1
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Weisbrod LJ, Thiraviyam A, Vengoji R, Shonka N, Jain M, Ho W, Batra SK, Salehi A. Diffuse intrinsic pontine glioma (DIPG): A review of current and emerging treatment strategies. Cancer Lett 2024; 590:216876. [PMID: 38609002 DOI: 10.1016/j.canlet.2024.216876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 04/14/2024]
Abstract
Diffuse intrinsic pontine glioma (DIPG) is a childhood malignancy of the brainstem with a dismal prognosis. Despite recent advances in its understanding at the molecular level, the prognosis of DIPG has remained unchanged. This article aims to review the current understanding of the genetic pathophysiology of DIPG and to highlight promising therapeutic targets. Various DIPG treatment strategies have been investigated in pre-clinical studies, several of which have shown promise and have been subsequently translated into ongoing clinical trials. Ultimately, a multifaceted therapeutic approach that targets cell-intrinsic alterations, the micro-environment, and augments the immune system will likely be necessary to eradicate DIPG.
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Affiliation(s)
- Luke J Weisbrod
- Department of Neurosurgery, University of Nebraska Medical Center, Omaha, NE, 68198-5870, USA
| | - Anand Thiraviyam
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68198-5870, USA
| | - Raghupathy Vengoji
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68198-5870, USA
| | - Nicole Shonka
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198-5870, USA; Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, 68198-5870, USA
| | - Maneesh Jain
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68198-5870, USA; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198-5870, USA; Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, 68198-5870, USA
| | - Winson Ho
- Department of Neurosurgery, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Surinder K Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68198-5870, USA; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198-5870, USA; Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, 68198-5870, USA
| | - Afshin Salehi
- Department of Neurosurgery, University of Nebraska Medical Center, Omaha, NE, 68198-5870, USA; Division of Pediatric Neurosurgery, Children's Nebraska, Omaha, NE, 68114, USA.
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2
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Spitzer A, Gritsch S, Nomura M, Jucht A, Fortin J, Raviram R, Weisman HR, Gonzalez Castro LN, Druck N, Chanoch-Myers R, Lee JJY, Mylvaganam R, Lee Servis R, Fung JM, Lee CK, Nagashima H, Miller JJ, Arrillaga-Romany I, Louis DN, Wakimoto H, Pisano W, Wen PY, Mak TW, Sanson M, Touat M, Landau DA, Ligon KL, Cahill DP, Suvà ML, Tirosh I. Mutant IDH inhibitors induce lineage differentiation in IDH-mutant oligodendroglioma. Cancer Cell 2024; 42:904-914.e9. [PMID: 38579724 PMCID: PMC11096020 DOI: 10.1016/j.ccell.2024.03.008] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 01/05/2024] [Accepted: 03/13/2024] [Indexed: 04/07/2024]
Abstract
A subset of patients with IDH-mutant glioma respond to inhibitors of mutant IDH (IDHi), yet the molecular underpinnings of such responses are not understood. Here, we profiled by single-cell or single-nucleus RNA-sequencing three IDH-mutant oligodendrogliomas from patients who derived clinical benefit from IDHi. Importantly, the tissues were sampled on-drug, four weeks from treatment initiation. We further integrate our findings with analysis of single-cell and bulk transcriptomes from independent cohorts and experimental models. We find that IDHi treatment induces a robust differentiation toward the astrocytic lineage, accompanied by a depletion of stem-like cells and a reduction of cell proliferation. Furthermore, mutations in NOTCH1 are associated with decreased astrocytic differentiation and may limit the response to IDHi. Our study highlights the differentiating potential of IDHi on the cellular hierarchies that drive oligodendrogliomas and suggests a genetic modifier that may improve patient stratification.
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Affiliation(s)
- Avishay Spitzer
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 761001, Israel; Department of Oncology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Simon Gritsch
- 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; Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
| | - Masashi Nomura
- 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
| | - Alexander Jucht
- 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
| | - Jerome Fortin
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada; Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, Canada
| | - Ramya Raviram
- New York Genome Center, New York, NY, USA; Weill Cornell Medicine, New York, NY, USA
| | - Hannah R Weisman
- 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
| | - L Nicolas Gonzalez Castro
- 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; Center for Neuro-Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
| | - Nicholas Druck
- 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
| | - Rony Chanoch-Myers
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 761001, Israel
| | - John J Y Lee
- 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
| | - Ravindra Mylvaganam
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Rachel Lee Servis
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Jeremy Man Fung
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Christine K Lee
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Hiroaki Nagashima
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Julie J Miller
- Pappas Center for Neuro-Oncology, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Isabel Arrillaga-Romany
- Departments of Neurology and Radiation Oncology, Division of Hematology/Oncology, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA
| | - David N Louis
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Hiroaki Wakimoto
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Will Pisano
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Patrick Y Wen
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Tak W Mak
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada; Centre for Oncology and Immunology, Hong Kong Science Park, Hong Kong SAR, China; Department of Pathology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Marc Sanson
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neurologie 2-Mazarin, Paris, France
| | - Mehdi Touat
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neurologie 2-Mazarin, Paris, France; Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
| | - Dan A Landau
- New York Genome Center, New York, NY, USA; Weill Cornell Medicine, New York, NY, USA
| | - Keith L Ligon
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA; Department of Pathology, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Daniel P Cahill
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
| | - Mario L Suvà
- 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.
| | - Itay Tirosh
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 761001, Israel.
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Jackson ER, Persson ML, Fish CJ, Findlay IJ, Mueller S, Nazarian J, Hulleman E, van der Lugt J, Duchatel RJ, Dun MD. A review of current therapeutics targeting the mitochondrial protease ClpP in diffuse midline glioma, H3 K27-altered. Neuro Oncol 2024; 26:S136-S154. [PMID: 37589388 PMCID: PMC11066926 DOI: 10.1093/neuonc/noad144] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Indexed: 08/18/2023] Open
Abstract
Diffuse midline gliomas (DMGs) are devastating pediatric brain tumors recognized as the leading cause of cancer-related death in children. DMGs are high-grade gliomas (HGGs) diagnosed along the brain's midline. Euchromatin is the hallmark feature of DMG, caused by global hypomethylation of H3K27 either through point mutations in histone H3 genes (H3K27M), or by overexpression of the enhancer of zeste homolog inhibitory protein. In a clinical trial for adults with progressive HGGs, a 22-year-old patient with a thalamic DMG, H3 K27-altered, showed a remarkable clinical and radiological response to dordaviprone (ONC201). This response in an H3 K27-altered HGG patient, coupled with the lack of response of patients harboring wildtype-H3 tumors, has increased the clinical interest in dordaviprone for the treatment of DMG. Additional reports of clinical benefit have emerged, but research defining mechanisms of action (MOA) fall behind dordaviprone's clinical use, with biomarkers of response unresolved. Here, we summarize dordaviprone's safety, interrogate its preclinical MOA identifying the mitochondrial protease "ClpP" as a biomarker of response, and discuss other ClpP agonists, expanding the arsenal of potential weapons in the fight against DMG. Finally, we discuss combination strategies including ClpP agonists, and their immunomodulatory effects suggestive of a role for the tumor microenvironment in DMG patient response.
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Affiliation(s)
- Evangeline R Jackson
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales , Australia
| | - Mika L Persson
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales , Australia
| | - Cameron J Fish
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales , Australia
| | - Izac J Findlay
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales , Australia
| | - Sabine Mueller
- DIPG/DMG Center Zurich, University Children’s Hospital Zürich, Zurich, Switzerland
- Department of Neurology, Neurosurgery and Pediatric, UCSF, San Francisco, California, USA
| | - Javad Nazarian
- DIPG/DMG Center Zurich, University Children’s Hospital Zürich, Zurich, Switzerland
- Center for Genetic Medicine Research, Children’s National Hospital, Washington, District of Columbia, USA
- The George Washington University, School of Medicine and Health Sciences, Washington, District of Columbia, USA
| | - Esther Hulleman
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands, Utrecht, Netherlands
| | - Jasper van der Lugt
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands, Utrecht, Netherlands
| | - Ryan J Duchatel
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales , Australia
| | - Matthew D Dun
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales , Australia
- Paediatric Program, Mark Hughes Foundation Centre for Brain Cancer Research, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
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Abstract
High-grade glioma (HGG) is the most common cause of cancer death in children and the most common primary central nervous system tumor in adults. While pediatric HGG was once thought to be biologically similar to the adult form of disease, research has shown these malignancies to be significantly molecularly distinct, necessitating distinct approaches to their clinical management. However, emerging data have shown shared molecular events in pediatric and adult HGG including the histone H3K27M mutation. This somatic missense mutation occurs in genes encoding one of two isoforms of the Histone H3 protein, H3F3A (H3.3), or HIST1H3B (H3.1), and is detected in up to 80% of pediatric diffuse midline gliomas and in up to 60% of adult diffuse gliomas. Importantly, the H3K27M mutation is associated with poorer overall survival and response to therapy compared to patients with H3 wild-type tumors. Here, we review the clinical features and biological underpinnings of pediatric and adult H3K27M mutant glioma, offering a groundwork for understanding current research and clinical approaches for the care of patients suffering with this challenging disease.
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Affiliation(s)
| | | | - Antonela Petrovic
- DMG Research Center, Department of Oncology, University Children’s Hospital, University of Zürich, Zürich, Switzerland
| | - Javad Nazarian
- Research Center for Genetic Medicine, Children’s National Health System, Washington, District of Columbia, USA
- Brain Tumor Institute, Children’s National Health System, Washington, District of Columbia, USA
- DMG Research Center, Department of Pediatrics, University Children’s Hospital, University of Zurich, Zürich, Switzerland
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5
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Mueller S, Kline C, Franson A, van der Lugt J, Prados M, Waszak SM, Plasschaert SLA, Molinaro AM, Koschmann C, Nazarian J. Rational combination platform trial design for children and young adults with diffuse midline glioma: A report from PNOC. Neuro Oncol 2024; 26:S125-S135. [PMID: 38124481 PMCID: PMC11066905 DOI: 10.1093/neuonc/noad181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [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: 05/23/2023] [Indexed: 12/23/2023] Open
Abstract
Background Diffuse midline glioma (DMG) is a devastating pediatric brain tumor unresponsive to hundreds of clinical trials. Approximately 80% of DMGs harbor H3K27M oncohistones, which reprogram the epigenome to increase the metabolic profile of the tumor cells. Methods We have previously shown preclinical efficacy of targeting both oxidative phosphorylation and glycolysis through treatment with ONC201, which activates the mitochondrial protease ClpP, and paxalisib, which inhibits PI3K/mTOR, respectively. Results ONC201 and paxalisib combination treatment aimed at inducing metabolic distress led to the design of the first DMG-specific platform trial PNOC022 (NCT05009992). Conclusions Here, we expand on the PNOC022 rationale and discuss various considerations, including liquid biome, microbiome, and genomic biomarkers, quality-of-life endpoints, and novel imaging modalities, such that we offer direction on future clinical trials in DMG.
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Affiliation(s)
- Sabine Mueller
- Department of Neurology, Neurosurgery and Pediatrics, University of California, San Francisco, California, USA
| | - Cassie Kline
- Division of Oncology, Department of Pediatrics, Children’s Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Andrea Franson
- Department of Pediatrics, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Michael Prados
- Department of Neurosurgery and Pediatrics, University of California, San Francisco, San Francisco, California, USA
| | - Sebastian M Waszak
- Department of Neurology, University of California, San Francisco, San Francisco, California, USA
- Laboratory of Computational Neuro-Oncology, Swiss Institute for Experimental Cancer Research, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | | | - Annette M Molinaro
- Division of Biomedical Statistics and Informatics, Department of Neurosurgery, University of California, San Francisco, San Francisco, California, USA
| | - Carl Koschmann
- Department of Pediatrics, University of Michigan, Ann Arbor, Michigan, USA
| | - Javad Nazarian
- Research Center for Genetic Medicine, Children’s National Health System, Washington, District of Columbia, USA
- Brain Tumor Institute, Children’s National Health System, Washington, District of Columbia, USA
- DMG Research Center, Department of Pediatrics, University Children’s Hospital, University of Zurich, Zürich, Switzerland
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Chen X, Yang W, Roberts CWM, Zhang J. Developmental origins shape the paediatric cancer genome. Nat Rev Cancer 2024:10.1038/s41568-024-00684-9. [PMID: 38698126 DOI: 10.1038/s41568-024-00684-9] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/18/2024] [Indexed: 05/05/2024]
Abstract
In the past two decades, technological advances have brought unprecedented insights into the paediatric cancer genome revealing characteristics distinct from those of adult cancer. Originating from developing tissues, paediatric cancers generally have low mutation burden and are driven by variants that disrupt the transcriptional activity, chromatin state, non-coding cis-regulatory regions and other biological functions. Within each tumour, there are multiple populations of cells with varying states, and the lineages of some can be tracked to their fetal origins. Genome-wide genetic screening has identified vulnerabilities associated with both the cell of origin and transcription deregulation in paediatric cancer, which have become a valuable resource for designing new therapeutic approaches including those for small molecules, immunotherapy and targeted protein degradation. In this Review, we present recent findings on these facets of paediatric cancer from a pan-cancer perspective and provide an outlook on future investigations.
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Affiliation(s)
- Xiaolong Chen
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Wentao Yang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Charles W M Roberts
- Comprehensive Cancer Center, St Jude Children's Research Hospital, Memphis, TN, USA
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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Lee MK, Azizgolshani N, Shapiro JA, Nguyen LN, Kolling FW, Zanazzi GJ, Frost HR, Christensen BC. Identifying tumor type and cell type-specific gene expression alterations in pediatric central nervous system tumors. Nat Commun 2024; 15:3634. [PMID: 38688897 PMCID: PMC11061189 DOI: 10.1038/s41467-024-47712-8] [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: 02/18/2023] [Accepted: 04/09/2024] [Indexed: 05/02/2024] Open
Abstract
Central nervous system (CNS) tumors are the leading cause of pediatric cancer death, and these patients have an increased risk for developing secondary neoplasms. Due to the low prevalence of pediatric CNS tumors, major advances in targeted therapies have been lagging compared to other adult tumors. We collect single nuclei RNA-seq data from 84,700 nuclei of 35 pediatric CNS tumors and three non-tumoral pediatric brain tissues and characterize tumor heterogeneity and transcriptomic alterations. We distinguish cell subpopulations associated with specific tumor types including radial glial cells in ependymomas and oligodendrocyte precursor cells in astrocytomas. In tumors, we observe pathways important in neural stem cell-like populations, a cell type previously associated with therapy resistance. Lastly, we identify transcriptomic alterations among pediatric CNS tumor types compared to non-tumor tissues, while accounting for cell type effects on gene expression. Our results suggest potential tumor type and cell type-specific targets for pediatric CNS tumor treatment. Here we address current gaps in understanding single nuclei gene expression profiles of previously under-investigated tumor types and enhance current knowledge of gene expression profiles of single cells of various pediatric CNS tumors.
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Affiliation(s)
- Min Kyung Lee
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Nasim Azizgolshani
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
- Department of Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | - Joshua A Shapiro
- Childhood Cancer Data Lab, Alex's Lemonade Stand Foundation, Bala Cynwyd, PA, USA
| | - Lananh N Nguyen
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | | | - George J Zanazzi
- Dartmouth Cancer Center, Lebanon, NH, USA
- Department of Pathology and Laboratory Medicine, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Hildreth Robert Frost
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.
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8
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Lee MK, Azizgolshani N, Zhang Z, Perreard L, Kolling FW, Nguyen LN, Zanazzi GJ, Salas LA, Christensen BC. Associations in cell type-specific hydroxymethylation and transcriptional alterations of pediatric central nervous system tumors. Nat Commun 2024; 15:3635. [PMID: 38688903 PMCID: PMC11061294 DOI: 10.1038/s41467-024-47943-9] [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: 02/18/2023] [Accepted: 04/16/2024] [Indexed: 05/02/2024] Open
Abstract
Although intratumoral heterogeneity has been established in pediatric central nervous system tumors, epigenomic alterations at the cell type level have largely remained unresolved. To identify cell type-specific alterations to cytosine modifications in pediatric central nervous system tumors, we utilize a multi-omic approach that integrated bulk DNA cytosine modification data (methylation and hydroxymethylation) with both bulk and single-cell RNA-sequencing data. We demonstrate a large reduction in the scope of significantly differentially modified cytosines in tumors when accounting for tumor cell type composition. In the progenitor-like cell types of tumors, we identify a preponderance differential Cytosine-phosphate-Guanine site hydroxymethylation rather than methylation. Genes with differential hydroxymethylation, like histone deacetylase 4 and insulin-like growth factor 1 receptor, are associated with cell type-specific changes in gene expression in tumors. Our results highlight the importance of epigenomic alterations in the progenitor-like cell types and its role in cell type-specific transcriptional regulation in pediatric central nervous system tumors.
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Affiliation(s)
- Min Kyung Lee
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.
| | - Nasim Azizgolshani
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
- Department of Surgery, Columbia University Medical Center, New York, NY, USA
| | - Ze Zhang
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Laurent Perreard
- Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Fred W Kolling
- Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Lananh N Nguyen
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - George J Zanazzi
- Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
- Department of Pathology and Laboratory Medicine, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Lucas A Salas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.
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9
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Donev K, Sundararajan V, Johnson D, Balan J, Chambers M, Paulson VA, Scherpelz KP, Abdullaev Z, Quezado M, Cimino PJ, Pratt D, Valerio E, Alves de Castro JV, Carraro DM, Torrezan GT, Wolff BM, Kulikowski LD, Costa FD, Aldape K, Ida CM. Diffuse hemispheric glioma with H3 p.K28M (K27M) mutation: Unusual non-midline presentation of diffuse midline glioma, H3 K27M-altered? J Neuropathol Exp Neurol 2024; 83:357-364. [PMID: 38447592 PMCID: PMC11029465 DOI: 10.1093/jnen/nlae018] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024] Open
Abstract
Diffuse midline glioma, H3 K27-altered (DMG-H3 K27) is an aggressive group of diffuse gliomas that predominantly occurs in pediatric patients, involves midline structures, and displays loss of H3 p.K28me3 (K27me3) expression by immunohistochemistry and characteristic genetic/epigenetic profile. Rare examples of a diffuse glioma with an H3 p.K28M (K27M) mutation and without involvement of the midline structures, so-called "diffuse hemispheric glioma with H3 p.K28M (K27M) mutation" (DHG-H3 K27), have been reported. Herein, we describe 2 additional cases of radiologically confirmed DHG-H3 K27 and summarize previously reported cases. We performed histological, immunohistochemical, molecular, and DNA methylation analysis and provided clinical follow-up in both cases. Overall, DHG-H3 K27 is an unusual group of diffuse gliomas that shows similar clinical, histopathological, genomic, and epigenetic features to DMG-H3 K27 as well as enrichment for activating alterations in MAPK pathway genes. These findings suggest that DHG-H3 K27 is closely related to DMG-H3 K27 and may represent an unusual presentation of DMG-H3 K27 without apparent midline involvement and with frequent MAPK pathway activation. Detailed reports of additional cases with clinical follow-up will be important to expand our understanding of this unusual group of diffuse gliomas and to better define the clinical outcome and how to classify DHG-H3 K27.
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Affiliation(s)
- Kliment Donev
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Scottsdale, Arizona, USA
| | - Vanitha Sundararajan
- OhioHealth Riverside Methodist Hospital, Columbus, Ohio, USA
- CORPath Pathology Services, Columbus, Ohio, USA
| | - Derek Johnson
- Department of Radiology, Mayo Clinic, Rochester, Minnesota, USA
| | - Jagadheshwar Balan
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USA
| | - Meagan Chambers
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Vera A Paulson
- Department of Laboratory Medicine and Pathology, Genetics and Solid Tumor Laboratory, University of Washington, Seattle, Washington, USA
| | - Kathryn P Scherpelz
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Zied Abdullaev
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Martha Quezado
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Patrick J Cimino
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Drew Pratt
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Ediel Valerio
- Department of Pathology, A.C. Camargo Cancer Center, Sao Paulo, Brazil
| | | | - Dirce Maria Carraro
- Genomics and Molecular Biology Group, International Center of Research CIPE, A.C. Camargo Cancer Center, Sao Paulo, Brazil
- National Institute of Science and Technology in Oncogenomics (INCITO), Sao Paulo, Brazil
| | - Giovana Tardin Torrezan
- Genomics and Molecular Biology Group, International Center of Research CIPE, A.C. Camargo Cancer Center, Sao Paulo, Brazil
- National Institute of Science and Technology in Oncogenomics (INCITO), Sao Paulo, Brazil
| | - Beatriz Martins Wolff
- Cytogenomic Laboratory, Department of Pathology, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Leslie Domenici Kulikowski
- Cytogenomic Laboratory, Department of Pathology, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Felipe D’Almeida Costa
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
- Dasa Laboratories, Sao Paulo, Brazil
| | - Kenneth Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Cristiane M Ida
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
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10
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Smith CM, Catchpoole D, Hutvagner G. MiRNAs from the Dlk1-Dio3 locus and miR-224/452 cluster contribute to glioblastoma tumor heterogeneity. Sci Rep 2024; 14:8570. [PMID: 38609422 PMCID: PMC11014907 DOI: 10.1038/s41598-024-58870-6] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
Glioblastoma is one of the most common and aggressive brain tumors and has seen few improvements in patient outcomes. Inter-tumor heterogeneity between tumors of different patients as well as intra-tumor heterogeneity of cells within the same tumor challenge the development of effective drugs. MiRNAs play an essential role throughout the developing brain and regulate many key genes involved in oncogenesis, yet their role in driving many of the processes underlying tumor heterogeneity remains unclear. In this study, we highlight miRNAs from the Dlk1-Dio3 and miR-224/452 clusters which may be expressed cell autonomously and have expression that is associated with cell state genes in glioblastoma, most prominently in neural progenitor-like and mesenchymal-like states respectively. These findings implicate these miRNA clusters as potential regulators of glioblastoma intra-tumoral heterogeneity and may serve as valuable biomarkers for cell state identification.
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Affiliation(s)
- Christopher M Smith
- School of Biomedical Engineering, Faculty of Engineering and IT, University of Technology Sydney, Sydney, Australia
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
| | - Daniel Catchpoole
- School of Computer Sciences, Faculty of Engineering and IT, University of Technology Sydney, Sydney, NSW, Australia
- The Tumour Bank, The Children's Cancer Research Unit, Kids Research, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Gyorgy Hutvagner
- School of Biomedical Engineering, Faculty of Engineering and IT, University of Technology Sydney, Sydney, Australia.
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11
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Li K, Zhu Q, Yang J, Zheng Y, Du S, Song M, Peng Q, Yang R, Liu Y, Qi L. Imaging and Liquid Biopsy for Distinguishing True Progression From Pseudoprogression in Gliomas, Current Advances and Challenges. Acad Radiol 2024:S1076-6332(24)00162-4. [PMID: 38614827 DOI: 10.1016/j.acra.2024.03.019] [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: 12/10/2023] [Revised: 01/14/2024] [Accepted: 03/18/2024] [Indexed: 04/15/2024]
Abstract
RATIONALE AND OBJECTIVES Gliomas are aggressive brain tumors with a poor prognosis. Assessing treatment response is challenging because magnetic resonance imaging (MRI) may not distinguish true progression (TP) from pseudoprogression (PsP). This review aims to discuss imaging techniques and liquid biopsies used to distinguish TP from PsP. MATERIALS AND METHODS This review synthesizes existing literature to examine advances in imaging techniques, such as magnetic resonance diffusion imaging (MRDI), perfusion-weighted imaging (PWI) MRI, and liquid biopsies, for identifying TP or PsP through tumor markers and tissue characteristics. RESULTS Advanced imaging techniques, including MRDI and PWI MRI, have proven effective in delineating tumor tissue properties, offering valuable insights into glioma behavior. Similarly, liquid biopsy has emerged as a potent tool for identifying tumor-derived markers in biofluids, offering a non-invasive glimpse into tumor evolution. Despite their promise, these methodologies grapple with significant challenges. Their sensitivity remains inconsistent, complicating the accurate differentiation between TP and PSP. Furthermore, the absence of standardized protocols across platforms impedes the reliability of comparisons, while inherent biological variability adds complexity to data interpretation. CONCLUSION Their potential applications have been highlighted, but gaps remain before routine clinical use. Further research is needed to develop and validate these promising methods for distinguishing TP from PsP in gliomas.
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Affiliation(s)
- Kaishu Li
- Department of Neurosurgery, Affiliated Qingyuan Hospital,Guangzhou Medical University,Qingyuan People's Hospital, Qingyuan 511518, China; Department of Neurosurgery & Medical Research Center, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), 1# Jiazi Road, Foshan, Guangdong 528300, China.; Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Qihui Zhu
- Department of Neurosurgery, Affiliated Qingyuan Hospital,Guangzhou Medical University,Qingyuan People's Hospital, Qingyuan 511518, China
| | - Junyi Yang
- Department of Neurosurgery, Affiliated Qingyuan Hospital,Guangzhou Medical University,Qingyuan People's Hospital, Qingyuan 511518, China
| | - Yin Zheng
- Department of Neurosurgery, Affiliated Qingyuan Hospital,Guangzhou Medical University,Qingyuan People's Hospital, Qingyuan 511518, China
| | - Siyuan Du
- Institute of Digestive Disease of Guangzhou Medical University, Affiliated Qingyuan Hospital,Guangzhou Medical University,Qingyuan People's Hospital, Qingyuan 511518, China
| | - Meihui Song
- Institute of Digestive Disease of Guangzhou Medical University, Affiliated Qingyuan Hospital,Guangzhou Medical University,Qingyuan People's Hospital, Qingyuan 511518, China
| | - Qian Peng
- Institute of Digestive Disease of Guangzhou Medical University, Affiliated Qingyuan Hospital,Guangzhou Medical University,Qingyuan People's Hospital, Qingyuan 511518, China
| | - Runwei Yang
- Department of Neurosurgery & Medical Research Center, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), 1# Jiazi Road, Foshan, Guangdong 528300, China
| | - Yawei Liu
- Department of Neurosurgery & Medical Research Center, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), 1# Jiazi Road, Foshan, Guangdong 528300, China
| | - Ling Qi
- Institute of Digestive Disease of Guangzhou Medical University, Affiliated Qingyuan Hospital,Guangzhou Medical University,Qingyuan People's Hospital, Qingyuan 511518, China.
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12
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Ganz J, Luquette LJ, Bizzotto S, Miller MB, Zhou Z, Bohrson CL, Jin H, Tran AV, Viswanadham VV, McDonough G, Brown K, Chahine Y, Chhouk B, Galor A, Park PJ, Walsh CA. Contrasting somatic mutation patterns in aging human neurons and oligodendrocytes. Cell 2024; 187:1955-1970.e23. [PMID: 38503282 PMCID: PMC11062076 DOI: 10.1016/j.cell.2024.02.025] [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: 01/09/2023] [Revised: 12/06/2023] [Accepted: 02/21/2024] [Indexed: 03/21/2024]
Abstract
Characterizing somatic mutations in the brain is important for disentangling the complex mechanisms of aging, yet little is known about mutational patterns in different brain cell types. Here, we performed whole-genome sequencing (WGS) of 86 single oligodendrocytes, 20 mixed glia, and 56 single neurons from neurotypical individuals spanning 0.4-104 years of age and identified >92,000 somatic single-nucleotide variants (sSNVs) and small insertions/deletions (indels). Although both cell types accumulate somatic mutations linearly with age, oligodendrocytes accumulated sSNVs 81% faster than neurons and indels 28% slower than neurons. Correlation of mutations with single-nucleus RNA profiles and chromatin accessibility from the same brains revealed that oligodendrocyte mutations are enriched in inactive genomic regions and are distributed across the genome similarly to mutations in brain cancers. In contrast, neuronal mutations are enriched in open, transcriptionally active chromatin. These stark differences suggest an assortment of active mutagenic processes in oligodendrocytes and neurons.
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Affiliation(s)
- Javier Ganz
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Lovelace J Luquette
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Sara Bizzotto
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Sorbonne Université, Institut du Cerveau (Paris Brain Institute) ICM, Inserm, CNRS, Hôpital de la Pitié Salpêtrière, 75013 Paris, France
| | - Michael B Miller
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Zinan Zhou
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Craig L Bohrson
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Hu Jin
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Antuan V Tran
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | | | - Gannon McDonough
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Katherine Brown
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Yasmine Chahine
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Brian Chhouk
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Alon Galor
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA; Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA.
| | - Christopher A Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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13
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Liu C, Kuang S, Huang T, Wu J, Zhang L, Gong X. Radiotherapy plus temozolomide with or without anlotinib in H3K27M-mutant diffuse midline glioma: A retrospective cohort study. CNS Neurosci Ther 2024; 30:e14730. [PMID: 38644565 PMCID: PMC11033330 DOI: 10.1111/cns.14730] [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: 01/15/2024] [Revised: 03/16/2024] [Accepted: 03/31/2024] [Indexed: 04/23/2024] Open
Abstract
BACKGROUND Besides the hallmark of H3K27M mutation, aberrant amplifications of receptor tyrosine kinases (RTKs) are commonly observed in diffuse midline glioma (DMG), a highly malignant brain tumor with dismal prognosis. Here, we intended to evaluate the efficacy and safety of a multitarget RTK inhibitor anlotinib in patients with H3K27M-DMG. METHODS A total of 40 newly diagnosed H3K27M-DMG patients including 15 with anlotinib and 25 without anlotinib treatment were retrospectively enrolled in this cohort. Progression-free survival (PFS), overall survival (OS), and toxicities were assessed and compared. RESULTS The median PFS and OS of all patients in this cohort were 8.5 months (95% CI, 6.5-11.3) and 15.5 months (95% CI, 12.6-17.1), respectively. According to the Response Assessment in Neuro-Oncology (RANO) criteria, the disease control rate in the anlotinib group [93.3%, 95% confidence interval (CI), 70.2-98.8] was significantly higher than those without anlotinib (64%, 95% CI: 40.5-79.8, p = 0.039). The median PFS of patients with and without anlotinib was 11.6 months (95% CI, 7.8-14.3) and 6.4 months (95% CI, 4.3-10.3), respectively. Both the median PFS and OS of DMG patients treated with anlotinib were longer than those without anlotinib in the infratentorial patients (PFS: 10.3 vs. 5.4 months, p = 0.006; OS: 16.6 vs. 8.7 months, p = 0.016). Multivariate analysis also indicated anlotinib (HR: 0.243, 95% CI: 0.066-0.896, p = 0.034) was an independent prognosticator for longer OS in the infratentorial subgroup. In addition, the adverse events of anlotinib administration were tolerable in the whole cohort. CONCLUSIONS This study first reported that anlotinib combined with Stupp regimen is a safe and feasible regimen for newly diagnosed patients with H3K27M-DMG. Further, anlotinib showed significant efficacy for H3K27M-DMG located in the infratentorial region.
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Affiliation(s)
- Chao Liu
- Department of OncologyXiangya Hospital, Central South UniversityChangshaChina
| | - Shuwen Kuang
- Department of OncologyXiangya Hospital, Central South UniversityChangshaChina
| | - Tianxiang Huang
- Department of NeurosurgeryXiangya Hospital, Central South UniversityChangshaChina
| | - Jun Wu
- Department of NeurosurgeryXiangya Hospital, Central South UniversityChangshaChina
| | - Longbo Zhang
- Department of NeurosurgeryXiangya Hospital, Central South UniversityChangshaChina
| | - Xuan Gong
- Department of NeurosurgeryXiangya Hospital, Central South UniversityChangshaChina
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14
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Hawly J, Murcar MG, Schcolnik-Cabrera A, Issa ME. Glioblastoma stem cell metabolism and immunity. Cancer Metastasis Rev 2024:10.1007/s10555-024-10183-w. [PMID: 38530545 DOI: 10.1007/s10555-024-10183-w] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 03/09/2024] [Indexed: 03/28/2024]
Abstract
Despite enormous efforts being invested in the development of novel therapies for brain malignancies, there remains a dire need for effective treatments, particularly for pediatric glioblastomas. Their poor prognosis has been attributed to the fact that conventional therapies target tumoral cells, but not glioblastoma stem cells (GSCs). GSCs are characterized by self-renewal, tumorigenicity, poor differentiation, and resistance to therapy. These characteristics represent the fundamental tools needed to recapitulate the tumor and result in a relapse. The mechanisms by which GSCs alter metabolic cues and escape elimination by immune cells are discussed in this article, along with potential strategies to harness effector immune cells against GSCs. As cellular immunotherapy is making significant advances in a variety of cancers, leveraging this underexplored reservoir may result in significant improvements in the treatment options for brain malignancies.
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Affiliation(s)
- Joseph Hawly
- Faculty of Medicine and Medical Sciences, University of Balamand, Dekouaneh, Lebanon
| | - Micaela G Murcar
- Department of Neurology, Massachusetts General Hospital, Charlestown, MA, USA
| | | | - Mark E Issa
- Department of Neurology, Massachusetts General Hospital, Charlestown, MA, USA.
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15
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Giacomini G, Piquet S, Chevallier O, Dabin J, Bai SK, Kim B, Siddaway R, Raught B, Coyaud E, Shan CM, Reid RJD, Toda T, Rothstein R, Barra V, Wilhelm T, Hamadat S, Bertin C, Crane A, Dubois F, Forne I, Imhof A, Bandopadhayay P, Beroukhim R, Naim V, Jia S, Hawkins C, Rondinelli B, Polo SE. Aberrant DNA repair reveals a vulnerability in histone H3.3-mutant brain tumors. Nucleic Acids Res 2024; 52:2372-2388. [PMID: 38214234 PMCID: PMC10954481 DOI: 10.1093/nar/gkad1257] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 05/26/2023] [Revised: 12/14/2023] [Accepted: 01/02/2024] [Indexed: 01/13/2024] Open
Abstract
Pediatric high-grade gliomas (pHGG) are devastating and incurable brain tumors with recurrent mutations in histone H3.3. These mutations promote oncogenesis by dysregulating gene expression through alterations of histone modifications. We identify aberrant DNA repair as an independent mechanism, which fosters genome instability in H3.3 mutant pHGG, and opens new therapeutic options. The two most frequent H3.3 mutations in pHGG, K27M and G34R, drive aberrant repair of replication-associated damage by non-homologous end joining (NHEJ). Aberrant NHEJ is mediated by the DNA repair enzyme polynucleotide kinase 3'-phosphatase (PNKP), which shows increased association with mutant H3.3 at damaged replication forks. PNKP sustains the proliferation of cells bearing H3.3 mutations, thus conferring a molecular vulnerability, specific to mutant cells, with potential for therapeutic targeting.
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Affiliation(s)
- Giulia Giacomini
- Epigenetics & Cell Fate Centre, CNRS/Université Paris Cité, Paris, France
| | - Sandra Piquet
- Epigenetics & Cell Fate Centre, CNRS/Université Paris Cité, Paris, France
| | - Odile Chevallier
- Epigenetics & Cell Fate Centre, CNRS/Université Paris Cité, Paris, France
| | - Juliette Dabin
- Epigenetics & Cell Fate Centre, CNRS/Université Paris Cité, Paris, France
| | - Siau-Kun Bai
- Epigenetics & Cell Fate Centre, CNRS/Université Paris Cité, Paris, France
| | - Byungjin Kim
- Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - Robert Siddaway
- Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Toronto, ON M5G1L7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Etienne Coyaud
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Toronto, ON M5G1L7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Université de Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000 Lille, France
| | - Chun-Min Shan
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Robert J D Reid
- Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Takenori Toda
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Rodney Rothstein
- Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Viviana Barra
- CNRS UMR9019 Genome Integrity and Cancers, Université Paris-Saclay, Gustave Roussy Institute, Villejuif, France
| | - Therese Wilhelm
- CNRS UMR9019 Genome Integrity and Cancers, Université Paris-Saclay, Gustave Roussy Institute, Villejuif, France
| | - Sabah Hamadat
- CNRS UMR9019 Genome Integrity and Cancers, Université Paris-Saclay, Gustave Roussy Institute, Villejuif, France
| | - Chloé Bertin
- CNRS UMR9019 Genome Integrity and Cancers, Université Paris-Saclay, Gustave Roussy Institute, Villejuif, France
| | - Alexander Crane
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - Frank Dubois
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - Ignasi Forne
- Protein Analysis Unit, BioMedical Center, Faculty of Medicine, Ludwig-Maximilians-University, Martinsried, Germany
| | - Axel Imhof
- Protein Analysis Unit, BioMedical Center, Faculty of Medicine, Ludwig-Maximilians-University, Martinsried, Germany
| | - Pratiti Bandopadhayay
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, USA
| | - Rameen Beroukhim
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - Valeria Naim
- CNRS UMR9019 Genome Integrity and Cancers, Université Paris-Saclay, Gustave Roussy Institute, Villejuif, France
| | - Songtao Jia
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Cynthia Hawkins
- Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
| | | | - Sophie E Polo
- Epigenetics & Cell Fate Centre, CNRS/Université Paris Cité, Paris, France
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16
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Fernández EC, Tomassoni L, Zhang X, Wang J, Obradovic A, Laise P, Griffin AT, Vlahos L, Minns HE, Morales DV, Simmons C, Gallitto M, Wei HJ, Martins TJ, Becker PS, Crawford JR, Tzaridis T, Wechsler-Reya RJ, Garvin J, Gartrell RD, Szalontay L, Zacharoulis S, Wu CC, Zhang Z, Califano A, Pavisic J. Elucidation and Pharmacologic Targeting of Master Regulator Dependencies in Coexisting Diffuse Midline Glioma Subpopulations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.17.585370. [PMID: 38559080 PMCID: PMC10979998 DOI: 10.1101/2024.03.17.585370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Diffuse Midline Gliomas (DMGs) are universally fatal, primarily pediatric malignancies affecting the midline structures of the central nervous system. Despite decades of clinical trials, treatment remains limited to palliative radiation therapy. A major challenge is the coexistence of molecularly distinct malignant cell states with potentially orthogonal drug sensitivities. To address this challenge, we leveraged established network-based methodologies to elucidate Master Regulator (MR) proteins representing mechanistic, non-oncogene dependencies of seven coexisting subpopulations identified by single-cell analysis-whose enrichment in essential genes was validated by pooled CRISPR/Cas9 screens. Perturbational profiles of 372 clinically relevant drugs helped identify those able to invert the activity of subpopulation-specific MRs for follow-up in vivo validation. While individual drugs predicted to target individual subpopulations-including avapritinib, larotrectinib, and ruxolitinib-produced only modest tumor growth reduction in orthotopic models, systemic co-administration induced significant survival extension, making this approach a valuable contribution to the rational design of combination therapy.
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17
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Tzaridis T, Wechsler-Reya RJ. Just a spoonful of metformin helps the medicine go down. J Clin Invest 2024; 134:e179144. [PMID: 38488006 PMCID: PMC10940077 DOI: 10.1172/jci179144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2024] Open
Abstract
Diffuse intrinsic pontine glioma (DIPG) is a devastating brain tumor with a need for novel therapies. So far, monotherapies have failed to prolong survival for these patients, and combinatorial strategies have often shown severe, dose-limiting toxicities. In this issue of the JCI, Duchatel, Jackson, and colleagues address this challenge by introducing a drug combination that mitigates side effects and overcomes resistance. After identifying the PI3K/mTOR pathway as a therapeutic vulnerability, they treated DIPG-bearing mice with paxalisib and saw responses but also observed hyperglycemia as a severe side effect. Combining paxalisib with metformin mitigated this toxicity, but also upregulated protein kinase C (PKC) signaling. To tackle this mechanism of resistance, the authors added the PKC inhibitor enzastaurin to their drug combination and showed that this triple therapy led to improved survival. This approach paves the way for improved outcomes for patients with DIPG and other brain tumors.
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Affiliation(s)
- Theophilos Tzaridis
- Cancer Genome and Epigenetics Program, NCI-Designated Cancer Center, Sanford Burnham, Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Robert J. Wechsler-Reya
- Cancer Genome and Epigenetics Program, NCI-Designated Cancer Center, Sanford Burnham, Prebys Medical Discovery Institute, La Jolla, California, USA
- Department of Neurology and Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, USA
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18
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Sussman JH, Oldridge DA, Yu W, Chen CH, Zellmer AM, Rong J, Parvaresh-Rizi A, Thadi A, Xu J, Bandyopadhyay S, Sun Y, Wu D, Emerson Hunter C, Brosius S, Ahn KJ, Baxter AE, Koptyra MP, Vanguri RS, McGrory S, Resnick AC, Storm PB, Amankulor NM, Santi M, Viaene AN, Zhang N, Raedt TD, Cole K, Tan K. A longitudinal single-cell and spatial multiomic atlas of pediatric high-grade glioma. bioRxiv 2024:2024.03.06.583588. [PMID: 38496580 PMCID: PMC10942465 DOI: 10.1101/2024.03.06.583588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Pediatric high-grade glioma (pHGG) is an incurable central nervous system malignancy that is a leading cause of pediatric cancer death. While pHGG shares many similarities to adult glioma, it is increasingly recognized as a molecularly distinct, yet highly heterogeneous disease. In this study, we longitudinally profiled a molecularly diverse cohort of 16 pHGG patients before and after standard therapy through single-nucleus RNA and ATAC sequencing, whole-genome sequencing, and CODEX spatial proteomics to capture the evolution of the tumor microenvironment during progression following treatment. We found that the canonical neoplastic cell phenotypes of adult glioblastoma are insufficient to capture the range of tumor cell states in a pediatric cohort and observed differential tumor-myeloid interactions between malignant cell states. We identified key transcriptional regulators of pHGG cell states and did not observe the marked proneural to mesenchymal shift characteristic of adult glioblastoma. We showed that essential neuromodulators and the interferon response are upregulated post-therapy along with an increase in non-neoplastic oligodendrocytes. Through in vitro pharmacological perturbation, we demonstrated novel malignant cell-intrinsic targets. This multiomic atlas of longitudinal pHGG captures the key features of therapy response that support distinction from its adult counterpart and suggests therapeutic strategies which are targeted to pediatric gliomas.
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Affiliation(s)
- Jonathan H. Sussman
- Medical Scientist Training Program, Perelman School of Medicine,
University of Pennsylvania, Philadelphia, PA
- Graduate Group in Genomics and Computational Biology, Perelman
School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Derek A. Oldridge
- Department of Pathology and Laboratory Medicine, Perelman School
of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Wenbao Yu
- Center for Childhood Cancer Research, Children’s Hospital
of Philadelphia, Philadelphia, PA
- Department of Pediatrics, University of Pennsylvania Perelman
School of Medicine, Philadelphia, PA
| | - Chia-Hui Chen
- Center for Childhood Cancer Research, Children’s Hospital
of Philadelphia, Philadelphia, PA
| | - Abigail M. Zellmer
- Department of Pathology and Laboratory Medicine, Perelman School
of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Jiazhen Rong
- Graduate Group in Genomics and Computational Biology, Perelman
School of Medicine, University of Pennsylvania, Philadelphia, PA
- Department of Statistics and Data Science, University of
Pennsylvania, Philadelphia, PA
| | | | - Anusha Thadi
- Center for Childhood Cancer Research, Children’s Hospital
of Philadelphia, Philadelphia, PA
| | - Jason Xu
- Medical Scientist Training Program, Perelman School of Medicine,
University of Pennsylvania, Philadelphia, PA
- Graduate Group in Genomics and Computational Biology, Perelman
School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Shovik Bandyopadhyay
- Medical Scientist Training Program, Perelman School of Medicine,
University of Pennsylvania, Philadelphia, PA
- Cellular and Molecular Biology Graduate Group, Perelman School of
Medicine, University of Pennsylvania, PA
| | - Yusha Sun
- Medical Scientist Training Program, Perelman School of Medicine,
University of Pennsylvania, Philadelphia, PA
- Neuroscience Graduate Group, Perelman School of Medicine,
University of Pennsylvania, PA
| | - David Wu
- Medical Scientist Training Program, Perelman School of Medicine,
University of Pennsylvania, Philadelphia, PA
- Graduate Group in Genomics and Computational Biology, Perelman
School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - C. Emerson Hunter
- Medical Scientist Training Program, Perelman School of Medicine,
University of Pennsylvania, Philadelphia, PA
- Graduate Group in Genomics and Computational Biology, Perelman
School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Stephanie Brosius
- Graduate Group in Genomics and Computational Biology, Perelman
School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Kyung Jin Ahn
- Center for Childhood Cancer Research, Children’s Hospital
of Philadelphia, Philadelphia, PA
| | - Amy E. Baxter
- Department of Pathology and Laboratory Medicine, Perelman School
of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Mateusz P. Koptyra
- Department of Neurosurgery, Children’s Hospital of
Philadelphia, Philadelphia, PA
| | - Rami S. Vanguri
- Department of Pathology and Laboratory Medicine, Perelman School
of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Stephanie McGrory
- Center for Childhood Cancer Research, Children’s Hospital
of Philadelphia, Philadelphia, PA
| | - Adam C. Resnick
- Department of Neurosurgery, Children’s Hospital of
Philadelphia, Philadelphia, PA
| | - Phillip B. Storm
- Department of Neurosurgery, Children’s Hospital of
Philadelphia, Philadelphia, PA
| | - Nduka M. Amankulor
- Department of Neurosurgery, Perelman School of Medicine,
Philadelphia, PA
| | - Mariarita Santi
- Department of Pathology and Laboratory Medicine, Perelman School
of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Angela N. Viaene
- Department of Pathology and Laboratory Medicine, Perelman School
of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Nancy Zhang
- Department of Statistics and Data Science, University of
Pennsylvania, Philadelphia, PA
| | - Thomas De Raedt
- Department of Pathology and Laboratory Medicine, Perelman School
of Medicine at the University of Pennsylvania, Philadelphia, PA
- Center for Childhood Cancer Research, Children’s Hospital
of Philadelphia, Philadelphia, PA
| | - Kristina Cole
- Center for Childhood Cancer Research, Children’s Hospital
of Philadelphia, Philadelphia, PA
- Department of Pediatrics, University of Pennsylvania Perelman
School of Medicine, Philadelphia, PA
| | - Kai Tan
- Center for Childhood Cancer Research, Children’s Hospital
of Philadelphia, Philadelphia, PA
- Department of Pediatrics, University of Pennsylvania Perelman
School of Medicine, Philadelphia, PA
- Center for Single Cell Biology, Children’s Hospital of
Philadelphia, Philadelphia, PA
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19
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Fernando D, Ahmed AU, Williams BRG. Therapeutically targeting the unique disease landscape of pediatric high-grade gliomas. Front Oncol 2024; 14:1347694. [PMID: 38525424 PMCID: PMC10957575 DOI: 10.3389/fonc.2024.1347694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/19/2024] [Indexed: 03/26/2024] Open
Abstract
Pediatric high-grade gliomas (pHGG) are a rare yet devastating malignancy of the central nervous system's glial support cells, affecting children, adolescents, and young adults. Tumors of the central nervous system account for the leading cause of pediatric mortality of which high-grade gliomas present a significantly grim prognosis. While the past few decades have seen many pediatric cancers experiencing significant improvements in overall survival, the prospect of survival for patients diagnosed with pHGGs has conversely remained unchanged. This can be attributed in part to tumor heterogeneity and the existence of the blood-brain barrier. Advances in discovery research have substantiated the existence of unique subgroups of pHGGs displaying alternate responses to different therapeutics and varying degrees of overall survival. This highlights a necessity to approach discovery research and clinical management of the disease in an alternative subtype-dependent manner. This review covers traditional approaches to the therapeutic management of pHGGs, limitations of such methods and emerging alternatives. Novel mutations which predominate the pHGG landscape are highlighted and the therapeutic potential of targeting them in a subtype specific manner discussed. Collectively, this provides an insight into issues in need of transformative progress which arise during the management of pHGGs.
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Affiliation(s)
- Dasun Fernando
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC, Australia
- Department of Molecular and Translational Sciences, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
| | - Afsar U. Ahmed
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC, Australia
- Department of Molecular and Translational Sciences, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
| | - Bryan R. G. Williams
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC, Australia
- Department of Molecular and Translational Sciences, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
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20
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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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21
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DeSisto J, Donson AM, Griesinger AM, Fu R, Riemondy K, Mulcahy Levy J, Siegenthaler JA, Foreman NK, Vibhakar R, Green AL. Tumor and immune cell types interact to produce heterogeneous phenotypes of pediatric high-grade glioma. Neuro Oncol 2024; 26:538-552. [PMID: 37934854 PMCID: PMC10912009 DOI: 10.1093/neuonc/noad207] [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: 11/16/2022] [Indexed: 11/09/2023] Open
Abstract
BACKGROUND Pediatric high-grade gliomas (PHGG) are aggressive brain tumors with 5-year survival rates ranging from <2% to 20% depending upon subtype. PHGG presents differently from patient to patient and is intratumorally heterogeneous, posing challenges in designing therapies. We hypothesized that heterogeneity occurs because PHGG comprises multiple distinct tumor and immune cell types in varying proportions, each of which may influence tumor characteristics. METHODS We obtained 19 PHGG samples from our institution's pediatric brain tumor bank. We constructed a comprehensive transcriptomic dataset at the single-cell level using single-cell RNA-Seq (scRNA-Seq), identified known glial and immune cell types, and performed differential gene expression and gene set enrichment analysis. We conducted multi-channel immunofluorescence (IF) staining to confirm the transcriptomic results. RESULTS Our PHGG samples included 3 principal predicted tumor cell types: astrocytes, oligodendrocyte progenitors (OPCs), and mesenchymal-like cells (Mes). These cell types differed in their gene expression profiles, pathway enrichment, and mesenchymal character. We identified a macrophage population enriched in mesenchymal and inflammatory gene expression as a possible source of mesenchymal tumor characteristics. We found evidence of T-cell exhaustion and suppression. CONCLUSIONS PHGG comprises multiple distinct proliferating tumor cell types. Microglia-derived macrophages may drive mesenchymal gene expression in PHGG. The predicted Mes tumor cell population likely derives from OPCs. The variable tumor cell populations rely on different oncogenic pathways and are thus likely to vary in their responses to therapy.
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Affiliation(s)
- John DeSisto
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Cell Biology, Stem Cells and Development Graduate Program, Aurora, Colorado, USA
| | - Andrew M Donson
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Andrea M Griesinger
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Rui Fu
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Kent Riemondy
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Jean Mulcahy Levy
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Center for Cancer and Blood Disorders, Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Julie A Siegenthaler
- Department of Pediatrics Section of Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Cell Biology, Stem Cells and Development Graduate Program, Aurora, Colorado, USA
| | - Nicholas K Foreman
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Center for Cancer and Blood Disorders, Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Rajeev Vibhakar
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Center for Cancer and Blood Disorders, Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Adam L Green
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Center for Cancer and Blood Disorders, Children’s Hospital Colorado, Aurora, Colorado, USA
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22
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Zheng C, Tu C, Wang J, Yu Y, Guo X, Sun J, Sun J, Cai W, Yang Q, Sun T. Deciphering Oligodendrocyte Lineages in the Human Fetal Central Nervous System Using Single-Cell RNA Sequencing. Mol Neurobiol 2024; 61:1737-1752. [PMID: 37775719 DOI: 10.1007/s12035-023-03661-9] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 09/12/2023] [Indexed: 10/01/2023]
Abstract
Oligodendrocytes form myelin sheaths and wrap axons of neurons to facilitate various crucial neurological functions. Oligodendrocyte progenitor cells (OPCs) persist in the embryonic, postnatal, and adult central nervous system (CNS). OPCs and mature oligodendrocytes are involved in a variety of biological processes such as memory, learning, and diseases. How oligodendrocytes are specified in different regions in the CNS, in particular in humans, remains obscure. We here explored oligodendrocyte development in three CNS regions, subpallium, brainstem, and spinal cord, in human fetuses from gestational week 8 (GW8) to GW12 using single-cell RNA sequencing. We detected multiple lineages of OPCs and illustrated distinct developmental trajectories of oligodendrocyte differentiation in three CNS regions. We also identified major genes, particularly transcription factors, which maintain status of OPC proliferation and promote generation of mature oligodendrocytes. Moreover, we discovered new marker genes that might be crucial for oligodendrocyte specification in humans, and detected common and distinct genes expressed in oligodendrocyte lineages in three CNS regions. Our study has demonstrated molecular heterogeneity of oligodendrocyte lineages in different CNS regions and provided references for further investigation of roles of important genes in oligodendrocyte development in humans.
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Affiliation(s)
- Chenlin Zheng
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, Fujian, China
| | - Chao Tu
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, Fujian, China
| | - Jing Wang
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, Fujian, China
| | - Yuan Yu
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, Fujian, China
| | - Xueyu Guo
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, Fujian, China
| | - Jason Sun
- Maple Glory United School, Xiamen, Fujian, China
- Xiamen Institute of Technology Attached School, Xiamen, Fujian, China
| | - Julianne Sun
- Maple Glory United School, Xiamen, Fujian, China
- Xiamen Institute of Technology Attached School, Xiamen, Fujian, China
| | - Wenjie Cai
- Department of Radiation Oncology, First Hospital of Quanzhou, Fujian Medical University, Quanzhou, Fujian, China
| | - Qingwei Yang
- Department of Neurology, Zhongshan Hospital, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Tao Sun
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, Fujian, China.
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23
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Sheng H, Li H, Zeng H, Zhang B, Lu Y, Liu X, Xu Z, Zhang J, Zhang L. Heterogeneity and tumoral origin of medulloblastoma in the single-cell era. Oncogene 2024; 43:839-850. [PMID: 38355808 PMCID: PMC10942862 DOI: 10.1038/s41388-024-02967-9] [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: 09/25/2023] [Accepted: 02/05/2024] [Indexed: 02/16/2024]
Abstract
Medulloblastoma is one of the most common malignant pediatric brain tumors derived from posterior fossa. The current treatment includes maximal safe surgical resection, radiotherapy, whole cranio-spinal radiation and adjuvant with chemotherapy. However, it can only limitedly prolong the survival time with severe side effects and relapse. Defining the intratumoral heterogeneity, cellular origin and identifying the interaction network within tumor microenvironment are helpful for understanding the mechanisms of medulloblastoma tumorigenesis and relapse. Due to technological limitations, the mechanisms of cellular heterogeneity and tumor origin have not been fully understood. Recently, the emergence of single-cell technology has provided a powerful tool for achieving the goal of understanding the mechanisms of tumorigenesis. Several studies have demonstrated the intratumoral heterogeneity and tumor origin for each subtype of medulloblastoma utilizing the single-cell RNA-seq, which has not been uncovered before using conventional technologies. In this review, we present an overview of the current progress in understanding of cellular heterogeneity and tumor origin of medulloblastoma and discuss novel findings in the age of single-cell technologies.
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Affiliation(s)
- Hui Sheng
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Haotai Li
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Han Zeng
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Bin Zhang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yu Lu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xixi Liu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Zhongwen Xu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jing Zhang
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Liguo Zhang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.
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24
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Leszczynska KB, Freitas-Huhtamäki A, Jayaprakash C, Dzwigonska M, Vitorino FNL, Horth C, Wojnicki K, Gielniewski B, Szadkowska P, Kaza B, Nazarian J, Ciolkowski MK, Trubicka J, Grajkowska W, Garcia BA, Majewski J, Kaminska B, Mieczkowski J. H2A.Z histone variants facilitate HDACi-dependent removal of H3.3K27M mutant protein in pediatric high-grade glioma cells. Cell Rep 2024; 43:113707. [PMID: 38306270 PMCID: PMC11026119 DOI: 10.1016/j.celrep.2024.113707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [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: 05/29/2023] [Revised: 10/22/2023] [Accepted: 01/11/2024] [Indexed: 02/04/2024] Open
Abstract
Diffuse intrinsic pontine gliomas (DIPGs) are deadly pediatric brain tumors, non-resectable due to brainstem localization and diffusive growth. Over 80% of DIPGs harbor a mutation in histone 3 (H3.3 or H3.1) resulting in a lysine-to-methionine substitution (H3K27M). Patients with DIPG have a dismal prognosis with no effective therapy. We show that histone deacetylase (HDAC) inhibitors lead to a significant reduction in the H3.3K27M protein (up to 80%) in multiple glioma cell lines. We discover that the SB939-mediated H3.3K27M loss is partially blocked by a lysosomal inhibitor, chloroquine. The H3.3K27M loss is facilitated by co-occurrence of H2A.Z, as evidenced by the knockdown of H2A.Z isoforms. Chromatin immunoprecipitation sequencing (ChIP-seq) analysis confirms the occupancy of H3.3K27M and H2A.Z at the same SB939-inducible genes. We discover a mechanism showing that HDAC inhibition in DIPG leads to pharmacological modulation of the oncogenic H3.3K27M protein levels. These findings show the possibility of directly targeting the H3.3K27M oncohistone.
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Affiliation(s)
- Katarzyna B Leszczynska
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland.
| | | | - Chinchu Jayaprakash
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Monika Dzwigonska
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Francisca N L Vitorino
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Cynthia Horth
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Kamil Wojnicki
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Bartlomiej Gielniewski
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Paulina Szadkowska
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Beata Kaza
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Javad Nazarian
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, USA; Department of Pediatrics, University Children's Hospital Zürich, Zürich, Switzerland
| | | | | | | | - Benjamin A Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Jacek Majewski
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Bozena Kaminska
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Jakub Mieczkowski
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland; 3P-Medicine Laboratory, Medical University of Gdansk, Gdansk, Poland.
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25
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Zang D, Dong Z, Liu Y, Chen Q. Single-cell RNA sequencing of anaplastic ependymoma and H3K27M-mutant diffuse midline glioma. BMC Neurol 2024; 24:74. [PMID: 38383423 PMCID: PMC10880286 DOI: 10.1186/s12883-024-03558-7] [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: 07/31/2023] [Accepted: 02/01/2024] [Indexed: 02/23/2024] Open
Abstract
BACKGROUND Anaplastic ependymoma and H3K27M-mutant diffuse midline glioma are two common subtypes of brain tumors with poor long-term prognosis. The present study analyzed and compared the differences in cell types between two tumors by single-cell RNA sequencing (scRNA-seq) technology. METHODS ScRNA-seq was performed to profile cells from cancer tissue from anaplastic ependymoma patient and H3K27M-mutant diffuse midline glioma patient. Cell clustering, marker gene identification, cell type annotation, copy number variation analysis and function analysis of differentially expressed genes were then performed. RESULTS A total of 11,219 cells were obtained from anaplastic ependymoma and H3K27M mutant diffuse midline glioma, and these cells categorized into 12 distinct clusters. Each cell cluster could be characterized with specific cell markers to indicate cellular heterogeneity. Five cell types were annotated in each sample, including astrocyte, oligodendrocytes, microglial cell, neural progenitor cell and immune cell. The cluster types and proportion of cell types were not consistent between the two brain tumors. Functional analyses suggest that these cell clusters are involved in tumor-associated pathways, with slight differences in the cells of origin between the two tumors. In addition, cell communication analysis showed that the NRG3-ERBB4 pair is a key Ligand-receptor pair for anaplastic ependymoma, while in H3K27M-mutant diffuse midline glioma it is the PTN-PTPRZ1 pair that establishes contact with other cells. CONCLUSION There was intratumor heterogeneity in anaplastic ependymoma and H3K27M mutant diffuse midline glioma, and that the subtype differences may be due to differences in the origin of the cells.
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Affiliation(s)
- Dongdong Zang
- Department of Neurosurgery, Shenzhen Children's Hospital, 7019 Yitian Road, Futian District, Shenzhen, Guangdong, China
| | - Zilong Dong
- Department of Neurosurgery, Shenzhen Children's Hospital, 7019 Yitian Road, Futian District, Shenzhen, Guangdong, China
| | - Yuecheng Liu
- Department of Neurosurgery, Shenzhen Children's Hospital, 7019 Yitian Road, Futian District, Shenzhen, Guangdong, China
| | - Qian Chen
- Department of Neurosurgery, Shenzhen Children's Hospital, 7019 Yitian Road, Futian District, Shenzhen, Guangdong, China.
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26
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Padilla O, Minns HE, Wei HJ, Fan W, Webster-Carrion A, Tazhibi M, McQuillan NM, Zhang X, Gallitto M, Yeh R, Zhang Z, Hei TK, Szalontay L, Pavisic J, Tan Y, Deoli N, Garty G, Garvin JH, Canoll PD, Vanpouille-Box C, Menon V, Olah M, Rabadan R, Wu CC, Gartrell RD. Immune Response following FLASH and Conventional Radiation in Diffuse Midline Glioma. Int J Radiat Oncol Biol Phys 2024:S0360-3016(24)00300-6. [PMID: 38364947 DOI: 10.1016/j.ijrobp.2024.01.219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 01/15/2024] [Accepted: 01/28/2024] [Indexed: 02/18/2024]
Abstract
PURPOSE Diffuse midline glioma (DMG) is a fatal tumor traditionally treated with radiation therapy (RT) and previously characterized as having a noninflammatory tumor immune microenvironment (TIME). FLASH is a novel RT technique using ultra-high dose rate that is associated with decreased toxicity and effective tumor control. However, the effect of FLASH and conventional (CONV) RT on the DMG TIME has not yet been explored. METHODS AND MATERIALS Here, we performed single-cell RNA sequencing (scRNA-seq) and flow cytometry on immune cells isolated from an orthotopic syngeneic murine model of brainstem DMG after the use of FLASH (90 Gy/sec) or CONV (2 Gy/min) dose-rate RT and compared to unirradiated tumor (SHAM). RESULTS At day 4 post-RT, FLASH exerted similar effects as CONV in the predominant microglial (MG) population, including the presence of two activated subtypes. However, at day 10 post-RT, we observed a significant increase in the type 1 interferon α/β receptor (IFNAR+) in MG in CONV and SHAM compared to FLASH. In the non-resident myeloid clusters of macrophages (MACs) and dendritic cells (DCs), we found increased type 1 interferon (IFN1) pathway enrichment for CONV compared to FLASH and SHAM by scRNA-seq. We observed this trend by flow cytometry at day 4 post-RT in IFNAR+ MACs and DCs, which equalized by day 10 post-RT. DMG control and murine survival were equivalent between RT dose rates. CONCLUSIONS Our work is the first to map CONV and FLASH immune alterations of the DMG TIME with single-cell resolution. Although DMG tumor control and survival were similar between CONV and FLASH, we found that changes in immune compartments differed over time. Importantly, although both RT modalities increased IFN1, we found that the timing of this response was cell-type and dose-rate dependent. These temporal differences, particularly in the context of tumor control, warrant further study.
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Affiliation(s)
- Oscar Padilla
- Department of Radiation Oncology, Columbia University Irving Medical Center, New York, New York; Department of Radiation Oncology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Hanna E Minns
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York; Oregon Health and Science University School of Medicine, Portland, Oregon
| | - Hong-Jian Wei
- Department of Radiation Oncology, Columbia University Irving Medical Center, New York, New York
| | - Weijia Fan
- Mailman School of Public Health, Columbia University, New York, New York
| | | | - Masih Tazhibi
- Department of Radiation Oncology, Columbia University Irving Medical Center, New York, New York
| | - Nicholas M McQuillan
- Department of Radiation Oncology, Columbia University Irving Medical Center, New York, New York
| | - Xu Zhang
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York; Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, New York; Department of Genetics and Development, Columbia University Irving Medical Center, New York, New York
| | - Matthew Gallitto
- Department of Radiation Oncology, Columbia University Irving Medical Center, New York, New York
| | - Rebecca Yeh
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York
| | - Zhiguo Zhang
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York; Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, New York; Department of Genetics and Development, Columbia University Irving Medical Center, New York, New York
| | - Tom K Hei
- Department of Radiation Oncology, Columbia University Irving Medical Center, New York, New York; Center for Radiological Research, Columbia University Irving Medical Center, New York, New York
| | - Luca Szalontay
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York
| | - Jovana Pavisic
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York
| | - Yuewen Tan
- Radiological Research Accelerator Facility, Columbia University Irving Medical Center, Irvington, New York
| | - Naresh Deoli
- Radiological Research Accelerator Facility, Columbia University Irving Medical Center, Irvington, New York
| | - Guy Garty
- Department of Radiation Oncology, Columbia University Irving Medical Center, New York, New York; Center for Radiological Research, Columbia University Irving Medical Center, New York, New York; Radiological Research Accelerator Facility, Columbia University Irving Medical Center, Irvington, New York
| | - James H Garvin
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York
| | - Peter D Canoll
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York
| | | | - Vilas Menon
- Department of Neurology, Columbia University Irving Medical Center, New York, New York; Center for Translational and Computational Neuroimmunology, Columbia University Irving Medical Center, New York, New York; Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York
| | - Marta Olah
- Department of Neurology, Columbia University Irving Medical Center, New York, New York; Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York
| | - Raul Rabadan
- Department of Systems Biology, Columbia University Irving Medical Center, New York, New York; Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, New York; Program for Mathematical Genomics, Columbia University Irving Medical Center, New York, New York
| | - Cheng-Chia Wu
- Department of Radiation Oncology, Columbia University Irving Medical Center, New York, New York
| | - Robyn D Gartrell
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York; Department of Oncology, Division of Pediatric Oncology, Johns Hopkins School of Medicine, Baltimore, Maryland.
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27
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Jacobo Jacobo M, Donnella HJ, Sobti S, Kaushik S, Goga A, Bandyopadhyay S. An inflamed tumor cell subpopulation promotes chemotherapy resistance in triple negative breast cancer. Sci Rep 2024; 14:3694. [PMID: 38355954 PMCID: PMC10866903 DOI: 10.1038/s41598-024-53999-w] [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: 10/11/2023] [Accepted: 02/07/2024] [Indexed: 02/16/2024] Open
Abstract
Individual cancers are composed of heterogeneous tumor cells with distinct phenotypes and genotypes, with triple negative breast cancers (TNBC) demonstrating the most heterogeneity among breast cancer types. Variability in transcriptional phenotypes could meaningfully limit the efficacy of monotherapies and fuel drug resistance, although to an unknown extent. To determine if transcriptional differences between tumor cells lead to differential drug responses we performed single cell RNA-seq on cell line and PDX models of breast cancer revealing cell subpopulations in states associated with resistance to standard-of-care therapies. We found that TNBC models contained a subpopulation in an inflamed cellular state, often also present in human breast cancer samples. Inflamed cells display evidence of heightened cGAS/STING signaling which we demonstrate is sufficient to cause tumor cell resistance to chemotherapy. Accordingly, inflamed cells were enriched in human tumors taken after neoadjuvant chemotherapy and associated with early recurrence, highlighting the potential for diverse tumor cell states to promote drug resistance.
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Affiliation(s)
- Mauricio Jacobo Jacobo
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Hayley J Donnella
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Sushil Sobti
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Swati Kaushik
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Andrei Goga
- Department of Cell & Tissue Biology, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Sourav Bandyopadhyay
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, 94143, USA.
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28
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Sojka C, Sloan SA. Gliomas: a reflection of temporal gliogenic principles. Commun Biol 2024; 7:156. [PMID: 38321118 PMCID: PMC10847444 DOI: 10.1038/s42003-024-05833-2] [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: 09/11/2023] [Accepted: 01/18/2024] [Indexed: 02/08/2024] Open
Abstract
The hijacking of early developmental programs is a canonical feature of gliomas where neoplastic cells resemble neurodevelopmental lineages and possess mechanisms of stem cell resilience. Given these parallels, uncovering how and when in developmental time gliomagenesis intersects with normal trajectories can greatly inform our understanding of tumor biology. Here, we review how elapsing time impacts the developmental principles of astrocyte (AS) and oligodendrocyte (OL) lineages, and how these same temporal programs are replicated, distorted, or circumvented in pathological settings such as gliomas. Additionally, we discuss how normal gliogenic processes can inform our understanding of the temporal progression of gliomagenesis, including when in developmental time gliomas originate, thrive, and can be pushed towards upon therapeutic coercion.
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Affiliation(s)
- Caitlin Sojka
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Steven A Sloan
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA.
- Emory Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA.
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29
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Duchatel RJ, Jackson ER, Parackal SG, Kiltschewskij D, Findlay IJ, Mannan A, Staudt DE, Thomas BC, Germon ZP, Laternser S, Kearney PS, Jamaluddin MFB, Douglas AM, Beitaki T, McEwen HP, Persson ML, Hocke EA, Jain V, Aksu M, Manning EE, Murray HC, Verrills NM, Sun CX, Daniel P, Vilain RE, Skerrett-Byrne DA, Nixon B, Hua S, de Bock CE, Colino-Sanguino Y, Valdes-Mora F, Tsoli M, Ziegler DS, Cairns MJ, Raabe EH, Vitanza NA, Hulleman E, Phoenix TN, Koschmann C, Alvaro F, Dayas CV, Tinkle CL, Wheeler H, Whittle JR, Eisenstat DD, Firestein R, Mueller S, Valvi S, Hansford JR, Ashley DM, Gregory SG, Kilburn LB, Nazarian J, Cain JE, Dun MD. PI3K/mTOR is a therapeutically targetable genetic dependency in diffuse intrinsic pontine glioma. J Clin Invest 2024; 134:e170329. [PMID: 38319732 PMCID: PMC10940093 DOI: 10.1172/jci170329] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 01/11/2024] [Indexed: 02/08/2024] Open
Abstract
Diffuse midline glioma (DMG), including tumors diagnosed in the brainstem (diffuse intrinsic pontine glioma; DIPG), are uniformly fatal brain tumors that lack effective treatment. Analysis of CRISPR/Cas9 loss-of-function gene deletion screens identified PIK3CA and MTOR as targetable molecular dependencies across patient derived models of DIPG, highlighting the therapeutic potential of the blood-brain barrier-penetrant PI3K/Akt/mTOR inhibitor, paxalisib. At the human-equivalent maximum tolerated dose, mice treated with paxalisib experienced systemic glucose feedback and increased insulin levels commensurate with patients using PI3K inhibitors. To exploit genetic dependence and overcome resistance while maintaining compliance and therapeutic benefit, we combined paxalisib with the antihyperglycemic drug metformin. Metformin restored glucose homeostasis and decreased phosphorylation of the insulin receptor in vivo, a common mechanism of PI3K-inhibitor resistance, extending survival of orthotopic models. DIPG models treated with paxalisib increased calcium-activated PKC signaling. The brain penetrant PKC inhibitor enzastaurin, in combination with paxalisib, synergistically extended the survival of multiple orthotopic patient-derived and immunocompetent syngeneic allograft models; benefits potentiated in combination with metformin and standard-of-care radiotherapy. Therapeutic adaptation was assessed using spatial transcriptomics and ATAC-Seq, identifying changes in myelination and tumor immune microenvironment crosstalk. Collectively, this study has identified what we believe to be a clinically relevant DIPG therapeutic combinational strategy.
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Affiliation(s)
- Ryan J. Duchatel
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
- Paediatric Stream, Mark Hughes Foundation Centre for Brain Cancer Research, College of Health, Medicine, and Wellbeing, Callaghan, New South Wales, Australia
| | - Evangeline R. Jackson
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
- Paediatric Stream, Mark Hughes Foundation Centre for Brain Cancer Research, College of Health, Medicine, and Wellbeing, Callaghan, New South Wales, Australia
| | - Sarah G. Parackal
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Dylan Kiltschewskij
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
- School of Biomedical Science and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
| | - Izac J. Findlay
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
- Paediatric Stream, Mark Hughes Foundation Centre for Brain Cancer Research, College of Health, Medicine, and Wellbeing, Callaghan, New South Wales, Australia
| | - Abdul Mannan
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - Dilana E. Staudt
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
- Paediatric Stream, Mark Hughes Foundation Centre for Brain Cancer Research, College of Health, Medicine, and Wellbeing, Callaghan, New South Wales, Australia
| | - Bryce C. Thomas
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
- Paediatric Stream, Mark Hughes Foundation Centre for Brain Cancer Research, College of Health, Medicine, and Wellbeing, Callaghan, New South Wales, Australia
| | - Zacary P. Germon
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - Sandra Laternser
- DIPG/DMG Research Center Zurich, Children’s Research Center, Department of Pediatrics, University Children’s Hospital Zürich, Zurich, Switzerland
| | - Padraic S. Kearney
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - M. Fairuz B. Jamaluddin
- School of Biomedical Science and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
| | - Alicia M. Douglas
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - Tyrone Beitaki
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - Holly P. McEwen
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - Mika L. Persson
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
- Paediatric Stream, Mark Hughes Foundation Centre for Brain Cancer Research, College of Health, Medicine, and Wellbeing, Callaghan, New South Wales, Australia
| | - Emily A. Hocke
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Vaibhav Jain
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Michael Aksu
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Elizabeth E. Manning
- School of Biomedical Science and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
| | - Heather C. Murray
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
- School of Biomedical Science and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
| | - Nicole M. Verrills
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
- School of Biomedical Science and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
| | - Claire Xin Sun
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Paul Daniel
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Ricardo E. Vilain
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - David A. Skerrett-Byrne
- Infertility and Reproduction Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - Brett Nixon
- Infertility and Reproduction Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - Susan Hua
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
- School of Biomedical Science and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
| | - Charles E. de Bock
- Children’s Cancer Institute, University of New South Wales (UNSW) Sydney, Kensington, New South Wales, Australia
- School of Clinical Medicine, UNSW Medicine and Health, UNSW Sydney, Kensington, New South Wales, Australia
| | - Yolanda Colino-Sanguino
- Children’s Cancer Institute, University of New South Wales (UNSW) Sydney, Kensington, New South Wales, Australia
- School of Clinical Medicine, UNSW Medicine and Health, UNSW Sydney, Kensington, New South Wales, Australia
| | - Fatima Valdes-Mora
- Children’s Cancer Institute, University of New South Wales (UNSW) Sydney, Kensington, New South Wales, Australia
- School of Clinical Medicine, UNSW Medicine and Health, UNSW Sydney, Kensington, New South Wales, Australia
| | - Maria Tsoli
- Children’s Cancer Institute, University of New South Wales (UNSW) Sydney, Kensington, New South Wales, Australia
- School of Clinical Medicine, UNSW Medicine and Health, UNSW Sydney, Kensington, New South Wales, Australia
| | - David S. Ziegler
- Children’s Cancer Institute, University of New South Wales (UNSW) Sydney, Kensington, New South Wales, Australia
- School of Clinical Medicine, UNSW Medicine and Health, UNSW Sydney, Kensington, New South Wales, Australia
- Kids Cancer Centre, Sydney Children’s Hospital, Randwick, New South Wales, Australia
| | - Murray J. Cairns
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
- School of Biomedical Science and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
| | - Eric H. Raabe
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Nicholas A. Vitanza
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, Washington, USA
- Department of Pediatrics, Seattle Children’s Hospital, University of Washington, Seattle, Washington, USA
| | - Esther Hulleman
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Timothy N. Phoenix
- Division of Pharmaceutical Sciences, James L. Winkle College of Pharmacy, University of Cincinnati, Cincinnati, Ohio, USA
| | - Carl Koschmann
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Michigan, Ann Arbor, Michigan, USA
| | - Frank Alvaro
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
- John Hunter Children’s Hospital, New Lambton Heights, New South Wales, Australia
| | - Christopher V. Dayas
- School of Biomedical Science and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
| | - Christopher L. Tinkle
- Department of Radiation Oncology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Helen Wheeler
- Department of Radiation Oncology Northern Sydney Cancer Centre, Royal North Shore Hospital, St Leonards, New South Wales, Australia
- The Brain Cancer group, St Leonards, New South Wales, Australia
- Sydney Medical School, University of Sydney, Sydney, Australia
| | - James R. Whittle
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - David D. Eisenstat
- Children’s Cancer Centre, The Royal Children’s Hospital Melbourne, Parkville, Victoria, Australia
- Neuro-Oncology Laboratory, Murdoch Children’s Research Institute, Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - Ron Firestein
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Sabine Mueller
- DIPG/DMG Research Center Zurich, Children’s Research Center, Department of Pediatrics, University Children’s Hospital Zürich, Zurich, Switzerland
- Department of Neurology, Neurosurgery, and Pediatrics, University of California, San Francisco, California, USA
| | - Santosh Valvi
- Department of Paediatric and Adolescent Oncology/Haematology, Perth Children’s Hospital, Nedlands, Washington, Australia
- Brain Tumour Research Laboratory, Telethon Kids Institute, Nedlands, Washington, Australia
- Division of Paediatrics, University of Western Australia Medical School, Nedlands, Western Australia, Australia
| | - Jordan R. Hansford
- Michael Rice Centre for Hematology and Oncology, Women’s and Children’s Hospital, North Adelaide, South Australia, Australia
- South Australia Health and Medical Research Institute, Adelaide, South Australia, Australia
- South Australian Immunogenomics Cancer Institute, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - David M. Ashley
- The Preston Robert Tisch Brain Tumor Center at Duke, Department of Neurosurgery, Duke University, Durham, North Carolina, USA
| | - Simon G. Gregory
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, North Carolina, USA
- The Preston Robert Tisch Brain Tumor Center at Duke, Department of Neurosurgery, Duke University, Durham, North Carolina, USA
| | - Lindsay B. Kilburn
- Center for Genetic Medicine Research, Children’s National Hospital, Washington, DC, USA
- The George Washington University, School of Medicine and Health Sciences, Washington, DC, USA
| | - Javad Nazarian
- DIPG/DMG Research Center Zurich, Children’s Research Center, Department of Pediatrics, University Children’s Hospital Zürich, Zurich, Switzerland
- Center for Genetic Medicine Research, Children’s National Hospital, Washington, DC, USA
- The George Washington University, School of Medicine and Health Sciences, Washington, DC, USA
| | - Jason E. Cain
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Matthew D. Dun
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
- Paediatric Stream, Mark Hughes Foundation Centre for Brain Cancer Research, College of Health, Medicine, and Wellbeing, Callaghan, New South Wales, Australia
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30
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Ghasemi DR, Okonechnikov K, Rademacher A, Tirier S, Maass KK, Schumacher H, Joshi P, Gold MP, Sundheimer J, Statz B, Rifaioglu AS, Bauer K, Schumacher S, Bortolomeazzi M, Giangaspero F, Ernst KJ, Clifford SC, Saez-Rodriguez J, Jones DTW, Kawauchi D, Fraenkel E, Mallm JP, Rippe K, Korshunov A, Pfister SM, Pajtler KW. Compartments in medulloblastoma with extensive nodularity are connected through differentiation along the granular precursor lineage. Nat Commun 2024; 15:269. [PMID: 38191550 PMCID: PMC10774372 DOI: 10.1038/s41467-023-44117-x] [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: 01/04/2023] [Accepted: 11/30/2023] [Indexed: 01/10/2024] Open
Abstract
Medulloblastomas with extensive nodularity are cerebellar tumors characterized by two distinct compartments and variable disease progression. The mechanisms governing the balance between proliferation and differentiation in MBEN remain poorly understood. Here, we employ a multi-modal single cell transcriptome analysis to dissect this process. In the internodular compartment, we identify proliferating cerebellar granular neuronal precursor-like malignant cells, along with stromal, vascular, and immune cells. In contrast, the nodular compartment comprises postmitotic, neuronally differentiated malignant cells. Both compartments are connected through an intermediate cell stage resembling actively migrating CGNPs. Notably, we also discover astrocytic-like malignant cells, found in proximity to migrating and differentiated cells at the transition zone between the two compartments. Our study sheds light on the spatial tissue organization and its link to the developmental trajectory, resulting in a more benign tumor phenotype. This integrative approach holds promise to explore intercompartmental interactions in other cancers with varying histology.
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Affiliation(s)
- David R Ghasemi
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro-oncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Konstantin Okonechnikov
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro-oncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Anne Rademacher
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Stephan Tirier
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
- Resolve BioSciences GmbH, Monheim am Rhein, Germany
| | - Kendra K Maass
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro-oncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Hanna Schumacher
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
| | - Piyush Joshi
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro-oncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Maxwell P Gold
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Julia Sundheimer
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro-oncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Britta Statz
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro-oncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ahmet S Rifaioglu
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
- Department of Electrical and Electronics Engineering, İskenderun Technical University, Hatay, Turkey
| | - Katharina Bauer
- Single-cell Open Lab, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sabrina Schumacher
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | | | - Felice Giangaspero
- Department of Radiological, Oncological and Anatomo-Pathological Sciences, Sapienza University of Rome, Rome, Italy
- Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Neuromed, Pozzilli, Italy
| | - Kati J Ernst
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Steven C Clifford
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Julio Saez-Rodriguez
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
| | - David T W Jones
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daisuke Kawauchi
- Department of Biochemistry and Cellular Biology, National Center of Neurology and Psychiatry (NCNP), Tokyo, Japan
| | - Ernest Fraenkel
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Edythe Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jan-Philipp Mallm
- Single-cell Open Lab, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Karsten Rippe
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Andrey Korshunov
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany.
| | - Stefan M Pfister
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
- Division of Pediatric Neuro-oncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Department of Pediatric Oncology, Hematology, and Immunology, Heidelberg University Hospital, Heidelberg, Germany.
| | - Kristian W Pajtler
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
- Division of Pediatric Neuro-oncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Department of Pediatric Oncology, Hematology, and Immunology, Heidelberg University Hospital, Heidelberg, Germany.
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31
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Koschmann C, Al-Holou WN, Alonso MM, Anastas J, Bandopadhayay P, Barron T, Becher O, Cartaxo R, Castro MG, Chung C, Clausen M, Dang D, Doherty R, Duchatel R, Dun M, Filbin M, Franson A, Galban S, Garcia Moure M, Garton H, Gowda P, Marques JG, Hawkins C, Heath A, Hulleman E, Ji S, Jones C, Kilburn L, Kline C, Koldobskiy MA, Lim D, Lowenstein PR, Lu QR, Lum J, Mack S, Magge S, Marini B, Martin D, Marupudi N, Messinger D, Mody R, Morgan M, Mota M, Muraszko K, Mueller S, Natarajan SK, Nazarian J, Niculcea M, Nuechterlein N, Okada H, Opipari V, Pai MP, Pal S, Peterson E, Phoenix T, Prensner JR, Pun M, Raju GP, Reitman ZJ, Resnick A, Rogawski D, Saratsis A, Sbergio SG, Souweidane M, Stafford JM, Tzaridis T, Venkataraman S, Vittorio O, Wadden J, Wahl D, Wechsler-Reya RJ, Yadav VN, Zhang X, Zhang Q, Venneti S. A road map for the treatment of pediatric diffuse midline glioma. Cancer Cell 2024; 42:1-5. [PMID: 38039965 PMCID: PMC11067690 DOI: 10.1016/j.ccell.2023.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/04/2023] [Accepted: 11/04/2023] [Indexed: 12/03/2023]
Abstract
Recent clinical trials for H3K27-altered diffuse midline gliomas (DMGs) have shown much promise. We present a consensus roadmap and identify three major barriers: (1) refinement of experimental models to include immune and brain-specific components; (2) collaboration among researchers, clinicians, and industry to integrate patient-derived data through sharing, transparency, and regulatory considerations; and (3) streamlining clinical efforts including biopsy, CNS-drug delivery, endpoint determination, and response monitoring. We highlight the importance of comprehensive collaboration to advance the understanding, diagnostics, and therapeutics for DMGs.
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Affiliation(s)
| | | | | | | | | | - Tara Barron
- Stanford University, Stanford, CA 94305, USA
| | - Oren Becher
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | | | - Chan Chung
- Daegu Gyeongbuk Institute of Science & Technology, Daegu, South Korea
| | | | - Derek Dang
- University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Ryan Duchatel
- University of Newcastle, Callaghan, NSW 2308, Australia
| | - Matthew Dun
- University of Newcastle, Callaghan, NSW 2308, Australia
| | | | | | | | | | - Hugh Garton
- University of Michigan, Ann Arbor, MI 48109, USA
| | | | | | | | - Allison Heath
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | | | - Sunjong Ji
- University of Michigan, Ann Arbor, MI 48109, USA
| | - Chris Jones
- Division of Molecular Pathology, Institute for Cancer Research, London SM2 5NG, UK
| | | | - Cassie Kline
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | | | - Daniel Lim
- University of California, San Francisco, San Francisco, CA 94143, USA
| | | | - Q Richard Lu
- Cincinnati Children's Hospital Medical Center, and University of Cincinnati, Cincinnati, OH 45229, USA
| | - Joanna Lum
- University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Suresh Magge
- University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Donna Martin
- University of Michigan, Ann Arbor, MI 48109, USA
| | | | | | - Rajen Mody
- University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Mateus Mota
- University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Sabine Mueller
- University of California, San Francisco, San Francisco, CA 94143, USA; Parker Institute for Cancer Immunotherapy, University of Zurich, Zurich, Switzerland
| | | | - Javad Nazarian
- Children's National, Washington, DC 20010, USA; University of Zurich, Zurich, Switzerland
| | | | - Nicholas Nuechterlein
- University of Michigan, Ann Arbor, MI 48109, USA; National Institutes of Health, Bethesda, MD, USA
| | - Hideho Okada
- University of California, San Francisco, San Francisco, CA 94143, USA
| | | | | | | | | | - Timothy Phoenix
- Cincinnati Children's Hospital Medical Center, and University of Cincinnati, Cincinnati, OH 45229, USA
| | | | - Matthew Pun
- University of Michigan, Ann Arbor, MI 48109, USA
| | - G Praveen Raju
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Adam Resnick
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | | | | | | | - Mark Souweidane
- Weill Cornell Medicine, New York Presbyterian and Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - James M Stafford
- Weill Cornell Medicine, New York Presbyterian and Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Theophilos Tzaridis
- Herbert Irving Comprehensive Cancer Center and Department of Neurology, Columbia University Medical Center, New York, NY 10032, USA
| | | | - Orazio Vittorio
- School of Biomedical Sciences, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
| | - Jack Wadden
- University of Michigan, Ann Arbor, MI 48109, USA
| | - Daniel Wahl
- University of Michigan, Ann Arbor, MI 48109, USA
| | | | | | - Xu Zhang
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Qiang Zhang
- University of Michigan, Ann Arbor, MI 48109, USA
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32
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Tetens AR, Martin AM, Arnold A, Novak OV, Idrizi A, Tryggvadottir R, Craig-Schwartz J, Liapodimitri A, Lunsford K, Barbato MI, Eberhart CG, Resnick AC, Raabe EH, Koldobskiy MA. DNA methylation landscapes in DIPG reveal methylome variability that can be modified pharmacologically. Neurooncol Adv 2024; 6:vdae023. [PMID: 38468866 PMCID: PMC10926944 DOI: 10.1093/noajnl/vdae023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024] Open
Abstract
Background Diffuse intrinsic pontine glioma (DIPG) is a uniformly lethal brainstem tumor of childhood, driven by histone H3 K27M mutation and resultant epigenetic dysregulation. Epigenomic analyses of DIPG have shown global loss of repressive chromatin marks accompanied by DNA hypomethylation. However, studies providing a static view of the epigenome do not adequately capture the regulatory underpinnings of DIPG cellular heterogeneity and plasticity. Methods To address this, we performed whole-genome bisulfite sequencing on a large panel of primary DIPG specimens and applied a novel framework for analysis of DNA methylation variability, permitting the derivation of comprehensive genome-wide DNA methylation potential energy landscapes that capture intrinsic epigenetic variation. Results We show that DIPG has a markedly disordered epigenome with increasingly stochastic DNA methylation at genes regulating pluripotency and developmental identity, potentially enabling cells to sample diverse transcriptional programs and differentiation states. The DIPG epigenetic landscape was responsive to treatment with the hypomethylating agent decitabine, which produced genome-wide demethylation and reduced the stochasticity of DNA methylation at active enhancers and bivalent promoters. Decitabine treatment elicited changes in gene expression, including upregulation of immune signaling such as the interferon response, STING, and MHC class I expression, and sensitized cells to the effects of histone deacetylase inhibition. Conclusions This study provides a resource for understanding the epigenetic instability that underlies DIPG heterogeneity. It suggests the application of epigenetic therapies to constrain the range of epigenetic states available to DIPG cells, as well as the use of decitabine in priming for immune-based therapies.
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Affiliation(s)
- Ashley R Tetens
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Allison M Martin
- Pediatric Hematology-Oncology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Antje Arnold
- Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Orlandi V Novak
- Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Adrian Idrizi
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Rakel Tryggvadottir
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jordyn Craig-Schwartz
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Athanasia Liapodimitri
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Kayleigh Lunsford
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Michael I Barbato
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Charles G Eberhart
- Neuropathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Adam C Resnick
- Center for Data-Driven Discovery in Biomedicine, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Division of Neurosurgery, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Eric H Raabe
- Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Neuropathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Michael A Koldobskiy
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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33
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Zhang Q, Tsui YM, Zhang VX, Lu AJ, Lee JMF, Lee E, Cheung GCH, Li PM, Cheung ETY, Chia NH, Lo ILO, Chan ACY, Cheung TT, Ng IOL, Ho DWH. Reciprocal interactions between malignant cells and macrophages enhance cancer stemness and M2 polarization in HBV-associated hepatocellular carcinoma. Theranostics 2024; 14:892-910. [PMID: 38169544 PMCID: PMC10758064 DOI: 10.7150/thno.87962] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 12/14/2023] [Indexed: 01/05/2024] Open
Abstract
Background: The tumor microenvironment of cancers has emerged as a crucial component in regulating cancer stemness and plays a pivotal role in cell-cell communication. However, the specific mechanisms underlying these phenomena remain poorly understood. Methods: We performed the single-cell RNA sequencing (scRNA-seq) on nine HBV-associated hepatocellular carcinoma (HCC) patients. The heterogeneity of the malignant cells in pathway functions, transcription factors (TFs) regulation, overall survival, stemness, as well as ligand-receptor-based intercellular communication with macrophages were characterized. The aggressive and stemness feature for the target tumor subclone was validated by the conduction of in vitro assays including sphere formation, proliferation, Annexin V apoptosis, flow cytometry, siRNA library screening assays, and multiple in vivo preclinical mouse models including mouse hepatoma cell and human HCC cell xenograft models with subcutaneous or orthotopic injection. Results: Our analysis yielded a comprehensive atlas of 31,664 cells, revealing a diverse array of malignant cell subpopulations. Notably, we identified a stemness-related subclone of HCC cells with concurrent upregulation of CD24, CD47, and ICAM1 expression that correlated with poorer overall survival. Functional characterization both in vitro and in vivo validated S100A11 as one of the top downstream mediators for tumor initiation and stemness maintenance of this subclone. Further investigation of cell-cell communication within the tumor microenvironment revealed a propensity for bi-directional crosstalk between this stemness-related subclone and tumor-associated macrophages (TAMs). Co-culture study showed that this interaction resulted in the maintenance of the expression of cancer stem cell markers and driving M2-like TAM polarization towards a pro-tumorigenic niche. We also consolidated an inverse relationship between the proportions of TAMs and tumor-infiltrating T cells. Conclusions: Our study highlighted the critical role of stemness-related cancer cell populations in driving an immunosuppressive tumor microenvironment and identified the S100A11 gene as a key mediator for stemness maintenance in HCC. Moreover, our study provides support that the maintenance of cancer stemness is more attributed to M2 polarization than the recruitment of the TAMs.
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Affiliation(s)
- Qingyang Zhang
- Department of Pathology, The University of Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong
| | - Yu-Man Tsui
- Department of Pathology, The University of Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong
| | - Vanilla Xin Zhang
- Department of Pathology, The University of Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong
| | - Anna Jingyi Lu
- Department of Pathology, The University of Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong
| | - Joyce Man-Fong Lee
- Department of Pathology, The University of Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong
| | - Eva Lee
- Department of Pathology, The University of Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong
| | - Gary Cheuk-Hang Cheung
- Department of Pathology, The University of Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong
| | - Po-Man Li
- Department of Pathology, The University of Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong
| | | | - Nam-Hung Chia
- Department of Surgery, Queen Elizabeth Hospital, Hong Kong
| | | | - Albert Chi-Yan Chan
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong
- Department of Surgery, The University of Hong Kong, Hong Kong
| | - Tan-To Cheung
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong
- Department of Surgery, The University of Hong Kong, Hong Kong
| | - Irene Oi-Lin Ng
- Department of Pathology, The University of Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong
| | - Daniel Wai-Hung Ho
- Department of Pathology, The University of Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong
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34
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Yu KKH, Basu S, Baquer G, Ahn R, Gantchev J, Jindal S, Regan MS, Abou-Mrad Z, Prabhu MC, Williams MJ, D'Souza AD, Malinowski SW, Hopland K, Elhanati Y, Stopka SA, Stortchevoi A, He Z, Sun J, Chen Y, Espejo AB, Chow KH, Yerrum S, Kao PL, Kerrigan BP, Norberg L, Nielsen D, Puduvalli VK, Huse J, Beroukhim R, Kim YSB, Goswami S, Boire A, Frisken S, Cima MJ, Holdhoff M, Lucas CHG, Bettegowda C, Levine SS, Bale TA, Brennan C, Reardon DA, Lang FF, Antonio Chiocca E, Ligon KL, White FM, Sharma P, Tabar V, Agar NYR. Investigative needle core biopsies for multi-omics in Glioblastoma. medRxiv 2023:2023.12.29.23300541. [PMID: 38234840 PMCID: PMC10793534 DOI: 10.1101/2023.12.29.23300541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Glioblastoma (GBM) is a primary brain cancer with an abysmal prognosis and few effective therapies. The ability to investigate the tumor microenvironment before and during treatment would greatly enhance both understanding of disease response and progression, as well as the delivery and impact of therapeutics. Stereotactic biopsies are a routine surgical procedure performed primarily for diagnostic histopathologic purposes. The role of investigative biopsies - tissue sampling for the purpose of understanding tumor microenvironmental responses to treatment using integrated multi-modal molecular analyses ('Multi-omics") has yet to be defined. Secondly, it is unknown whether comparatively small tissue samples from brain biopsies can yield sufficient information with such methods. Here we adapt stereotactic needle core biopsy tissue in two separate patients. In the first patient with recurrent GBM we performed highly resolved multi-omics analysis methods including single cell RNA sequencing, spatial-transcriptomics, metabolomics, proteomics, phosphoproteomics, T-cell clonotype analysis, and MHC Class I immunopeptidomics from biopsy tissue that was obtained from a single procedure. In a second patient we analyzed multi-regional core biopsies to decipher spatial and genomic variance. We also investigated the utility of stereotactic biopsies as a method for generating patient derived xenograft models in a separate patient cohort. Dataset integration across modalities showed good correspondence between spatial modalities, highlighted immune cell associated metabolic pathways and revealed poor correlation between RNA expression and the tumor MHC Class I immunopeptidome. In conclusion, stereotactic needle biopsy cores are of sufficient quality to generate multi-omics data, provide data rich insight into a patient's disease process and tumor immune microenvironment and can be of value in evaluating treatment responses. One sentence summary Integrative multi-omics analysis of stereotactic needle core biopsies in glioblastoma.
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35
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Long C, Song Y, Pan Y, Wu C. Identification of molecular subtypes and a risk model based on inflammation-related genes in patients with low grade glioma. Heliyon 2023; 9:e22429. [PMID: 38046156 PMCID: PMC10686866 DOI: 10.1016/j.heliyon.2023.e22429] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 11/07/2023] [Accepted: 11/13/2023] [Indexed: 12/05/2023] Open
Abstract
Lower grade gliomas (LGGs) exhibit invasiveness and heterogeneity as distinguishing features. The outcome of patients with LGG differs greatly. Recently, more and more studies have suggested that infiltrating inflammation cells and inflammation-related genes (IRGs) play an essential role in tumorigenesis, prognosis, and treatment responses. Nevertheless, the role of IRGs in LGG remains unclear. In The Cancer Genome Atlas (TCGA) cohort, we conducted a thorough examination of the predictive significance of IRGs and identified 245 IRGs that correlated with the clinical prognosis of individuals diagnosed with LGG. Based on unsupervised cluster analysis, we identified two inflammation-associated molecular clusters, which presented different tumor immune microenvironments, tumorigenesis scores, and tumor stemness indices. Furthermore, a prognostic risk model including ten prognostic IRGs (ADRB2, CD274, CXCL12, IL12B, NFE2L2, PRF1, SFTPC, TBX21, TNFRSF11B, and TTR) was constructed. The survival analysis indicated that the IRGs risk model independently predicted the prognosis of patients with LGG, which was validated in an independent LGG cohort. Moreover, the risk model significantly correlated with the infiltrative level of immune cells, tumor mutation burden, expression of HLA and immune checkpoint genes, tumorigenesis scores, and tumor stemness indices in LGG. Additionally, we found that our risk model could predict the chemotherapy response of some drugs in patients with LGG. This study may enhance the advancement of personalized therapy and improve outcomes of LGG.
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Affiliation(s)
- Cheng Long
- Department of Orthopedics, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Ya Song
- Department of Orthopedics, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Yimin Pan
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Changwu Wu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China
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36
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Taylor KR, Monje M. Neuron-oligodendroglial interactions in health and malignant disease. Nat Rev Neurosci 2023; 24:733-746. [PMID: 37857838 PMCID: PMC10859969 DOI: 10.1038/s41583-023-00744-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Accepted: 09/14/2023] [Indexed: 10/21/2023]
Abstract
Experience sculpts brain structure and function. Activity-dependent modulation of the myelinated infrastructure of the nervous system has emerged as a dimension of adaptive change during childhood development and in adulthood. Myelination is a richly dynamic process, with neuronal activity regulating oligodendrocyte precursor cell proliferation, oligodendrogenesis and myelin structural changes in some axonal subtypes and in some regions of the nervous system. This myelin plasticity and consequent changes to conduction velocity and circuit dynamics can powerfully influence neurological functions, including learning and memory. Conversely, disruption of the mechanisms mediating adaptive myelination can contribute to cognitive impairment. The robust effects of neuronal activity on normal oligodendroglial precursor cells, a putative cellular origin for many forms of glioma, indicates that dysregulated or 'hijacked' mechanisms of myelin plasticity could similarly promote growth in this devastating group of brain cancers. Indeed, neuronal activity promotes the pathogenesis of many forms of glioma in preclinical models through activity-regulated paracrine factors and direct neuron-to-glioma synapses. This synaptic integration of glioma into neural circuits is central to tumour growth and invasion. Thus, not only do neuron-oligodendroglial interactions modulate neural circuit structure and function in the healthy brain, but neuron-glioma interactions also have important roles in the pathogenesis of glial malignancies.
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Affiliation(s)
- Kathryn R Taylor
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Michelle Monje
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
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37
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Martin BJE, Ablondi EF, Goglia C, Mimoso CA, Espinel-Cabrera PR, Adelman K. Global identification of SWI/SNF targets reveals compensation by EP400. Cell 2023; 186:5290-5307.e26. [PMID: 37922899 DOI: 10.1016/j.cell.2023.10.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 08/11/2023] [Accepted: 10/03/2023] [Indexed: 11/07/2023]
Abstract
Mammalian SWI/SNF chromatin remodeling complexes move and evict nucleosomes at gene promoters and enhancers to modulate DNA access. Although SWI/SNF subunits are commonly mutated in disease, therapeutic options are limited by our inability to predict SWI/SNF gene targets and conflicting studies on functional significance. Here, we leverage a fast-acting inhibitor of SWI/SNF remodeling to elucidate direct targets and effects of SWI/SNF. Blocking SWI/SNF activity causes a rapid and global loss of chromatin accessibility and transcription. Whereas repression persists at most enhancers, we uncover a compensatory role for the EP400/TIP60 remodeler, which reestablishes accessibility at most promoters during prolonged loss of SWI/SNF. Indeed, we observe synthetic lethality between EP400 and SWI/SNF in cancer cell lines and human cancer patient data. Our data define a set of molecular genomic features that accurately predict gene sensitivity to SWI/SNF inhibition in diverse cancer cell lines, thereby improving the therapeutic potential of SWI/SNF inhibitors.
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Affiliation(s)
- Benjamin J E Martin
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Ludwig Center at Harvard, Boston, MA 02115, USA
| | - Eileen F Ablondi
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Christine Goglia
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Claudia A Mimoso
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Piero R Espinel-Cabrera
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Karen Adelman
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Ludwig Center at Harvard, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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Pericoli G, Galardi A, Paolini A, Petrilli LL, Pepe G, Palma A, Colletti M, Ferretti R, Giorda E, Levi Mortera S, Burford A, Carai A, Mastronuzzi A, Mackay A, Putignani L, Jones C, Pascucci L, Peinado H, Helmer-Citterich M, de Billy E, Masotti A, Locatelli F, Di Giannatale A, Vinci M. Inhibition of exosome biogenesis affects cell motility in heterogeneous sub-populations of paediatric-type diffuse high-grade gliomas. Cell Biosci 2023; 13:207. [PMID: 37957701 PMCID: PMC10641969 DOI: 10.1186/s13578-023-01166-5] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 11/05/2023] [Indexed: 11/15/2023] Open
Abstract
BACKGROUND Paediatric-type diffuse High-Grade Gliomas (PDHGG) are highly heterogeneous tumours which include distinct cell sub-populations co-existing within the same tumour mass. We have previously shown that primary patient-derived and optical barcoded single-cell-derived clones function as interconnected networks. Here, we investigated the role of exosomes as a route for inter-clonal communication mediating PDHGG migration and invasion. RESULTS A comprehensive characterisation of seven optical barcoded single-cell-derived clones obtained from two patient-derived cell lines was performed. These analyses highlighted extensive intra-tumour heterogeneity in terms of genetic and transcriptional profiles between clones as well as marked phenotypic differences including distinctive motility patterns. Live single-cell tracking analysis of 3D migration and invasion assays showed that the single-cell-derived clones display a higher speed and longer travelled distance when in co-culture compared to mono-culture conditions. To determine the role of exosomes in PDHGG inter-clonal cross-talks, we isolated exosomes released by different clones and characterised them in terms of marker expression, size and concentration. We demonstrated that exosomes are actively internalized by the cells and that the inhibition of their biogenesis, using the phospholipase inhibitor GW4689, significantly reduced the cell motility in mono-culture and more prominently when the cells from the clones were in co-culture. Analysis of the exosomal miRNAs, performed with a miRNome PCR panel, identified clone-specific miRNAs and a set of miRNA target genes involved in the regulation of cell motility/invasion/migration. These genes were found differentially expressed in co-culture versus mono-culture conditions and their expression levels were significantly modulated upon inhibition of exosome biogenesis. CONCLUSIONS In conclusion, our study highlights for the first time a key role for exosomes in the inter-clonal communication in PDHGG and suggests that interfering with the exosome biogenesis pathway may be a valuable strategy to inhibit cell motility and dissemination for these specific diseases.
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Affiliation(s)
- Giulia Pericoli
- Department of Onco-hematology, Gene and Cell Therapy, Bambino Gesù Children's Hospital-IRCCS, Rome, Italy
| | - Angela Galardi
- Department of Onco-hematology, Gene and Cell Therapy, Bambino Gesù Children's Hospital-IRCCS, Rome, Italy
| | - Alessandro Paolini
- Multifactorial and Complex Phenotype Research Area, Bambino Gesù Children's Hospital-IRCCS, Rome, Italy
| | - Lucia Lisa Petrilli
- Department of Onco-hematology, Gene and Cell Therapy, Bambino Gesù Children's Hospital-IRCCS, Rome, Italy
| | - Gerardo Pepe
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Alessandro Palma
- Department of Onco-hematology, Gene and Cell Therapy, Bambino Gesù Children's Hospital-IRCCS, Rome, Italy
| | - Marta Colletti
- Department of Onco-hematology, Gene and Cell Therapy, Bambino Gesù Children's Hospital-IRCCS, Rome, Italy
| | - Roberta Ferretti
- Department of Onco-hematology, Gene and Cell Therapy, Bambino Gesù Children's Hospital-IRCCS, Rome, Italy
| | - Ezio Giorda
- Core Facilities research laboratories, Bambino Gesù Children's Hospital-IRCCS, Rome, Italy
| | - Stefano Levi Mortera
- Multimodal Laboratory Medicine Research Area, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Anna Burford
- Department of Molecular Pathology, The Institute of Cancer Research, Sutton, UK
| | - Andrea Carai
- Oncological Neurosurgery Unit, Department of Neuroscience and Neurorehabilitation, Bambino Gesù Children's Hospital-IRCCS, Rome, Italy
| | - Angela Mastronuzzi
- Department of Onco-hematology, Gene and Cell Therapy, Bambino Gesù Children's Hospital-IRCCS, Rome, Italy
| | - Alan Mackay
- Department of Molecular Pathology, The Institute of Cancer Research, Sutton, UK
| | - Lorenza Putignani
- Multimodal Laboratory Medicine Research Area, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Chris Jones
- Department of Molecular Pathology, The Institute of Cancer Research, Sutton, UK
| | - Luisa Pascucci
- Department of Veterinary Medicine, University of Perugia, Perugia, Italy
| | - Hector Peinado
- Microenvironment & Metastasis Group, Molecular Oncology Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | | | - Emmanuel de Billy
- Department of Onco-hematology, Gene and Cell Therapy, Bambino Gesù Children's Hospital-IRCCS, Rome, Italy
| | - Andrea Masotti
- Multifactorial and Complex Phenotype Research Area, Bambino Gesù Children's Hospital-IRCCS, Rome, Italy
| | - Franco Locatelli
- Department of Onco-hematology, Gene and Cell Therapy, Bambino Gesù Children's Hospital-IRCCS, Rome, Italy
| | - Angela Di Giannatale
- Department of Onco-hematology, Gene and Cell Therapy, Bambino Gesù Children's Hospital-IRCCS, Rome, Italy
| | - Maria Vinci
- Department of Onco-hematology, Gene and Cell Therapy, Bambino Gesù Children's Hospital-IRCCS, Rome, Italy.
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Taylor KR, Barron T, Hui A, Spitzer A, Yalçin B, Ivec AE, Geraghty AC, Hartmann GG, Arzt M, Gillespie SM, Kim YS, Maleki Jahan S, Zhang H, Shamardani K, Su M, Ni L, Du PP, Woo PJ, Silva-Torres A, Venkatesh HS, Mancusi R, Ponnuswami A, Mulinyawe S, Keough MB, Chau I, Aziz-Bose R, Tirosh I, Suvà ML, Monje M. Glioma synapses recruit mechanisms of adaptive plasticity. Nature 2023; 623:366-374. [PMID: 37914930 PMCID: PMC10632140 DOI: 10.1038/s41586-023-06678-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [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: 11/01/2021] [Accepted: 09/26/2023] [Indexed: 11/03/2023]
Abstract
The role of the nervous system in the regulation of cancer is increasingly appreciated. In gliomas, neuronal activity drives tumour progression through paracrine signalling factors such as neuroligin-3 and brain-derived neurotrophic factor1-3 (BDNF), and also through electrophysiologically functional neuron-to-glioma synapses mediated by AMPA (α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid) receptors4,5. The consequent glioma cell membrane depolarization drives tumour proliferation4,6. In the healthy brain, activity-regulated secretion of BDNF promotes adaptive plasticity of synaptic connectivity7,8 and strength9-15. Here we show that malignant synapses exhibit similar plasticity regulated by BDNF. Signalling through the receptor tropomyosin-related kinase B16 (TrkB) to CAMKII, BDNF promotes AMPA receptor trafficking to the glioma cell membrane, resulting in increased amplitude of glutamate-evoked currents in the malignant cells. Linking plasticity of glioma synaptic strength to tumour growth, graded optogenetic control of glioma membrane potential demonstrates that greater depolarizing current amplitude promotes increased glioma proliferation. This potentiation of malignant synaptic strength shares mechanistic features with synaptic plasticity17-22 that contributes to memory and learning in the healthy brain23-26. BDNF-TrkB signalling also regulates the number of neuron-to-glioma synapses. Abrogation of activity-regulated BDNF secretion from the brain microenvironment or loss of glioma TrkB expression robustly inhibits tumour progression. Blocking TrkB genetically or pharmacologically abrogates these effects of BDNF on glioma synapses and substantially prolongs survival in xenograft models of paediatric glioblastoma and diffuse intrinsic pontine glioma. Together, these findings indicate that BDNF-TrkB signalling promotes malignant synaptic plasticity and augments tumour progression.
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Affiliation(s)
- Kathryn R Taylor
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Tara Barron
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Alexa Hui
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Avishay Spitzer
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Belgin Yalçin
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Alexis E Ivec
- 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
| | - Griffin G Hartmann
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Marlene Arzt
- 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
| | - Yoon Seok Kim
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Samin Maleki Jahan
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Helena Zhang
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Kiarash Shamardani
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Minhui Su
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Lijun Ni
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Peter P Du
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Pamelyn J Woo
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Arianna Silva-Torres
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Humsa S Venkatesh
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Rebecca Mancusi
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Anitha Ponnuswami
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Sara Mulinyawe
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Michael B Keough
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Isabelle Chau
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Razina Aziz-Bose
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Itay Tirosh
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Mario L Suvà
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Boston, MA, USA
| | - Michelle Monje
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA.
- Department of Pediatrics, 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 California, Stanford, CA, USA.
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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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Saqib J, Park B, Jin Y, Seo J, Mo J, Kim J. Identification of Niche-Specific Gene Signatures between Malignant Tumor Microenvironments by Integrating Single Cell and Spatial Transcriptomics Data. Genes (Basel) 2023; 14:2033. [PMID: 38002976 PMCID: PMC10671538 DOI: 10.3390/genes14112033] [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: 10/05/2023] [Revised: 10/29/2023] [Accepted: 10/30/2023] [Indexed: 11/26/2023] Open
Abstract
The tumor microenvironment significantly affects the transcriptomic states of tumor cells. Single-cell RNA sequencing (scRNA-seq) helps elucidate the transcriptomes of individual cancer cells and their neighboring cells. However, cell dissociation results in the loss of information on neighboring cells. To address this challenge and comprehensively assess the gene activity in tissue samples, it is imperative to integrate scRNA-seq with spatial transcriptomics. In our previous study on physically interacting cell sequencing (PIC-seq), we demonstrated that gene expression in single cells is affected by neighboring cell information. In the present study, we proposed a strategy to identify niche-specific gene signatures by harmonizing scRNA-seq and spatial transcriptomic data. This approach was applied to the paired or matched scRNA-seq and Visium platform data of five cancer types: breast cancer, gastrointestinal stromal tumor, liver hepatocellular carcinoma, uterine corpus endometrial carcinoma, and ovarian cancer. We observed distinct gene signatures specific to cellular niches and their neighboring counterparts. Intriguingly, these niche-specific genes display considerable dissimilarity to cell type markers and exhibit unique functional attributes independent of the cancer types. Collectively, these results demonstrate the potential of this integrative approach for identifying novel marker genes and their spatial relationships.
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Affiliation(s)
| | | | | | | | | | - Junil Kim
- School of Systems Biomedical Science, Soongsil University, 369 Sangdo-Ro, Dongjak-Gu, Seoul 06978, Republic of Korea; (J.S.); (Y.J.); (J.M.)
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42
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Xing YL, Panovska D, Petritsch CK. Successes and challenges in modeling heterogeneous BRAF V600E mutated central nervous system neoplasms. Front Oncol 2023; 13:1223199. [PMID: 37920169 PMCID: PMC10619673 DOI: 10.3389/fonc.2023.1223199] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 09/18/2023] [Indexed: 11/04/2023] Open
Abstract
Central nervous system (CNS) neoplasms are difficult to treat due to their sensitive location. Over the past two decades, the availability of patient tumor materials facilitated large scale genomic and epigenomic profiling studies, which have resulted in detailed insights into the molecular underpinnings of CNS tumorigenesis. Based on results from these studies, CNS tumors have high molecular and cellular intra-tumoral and inter-tumoral heterogeneity. CNS cancer models have yet to reflect the broad diversity of CNS tumors and patients and the lack of such faithful cancer models represents a major bottleneck to urgently needed innovations in CNS cancer treatment. Pediatric cancer model development is lagging behind adult tumor model development, which is why we focus this review on CNS tumors mutated for BRAFV600E which are more prevalent in the pediatric patient population. BRAFV600E-mutated CNS tumors exhibit high inter-tumoral heterogeneity, encompassing clinically and histopathological diverse tumor types. Moreover, BRAFV600E is the second most common alteration in pediatric low-grade CNS tumors, and low-grade tumors are notoriously difficult to recapitulate in vitro and in vivo. Although the mutation predominates in low-grade CNS tumors, when combined with other mutations, most commonly CDKN2A deletion, BRAFV600E-mutated CNS tumors are prone to develop high-grade features, and therefore BRAFV600E-mutated CNS are a paradigm for tumor progression. Here, we describe existing in vitro and in vivo models of BRAFV600E-mutated CNS tumors, including patient-derived cell lines, patient-derived xenografts, syngeneic models, and genetically engineered mouse models, along with their advantages and shortcomings. We discuss which research gaps each model might be best suited to answer, and identify those areas in model development that need to be strengthened further. We highlight areas of potential research focus that will lead to the heightened predictive capacity of preclinical studies, allow for appropriate validation, and ultimately improve the success of "bench to bedside" translational research.
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Affiliation(s)
| | | | - Claudia K. Petritsch
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, United States
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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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Sharma M, Barravecchia I, Magnuson B, Ferris SF, Apfelbaum A, Mbah NE, Cruz J, Krishnamoorthy V, Teis R, Kauss M, Koschmann C, Lyssiotis CA, Ljungman M, Galban S. Histone H3 K27M-mediated regulation of cancer cell stemness and differentiation in diffuse midline glioma. Neoplasia 2023; 44:100931. [PMID: 37647805 PMCID: PMC10474232 DOI: 10.1016/j.neo.2023.100931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [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: 02/22/2023] [Revised: 08/22/2023] [Accepted: 08/22/2023] [Indexed: 09/01/2023]
Abstract
Therapeutic resistance remains a major obstacle to preventing progression of H3K27M-altered Diffuse Midline Glioma (DMG). Resistance is driven in part by ALDH-positive cancer stem cells (CSC), with high ALDH1A3 expression observed in H3K27M-mutant DMG biopsies. We hypothesized that ALDH-mediated stemness and resistance may in part be driven by the oncohistone itself. Upon deletion of H3K27M, ALDH1A3 expression decreased dramatically and was accompanied by a gain in astrocytic marker expression and a loss of neurosphere forming potential, indicative of differentiation. Here we show that the oncohistone regulates histone acetylation through ALDH1A3 in a Wnt-dependent manner and that loss of H3K27M expression results in sensitization of DMGs to radiotherapy. The observed elevated Wnt signaling in H3K27M-altered DMG likely stems from a dramatic suppression of mRNA and protein expression of the Wnt inhibitor EYA4 driven by the oncohistone. Thus, our findings identify EYA4 as a bona fide tumor suppressor in DMG that upon suppression, results in aberrant Wnt signaling to orchestrate stemness and differentiation. Future studies will explore whether overexpression of EYA4 in DMG can impede growth and invasion. In summary, we have gained mechanistic insight into H3K27M-mediated regulation of cancer stemness and differentiation, which provides rationale for exploring new therapeutic targets for DMG.
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Affiliation(s)
- Monika Sharma
- Center for Molecular Imaging, The University of Michigan Medical School, Ann Arbor, MI 48109, United States; Department of Radiology, The University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Ivana Barravecchia
- Center for Molecular Imaging, The University of Michigan Medical School, Ann Arbor, MI 48109, United States; Department of Radiology, The University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Brian Magnuson
- Rogel Cancer Center, The University of Michigan Medical School, Ann Arbor, MI 48109, United States; Department of Biostatistics, School of Public Health, The University of Michigan, Ann Arbor, MI 48109, United States
| | - Sarah F Ferris
- Center for Molecular Imaging, The University of Michigan Medical School, Ann Arbor, MI 48109, United States; Department of Radiology, The University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - April Apfelbaum
- Center for Molecular Imaging, The University of Michigan Medical School, Ann Arbor, MI 48109, United States; Department of Radiology, The University of Michigan Medical School, Ann Arbor, MI 48109, United States; Rogel Cancer Center, The University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Nneka E Mbah
- Department of Molecular & Integrative Physiology, The University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Jeanette Cruz
- Center for Molecular Imaging, The University of Michigan Medical School, Ann Arbor, MI 48109, United States; Department of Radiology, The University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Varunkumar Krishnamoorthy
- Center for Molecular Imaging, The University of Michigan Medical School, Ann Arbor, MI 48109, United States; Department of Radiology, The University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Robert Teis
- Center for Molecular Imaging, The University of Michigan Medical School, Ann Arbor, MI 48109, United States; Department of Radiology, The University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - McKenzie Kauss
- Center for Molecular Imaging, The University of Michigan Medical School, Ann Arbor, MI 48109, United States; Department of Radiology, The University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Carl Koschmann
- Department of Pediatrics, The University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Costas A Lyssiotis
- Rogel Cancer Center, The University of Michigan Medical School, Ann Arbor, MI 48109, United States; Department of Molecular & Integrative Physiology, The University of Michigan Medical School, Ann Arbor, MI 48109, United States; Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Mats Ljungman
- Rogel Cancer Center, The University of Michigan Medical School, Ann Arbor, MI 48109, United States; Department of Radiation Oncology, The University of Michigan Medical School, Ann Arbor, MI 48109, United States; Center for RNA Biomedicine, The University of Michigan, Ann Arbor, MI 48109, United States
| | - Stefanie Galban
- Center for Molecular Imaging, The University of Michigan Medical School, Ann Arbor, MI 48109, United States; Department of Radiology, The University of Michigan Medical School, Ann Arbor, MI 48109, United States; Rogel Cancer Center, The University of Michigan Medical School, Ann Arbor, MI 48109, United States.
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45
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Shi Q, Chen X, Zhang Z. Decoding Human Biology and Disease Using Single-cell Omics Technologies. Genomics Proteomics Bioinformatics 2023; 21:926-949. [PMID: 37739168 PMCID: PMC10928380 DOI: 10.1016/j.gpb.2023.06.003] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 05/22/2023] [Accepted: 06/08/2023] [Indexed: 09/24/2023]
Abstract
Over the past decade, advances in single-cell omics (SCO) technologies have enabled the investigation of cellular heterogeneity at an unprecedented resolution and scale, opening a new avenue for understanding human biology and disease. In this review, we summarize the developments of sequencing-based SCO technologies and computational methods, and focus on considerable insights acquired from SCO sequencing studies to understand normal and diseased properties, with a particular emphasis on cancer research. We also discuss the technological improvements of SCO and its possible contribution to fundamental research of the human, as well as its great potential in clinical diagnoses and personalized therapies of human disease.
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Affiliation(s)
- Qiang Shi
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xueyan Chen
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing 100871, China
| | - Zemin Zhang
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; Changping Laboratory, Beijing 102206, China.
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Abstract
Cancer has been a leading cause of death for decades. This dismal statistic has increased efforts to prevent the disease or to detect it early, when treatment is less invasive, relatively inexpensive and more likely to cure. But precisely how tissues are transformed continues to provoke controversy and debate, hindering cancer prevention and early intervention strategies. Various theories of cancer origins have emerged, including the suggestion that it is 'bad luck': the inevitable consequence of random mutations in proliferating stem cells. In this Review, we discuss the principal theories of cancer origins and the relative importance of the factors that underpin them. The body of available evidence suggests that developing and ageing tissues 'walk a tightrope', retaining adequate levels of cell plasticity to generate and maintain tissues while avoiding overstepping into transformation. Rather than viewing cancer as 'bad luck', understanding the complex choreography of cell intrinsic and extrinsic factors that characterize transformation holds promise to discover effective new ways to prevent, detect and stop cancer before it becomes incurable.
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Affiliation(s)
- Amir Jassim
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Eric P Rahrmann
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Ben D Simons
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Cambridge, UK
| | - Richard J Gilbertson
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK.
- Department of Oncology, University of Cambridge, Cambridge, UK.
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47
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Ashouri A, Zhang C, Gaiti F. Decoding Cancer Evolution: Integrating Genetic and Non-Genetic Insights. Genes (Basel) 2023; 14:1856. [PMID: 37895205 PMCID: PMC10606072 DOI: 10.3390/genes14101856] [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: 09/01/2023] [Revised: 09/19/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
The development of cancer begins with cells transitioning from their multicellular nature to a state akin to unicellular organisms. This shift leads to a breakdown in the crucial regulators inherent to multicellularity, resulting in the emergence of diverse cancer cell subpopulations that have enhanced adaptability. The presence of different cell subpopulations within a tumour, known as intratumoural heterogeneity (ITH), poses challenges for cancer treatment. In this review, we delve into the dynamics of the shift from multicellularity to unicellularity during cancer onset and progression. We highlight the role of genetic and non-genetic factors, as well as tumour microenvironment, in promoting ITH and cancer evolution. Additionally, we shed light on the latest advancements in omics technologies that allow for in-depth analysis of tumours at the single-cell level and their spatial organization within the tissue. Obtaining such detailed information is crucial for deepening our understanding of the diverse evolutionary paths of cancer, allowing for the development of effective therapies targeting the key drivers of cancer evolution.
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Affiliation(s)
- Arghavan Ashouri
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada
| | - Chufan Zhang
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Federico Gaiti
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
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48
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Li J, Zhang P, Qu L, Sun T, Duan Y, Wu M, Weng J, Li Z, Gong X, Liu X, Wang Y, Jia W, Su X, Yue Q, Li J, Zhang Z, Barkhof F, Huang RY, Chang K, Sair H, Ye C, Zhang L, Zhuo Z, Liu Y. Deep Learning for Noninvasive Assessment of H3 K27M Mutation Status in Diffuse Midline Gliomas Using MR Imaging. J Magn Reson Imaging 2023; 58:850-861. [PMID: 36692205 DOI: 10.1002/jmri.28606] [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: 10/21/2022] [Revised: 01/05/2023] [Accepted: 01/07/2023] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Determination of H3 K27M mutation in diffuse midline glioma (DMG) is key for prognostic assessment and stratifying patient subgroups for clinical trials. MRI can noninvasively depict morphological and metabolic characteristics of H3 K27M mutant DMG. PURPOSE This study aimed to develop a deep learning (DL) approach to noninvasively predict H3 K27M mutation in DMG using T2-weighted images. STUDY TYPE Retrospective and prospective. POPULATION For diffuse midline brain gliomas, 341 patients from Center-1 (27 ± 19 years, 184 males), 42 patients from Center-2 (33 ± 19 years, 27 males) and 35 patients (37 ± 18 years, 24 males). For diffuse spinal cord gliomas, 133 patients from Center-1 (30 ± 15 years, 80 males). FIELD STRENGTH/SEQUENCE 5T and 3T, T2-weighted turbo spin echo imaging. ASSESSMENT Conventional radiological features were independently reviewed by two neuroradiologists. H3 K27M status was determined by histopathological examination. The Dice coefficient was used to evaluate segmentation performance. Classification performance was evaluated using accuracy, sensitivity, specificity, and area under the curve. STATISTICAL TESTS Pearson's Chi-squared test, Fisher's exact test, two-sample Student's t-test and Mann-Whitney U test. A two-sided P value <0.05 was considered statistically significant. RESULTS In the testing cohort, Dice coefficients of tumor segmentation using DL were 0.87 for diffuse midline brain and 0.81 for spinal cord gliomas. In the internal prospective testing dataset, the predictive accuracies, sensitivities, and specificities of H3 K27M mutation status were 92.1%, 98.2%, 82.9% in diffuse midline brain gliomas and 85.4%, 88.9%, 82.6% in spinal cord gliomas. Furthermore, this study showed that the performance generalizes to external institutions, with predictive accuracies of 85.7%-90.5%, sensitivities of 90.9%-96.0%, and specificities of 82.4%-83.3%. DATA CONCLUSION In this study, an automatic DL framework was developed and validated for accurately predicting H3 K27M mutation using T2-weighted images, which could contribute to the noninvasive determination of H3 K27M status for clinical decision-making. EVIDENCE LEVEL 2 Technical Efficacy: Stage 2.
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Affiliation(s)
- Junjie Li
- Department of Radiology, Beijing Tiantan Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Peng Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Liying Qu
- Department of Radiology, Beijing Tiantan Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Ting Sun
- Department of Radiology, Beijing Tiantan Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Yunyun Duan
- Department of Radiology, Beijing Tiantan Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Minghao Wu
- Department of Radiology, Beijing Tiantan Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Jinyuan Weng
- Department of Medical Imaging Product, Neusoft, Group Ltd., Shenyang, People's Republic of China
| | - Zhaohui Li
- BioMind Inc., Beijing, People's Republic of China
| | - Xiaodong Gong
- Department of Medical Imaging Product, Neusoft, Group Ltd., Shenyang, People's Republic of China
| | - Xing Liu
- Department of Pathology, Beijing Tiantan Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Yongzhi Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Wenqing Jia
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Xiaorui Su
- Department of Radiology, West China Hospital of Sichuan University, Chengdu, People's Republic of China
| | - Qiang Yue
- Department of Radiology, West China Hospital of Sichuan University, Chengdu, People's Republic of China
| | - Jianrui Li
- Department of Diagnostic Radiology, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, People's Republic of China
| | - Zhiqiang Zhang
- Department of Diagnostic Radiology, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, People's Republic of China
| | - Frederik Barkhof
- UCL Institutes of Neurology and Healthcare Engineering, London, UK
- Department of Radiology & Nuclear Medicine, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Raymond Y Huang
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Ken Chang
- Department of Radiology, Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Haris Sair
- Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Chuyang Ye
- School of Information and Electronics, Beijing Institute of Technology, Beijing, People's Republic of China
| | - Liwei Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Zhizheng Zhuo
- Department of Radiology, Beijing Tiantan Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Yaou Liu
- Department of Radiology, Beijing Tiantan Hospital, Capital Medical University, Beijing, People's Republic of China
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49
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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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50
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Zhang Y, Jiang S, He F, Tian Y, Hu H, Gao L, Zhang L, Chen A, Hu Y, Fan L, Yang C, Zhou B, Liu D, Zhou Z, Su Y, Qin L, Wang Y, He H, Lu J, Xiao P, Hu S, Wang QF. Single-cell transcriptomics reveals multiple chemoresistant properties in leukemic stem and progenitor cells in pediatric AML. Genome Biol 2023; 24:199. [PMID: 37653425 PMCID: PMC10472599 DOI: 10.1186/s13059-023-03031-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 08/02/2023] [Indexed: 09/02/2023] Open
Abstract
BACKGROUND Cancer patients can achieve dramatic responses to chemotherapy yet retain resistant tumor cells, which ultimately results in relapse. Although xenograft model studies have identified several cellular and molecular features that are associated with chemoresistance in acute myeloid leukemia (AML), to what extent AML patients exhibit these properties remains largely unknown. RESULTS We apply single-cell RNA sequencing to paired pre- and post-chemotherapy whole bone marrow samples obtained from 13 pediatric AML patients who had achieved disease remission, and distinguish AML clusters from normal cells based on their unique transcriptomic profiles. Approximately 50% of leukemic stem and progenitor populations actively express leukemia stem cell (LSC) and oxidative phosphorylation (OXPHOS) signatures, respectively. These clusters have a higher chance of tolerating therapy and exhibit an enhanced metabolic program in response to treatment. Interestingly, the transmembrane receptor CD69 is highly expressed in chemoresistant hematopoietic stem cell (HSC)-like populations (named the CD69+ HSC-like subpopulation). Furthermore, overexpression of CD69 results in suppression of the mTOR signaling pathway and promotion of cell quiescence and adhesion in vitro. Finally, the presence of CD69+ HSC-like cells is associated with unfavorable genetic mutations, the persistence of residual tumor cells in chemotherapy, and poor outcomes in independent pediatric and adult public AML cohorts. CONCLUSIONS Our analysis reveals leukemia stem cell and OXPHOS as two major chemoresistant features in human AML patients. CD69 may serve as a potential biomarker in defining a subpopulation of chemoresistant leukemia stem cells. These findings have important implications for targeting residual chemo-surviving AML cells.
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Affiliation(s)
- Yongping Zhang
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, 215025, China
| | - Shuting Jiang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fuhong He
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuanyuan Tian
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, 215025, China
| | - Haiyang Hu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li Gao
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, 215025, China
| | - Lin Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Aili Chen
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yixin Hu
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, 215025, China
| | - Liyan Fan
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, 215025, China
| | - Chun Yang
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, 215025, China
| | - Bi Zhou
- SuZhou Hospital of Anhui Medical University, Suzhou, China
| | - Dan Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
| | - Zihan Zhou
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanxun Su
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lei Qin
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yi Wang
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, 215025, China
| | - Hailong He
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, 215025, China
| | - Jun Lu
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, 215025, China
| | - Peifang Xiao
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, 215025, China
| | - Shaoyan Hu
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, 215025, China.
| | - Qian-Fei Wang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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