathology, University of California, San Francisco, CA, 94132, USA
- Department of Neurological Surgery, University of California, San Francisco, CA, USA. 94132
| | - Miriam Bornhorst
- Research Center for Genetic Medicine, Children's National Health System, Washington DC, 20012, USA
- Brain Tumor Institute, Children's National Health System, Washington, DC 20012, USA
| | - Andrea M Griesinger
- Department of Pediatrics, University of Colorado Denver, Aurora, 80045, Colorado
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, 80045, Colorado
| | - Andrew M Donson
- Department of Pediatrics, University of Colorado Denver, Aurora, 80045, Colorado
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, 80045, Colorado
| | - Nicholas K Foreman
- Department of Pediatrics, University of Colorado Denver, Aurora, 80045, Colorado
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, 80045, Colorado
| | - Hugh J.L. Garton
- Department of Neurosurgery, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jason Heth
- Department of Neurosurgery, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Karin Muraszko
- Department of Neurosurgery, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Javad Nazarian
- Research Center for Genetic Medicine, Children's National Health System, Washington DC, 20012, USA
- Brain Tumor Institute, Children's National Health System, Washington, DC 20012, USA
- DMG Research Center Department of Oncology University Children's Hospital, CH-8032 Zürich
| | - Carl Koschmann
- Department of Pediatrics, Michigan Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Li Jiang
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02115, USA
| | - Mariella G. Filbin
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02115, USA
| | - Deepak Nagrath
- Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Marcel Kool
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, 69120, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, 69120, Germany
- Princess Máxima Center for Pediatric Oncology, Utrecht, 3584, the Netherlands
| | - Andrey Korshunov
- Department of Neuropathology, German Cancer Research Center (DKFZ), University Hospital Heidelberg and CCU Neuropathology, Heidelberg, 69120, Germany
| | - Stefan M. Pfister
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, 69120, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, 69120, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, 69120, Germany
| | | | - C. David Allis
- Laboratory of Chromatin Biology & Epigenetics, The Rockefeller University, New York, NY, 10065, USA
| | - Arul Chinnaiyan
- Laboratory of Brain Tumor Metabolism and Epigenetics, Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Sophia Y. Lunt
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48823, USA
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, 48823, USA
| | - Stefan Blüml
- Department of Radiology, Children’s Hospital Los Angeles, Keck School of Medicine University of Southern California, Los Angeles, CA, 90027, USA
| | - Alexander R. Judkins
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Keck School of Medicine University of Southern California, Los Angeles, CA, 90027, USA
| | - Sriram Venneti
- Laboratory of Brain Tumor Metabolism and Epigenetics, Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Pediatrics, Michigan Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
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Lötsch D, Kirchhofer D, Englinger B, Jiang L, Okonechnikov K, Senfter D, Laemmerer A, Gabler L, Pirker C, Donson AM, Bannauer P, Korbel P, Jaunecker CN, Hübner JM, Mayr L, Madlener S, Schmook MT, Ricken G, Maaß K, Grusch M, Holzmann K, Grasl-Kraupp B, Spiegl-Kreinecker S, Hsu J, Dorfer C, Rössler K, Azizi AA, Foreman NK, Peyrl A, Haberler C, Czech T, Slavc I, Filbin MG, Pajtler KW, Kool M, Berger W, Gojo J. Targeting fibroblast growth factor receptors to combat aggressive ependymoma. Acta Neuropathol 2021; 142:339-360. [PMID: 34046693 PMCID: PMC8270873 DOI: 10.1007/s00401-021-02327-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 04/10/2021] [Accepted: 05/10/2021] [Indexed: 12/16/2022]
Abstract
Ependymomas (EPN) are central nervous system tumors comprising both aggressive and more benign molecular subtypes. However, therapy of the high-risk subtypes posterior fossa group A (PF-A) and supratentorial RELA-fusion positive (ST-RELA) is limited to gross total resection and radiotherapy, as effective systemic treatment concepts are still lacking. We have recently described fibroblast growth factor receptors 1 and 3 (FGFR1/FGFR3) as oncogenic drivers of EPN. However, the underlying molecular mechanisms and their potential as therapeutic targets have not yet been investigated in detail. Making use of transcriptomic data across 467 EPN tissues, we found that FGFR1 and FGFR3 were both widely expressed across all molecular groups. FGFR3 mRNA levels were enriched in ST-RELA showing the highest expression among EPN as well as other brain tumors. We further identified high expression levels of fibroblast growth factor 1 and 2 (FGF1, FGF2) across all EPN subtypes while FGF9 was elevated in ST-EPN. Interrogation of our EPN single-cell RNA-sequencing data revealed that FGFR3 was further enriched in cycling and progenitor-like cell populations. Corroboratively, we found FGFR3 to be predominantly expressed in radial glia cells in both mouse embryonal and human brain datasets. Moreover, we detected alternative splicing of the FGFR1/3-IIIc variant, which is known to enhance ligand affinity and FGFR signaling. Dominant-negative interruption of FGFR1/3 activation in PF-A and ST-RELA cell models demonstrated inhibition of key oncogenic pathways leading to reduced cell growth and stem cell characteristics. To explore the feasibility of therapeutically targeting FGFR, we tested a panel of FGFR inhibitors in 12 patient-derived EPN cell models revealing sensitivity in the low-micromolar to nano-molar range. Finally, we gain the first clinical evidence for the activity of the FGFR inhibitor nintedanib in the treatment of a patient with recurrent ST-RELA. Together, these preclinical and clinical data suggest FGFR inhibition as a novel and feasible approach to combat aggressive EPN.
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MESH Headings
- Animals
- Central Nervous System Neoplasms/genetics
- Central Nervous System Neoplasms/pathology
- Ependymoma/genetics
- Ependymoma/pathology
- Humans
- Mice
- Neoplasm Recurrence, Local/genetics
- Neoplasm Recurrence, Local/metabolism
- Neoplasm Recurrence, Local/pathology
- Receptor, Fibroblast Growth Factor, Type 1/genetics
- Receptor, Fibroblast Growth Factor, Type 1/metabolism
- Receptor, Fibroblast Growth Factor, Type 3/metabolism
- Receptors, Fibroblast Growth Factor/genetics
- Receptors, Fibroblast Growth Factor/metabolism
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Affiliation(s)
- Daniela Lötsch
- Department of Neurosurgery, Medical University of Vienna, Vienna, Austria
- Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Dominik Kirchhofer
- Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Bernhard Englinger
- Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, USA
| | - Li Jiang
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, USA
| | - Konstantin Okonechnikov
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Daniel Senfter
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Anna Laemmerer
- Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Lisa Gabler
- Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Christine Pirker
- Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Andrew M Donson
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, USA
- Department of Pediatrics, University of Colorado Denver, Aurora, CO, USA
| | - Peter Bannauer
- Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Pia Korbel
- Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Carola N Jaunecker
- Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Jens-Martin Hübner
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Lisa Mayr
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Sibylle Madlener
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Maria T Schmook
- Department of Biomedical Imaging and Image-Guided Therapy, Medical University of Vienna, Vienna, Austria
| | - Gerda Ricken
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Kendra Maaß
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Michael Grusch
- Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Klaus Holzmann
- Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Bettina Grasl-Kraupp
- Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Sabine Spiegl-Kreinecker
- Department of Neurosurgery, Kepler University Hospital GmbH, Johannes Kepler University, Linz, Austria
| | - Jennifer Hsu
- Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Christian Dorfer
- Department of Neurosurgery, Medical University of Vienna, Vienna, Austria
| | - Karl Rössler
- Department of Neurosurgery, Medical University of Vienna, Vienna, Austria
| | - Amedeo A Azizi
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Nicholas K Foreman
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, USA
- Department of Pediatrics, University of Colorado Denver, Aurora, CO, USA
| | - Andreas Peyrl
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Christine Haberler
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Thomas Czech
- Department of Neurosurgery, Medical University of Vienna, Vienna, Austria
| | - Irene Slavc
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Mariella G Filbin
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, USA
| | - Kristian W Pajtler
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Haematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Marcel Kool
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Walter Berger
- Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Johannes Gojo
- Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria.
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria.
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany.
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Dorfer C, Czech T, Gojo J, Hosmann A, Peyrl A, Azizi AA, Kasprian G, Dieckmann K, Filbin MG, Haberler C, Roessler K, Slavc I. Infiltrative gliomas of the thalamus in children: the role of surgery in the era of H3 K27M mutant midline gliomas. Acta Neurochir (Wien) 2021; 163:2025-2035. [PMID: 33090244 PMCID: PMC8195935 DOI: 10.1007/s00701-020-04589-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 09/16/2020] [Indexed: 12/28/2022]
Abstract
Background The role of surgery in the management of pediatric non-pilocytic infiltrative thalamic gliomas needs to be revisited specifically with regard to molecularly defined subtypes. Methods A retrospective review of a consecutive series of children operated on a thalamic tumor between 1992 and May 2018 was performed. Neuroimaging data were reviewed for localization and extent of resection; pathology was re-reviewed according to the current WHO classification, including assessment of histone H3 K27 mutational status. Results Forty-nine patients with a thalamic tumor aged < 18 years at diagnosis were identified. Twenty-five patients (51%) had a non-pilocytic infiltrative glioma, of which the H3 K27M status was available in 22. Fourteen patients were diagnosed as diffuse midline glioma (DMG) H3 K27M mutant. There was no statistically significant difference in survival between patients harboring the H3 K27M mutation and wildtype. Resection (“any resection > 50%” vs “biopsy”) and histological tumor grade (“°II” vs “°III+°IV”) were statistically significant predictors of survival (univariate: p = 0.044 and p = 0.013, respectively). These results remained significant on multivariate analysis (HR 0.371/p = 0.048, HR 9.433/p = 0.035). Conclusion We advocate to still consider an attempt at maximal safe resection in the multidisciplinary treatment of unilateral thalamic non-pilocytic gliomas irrespective of their H3 K27-mutational status.
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Affiliation(s)
- Christian Dorfer
- Department of Neurosurgery, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
- Comprehensive Cancer Center-CCC CNS Unit, Medical University of Vienna, Vienna, Austria
| | - Thomas Czech
- Department of Neurosurgery, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria.
- Comprehensive Cancer Center-CCC CNS Unit, Medical University of Vienna, Vienna, Austria.
| | - Johannes Gojo
- Comprehensive Cancer Center-CCC CNS Unit, Medical University of Vienna, Vienna, Austria
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | - Arthur Hosmann
- Department of Neurosurgery, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
- Comprehensive Cancer Center-CCC CNS Unit, Medical University of Vienna, Vienna, Austria
| | - Andreas Peyrl
- Comprehensive Cancer Center-CCC CNS Unit, Medical University of Vienna, Vienna, Austria
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | - Amedeo A Azizi
- Comprehensive Cancer Center-CCC CNS Unit, Medical University of Vienna, Vienna, Austria
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | - Gregor Kasprian
- Comprehensive Cancer Center-CCC CNS Unit, Medical University of Vienna, Vienna, Austria
- Department of Biomedical Imaging and Image-Guided Therapy, Medical University of Vienna, Vienna, Austria
| | - Karin Dieckmann
- Comprehensive Cancer Center-CCC CNS Unit, Medical University of Vienna, Vienna, Austria
- Department of Radiotherapy, Medical University of Vienna, Vienna, Austria
| | - Mariella G Filbin
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Christine Haberler
- Comprehensive Cancer Center-CCC CNS Unit, Medical University of Vienna, Vienna, Austria
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Karl Roessler
- Department of Neurosurgery, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
- Comprehensive Cancer Center-CCC CNS Unit, Medical University of Vienna, Vienna, Austria
| | - Irene Slavc
- Comprehensive Cancer Center-CCC CNS Unit, Medical University of Vienna, Vienna, Austria
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
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32
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Ausejo-Mauleon I, Labiano S, Laspidea V, Garcia-Moure M, de la Nava D, Puigdelloses M, Becher OJ, Jiang L, Filbin MG, Pastor F, Alonso MM. IMMU-08. MICROENVIRONMENT MODULATION BY TIM-3 BLOCKADE IMPROVES THE OUTCOME OF PRECLINICAL DIPG MODELS. Neuro Oncol 2021. [PMCID: PMC8168128 DOI: 10.1093/neuonc/noab090.116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Diffuse Midline Gliomas (DMGs), encompassing Diffuse Intrinsic Pontine Gliomas (DIPGs), are the most aggressive pediatric brain tumors. Their meagre survival has not changed despite the combination of radiotherapy with targeted therapies emphasizing the urgent need for effective treatments. Recent research suggested that the DIPG tumor microenvironment is neither highly immunosuppressive nor inflammatory. These analyses showed the lack of infiltrating lymphocytes and the abundance of CD11b+ cells. TIM-3 (HAVCR2) is a member of the T-cell immunoglobulin and mucin domain protein family which is expressed on multiple immune cell types including T cells, Tregs, NK cells, monocytes, dendritic cells and microglia, where it potently regulates not only adaptive immunity but also innate immunity. Therefore, the central hypothesis of this study is that TIM-3 inhibitors could stimulate a cytotoxic immune effect and challenge several components in the tumor microenvironment including microglia, thereby providing a potential effective treatment for DMGs. In silico assessment of TIM-3 expression in a DIPG datasets showed a robust expression of this gene. Moreover, single-cell sequencing analyses of DIPG biopsies uncover its expression on tumor cells, especially in the OPCs compartment. In vivo efficacy studies showed that treatment with anti-TIM-3 antibody significantly increase the overall survival in two DIPG immunocompetent orthotopic animal models (doubling the median), lead to long-term survivors (50%) and showed immune memory. Analyses of CD45+ populations in the tumor microenvironment showed a significant increase in B, NK and CD8+ cells corresponding with a T-cell activate phenotype in treated-mice. The potential therapeutic involvement of NK cells was certified using nude mice and functional studies. Involvement of microglia in currently being analysed. In summary, these data underscore TIM-3 as a potential target DIPGs and uncover the potential involvement of NKs and other immune mechanisms in the efficacy of anti-TIM-3 therapy.
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Affiliation(s)
- Iker Ausejo-Mauleon
- Department of Pediatrics, Clinica Universidad de Navarra, Pamplona, Navarra, Spain
- Health Research Institute os Navarra (IdiSNA), Pamplona, Navarra, Spain
| | - Sara Labiano
- Department of Pediatrics, Clinica Universidad de Navarra, Pamplona, Navarra, Spain
- Health Research Institute os Navarra (IdiSNA), Pamplona, Navarra, Spain
| | - Virginia Laspidea
- Department of Pediatrics, Clinica Universidad de Navarra, Pamplona, Navarra, Spain
- Health Research Institute os Navarra (IdiSNA), Pamplona, Navarra, Spain
| | - Marc Garcia-Moure
- Department of Pediatrics, Clinica Universidad de Navarra, Pamplona, Navarra, Spain
- Health Research Institute os Navarra (IdiSNA), Pamplona, Navarra, Spain
| | - Daniel de la Nava
- Department of Pediatrics, Clinica Universidad de Navarra, Pamplona, Navarra, Spain
- Health Research Institute os Navarra (IdiSNA), Pamplona, Navarra, Spain
| | - Montserrat Puigdelloses
- Department of Pediatrics, Clinica Universidad de Navarra, Pamplona, Navarra, Spain
- Health Research Institute os Navarra (IdiSNA), Pamplona, Navarra, Spain
| | - Oren J Becher
- Division of Hematology, Oncology, Neuro-Oncology and Stem Cell Transplantation, Ann and Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL, USA
| | - Li Jiang
- Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
| | - Mariella G Filbin
- Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
| | - Fernando Pastor
- Molecular Therapeutics Program, Center for Applied Medical Research, CIMA, University of Navarra, Pamplona, Navarra, Spain
| | - Marta M Alonso
- Department of Pediatrics, Clinica Universidad de Navarra, Pamplona, Navarra, Spain
- Health Research Institute os Navarra (IdiSNA), Pamplona, Navarra, Spain
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33
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Liu I, Bjerke L, Cruzeiro GAV, Rogers RF, Grabovska Y, Panditharatna E, Mackay A, Barron T, Shaw M, Hoffman SE, Hack OA, Quezada MA, Dempster J, Temelso S, Englinger B, Molinari V, Mire HM, Jiang L, Madlener S, Mayr L, Dorfer C, Geyeregger R, Rota C, Ricken G, Alexandrescu S, Braun E, Danan-Gotthold M, Hu L, Siletti K, Sundstroem E, Hodge R, Lein E, Agnihotri S, Eisenstat DD, Carceller F, Stapleton S, Bleil C, Mastronuzzi A, Cole KA, Waanders AJ, Carcaboso AM, Vinci M, Hargrave D, Haberler C, Gojo J, Slavc I, Linnarsson S, Monje M, Jones C, Filbin MG. HGG-06. EARLY GABAERGIC NEURONAL LINEAGE DEFINES DEPENDENCIES IN HISTONE H3 G34R/V GLIOMA. Neuro Oncol 2021. [PMCID: PMC8168148 DOI: 10.1093/neuonc/noab090.072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
High-grade gliomas harboring H3 G34R/V mutations exclusively occur in the cerebral hemispheres of adolescents and young adults, suggesting a distinct neurodevelopmental origin. Combining multimodal bulk and single-cell genomics with unbiased genome-scale CRISPR/Cas9 approaches, we here describe a GABAergic interneuron progenitor lineage as the most likely context from which these H3 G34R/V mutations drive gliomagenesis, conferring unique and tumor-selective gene targets essential for glioma cell survival, as validated genetically and pharmacologically. Phenotypically, we demonstrate that while H3 G34R/V glioma cells harbor the neurotransmitter GABA, they are developmentally stalled, and do not induce the neuronal hyperexcitability described in other glioma subtypes. These findings offer a striking counter-example to the prevailing view of glioma origins in glial precursor cells, resulting in distinct cellular, microenvironmental, and therapeutic consequences.
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Affiliation(s)
- Ilon Liu
- Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
| | | | | | | | | | - Eshini Panditharatna
- Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
| | | | - Tara Barron
- Stanford University School of Medicine, Stanford, CA, USA
| | - McKenzie Shaw
- Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
| | - Samantha E Hoffman
- Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
| | - Olivia A Hack
- Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
| | | | | | | | - Bernhard Englinger
- Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
| | | | - Hafsa M Mire
- Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
| | - Li Jiang
- Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
| | | | - Lisa Mayr
- Medical University of Vienna, Vienna, Austria
| | | | | | | | | | | | | | | | - Lijuan Hu
- Karolinska Institute, Stockholm, Sweden
| | | | | | | | - Ed Lein
- Allen Institute, Seattle, WA, USA
| | | | | | | | | | | | | | | | | | | | - Maria Vinci
- Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Darren Hargrave
- UCL Great Ormond Street Institute for Child Health, London, UK
| | | | | | - Irene Slavc
- Medical University of Vienna, Vienna, Austria
| | | | - Michelle Monje
- Stanford University School of Medicine, Stanford, CA, USA
| | | | - Mariella G Filbin
- Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
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Przystal* JM, Yadavilli* S, Abadi* CC, Yadav VN, Laternser S, Cosentino CC, Waszak SM, Cartaxo R, Biery M, Myers C, Jayasekara S, Olson JM, Filbin MG, Vitanza NA, Cain J, Koschmann# C, Müller# S, Nazarian# J. DIPG-64. INTERNATIONAL PRECLINICAL DRUG DISCOVERY AND BIOMARKER PROGRAM INFORMING AN ADOPTIVE COMBINATORIAL TRIAL FOR DIFFUSE MIDLINE GLIOMAS. Neuro Oncol 2020. [PMCID: PMC7715218 DOI: 10.1093/neuonc/noaa222.109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
INTRODUCTION DMG-ACT (DMG- multi-arm Adaptive and Combinatorial Trial) aims to implement a highly innovative clinical trial design of combinatorial arms for patients with diffuse midline gliomas (DMGs) at all disease stages that is adaptive to pre-clinical data generated in eight collaborating institutions. The goals of the team are to: i) rapidly identify and validate promising drugs for clinical use, and ii) predict biomarkers for promising drugs. METHODS In vitro (n=15) and in vivo (n=8) models of DMGs across seven institutions were used to assess single and combination treatments with ONC201, ONC206, marizomib, panobinostat, Val-083, and TAK228. In vivo pharmacokinetic assays using clinically relevant dosing of ONC201, ONC206, and panobinostat were performed. Predictive biomarkers for ONC201 and ONC206 were identified using extensive molecular assays including CRISPR, RNAseq, ELISA, FACS, and IHC. RESULTS Inhibitory concentrations (IC50) were established and validated across participating sites. In vivo validation of single and combination drug assays confirmed drug efficacy as increased survival for: ONC201 (p=0.01), ONC206 (p=0.01), ONC201+ONC206 (p=0.02), and ONC201+panobinostat (p=0.01). Marizomib showed toxicity in murine/zebrafish PDXs models. Murine pharmacokinetic analysis showed peak brain levels of ONC201 and ONC206 above pre-clinical IC50. Molecular testing and analyses of existing drug screen across 537 cancer cell lines validated mitochondrial stress and ATF4 as the main targets induced by ONC201/6. CONCLUSION Thorough preclinical testing in a multi-site laboratory setting is feasible and identified ONC201 in combination with ONC206 as promising therapeutics for DMGs. Preclinical and correlative-clinical studies are ongoing.
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Affiliation(s)
- Justyna M Przystal*
- Oncology Department, University Children’s Hospital Zurich, Zürich, Switzerland
| | - Sridevi Yadavilli*
- Center for Genetic Medicine Research, Children’s National Medical Center, Washington DC, USA
| | | | | | - Sandra Laternser
- Oncology Department, University Children’s Hospital Zurich, Zürich, Switzerland
| | | | | | - Rodrigo Cartaxo
- Department of Pediatrics, Michigan Medicine, Ann Arbor, MI, USA
| | - Matt Biery
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Carrie Myers
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Samantha Jayasekara
- Developmental and Cancer Biology Centre for Cancer Research Hudson Institute of Medical Research, Melbourne, Australia
| | - James M Olson
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Mariella G Filbin
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Nicholas A Vitanza
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Washington, Seattle Children’s Hospital, Seattle, WA, USA
| | - Jason Cain
- Developmental and Cancer Biology Centre for Cancer Research Hudson Institute of Medical Research, Melbourne, Australia
| | - Carl Koschmann#
- Department of Pediatrics, Michigan Medicine, Ann Arbor, MI, USA
| | - Sabine Müller#
- Oncology Department, University Children’s Hospital Zurich, Zürich, Switzerland
- UCSF Department of Neurology, Neurosurgery and Pediatrics, San Francisco, California, USA
| | - Javad Nazarian#
- Oncology Department, University Children’s Hospital Zurich, Zürich, Switzerland
- Center for Genetic Medicine Research, Children’s National Medical Center, Washington DC, USA
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Hack OA, Babikir H, Jiang L, Shamardani K, Liu I, Shaw M, Cunliffe-Koehler K, Resnick A, Prados M, Monje M, Diaz A, Filbin MG. HGG-53. PROJECT HOPE: “PEDIATRIC AND AYA HIGH-GRADE GLIOMA OMICS PROJECT”- A LONGITUDINAL MOLECULAR LANDSCAPE OF HIGH-GRADE GLIOMAS RESOLVED AT SINGLE-CELL LEVEL. Neuro Oncol 2020. [PMCID: PMC7715324 DOI: 10.1093/neuonc/noaa222.333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
High-grade gliomas (HGG) are among the most prevalent and fatal cancers in pediatric, adolescent, and young adult (AYA) patients. Especially understudied are older children and young adults, aged 16–39 years. Previously, we profiled primary pediatric HGGs through single-cell transcriptomics and identified the genetic, epigenetic and developmental programs that drive their malignant progression. However, the questions of how these programs compare to those in older HGG patients, what the mechanisms are by which these tumors ultimately evolve to drive recurrence and treatment resistance, and how distinct tumor cell subpopulations bidirectionally communicate with their microenvironment remain to be elucidated. Here, we use single-nucleus RNA sequencing to compare 11 paired, matched high-grade gliomas at diagnosis and recurrence and 15 additional H3K27M primary and recurrent DMG samples in pediatric and AYA patients. In all tumors, we find both undifferentiated and differentiated tumor cells recapitulating distinct glial lineages, as well as diverse microenvironmental cell populations. When longitudinally comparing this tumor architecture within matched pairs, we find substantial differences in transcriptional program expressions. Diagnostic samples include more differentiated, astrocyte-like tumor cells, while cells from recurrent samples more highly express ribosomal and heat-shock protein genes, suggesting tumor progression- and treatment-related shifts. Ongoing sequencing and analysis will allow for unprecedented insight into the evolutionary dynamics of pediatric and AYA high-grade gliomas as well as delineate differences in the biology of DMGs occurring in different age groups. This multi-institutional project was funded by the National Institute of Health.
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Affiliation(s)
- Olivia A Hack
- Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Husam Babikir
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Li Jiang
- Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Karin Shamardani
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Ilon Liu
- Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - McKenzie Shaw
- Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Adam Resnick
- Center for Data Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Michael Prados
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Michelle Monje
- Department of Neurology, Stanford University, Stanford, CA, USA
- Department of Neurosurgery, Stanford University, Stanford, CA, USA
| | - Aaron Diaz
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Mariella G Filbin
- Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
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36
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Gudenas B, Englinger B, Liu APY, Tong Y, Meredith D, Pfaff E, Lin T, Orr BA, Klimo P, Bihannic L, Paul L, Kumar R, Bouffet E, Gururangan S, Crawford JR, Kellie SJ, Chintagumpala M, Fisher MJ, Bowers DC, Hassall T, Indelicato DJ, Ellison DW, Boop FA, Merchant TE, Chiang J, Robinson GW, Gajjar A, Alexandrescu S, Jones DTW, Filbin MG, Northcott PA. ETMR-06. DISSECTING THE MOLECULAR AND DEVELOPMENTAL BASIS OF PINEOBLASTOMA THROUGH GENOMICS. Neuro Oncol 2020. [PMCID: PMC7715543 DOI: 10.1093/neuonc/noaa222.210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pineoblastoma (PB) is an aggressive embryonal brain tumor comprising 1% of pediatric CNS tumors. The clinico-molecular heterogeneity and developmental origins underlying PB are poorly understood; therefore, we have assembled a molecular cohort of histologically defined PBs (n=43) with corresponding outcome data. Methylation profiling revealed four molecularly and clinically distinct PB subgroups, including two novel entities. Mutational and transcriptional analysis identified characteristic molecular features of each subgroup, such as mutations in the miRNA processing pathway or FOXR2 proto-oncogene overexpression. Furthermore, subgroups exhibited differences in propensity for metastasis, cytogenetics, and clinical outcomes. To dissect PB developmental origins and resolve PB subgroup biology, we have employed a combination of single-cell genomics and genetically engineered mouse modeling. We created a single-cell transcriptional atlas of the developing murine pineal gland across 11 timepoints and are currently integrating these data with single nuclei RNA-seq data of human PB (n=25). Single-cell analysis of the developing pineal gland revealed three distinct populations of pinealocytes, referred to as early, mid and late pinealocytes, which segregate by developmental stage yet lie along a single developmental trajectory. Preliminary results implicate significant associations between PBs and the early pinealocyte population as well as subgroup-specific differences in intratumoral heterogeneity. Furthermore, this knowledge has informed the downstream generation of biologically faithful disease models, including a transgenic mouse model of the PB-RB subgroup. Remarkably, this model shows up-regulation of key markers of PB such as Crx, Asmt and Otx2 and substantiates early pinealocytes as the probable cell-of-origin for this PB subgroup.
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Affiliation(s)
- Brian Gudenas
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Bernhard Englinger
- Department of Pediatric Oncology, Dana-Farber/Boston Children’s Cancer and Blood Disorder Center and Harvard Medical School, Boston, MA, USA
| | - Anthony P Y Liu
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Yiai Tong
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - David Meredith
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Elke Pfaff
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Pediatric Glioma Research Group (B360), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tong Lin
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Brent A Orr
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Paul Klimo
- Department of Surgery, St. Jude Children’s Research Hospital, Memphis, TN, USA
- Department of Neurosurgery, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Laure Bihannic
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Leena Paul
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Rahul Kumar
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Eric Bouffet
- Pediatric Brain Tumor Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Sridharan Gururangan
- Preston A, Wells Jr, Center of Brain Tumor Therapy, University of Florida, Gainesville, FL, USA
| | - John R Crawford
- University of California San Diego and Rady Children’s Hospital, San Diego, CA, USA
| | - Stewart J Kellie
- Children’s Cancer Centre, The Children’s Hospital at Westmead & University of Sydney, Sydney, Australia
| | - Murali Chintagumpala
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Michael J Fisher
- Department of Pediatrics, Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Daniel C Bowers
- Division of Pediatric Hematology and Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Tim Hassall
- Queensland Children’s Hospital, Brisbane, QLD, Australia
| | - Daniel J Indelicato
- Department of Radiation Oncology, University of Florida, Jacksonville, FL, USA
| | - David W Ellison
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Frederick A Boop
- Department of Surgery, St. Jude Children’s Research Hospital, Memphis, TN, USA
- Department of Neurosurgery, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Thomas E Merchant
- Department of Radiation Oncology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Jason Chiang
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Giles W Robinson
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Amar Gajjar
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Sanda Alexandrescu
- Department of Pathology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - David T W Jones
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Pediatric Glioma Research Group (B360), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mariella G Filbin
- Department of Pediatric Oncology, Dana-Farber/Boston Children’s Cancer and Blood Disorder Center and Harvard Medical School, Boston, MA, USA
| | - Paul A Northcott
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN, USA
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Chen CCL, Deshmukh S, Jessa S, Hadjadj D, Lisi V, Andrade AF, Faury D, Jawhar W, Dali R, Suzuki H, Pathania M, A D, Dubois F, Woodward E, Hébert S, Coutelier M, Karamchandani J, Albrecht S, Brandner S, De Jay N, Gayden T, Bajic A, Harutyunyan AS, Marchione DM, Mikael LG, Juretic N, Zeinieh M, Russo C, Maestro N, Bassenden AV, Hauser P, Virga J, Bognar L, Klekner A, Zapotocky M, Vicha A, Krskova L, Vanova K, Zamecnik J, Sumerauer D, Ekert PG, Ziegler DS, Ellezam B, Filbin MG, Blanchette M, Hansford JR, Khuong-Quang DA, Berghuis AM, Weil AG, Garcia BA, Garzia L, Mack SC, Beroukhim R, Ligon KL, Taylor MD, Bandopadhayay P, Kramm C, Pfister SM, Korshunov A, Sturm D, Jones DTW, Salomoni P, Kleinman CL, Jabado N. Histone H3.3G34-Mutant Interneuron Progenitors Co-opt PDGFRA for Gliomagenesis. Cell 2020; 183:1617-1633.e22. [PMID: 33259802 DOI: 10.1016/j.cell.2020.11.012] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 10/01/2020] [Accepted: 11/06/2020] [Indexed: 12/15/2022]
Abstract
Histone H3.3 glycine 34 to arginine/valine (G34R/V) mutations drive deadly gliomas and show exquisite regional and temporal specificity, suggesting a developmental context permissive to their effects. Here we show that 50% of G34R/V tumors (n = 95) bear activating PDGFRA mutations that display strong selection pressure at recurrence. Although considered gliomas, G34R/V tumors actually arise in GSX2/DLX-expressing interneuron progenitors, where G34R/V mutations impair neuronal differentiation. The lineage of origin may facilitate PDGFRA co-option through a chromatin loop connecting PDGFRA to GSX2 regulatory elements, promoting PDGFRA overexpression and mutation. At the single-cell level, G34R/V tumors harbor dual neuronal/astroglial identity and lack oligodendroglial programs, actively repressed by GSX2/DLX-mediated cell fate specification. G34R/V may become dispensable for tumor maintenance, whereas mutant-PDGFRA is potently oncogenic. Collectively, our results open novel research avenues in deadly tumors. G34R/V gliomas are neuronal malignancies where interneuron progenitors are stalled in differentiation by G34R/V mutations and malignant gliogenesis is promoted by co-option of a potentially targetable pathway, PDGFRA signaling.
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Affiliation(s)
- Carol C L Chen
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Shriya Deshmukh
- Division of Experimental Medicine, Department of Medicine, McGill University, Montreal, QC H4A 3J1, Canada
| | - Selin Jessa
- Quantitative Life Sciences, McGill University, Montreal, QC H3A 2A7, Canada; Lady Davis Research Institute, Jewish General Hospital, Montreal, QC H3T 1E2, Canada
| | - Djihad Hadjadj
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Véronique Lisi
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | | | - Damien Faury
- Department of Pediatrics, McGill University, and The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Wajih Jawhar
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Rola Dali
- Canadian Centre for Computational Genomics, McGill University, Montreal, QC H3A 0E9, Canada
| | - Hiromichi Suzuki
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Manav Pathania
- Department of Oncology and The Milner Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; CRUK Children's Brain Tumour Centre of Excellence, University of Cambridge, Cambridge CB2 0RE, UK
| | - Deli A
- Nuclear Function in CNS Pathophysiology, German Center for Neurodegenerative Diseases (DZNE), Bonn 53127, Germany
| | - Frank Dubois
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02215, USA
| | - Eleanor Woodward
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02215, USA
| | - Steven Hébert
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; Lady Davis Research Institute, Jewish General Hospital, Montreal, QC H3T 1E2, Canada
| | - Marie Coutelier
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; Lady Davis Research Institute, Jewish General Hospital, Montreal, QC H3T 1E2, Canada
| | - Jason Karamchandani
- Department of Pathology, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | - Steffen Albrecht
- Department of Pathology, Montreal Children's Hospital, McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | | | - Nicolas De Jay
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; Lady Davis Research Institute, Jewish General Hospital, Montreal, QC H3T 1E2, Canada
| | - Tenzin Gayden
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Andrea Bajic
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Ashot S Harutyunyan
- Department of Pediatrics, McGill University, and The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Dylan M Marchione
- Department of Biochemistry and Biophysics and Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6073, USA
| | - Leonie G Mikael
- Department of Pediatrics, McGill University, and The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Nikoleta Juretic
- Department of Pediatrics, McGill University, and The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Michele Zeinieh
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Caterina Russo
- Department of Pediatrics, McGill University, and The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Nicola Maestro
- Department of Oncology and The Milner Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK
| | | | - Peter Hauser
- Second Department of Paediatrics, Semmelweis University, Budapest 1094, Hungary
| | - József Virga
- Department of Neurosurgery, University of Debrecen, Debrecen 4032, Hungary; Department of Oncology, Faculty of Medicine, University of Debrecen, Debrecen 4032, Hungary
| | - Laszlo Bognar
- Department of Neurosurgery, University of Debrecen, Debrecen 4032, Hungary
| | - Almos Klekner
- Department of Neurosurgery, University of Debrecen, Debrecen 4032, Hungary
| | - Michal Zapotocky
- Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague 150 06, Czech Republic
| | - Ales Vicha
- Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague 150 06, Czech Republic
| | - Lenka Krskova
- Department of Pathology and Molecular Medicine, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague 150 06, Czech Republic
| | - Katerina Vanova
- Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague 150 06, Czech Republic
| | - Josef Zamecnik
- Department of Pathology and Molecular Medicine, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague 150 06, Czech Republic
| | - David Sumerauer
- Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague 150 06, Czech Republic
| | - Paul G Ekert
- Children's Cancer Center, The Royal Children's Hospital; Murdoch Children's Research Institute; Department of Pediatrics, University of Melbourne, Parkville, VIC 3052, Australia
| | - David S Ziegler
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW 2031, Australia; School of Women's and Children's Health, UNSW Sydney, Kensington, NSW 2052, Australia
| | - Benjamin Ellezam
- Department of Pathology, Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, QC H3T 1C5, Canada
| | - Mariella G Filbin
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA 02215, USA
| | - Mathieu Blanchette
- School of Computer Science, McGill University, Montreal, QC H3A 2A7, Canada
| | - Jordan R Hansford
- Children's Cancer Center, The Royal Children's Hospital; Murdoch Children's Research Institute; Department of Pediatrics, University of Melbourne, Parkville, VIC 3052, Australia
| | - Dong-Anh Khuong-Quang
- Children's Cancer Center, The Royal Children's Hospital; and Murdoch Children's Research Institute; Parkville, VIC 3052, Australia
| | - Albert M Berghuis
- Department of Biochemistry, McGill University, Montreal, QC H3A 1A3, Canada
| | - Alexander G Weil
- Department of Pediatric Neurosurgery, Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, QC H3T 1C5, Canada
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics and Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6073, USA
| | - Livia Garzia
- Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; Division of Orthopedic Surgery, Faculty of Surgery, McGill University, Montreal, QC H3G 1A4, Canada
| | - Stephen C Mack
- Department of Pediatrics, Division of Hematology and Oncology, Texas Children's Cancer and Hematology Centers, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rameen Beroukhim
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215-5450, USA; Broad Institute of MIT and Harvard, Boston, MA 02142, USA
| | - Keith L Ligon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215-5450, USA; Department of Pathology, Boston Children's Hospital and Brigham and Women's Hospital, Harvard Medical School, and Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Michael D Taylor
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Pratiti Bandopadhayay
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02215, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215-5450, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Christoph Kramm
- Division of Pediatric Hematology and Oncology, University Medical Center Goettingen, Goettingen 37075, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ) and Department of Pediatric Oncology, Hematology and Immunology, University Hospital Heidelberg, Heidelberg 69120, Germany; Division of Pediatric Neurooncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg 69120, Germany; Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg 69120, Germany
| | - Andrey Korshunov
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg 69120, Germany; Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Dominik Sturm
- Division of Pediatric Hematology and Oncology, University Medical Center Goettingen, Goettingen 37075, Germany; Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - David T W Jones
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany; Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg 69120, Germany
| | - Paolo Salomoni
- Department of Oncology and The Milner Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Nuclear Function in CNS Pathophysiology, German Center for Neurodegenerative Diseases (DZNE), Bonn 53127, Germany
| | - Claudia L Kleinman
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; Lady Davis Research Institute, Jewish General Hospital, Montreal, QC H3T 1E2, Canada.
| | - Nada Jabado
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; Division of Experimental Medicine, Department of Medicine, McGill University, Montreal, QC H4A 3J1, Canada; Department of Pediatrics, McGill University, and The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada.
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38
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Kim GB, Pacheco DRF, Saxon D, Yang A, Sabat S, Dutra-Clarke M, Levy R, Watkins A, Park H, Akhtar AA, Linesch PW, Kobritz N, Shandra SS, Grausam K, Ayala-Sarmiento A, Molina J, Sedivakova K, Gareau DS, Filbin MG, Bannykh S, Tang J, Suva ML, Chen B, Danielpour M, Breunig JJ. Abstract NG01: MADR: Rapid generation of somatic mosaics to model cancer in mice and human organoids. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-ng01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
In situ transgenesis methods such as virus and electroporation can create somatic transgenic mice quickly, but they lack the exquisite control over copy number, zygosity, and locus specificity. We have recently established mosaic analysis by dual recombinase-mediated cassette exchange (MADR), which permits stable labeling of mutant cells expressing transgenic elements from precisely-defined chromosomal loci. MADR provides a toolkit of elements for combinatorial labeling, inducible/reversible transgene manipulation, VCre recombinase expression, and genetic manipulation of human cells. Further, we have demonstrated the versatility of MADR by creating glioma models with mixed, reporter-identified zygosity or with “personalized” driver mutations from pediatric glioma. For example, introducing H3f3a mutation variants with MADR regulates the spatiotemporal profile of glioma, and single-cell RNA and ATAC sequencing analysis demonstrates a recapitulation of developmental hierarchy seen in K27M-mutant human glioma. Moreover, we have generated novel models of supratentorial ependymoma using patient-derived oncofusion transgenes. These models display a high degree of fidelity and we now compare these models on a single-cell level with our previous models and human tumor cell transcriptomes. In addition, we now demonstrate the ability to generalize the MADR technology to other non-CNS tissues using local plasmid delivery. Finally, we have engineered human cells to allow for MADR transgenesis and somatic transgenic organoids. These combined approaches will enable researchers to discovery disease mechanisms and test therapeutics in more physiologically relevant cancer models.MADR is extensible to thousands of existing mouse lines and can be adapted to human cells, providing a flexible platform to democratize the generation of somatic transgenic disease models.
Citation Format: Gi Bum Kim, David Rincon Fernandez Pacheco, David Saxon, Amy Yang, Sara Sabat, Marina Dutra-Clarke, Rachelle Levy, Ashley Watkins, Hannah Park, Aslam Abbasi Akhtar, Paul W. Linesch, Naomi Kobritz, Swasty S. Shandra, Katie Grausam, Alberto Ayala-Sarmiento, Jessica Molina, Kristyna Sedivakova, Daniel S. Gareau, Mariella G. Filbin, Serguei Bannykh, Jie Tang, Mario L. Suva, Bin Chen, Moise Danielpour, Joshua J. Breunig. MADR: Rapid generation of somatic mosaics to model cancer in mice and human organoids [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr NG01.
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Affiliation(s)
- Gi Bum Kim
- Cedars-Sinai Medical Center, Los Angeles, CA, Rockefeller University, New York, NY, Dana Farber Boston Children's Cancer and Blood Disorder Center, Boston, MA, Broad Institute of MIT and Harvard, Cambridge, MA, University of California Santa Cruz, Santa Cruz, CA
| | - David Rincon Fernandez Pacheco
- Cedars-Sinai Medical Center, Los Angeles, CA, Rockefeller University, New York, NY, Dana Farber Boston Children's Cancer and Blood Disorder Center, Boston, MA, Broad Institute of MIT and Harvard, Cambridge, MA, University of California Santa Cruz, Santa Cruz, CA
| | - David Saxon
- Cedars-Sinai Medical Center, Los Angeles, CA, Rockefeller University, New York, NY, Dana Farber Boston Children's Cancer and Blood Disorder Center, Boston, MA, Broad Institute of MIT and Harvard, Cambridge, MA, University of California Santa Cruz, Santa Cruz, CA
| | - Amy Yang
- Cedars-Sinai Medical Center, Los Angeles, CA, Rockefeller University, New York, NY, Dana Farber Boston Children's Cancer and Blood Disorder Center, Boston, MA, Broad Institute of MIT and Harvard, Cambridge, MA, University of California Santa Cruz, Santa Cruz, CA
| | - Sara Sabat
- Cedars-Sinai Medical Center, Los Angeles, CA, Rockefeller University, New York, NY, Dana Farber Boston Children's Cancer and Blood Disorder Center, Boston, MA, Broad Institute of MIT and Harvard, Cambridge, MA, University of California Santa Cruz, Santa Cruz, CA
| | - Marina Dutra-Clarke
- Cedars-Sinai Medical Center, Los Angeles, CA, Rockefeller University, New York, NY, Dana Farber Boston Children's Cancer and Blood Disorder Center, Boston, MA, Broad Institute of MIT and Harvard, Cambridge, MA, University of California Santa Cruz, Santa Cruz, CA
| | - Rachelle Levy
- Cedars-Sinai Medical Center, Los Angeles, CA, Rockefeller University, New York, NY, Dana Farber Boston Children's Cancer and Blood Disorder Center, Boston, MA, Broad Institute of MIT and Harvard, Cambridge, MA, University of California Santa Cruz, Santa Cruz, CA
| | - Ashley Watkins
- Cedars-Sinai Medical Center, Los Angeles, CA, Rockefeller University, New York, NY, Dana Farber Boston Children's Cancer and Blood Disorder Center, Boston, MA, Broad Institute of MIT and Harvard, Cambridge, MA, University of California Santa Cruz, Santa Cruz, CA
| | - Hannah Park
- Cedars-Sinai Medical Center, Los Angeles, CA, Rockefeller University, New York, NY, Dana Farber Boston Children's Cancer and Blood Disorder Center, Boston, MA, Broad Institute of MIT and Harvard, Cambridge, MA, University of California Santa Cruz, Santa Cruz, CA
| | - Aslam Abbasi Akhtar
- Cedars-Sinai Medical Center, Los Angeles, CA, Rockefeller University, New York, NY, Dana Farber Boston Children's Cancer and Blood Disorder Center, Boston, MA, Broad Institute of MIT and Harvard, Cambridge, MA, University of California Santa Cruz, Santa Cruz, CA
| | - Paul W. Linesch
- Cedars-Sinai Medical Center, Los Angeles, CA, Rockefeller University, New York, NY, Dana Farber Boston Children's Cancer and Blood Disorder Center, Boston, MA, Broad Institute of MIT and Harvard, Cambridge, MA, University of California Santa Cruz, Santa Cruz, CA
| | - Naomi Kobritz
- Cedars-Sinai Medical Center, Los Angeles, CA, Rockefeller University, New York, NY, Dana Farber Boston Children's Cancer and Blood Disorder Center, Boston, MA, Broad Institute of MIT and Harvard, Cambridge, MA, University of California Santa Cruz, Santa Cruz, CA
| | - Swasty S. Shandra
- Cedars-Sinai Medical Center, Los Angeles, CA, Rockefeller University, New York, NY, Dana Farber Boston Children's Cancer and Blood Disorder Center, Boston, MA, Broad Institute of MIT and Harvard, Cambridge, MA, University of California Santa Cruz, Santa Cruz, CA
| | - Katie Grausam
- Cedars-Sinai Medical Center, Los Angeles, CA, Rockefeller University, New York, NY, Dana Farber Boston Children's Cancer and Blood Disorder Center, Boston, MA, Broad Institute of MIT and Harvard, Cambridge, MA, University of California Santa Cruz, Santa Cruz, CA
| | - Alberto Ayala-Sarmiento
- Cedars-Sinai Medical Center, Los Angeles, CA, Rockefeller University, New York, NY, Dana Farber Boston Children's Cancer and Blood Disorder Center, Boston, MA, Broad Institute of MIT and Harvard, Cambridge, MA, University of California Santa Cruz, Santa Cruz, CA
| | - Jessica Molina
- Cedars-Sinai Medical Center, Los Angeles, CA, Rockefeller University, New York, NY, Dana Farber Boston Children's Cancer and Blood Disorder Center, Boston, MA, Broad Institute of MIT and Harvard, Cambridge, MA, University of California Santa Cruz, Santa Cruz, CA
| | - Kristyna Sedivakova
- Cedars-Sinai Medical Center, Los Angeles, CA, Rockefeller University, New York, NY, Dana Farber Boston Children's Cancer and Blood Disorder Center, Boston, MA, Broad Institute of MIT and Harvard, Cambridge, MA, University of California Santa Cruz, Santa Cruz, CA
| | - Daniel S. Gareau
- Cedars-Sinai Medical Center, Los Angeles, CA, Rockefeller University, New York, NY, Dana Farber Boston Children's Cancer and Blood Disorder Center, Boston, MA, Broad Institute of MIT and Harvard, Cambridge, MA, University of California Santa Cruz, Santa Cruz, CA
| | - Mariella G. Filbin
- Cedars-Sinai Medical Center, Los Angeles, CA, Rockefeller University, New York, NY, Dana Farber Boston Children's Cancer and Blood Disorder Center, Boston, MA, Broad Institute of MIT and Harvard, Cambridge, MA, University of California Santa Cruz, Santa Cruz, CA
| | - Serguei Bannykh
- Cedars-Sinai Medical Center, Los Angeles, CA, Rockefeller University, New York, NY, Dana Farber Boston Children's Cancer and Blood Disorder Center, Boston, MA, Broad Institute of MIT and Harvard, Cambridge, MA, University of California Santa Cruz, Santa Cruz, CA
| | - Jie Tang
- Cedars-Sinai Medical Center, Los Angeles, CA, Rockefeller University, New York, NY, Dana Farber Boston Children's Cancer and Blood Disorder Center, Boston, MA, Broad Institute of MIT and Harvard, Cambridge, MA, University of California Santa Cruz, Santa Cruz, CA
| | - Mario L. Suva
- Cedars-Sinai Medical Center, Los Angeles, CA, Rockefeller University, New York, NY, Dana Farber Boston Children's Cancer and Blood Disorder Center, Boston, MA, Broad Institute of MIT and Harvard, Cambridge, MA, University of California Santa Cruz, Santa Cruz, CA
| | - Bin Chen
- Cedars-Sinai Medical Center, Los Angeles, CA, Rockefeller University, New York, NY, Dana Farber Boston Children's Cancer and Blood Disorder Center, Boston, MA, Broad Institute of MIT and Harvard, Cambridge, MA, University of California Santa Cruz, Santa Cruz, CA
| | - Moise Danielpour
- Cedars-Sinai Medical Center, Los Angeles, CA, Rockefeller University, New York, NY, Dana Farber Boston Children's Cancer and Blood Disorder Center, Boston, MA, Broad Institute of MIT and Harvard, Cambridge, MA, University of California Santa Cruz, Santa Cruz, CA
| | - Joshua J. Breunig
- Cedars-Sinai Medical Center, Los Angeles, CA, Rockefeller University, New York, NY, Dana Farber Boston Children's Cancer and Blood Disorder Center, Boston, MA, Broad Institute of MIT and Harvard, Cambridge, MA, University of California Santa Cruz, Santa Cruz, CA
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Abstract
Posterior fossa type A (PFA) ependymoma is a lethal pediatric brain tumor proposed to be driven solely by epigenetic deregulation. Michealraj et al. (2020) demonstrate that hypoxia reprograms PFA metabolism and, subsequently, the epigenome toward H3K27 hypomethylation, mirroring transcriptional and metabolic signatures of gliogenic progenitors involved in embryonal hindbrain development.
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Affiliation(s)
- Bernhard Englinger
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Olivia A Hack
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Mariella G Filbin
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
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40
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Filbin MG. Abstract IA29: Developmental and oncogenic programs in pediatric brain tumors dissected by single-cell RNA-sequencing. Cancer Res 2020. [DOI: 10.1158/1538-7445.pedca19-ia29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
During development, the multiple cell types of human brain arise from pluripotent stem cells via progressively more committed progenitor cells. Emerging data suggest that pediatric brain tumors arise from progenitors that have become developmentally stalled. In preliminary studies, our lab used single-cell RNA-seq to display the expression profiles of individual cells within pediatric midline and hemispheric high-grade gliomas. Our data show that these tumors are composed of (i) replicating cells that resemble glial and neural progenitors and (ii) maturing cells resembling astrocytes, oligodendrocytes, or mesenchymal cells. In this presentation I will address how single-cell RNA-sequencing has revolutionized our understanding of the developmental hierarchy and oncogenic programs in pediatric brain tumors. Our recent findings pointing towards potential cells of origin of midline and hemispheric pediatric high-grade gliomas as well as plasticity of different cancer cell states will be discussed.
Citation Format: Mariella G. Filbin. Developmental and oncogenic programs in pediatric brain tumors dissected by single-cell RNA-sequencing [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr IA29.
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Torre M, Vasudevaraja V, Serrano J, DeLorenzo M, Malinowski S, Blandin AF, Pages M, Ligon AH, Dong F, Meredith DM, Nasrallah MP, Horbinski C, Dahiya S, Ligon KL, Santi M, Ramkissoon SH, Filbin MG, Snuderl M, Alexandrescu S. Molecular and clinicopathologic features of gliomas harboring NTRK fusions. Acta Neuropathol Commun 2020; 8:107. [PMID: 32665022 PMCID: PMC7362646 DOI: 10.1186/s40478-020-00980-z] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 06/24/2020] [Indexed: 01/07/2023] Open
Abstract
Fusions involving neurotrophic tyrosine receptor kinase (NTRK) genes are detected in ≤2% of gliomas and can promote gliomagenesis. The remarkable therapeutic efficacy of TRK inhibitors, which are among the first Food and Drug Administration-approved targeted therapies for NTRK-fused gliomas, has generated significant clinical interest in characterizing these tumors. In this multi-institutional retrospective study of 42 gliomas with NTRK fusions, next generation DNA sequencing (n = 41), next generation RNA sequencing (n = 1), RNA-sequencing fusion panel (n = 16), methylation profile analysis (n = 18), and histologic evaluation (n = 42) were performed. All infantile NTRK-fused gliomas (n = 7) had high-grade histology and, with one exception, no other significant genetic alterations. Pediatric NTRK-fused gliomas (n = 13) typically involved NTRK2, ranged from low- to high-histologic grade, and demonstrated histologic overlap with desmoplastic infantile ganglioglioma, pilocytic astrocytoma, ganglioglioma, and glioblastoma, among other entities, but they rarely matched with high confidence to known methylation class families or with each other; alterations involving ATRX, PTEN, and CDKN2A/2B were present in a subset of cases. Adult NTRK-fused gliomas (n = 22) typically involved NTRK1 and had predominantly high-grade histology; genetic alterations involving IDH1, ATRX, TP53, PTEN, TERT promoter, RB1, CDKN2A/2B, NF1, and polysomy 7 were common. Unsupervised principal component analysis of methylation profiles demonstrated no obvious grouping by histologic grade, NTRK gene involved, or age group. KEGG pathway analysis detected methylation differences in genes involved in PI3K/AKT, MAPK, and other pathways. In summary, the study highlights the clinical, histologic, and molecular heterogeneity of NTRK-fused gliomas, particularly when stratified by age group.
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Affiliation(s)
- Matthew Torre
- grid.62560.370000 0004 0378 8294Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, 75 Francis Street, Boston, MA 02115 USA ,grid.2515.30000 0004 0378 8438Department of Pathology, Boston Children’s Hospital and Harvard Medical School, 300 Longwood Ave, Bader Building, Boston, MA 02115 USA
| | - Varshini Vasudevaraja
- grid.137628.90000 0004 1936 8753Department of Pathology, NYU Langone Health, 550 First Avenue, New York, NY 10016 USA
| | - Jonathan Serrano
- grid.137628.90000 0004 1936 8753Department of Pathology, NYU Langone Health, 550 First Avenue, New York, NY 10016 USA
| | - Michael DeLorenzo
- grid.137628.90000 0004 1936 8753Department of Pathology, NYU Langone Health, 550 First Avenue, New York, NY 10016 USA
| | - Seth Malinowski
- grid.65499.370000 0001 2106 9910Department of Oncologic Pathology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02115 USA
| | - Anne-Florence Blandin
- grid.65499.370000 0001 2106 9910Department of Oncologic Pathology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02115 USA
| | - Melanie Pages
- grid.414435.30000 0001 2200 9055Department of Neuropathology, GHU Paris Sainte-Anne Hospital, 1 Rue Cabanis, 75014 Paris, France
| | - Azra H. Ligon
- grid.62560.370000 0004 0378 8294Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, 75 Francis Street, Boston, MA 02115 USA ,grid.62560.370000 0004 0378 8294Center for Advanced Molecular Diagnostics, Brigham and Women’s Hospital and Harvard Medical School, 75 Francis Street, Boston, MA 02115 USA
| | - Fei Dong
- grid.62560.370000 0004 0378 8294Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, 75 Francis Street, Boston, MA 02115 USA
| | - David M. Meredith
- grid.62560.370000 0004 0378 8294Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, 75 Francis Street, Boston, MA 02115 USA
| | - MacLean P. Nasrallah
- grid.25879.310000 0004 1936 8972Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, 3400 Spruce Street 34th St, Philadelphia, PA 19104 USA
| | - Craig Horbinski
- grid.16753.360000 0001 2299 3507Department of Neurological Surgery, Northwestern University, Chicago, IL USA ,grid.16753.360000 0001 2299 3507Department of Pathology, Northwestern University, 303 East Chicago Avenue, Chicago, IL 60611 USA
| | - Sonika Dahiya
- grid.4367.60000 0001 2355 7002Division of Neuropathology, Department of Pathology and Immunology, Washington University School of Medicine, 660 South Euclid Avenue, Campus Box 8118, St. Louis, MO 63110 USA
| | - Keith L. Ligon
- grid.62560.370000 0004 0378 8294Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, 75 Francis Street, Boston, MA 02115 USA ,grid.2515.30000 0004 0378 8438Department of Pathology, Boston Children’s Hospital and Harvard Medical School, 300 Longwood Ave, Bader Building, Boston, MA 02115 USA ,grid.65499.370000 0001 2106 9910Department of Oncologic Pathology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02115 USA
| | - Mariarita Santi
- grid.25879.310000 0004 1936 8972Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, 3400 Spruce Street 34th St, Philadelphia, PA 19104 USA ,grid.239552.a0000 0001 0680 8770Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA USA
| | - Shakti H. Ramkissoon
- Foundation Medicine, 7010 Kit Creek Road, Morrisville, NC 27560 USA ,grid.241167.70000 0001 2185 3318Wake Forest Comprehensive Cancer Center and Department of Pathology, Wake Forest School of Medicine, Winston-Salem, 27157 NC USA
| | - Mariella G. Filbin
- grid.38142.3c000000041936754XDepartment of Pediatric Oncology, Dana Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215 USA
| | - Matija Snuderl
- grid.137628.90000 0004 1936 8753Department of Pathology, NYU Langone Health, 550 First Avenue, New York, NY 10016 USA
| | - Sanda Alexandrescu
- grid.62560.370000 0004 0378 8294Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, 75 Francis Street, Boston, MA 02115 USA ,grid.2515.30000 0004 0378 8438Department of Pathology, Boston Children’s Hospital and Harvard Medical School, 300 Longwood Ave, Bader Building, Boston, MA 02115 USA
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42
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Gojo J, Englinger B, Jiang L, Hübner JM, Shaw ML, Hack OA, Madlener S, Kirchhofer D, Liu I, Pyrdol J, Hovestadt V, Mazzola E, Mathewson ND, Trissal M, Lötsch D, Dorfer C, Haberler C, Halfmann A, Mayr L, Peyrl A, Geyeregger R, Schwalm B, Mauermann M, Pajtler KW, Milde T, Shore ME, Geduldig JE, Pelton K, Czech T, Ashenberg O, Wucherpfennig KW, Rozenblatt-Rosen O, Alexandrescu S, Ligon KL, Pfister SM, Regev A, Slavc I, Berger W, Suvà ML, Kool M, Filbin MG. Single-Cell RNA-Seq Reveals Cellular Hierarchies and Impaired Developmental Trajectories in Pediatric Ependymoma. Cancer Cell 2020; 38:44-59.e9. [PMID: 32663469 PMCID: PMC7479515 DOI: 10.1016/j.ccell.2020.06.004] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 03/26/2020] [Accepted: 06/03/2020] [Indexed: 02/07/2023]
Abstract
Ependymoma is a heterogeneous entity of central nervous system tumors with well-established molecular groups. Here, we apply single-cell RNA sequencing to analyze ependymomas across molecular groups and anatomic locations to investigate their intratumoral heterogeneity and developmental origins. Ependymomas are composed of a cellular hierarchy initiating from undifferentiated populations, which undergo impaired differentiation toward three lineages of neuronal-glial fate specification. While prognostically favorable groups of ependymoma predominantly harbor differentiated cells, aggressive groups are enriched for undifferentiated cell populations. The delineated transcriptomic signatures correlate with patient survival and define molecular dependencies for targeted treatment approaches. Taken together, our analyses reveal a developmental hierarchy underlying ependymomas relevant to biological and clinical behavior.
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Affiliation(s)
- Johannes Gojo
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA 02215, USA; Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
| | - Bernhard Englinger
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Li Jiang
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Jens M Hübner
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - McKenzie L Shaw
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Olivia A Hack
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Sibylle Madlener
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
| | - Dominik Kirchhofer
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria; Institute of Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
| | - Ilon Liu
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Jason Pyrdol
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Volker Hovestadt
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Emanuele Mazzola
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Nathan D Mathewson
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Maria Trissal
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Daniela Lötsch
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria; Institute of Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria; Department of Neurosurgery, Medical University of Vienna, 1090 Vienna, Austria
| | - Christian Dorfer
- Department of Neurosurgery, Medical University of Vienna, 1090 Vienna, Austria
| | - Christine Haberler
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, 1090 Vienna, Austria
| | - Angela Halfmann
- Clinical Cell Biology, Children's Cancer Research Institute (CCRI), 1090 Vienna, Austria
| | - Lisa Mayr
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
| | - Andreas Peyrl
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
| | - Rene Geyeregger
- Clinical Cell Biology, Children's Cancer Research Institute (CCRI), 1090 Vienna, Austria
| | - Benjamin Schwalm
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Monica Mauermann
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Kristian W Pajtler
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Department of Paediatric Haematology and Oncology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Till Milde
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Department of Paediatric Haematology and Oncology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Marni E Shore
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Jack E Geduldig
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Kristine Pelton
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Thomas Czech
- Department of Neurosurgery, Medical University of Vienna, 1090 Vienna, Austria
| | - Orr Ashenberg
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Kai W Wucherpfennig
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Orit Rozenblatt-Rosen
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sanda Alexandrescu
- Department of Pathology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Keith L Ligon
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Pathology, Brigham and Women's Hospital, Boston Children's Hospital, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Stefan M Pfister
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Department of Paediatric Haematology and Oncology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Aviv Regev
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02140, USA
| | - Irene Slavc
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
| | - Walter Berger
- Institute of Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
| | - Mario L Suvà
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Marcel Kool
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, the Netherlands
| | - Mariella G Filbin
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
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43
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Kim GB, Rincon Fernandez Pacheco D, Saxon D, Yang A, Sabet S, Dutra-Clarke M, Levy R, Watkins A, Park H, Abbasi Akhtar A, Linesch PW, Kobritz N, Chandra SS, Grausam K, Ayala-Sarmiento A, Molina J, Sedivakova K, Hoang K, Tsyporin J, Gareau DS, Filbin MG, Bannykh S, Santiskulvong C, Wang Y, Tang J, Suva ML, Chen B, Danielpour M, Breunig JJ. Rapid Generation of Somatic Mouse Mosaics with Locus-Specific, Stably Integrated Transgenic Elements. Cell 2020; 179:251-267.e24. [PMID: 31539496 DOI: 10.1016/j.cell.2019.08.013] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 05/24/2019] [Accepted: 08/06/2019] [Indexed: 12/11/2022]
Abstract
In situ transgenesis methods such as viruses and electroporation can rapidly create somatic transgenic mice but lack control over copy number, zygosity, and locus specificity. Here we establish mosaic analysis by dual recombinase-mediated cassette exchange (MADR), which permits stable labeling of mutant cells expressing transgenic elements from precisely defined chromosomal loci. We provide a toolkit of MADR elements for combination labeling, inducible and reversible transgene manipulation, VCre recombinase expression, and transgenesis of human cells. Further, we demonstrate the versatility of MADR by creating glioma models with mixed reporter-identified zygosity or with "personalized" driver mutations from pediatric glioma. MADR is extensible to thousands of existing mouse lines, providing a flexible platform to democratize the generation of somatic mosaic mice. VIDEO ABSTRACT.
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Affiliation(s)
- Gi Bum Kim
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | | | - David Saxon
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Amy Yang
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Sara Sabet
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Marina Dutra-Clarke
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Rachelle Levy
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Ashley Watkins
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Hannah Park
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Aslam Abbasi Akhtar
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Paul W Linesch
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Naomi Kobritz
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Swasty S Chandra
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Katie Grausam
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Alberto Ayala-Sarmiento
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jessica Molina
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Kristyna Sedivakova
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Kendy Hoang
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, 1156 High St., Santa Cruz, CA 95064, USA
| | - Jeremiah Tsyporin
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, 1156 High St., Santa Cruz, CA 95064, USA
| | - Daniel S Gareau
- Laboratory for Investigative Dermatology, The Rockefeller University, New York, NY 10065, USA
| | - Mariella G Filbin
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Serguei Bannykh
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Chintda Santiskulvong
- Center for Neural Sciences in Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Yizhou Wang
- Center for Neural Sciences in Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jie Tang
- Center for Neural Sciences in Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Mario L Suva
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Bin Chen
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, 1156 High St., Santa Cruz, CA 95064, USA
| | - Moise Danielpour
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Neurosurgery, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Joshua J Breunig
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Center for Neural Sciences in Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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44
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Kim GB, Pacheco DRF, Saxon D, Yang A, Sabet S, Dutra-Clarke M, Levy R, Watkins A, Park H, Akhtar AA, Linesch PW, Kobritz N, Chandra SS, Grausam K, Sarmiento AA, Molina J, Sedivakova K, Gareau DS, Filbin MG, Bannykh S, Tang J, Suva M, Chen B, Danielpour M, Breunig JJ. Abstract PR11: MADR: Rapid generation of somatic mosaics with locus-specific, stably integrated transgenic elements for generation of “personalized” mouse models and human organoid tumor models. Cancer Res 2020. [DOI: 10.1158/1538-7445.camodels2020-pr11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
In situ transgenesis methods such as virus and electroporation can create somatic transgenic mice quickly, but they lack the exquisite control over copy number, zygosity, and locus specificity. We have recently established mosaic analysis by dual recombinase-mediated cassette exchange (MADR), which permits stable labeling of mutant cells expressing transgenic elements from precisely defined chromosomal loci. MADR provides a toolkit of elements for combinatorial labeling, inducible/reversible transgene manipulation, VCre recombinase expression, and genetic manipulation of human cells. Further, we have demonstrated the versatility of MADR by creating glioma models with mixed, reporter-identified zygosity or with “personalized” driver mutations from pediatric glioma. For example, introducing H3f3a mutation variants with MADR regulates the spatiotemporal profile of glioma, and single-cell RNA and ATAC sequencing analysis demonstrates a recapitulation of developmental hierarchy seen in K27M mutant human glioma. Moreover, we have generated novel models of supratentorial ependymoma using patient-derived oncofusion transgenes. These models display a high degree of fidelity, and we now compare these models on a single-cell level with our previous models and human tumor cell transcriptomes. In addition, we now demonstrate the ability to generalize the MADR technology to other non-CNS tissues using local plasmid delivery. Finally, we have engineered human cells to allow for MADR transgenesis and somatic transgenic organoids. These combined approaches will enable researchers to discover disease mechanisms and test therapeutics in more physiologically relevant cancer models. MADR is extensible to thousands of existing mouse lines and can be adapted to human cells, providing a flexible platform to democratize the generation of somatic transgenic disease models.
This abstract is also being presented as Poster B46.
Citation Format: Gi Bum Kim, David Rincon Fernandez Pacheco, David Saxon, Amy Yang, Sara Sabet, Marina Dutra-Clarke, Rachelle Levy, Ashley Watkins, Hannah Park, Aslam Abbasi Akhtar, Paul W. Linesch, Naomi Kobritz, Swasty S. Chandra, Katie Grausam, Alberto Ayala- Sarmiento, Jessica Molina, Kristyna Sedivakova, Daniel S. Gareau, Mariella G. Filbin, Serguei Bannykh, Jie Tang, Mario Suva, Bin Chen, Moise Danielpour, Joshua J. Breunig. MADR: Rapid generation of somatic mosaics with locus-specific, stably integrated transgenic elements for generation of “personalized” mouse models and human organoid tumor models [abstract]. In: Proceedings of the AACR Special Conference on the Evolving Landscape of Cancer Modeling; 2020 Mar 2-5; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2020;80(11 Suppl):Abstract nr PR11.
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Affiliation(s)
- Gi Bum Kim
- 1Cedars-Sinai Medical Center, Los Angeles, CA,
| | | | - David Saxon
- 1Cedars-Sinai Medical Center, Los Angeles, CA,
| | - Amy Yang
- 1Cedars-Sinai Medical Center, Los Angeles, CA,
| | - Sara Sabet
- 1Cedars-Sinai Medical Center, Los Angeles, CA,
| | | | | | | | - Hannah Park
- 1Cedars-Sinai Medical Center, Los Angeles, CA,
| | | | | | | | | | | | | | | | | | | | | | | | - Jie Tang
- 1Cedars-Sinai Medical Center, Los Angeles, CA,
| | - Mario Suva
- 4Broad Institute and Massachusetts Institute of Technology, Cambridge, MA,
| | - Bin Chen
- 5University of California Santa Cruz, Santa Cruz, CA
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45
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Abstract
PURPOSE OF REVIEW Altered epigenetics is central to oncogenesis in many pediatric cancers. Aberrant epigenetic states are induced by mutations in histones or epigenetic regulatory genes, aberrant expression of genes regulating chromatin complexes, altered DNA methylation patterns, or dysregulated expression of noncoding RNAs. Developmental contexts of dysregulated epigenetic states are equally important for initiation and progression of many childhood cancers. As an improved understanding of disease-specific roles and molecular consequences of epigenetic alterations in oncogenesis is emerging, targeting these mechanisms of disease in childhood cancers is increasingly becoming important. RECENT FINDINGS In addition to disease-causing epigenetic events, DNA methylation patterns and specific oncohistone mutations are being utilized for the diagnosis of pediatric central nervous system (CNS) and solid tumors. These discoveries have improved the classification of poorly differentiated tumors and laid the foundation for future improved clinical management. On the therapeutic side, the first therapies targeting epigenetic alterations have recently entered clinical trials. Current clinical trials include pharmacological inhibition of histone and DNA modifiers in aggressive types of pediatric cancer. SUMMARY Targeting novel epigenetic vulnerabilities, either by themselves, or coupled with targeting altered transcriptional states, developmental cell states or immunomodulation will result in innovative approaches for treating deadly pediatric cancers.
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Affiliation(s)
- Eshini Panditharatna
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Broad Institute of Harvard and MIT, Cambridge, MA
| | - Mariella G Filbin
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Broad Institute of Harvard and MIT, Cambridge, MA.,Boston Children's Cancer and Blood Disorder Center, Boston, Massachusetts, USA
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46
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Jessa S, Blanchet-Cohen A, Krug B, Vladoiu M, Coutelier M, Faury D, Poreau B, De Jay N, Hébert S, Monlong J, Farmer WT, Donovan LK, Hu Y, McConechy MK, Cavalli FMG, Mikael LG, Ellezam B, Richer M, Allaire A, Weil AG, Atkinson J, Farmer JP, Dudley RWR, Larouche V, Crevier L, Albrecht S, Filbin MG, Sartelet H, Lutz PE, Nagy C, Turecki G, Costantino S, Dirks PB, Murai KK, Bourque G, Ragoussis J, Garzia L, Taylor MD, Jabado N, Kleinman CL. Stalled developmental programs at the root of pediatric brain tumors. Nat Genet 2019; 51:1702-1713. [PMID: 31768071 PMCID: PMC6885128 DOI: 10.1038/s41588-019-0531-7] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 10/18/2019] [Indexed: 02/08/2023]
Abstract
Childhood brain tumors have suspected prenatal origins. To identify vulnerable developmental states, we generated a single-cell transcriptome atlas of >65,000 cells from embryonal pons and forebrain, two major tumor locations. We derived signatures for 191 distinct cell populations and defined regional cellular diversity and differentiation dynamics. Projection of bulk tumor transcriptomes onto this dataset shows that WNT medulloblastomas match the rhombic lip-derived mossy fiber neuronal lineage, embryonal tumors with multilayered rosettes fully recapitulate a neuronal lineage, while Group 2a/b atypical teratoid/rhabdoid tumors may originate outside of the neuroectoderm. Importantly, single-cell tumor profiles reveal highly defined cell hierarchies mirroring transcriptional programs of the corresponding normal lineages. Our findings identify impaired differentiation of specific neural progenitors as a common mechanism underlying these pediatric cancers and provide a rational framework for future modeling and therapeutic interventions.
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Affiliation(s)
- Selin Jessa
- Quantitative Life Sciences, McGill University, Montreal, Quebec, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Alexis Blanchet-Cohen
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada.,Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Brian Krug
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Maria Vladoiu
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada.,The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Marie Coutelier
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada.,Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Damien Faury
- Department of Pediatrics, McGill University, Montreal, Quebec, Canada.,The Research Institute of the McGill University Health Center, Montreal, Quebec, Canada
| | - Brice Poreau
- Department of Pediatrics, McGill University, Montreal, Quebec, Canada.,The Research Institute of the McGill University Health Center, Montreal, Quebec, Canada.,Service de Génétique et Procréation, Centre Hospitalier Universitaire, Grenoble-Alpes, Grenoble, France
| | - Nicolas De Jay
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada.,Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Steven Hébert
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada.,Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Jean Monlong
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - W Todd Farmer
- Centre for Research in Neuroscience, Brain Repair and Integrative Neuroscience Program, The Research Institute of the McGill University Health Centre, Montreal General Hospital, Montreal, Quebec, Canada.,Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Laura K Donovan
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada.,The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Yixing Hu
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada.,Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | | | - Florence M G Cavalli
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada.,The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Leonie G Mikael
- Department of Pediatrics, McGill University, Montreal, Quebec, Canada.,The Research Institute of the McGill University Health Center, Montreal, Quebec, Canada
| | - Benjamin Ellezam
- Department of Pathology, Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montreal, Quebec, Canada
| | - Maxime Richer
- Department of Pathology, Centre Hospitalier Universitaire de Sherbrooke, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Andréa Allaire
- Department of Pathology, Centre Hospitalier Universitaire de Sherbrooke, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Alexander G Weil
- Department of Pediatric Neurosurgery, Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montreal, Quebec, Canada
| | - Jeffrey Atkinson
- Department of Pediatric Surgery, Division of Neurosurgery, Montreal Children's Hospital, McGill University, Montreal, Querbec, Canada
| | - Jean-Pierre Farmer
- Department of Pediatric Surgery, Division of Neurosurgery, Montreal Children's Hospital, McGill University, Montreal, Querbec, Canada
| | - Roy W R Dudley
- Department of Pediatric Surgery, Division of Neurosurgery, Montreal Children's Hospital, McGill University, Montreal, Querbec, Canada
| | - Valerie Larouche
- Department of Pediatrics, Centre mère-enfant Soleil du CHU de Québec-Université Laval, Quebec City, Quebec, Canada
| | - Louis Crevier
- Department of Surgery, Université de Laval, Quebec City, Quebec, Canada
| | - Steffen Albrecht
- Department of Pathology, Montreal Children's Hospital, McGill University Health Center, Montreal, Quebec, Canada
| | - Mariella G Filbin
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorder Center, Boston, MA, USA
| | - Hervé Sartelet
- Department of Pathology, Centre Hospitalier Universitaire de Grenoble, Grenoble, France
| | - Pierre-Eric Lutz
- Centre National de la Recherche Scientifique, Institut des Neurosciences Cellulaires et Intégratives, Université de Strasbourg, Fédération de Médecine Translationnelle de Strasbourg, Strasbourg, France.,Department of Psychiatry, McGill University, Montreal, Quebec, Canada.,Douglas Mental Health University Institute, McGill University, Montreal, Quebec, Canada
| | - Corina Nagy
- Department of Psychiatry, McGill University, Montreal, Quebec, Canada.,Douglas Mental Health University Institute, McGill University, Montreal, Quebec, Canada
| | - Gustavo Turecki
- Department of Psychiatry, McGill University, Montreal, Quebec, Canada.,Douglas Mental Health University Institute, McGill University, Montreal, Quebec, Canada
| | - Santiago Costantino
- Maisonneuve-Rosemont Hospital Research Center, Montreal, Quebec, Canada.,Department of Ophthalmology, Université de Montréal, Montreal, Quebec, Canada
| | - Peter B Dirks
- Department of Surgery, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Keith K Murai
- Centre for Research in Neuroscience, Brain Repair and Integrative Neuroscience Program, The Research Institute of the McGill University Health Centre, Montreal General Hospital, Montreal, Quebec, Canada.,Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada.,Canadian Center for Computational Genomics, Montreal, Quebec, Canada
| | - Jiannis Ragoussis
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Livia Garzia
- Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada.,Division of Orthopedic Surgery, Faculty of Surgery, McGill University, Montreal, Quebec, Canada
| | - Michael D Taylor
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada. .,The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada. .,Department of Surgery, University of Toronto, Toronto, Ontario, Canada. .,Division of Neurosurgery, The Hospital for Sick Children, Toronto, Ontario, Canada. .,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada. .,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
| | - Nada Jabado
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada. .,Department of Pediatrics, McGill University, Montreal, Quebec, Canada. .,The Research Institute of the McGill University Health Center, Montreal, Quebec, Canada.
| | - Claudia L Kleinman
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada. .,Department of Human Genetics, McGill University, Montreal, Quebec, Canada.
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47
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Anastas JN, Zee BM, Kalin JH, Kim M, Guo R, Alexandrescu S, Blanco MA, Giera S, Gillespie SM, Das J, Wu M, Nocco S, Bonal DM, Nguyen QD, Suva ML, Bernstein BE, Alani R, Golub TR, Cole PA, Filbin MG, Shi Y. Re-programing Chromatin with a Bifunctional LSD1/HDAC Inhibitor Induces Therapeutic Differentiation in DIPG. Cancer Cell 2019; 36:528-544.e10. [PMID: 31631026 DOI: 10.1016/j.ccell.2019.09.005] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 08/02/2019] [Accepted: 09/12/2019] [Indexed: 02/01/2023]
Abstract
H3K27M mutations resulting in epigenetic dysfunction are frequently observed in diffuse intrinsic pontine glioma (DIPGs), an incurable pediatric cancer. We conduct a CRISPR screen revealing that knockout of KDM1A encoding lysine-specific demethylase 1 (LSD1) sensitizes DIPG cells to histone deacetylase (HDAC) inhibitors. Consistently, Corin, a bifunctional inhibitor of HDACs and LSD1, potently inhibits DIPG growth in vitro and in xenografts. Mechanistically, Corin increases H3K27me3 levels suppressed by H3K27M histones, and simultaneously increases HDAC-targeted H3K27ac and LSD1-targeted H3K4me1 at differentiation-associated genes. Corin treatment induces cell death, cell-cycle arrest, and a cellular differentiation phenotype and drives transcriptional changes correlating with increased survival time in DIPG patients. These data suggest a strategy for treating DIPG by simultaneously inhibiting LSD1 and HDACs.
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Affiliation(s)
- Jamie N Anastas
- Division of Newborn Medicine and Epigenetics Program, Department of Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Barry M Zee
- Division of Newborn Medicine and Epigenetics Program, Department of Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Jay H Kalin
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Division of Genetics, Department of Medicine, Brigham and Womens Hospital, Boston, MA 02115, USA
| | - Mirhee Kim
- NYU Medical School, New York, NY 10016, USA
| | - Robyn Guo
- Duke University, Durham, NC 27708, USA
| | - Sanda Alexandrescu
- Department of Pathology Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute and Children's Hospital Cancer Center, Boston, MA 02215, USA
| | - Mario Andres Blanco
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Shawn M Gillespie
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Jayanta Das
- Eshelman School of Pharmacy, UNC Chapel Hill, Chapel Hill, NC 27599, USA
| | - Muzhou Wu
- Department of Dermatology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Sarah Nocco
- Department of Dermatology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Dennis M Bonal
- Lurie Family Imaging Center, Center for Biomedical Imaging in Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Quang-De Nguyen
- Lurie Family Imaging Center, Center for Biomedical Imaging in Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Mario L Suva
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Bradley E Bernstein
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Rhoda Alani
- Department of Dermatology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Todd R Golub
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, 20815 MD, USA
| | - Philip A Cole
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Division of Genetics, Department of Medicine, Brigham and Womens Hospital, Boston, MA 02115, USA
| | - Mariella G Filbin
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Children's Hospital Cancer Center, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
| | - Yang Shi
- Division of Newborn Medicine and Epigenetics Program, Department of Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
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Nagaraja S, Quezada MA, Gillespie SM, Arzt M, Lennon JJ, Woo PJ, Hovestadt V, Kambhampati M, Filbin MG, Suva ML, Nazarian J, Monje M. Histone Variant and Cell Context Determine H3K27M Reprogramming of the Enhancer Landscape and Oncogenic State. Mol Cell 2019; 76:965-980.e12. [PMID: 31588023 DOI: 10.1016/j.molcel.2019.08.030] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 08/06/2019] [Accepted: 08/29/2019] [Indexed: 01/03/2023]
Abstract
Development of effective targeted cancer therapies is fundamentally limited by our molecular understanding of disease pathogenesis. Diffuse intrinsic pontine glioma (DIPG) is a fatal malignancy of the childhood pons characterized by a unique substitution to methionine in histone H3 at lysine 27 (H3K27M) that results in globally altered epigenetic marks and oncogenic transcription. Through primary DIPG tumor characterization and isogenic oncohistone expression, we show that the same H3K27M mutation displays distinct modes of oncogenic reprogramming and establishes distinct enhancer architecture depending upon both the variant of histone H3 and the cell context in which the mutation occurs. Compared with non-malignant pediatric pontine tissue, we identify and functionally validate both shared and variant-specific pathophysiology. Altogether, we provide a powerful resource of epigenomic data in 25 primary DIPG samples and 5 rare normal pediatric pontine tissue samples, revealing clinically relevant functional distinctions previously unidentified in DIPG.
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Affiliation(s)
- Surya Nagaraja
- Department of Neurology, Stanford University School of Medicine, Stanford, CA, USA; Stanford Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael A Quezada
- Department of Neurology, Stanford University School of Medicine, Stanford, CA, USA
| | - Shawn M Gillespie
- Department of Neurology, Stanford University School of Medicine, Stanford, CA, USA
| | - Marlene Arzt
- Department of Neurology, Stanford University School of Medicine, Stanford, CA, USA
| | - James J Lennon
- Department of Neurology, Stanford University School of Medicine, Stanford, CA, USA
| | - Pamelyn J Woo
- Department of Neurology, Stanford University School of Medicine, Stanford, CA, USA
| | - Volker Hovestadt
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Klarman Cell Observatory, Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA 02142, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Madhuri Kambhampati
- Research Center for Genetic Medicine, Children's National Health System, Washington, DC, USA
| | - Mariella G Filbin
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorder Center and Harvard Medical School, Boston, MA, USA
| | - Mario L Suva
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Klarman Cell Observatory, Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA 02142, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Javad Nazarian
- Research Center for Genetic Medicine, Children's National Health System, Washington, DC, USA; Department of Integrative Systems Biology, George Washington University School of Medicine and Health Sciences, Washington, DC, USA; Department of Oncology, University Children's Hospital, Zurich, Switzerland
| | - Michelle Monje
- Department of Neurology, Stanford University School of Medicine, Stanford, CA, USA; Stanford Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA; Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA; Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
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49
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Ahrendsen JT, Filbin MG, Chi SN, Manley PE, Wright KD, Bandopadhayay P, Clymer JR, Yeo KK, Kieran MW, Jones R, Lidov HG, Ligon KL, Alexandrescu S. Increasing value of autopsies in patients with brain tumors in the molecular era. J Neurooncol 2019; 145:349-355. [PMID: 31571114 DOI: 10.1007/s11060-019-03302-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 09/24/2019] [Indexed: 12/27/2022]
Abstract
BACKGROUND Pediatric brain tumors are associated with high morbidity and mortality, in part due to insufficient understanding of tumor biology. With limited tissue allocation for research from surgical specimens, a key barrier to improving biological understanding, brain tumor autopsies have become an increasingly valuable resource. This study reviews the brain tumor autopsy practice at our institution and describes specific emerging research utilization patterns beyond the clinical autopsy report. METHODS We performed a retrospective analysis of brain tumor autopsies at Boston Children's Hospital (BCH) between 2007 and 2017 and reviewed their consents, neuropathology reports and final diagnoses. We reviewed the method of tissue triaging for research consented autopsies (bioregistry, frozen and fresh tissue) and documented their specific uses. RESULTS Ninety-six deaths at BCH were due to brain tumors; 56 autopsies were performed (58.3%), of which 49 (87.5%) were consented for research. Tumor mapping was performed on all cases and tissue was allocated for DNA- and RNA-based sequencing studies (published and ongoing). Three tissue allocations with a postmortem interval of 8 h or less resulted in successful cell lines. Tissue from 14 autopsies was contributed to the National DIPG Registry. CONCLUSION Our institutional pediatric brain tumor autopsy clinical experience demonstrates the increased utility and wide utilization of autopsy-derived tissue for multiple types of research. These results support the increased efforts to obtain research consent for brain tumor autopsy and active collection of unfixed autopsy material in the molecular era.
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Affiliation(s)
- Jared T Ahrendsen
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, USA
| | - Mariella G Filbin
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - Susan N Chi
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - Peter E Manley
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - Karen D Wright
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, USA
| | | | - Jessica R Clymer
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - Kee Kiat Yeo
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - Mark W Kieran
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, USA.,Brystol Meyers Squibb, New York, USA
| | - Robert Jones
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - Hart G Lidov
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, 300 Longwood Ave, Boston, MA, 02215, USA
| | - Keith L Ligon
- Department of Pathology, Brigham and Women's Hospital, Boston, USA.,Department of Pathology, Boston Children's Hospital, Harvard Medical School, 300 Longwood Ave, Boston, MA, 02215, USA
| | - Sanda Alexandrescu
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, USA. .,Department of Pathology, Boston Children's Hospital, Harvard Medical School, 300 Longwood Ave, Boston, MA, 02215, USA.
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50
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Reitman ZJ, Paolella B, Bergthold G, Pelton K, Jones R, Becker S, Sinai CE, Malkin H, Huang Y, Grimmett L, Herbert ZT, Sun Y, Weatherbee J, Alberta J, Daley J, Rozenblatt-Rosen O, Segal R, Haas-Kogan D, Filbin MG, Suva ML, Regev A, Stiles C, Kieran MW, Goumnerova L, Ligon KL, Shalek AK, Bandopadhayay P, Beroukhim R. Abstract 3647: Single cell RNA sequencing reveals mitogenic and progenitor gene programs inBRAF-rearranged pilocytic astrocytomas. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-3647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Single-cell RNA sequencing (scRNAseq) has been performed across a range of intermediate to high-grade gliomas that each harbor multiple driver mutations. Pilocytic astrocytoma (PA), the most common childhood brain tumor, is a low-grade glioma. PAs frequently harbor oncogenic KIAA1549-BRAF fusions, and exhibit low rates of other driver mutations. While PAs exhibit a favorable prognosis compared to the higher-grade gliomas, treatment morbidity and tumor recurrence can represent major challenges for some PA patients. We performed scRNAseq of both tumor and non-tumor cells in newly-diagnosed PAs that contained KIAA1549-BRAF rearrangements. To confidently distinguish tumor cells from nontumor cells, we sorted cells by glial progenitor marker A2B5 status and profiled KIAA1549-BRAF fusion status of cells using a sensitive quantitative PCR-based assay. Results were validated using RNA in situ hybridization. When compared to higher-grade gliomas, a higher proportion of the PA tumor cells exhibited a differentiated, astrocyte-like phenotype. A smaller proportion of cells exhibited a progenitor-like phenotype with evidence of proliferation. These progenitor-like tumor cells expressed a mitogen-activated protein kinase (MAPK) program that was absent from higher-grade gliomas. Similar patterns of expression of genes associated with the astrocyte-like and MAPK gene programs were also seen in formalin fixed, paraffin embedded PA tissues using RNA in situ hybridization. Immune cells, especially microglia, comprised almost half of all cells in the PAs and accounted for differences in bulk expression profiles between tumor locations and subtypes. These single cell transcriptional data reveal a transcriptional developmental hierarchy in a pediatric low grade glioma that is skewed towards more mature brain cells compared to higher-grade gliomas. The results indicate that future analyses of bulk PA tissues should attempt to account for considerable infiltration by nontumor cells. Finally, the finding that a MAPK gene program is not uniformly expressed in PA tumor cells has implications for ongoing clinical investigations of therapies directed at the MAPK pathway for the treatment of PA.
Citation Format: Zachary J. Reitman, Brenton Paolella, Guillaume Bergthold, Kristine Pelton, Robert Jones, Sarah Becker, Claire E. Sinai, Haley Malkin, Ying Huang, Leslie Grimmett, Zachary T. Herbert, Yu Sun, Jessica Weatherbee, John Alberta, John Daley, Orit Rozenblatt-Rosen, Rosalind Segal, Daphne Haas-Kogan, Mariella G. Filbin, Mario L. Suva, Aviv Regev, Charles Stiles, Mark W. Kieran, Liliana Goumnerova, Keith L. Ligon, Alex K. Shalek, Pratiti Bandopadhayay, Rameen Beroukhim. Single cell RNA sequencing reveals mitogenic and progenitor gene programs inBRAF-rearranged pilocytic astrocytomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3647.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Ying Huang
- 1Dana-Farber Cancer Institute, Boston, MA
| | | | | | - Yu Sun
- 1Dana-Farber Cancer Institute, Boston, MA
| | | | | | - John Daley
- 1Dana-Farber Cancer Institute, Boston, MA
| | | | | | | | | | | | - Aviv Regev
- 2Broad Institute of Harvard and MIT, Cambridge, MA
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