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Arfuso M, Kuril S, Shah H, Hanson D. Pediatric Neuroglial Tumors: A Review of Ependymoma and Dysembryoplastic Neuroepithelial Tumor. Pediatr Neurol 2024; 156:139-146. [PMID: 38781722 DOI: 10.1016/j.pediatrneurol.2024.04.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/22/2024] [Accepted: 04/24/2024] [Indexed: 05/25/2024]
Affiliation(s)
- Melissa Arfuso
- Joseph M. Sanzari Children's Hospital, Hackensack University Medical Center, Hackensack, New Jersey
| | | | - Harshal Shah
- Hackensack Meridian School of Medicine, Nutley, New Jersey
| | - Derek Hanson
- Joseph M. Sanzari Children's Hospital, Hackensack University Medical Center, Hackensack, New Jersey; Hackensack Meridian School of Medicine, Nutley, New Jersey.
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2
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Amissah HA, Combs SE, Shevtsov M. Tumor Dormancy and Reactivation: The Role of Heat Shock Proteins. Cells 2024; 13:1087. [PMID: 38994941 PMCID: PMC11240553 DOI: 10.3390/cells13131087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 06/19/2024] [Accepted: 06/20/2024] [Indexed: 07/13/2024] Open
Abstract
Tumors are a heterogeneous group of cell masses originating in various organs or tissues. The cellular composition of the tumor cell mass interacts in an intricate manner, influenced by humoral, genetic, molecular, and tumor microenvironment cues that dictate tumor growth or suppression. As a result, tumors undergo a period of a dormant state before their clinically discernible stage, which surpasses the clinical dormancy threshold. Moreover, as a genetically imprinted strategy, early-seeder cells, a distinct population of tumor cells, break off to dock nearby or extravasate into blood vessels to secondary tissues, where they form disseminated solitary dormant tumor cells with reversible capacity. Among the various mechanisms underlying the dormant tumor mass and dormant tumor cell formation, heat shock proteins (HSPs) might play one of the most important roles in how the dormancy program plays out. It is known that numerous aberrant cellular processes, such as malignant transformation, cancer cell stemness, tumor invasion, metastasis, angiogenesis, and signaling pathway maintenance, are influenced by the HSPs. An accumulating body of knowledge suggests that HSPs may be involved in the angiogenic switch, immune editing, and extracellular matrix (ECM) remodeling cascades, crucial genetically imprinted strategies important to the tumor dormancy initiation and dormancy maintenance program. In this review, we highlight the biological events that orchestrate the dormancy state and the body of work that has been conducted on the dynamics of HSPs in a tumor mass, as well as tumor cell dormancy and reactivation. Additionally, we propose a conceptual framework that could possibly underlie dormant tumor reactivation in metastatic relapse.
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Affiliation(s)
- Haneef Ahmed Amissah
- Institute of Life Sciences and Biomedicine, Department of Medical Biology and Medical Biology, FEFU Campus, Far Eastern Federal University, 690922 Vladivostok, Russia
- Diagnostics Laboratory Department, Trauma and Specialist Hospital, CE-122-2486, Central Region, Winneba P.O. Box 326, Ghana
| | - Stephanie E Combs
- Department of Radiation Oncology, Technische Universität München (TUM), Klinikum Rechts der Isar, 81675 Munich, Germany
| | - Maxim Shevtsov
- Department of Radiation Oncology, Technische Universität München (TUM), Klinikum Rechts der Isar, 81675 Munich, Germany
- Laboratory of Biomedical Nanotechnologies, Institute of Cytology of the Russian Academy of Sciences (RAS), 194064 Saint Petersburg, Russia
- Personalized Medicine Centre, Almazov National Medical Research Centre, 197341 Saint Petersburg, Russia
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3
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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] [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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4
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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] [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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5
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Griesinger AM, Calzadilla AJ, Grimaldo E, Donson AM, Amani V, Pierce AM, Steiner J, Kargar S, Serkova NJ, Bertrand KC, Wright KD, Vibhakar R, Hankinson T, Handler M, Lindsay HB, Foreman NK, Dorris K. Development of Chromosome 1q+ Specific Treatment for Highest Risk Pediatric Posterior Fossa Ependymoma. Clin Cancer Res 2024; 30:1544-1554. [PMID: 38334950 PMCID: PMC11018467 DOI: 10.1158/1078-0432.ccr-23-3156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/05/2024] [Accepted: 02/07/2024] [Indexed: 02/10/2024]
Abstract
PURPOSE There are no effective treatment strategies for children with highest-risk posterior fossa group A ependymoma (PFA). Chromosome 1q gains (1q+) are present in approximately 25% of newly diagnosed PFA tumors, and this number doubles at recurrence. Seventy percent of children with chromosome 1q+ PFA will die because of the tumor, highlighting the urgent need to develop new therapeutic strategies for this population. EXPERIMENTAL DESIGN In this study, we utilize 1q+ PFA in vitro and in vivo models to test the efficacy of combination radiation and chemotherapy in a preclinical setting. RESULTS 5-fluorouracil (5FU) enhances radiotherapy in 1q+ PFA cell lines. Specifically, 5FU increases p53 activity mediated by the extra copy of UCK2 located on chromosome 1q in 1q+ PFA. Experimental downregulation of UCK2 resulted in decreased 5FU sensitivity in 1q+ PFA cells. In in vitro studies, a combination of 5FU, retinoid tretinoin (ATRA), and radiation provided the greatest reduction in cellular proliferation and greatest increase in markers of apoptosis in 1q+ PFA cell lines compared with other treatment arms. Similarly, in vivo experiments demonstrated significant enhancement of survival in mice treated with combination radiation and 5FU and ATRA. CONCLUSIONS These results are the first to identify a chromosome 1q+ specific therapy approach in 1q+ PFA. Existing phase I studies have already established single-agent pediatric safety and dosages of 5FU and ATRA, allowing for expedited clinical application as phase II trials for children with high-risk PFA.
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Affiliation(s)
- Andrea M Griesinger
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, Colorado
- Department of Pediatrics, University of Colorado Anscutz Medical Campus, Aurora, Colorado
| | - Annaliese J Calzadilla
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, Colorado
- Department of Pediatrics, University of Colorado Anscutz Medical Campus, Aurora, Colorado
| | - Enrique Grimaldo
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, Colorado
- Department of Pediatrics, University of Colorado Anscutz Medical Campus, Aurora, Colorado
| | - Andrew M Donson
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, Colorado
- Department of Pediatrics, University of Colorado Anscutz Medical Campus, Aurora, Colorado
| | - Vladimir Amani
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, Colorado
- Department of Pediatrics, University of Colorado Anscutz Medical Campus, Aurora, Colorado
| | - Angela M Pierce
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, Colorado
- Department of Pediatrics, University of Colorado Anscutz Medical Campus, Aurora, Colorado
| | - Jenna Steiner
- Department of Radiology, University of Colorado Anschutz Medical Campus and University of Colorado Cancer Center, Aurora, Colorado
| | - Soudabeh Kargar
- Department of Radiology, University of Colorado Anschutz Medical Campus and University of Colorado Cancer Center, Aurora, Colorado
| | - Natalie J Serkova
- Department of Radiology, University of Colorado Anschutz Medical Campus and University of Colorado Cancer Center, Aurora, Colorado
| | - Kelsey C Bertrand
- Department of Pediatric Hematology and Oncology, St Jude Children's Research Hospital, Memphis, Tennessee
| | - Karen D Wright
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
| | - Rajeev Vibhakar
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, Colorado
- Department of Pediatrics, University of Colorado Anscutz Medical Campus, Aurora, Colorado
| | - Todd Hankinson
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, Colorado
- Department of Neurosurgery, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Michael Handler
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, Colorado
- Department of Neurosurgery, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Holly B Lindsay
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, Colorado
- Department of Pediatrics, University of Colorado Anscutz Medical Campus, Aurora, Colorado
| | - Nicholas K Foreman
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, Colorado
- Department of Pediatrics, University of Colorado Anscutz Medical Campus, Aurora, Colorado
| | - Kathleen Dorris
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, Colorado
- Department of Pediatrics, University of Colorado Anscutz Medical Campus, Aurora, Colorado
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Zahedi S, Riemondy K, Griesinger AM, Donson AM, Fu R, Crespo M, DeSisto J, Groat MM, Bratbak E, Green A, Hankinson TC, Handler M, Vibhakar R, Willard N, Foreman NK, Levy JM. Multi-pronged analysis of pediatric low-grade glioma reveals a unique tumor microenvironment associated with BRAF alterations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.05.588294. [PMID: 38645202 PMCID: PMC11030246 DOI: 10.1101/2024.04.05.588294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Pediatric low-grade gliomas (pLGG) comprise 35% of all brain tumors. Despite favorable survival, patients experience significant morbidity from disease and treatments. A deeper understanding of pLGG biology is essential to identify novel, more effective, and less toxic therapies. We utilized single cell RNA sequencing (scRNA-seq), spatial transcriptomics, and cytokine analyses to characterize and understand tumor and immune cell heterogeneity across pLGG. scRNA-seq revealed tumor and immune cells within the tumor microenvironment (TME). Tumor cell subsets revealed a developmental hierarchy with progenitor and mature cell populations. Immune cells included myeloid and lymphocytic cells. There was a significant difference between the prevalence of two major myeloid subclusters between pilocytic astrocytoma (PA) and ganglioglioma (GG). Bulk and single-cell cytokine analyses evaluated the immune cell signaling cascade with distinct immune phenotypes among tumor samples. KIAA1549-BRAF tumors appeared more immunogenic, secreting higher levels of immune cell activators and chemokines, compared to BRAF V600E tumors. Spatial transcriptomics revealed the differential gene expression of these chemokines and their location within the TME. A multi-pronged analysis of pLGG demonstrated the complexity of the pLGG TME and differences between genetic drivers that may influence their response to immunotherapy. Further investigation of immune cell infiltration and tumor-immune interactions is warranted. Key points There is a developmental hierarchy in neoplastic population comprising of both progenitor-like and mature cell types in both PA and GG.A more immunogenic, immune activating myeloid population is present in PA compared to GG. Functional analysis and spatial transcriptomics show higher levels of immune mobilizing chemokines in KIAA1549-BRAF fusion PA tumor samples compared to BRAF V600E GG samples. Importance of the Study While scRNA seq provides information on cellular heterogeneity within the tumor microenvironment (TME), it does not provide a complete picture of how these cells are interacting or where they are located. To expand on this, we used a three-pronged approach to better understand the biology of pediatric low-grade glioma (pLGG). By analyzing scRNA-seq, secreted cytokines and spatial orientation of cells within the TME, we strove to gain a more complete picture of the complex interplay between tumor and immune cells within pLGG. Our data revealed a complex heterogeneity in tumor and immune populations and identified an interesting difference in the immune phenotype among different subtypes.
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Zhao S, Li Y, Xu J, Shen L. APOBEC3C is a novel target for the immune treatment of lower-grade gliomas. Neurol Res 2024; 46:227-242. [PMID: 38007705 DOI: 10.1080/01616412.2023.2287340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 11/21/2023] [Indexed: 11/28/2023]
Abstract
BACKGROUND Apolipoprotein B mRNA editing catalytic polypeptide-like (APOBEC) type 3C (A3C) has been identified as a cancer molecular biomarker in the past decade. However, the practical role of A3C in lower-grade gliomas (LGGs) in improving the clinical outcome remains unclear. This study aims to discuss the function of A3C in immunotherapy in LGGs. METHODS The RNA-Sequencing (RNA-seq) and corresponding clinical data were extracted from UCSC Xena and the results were verified in the Chinese Glioma Genome Atlas (CGGA). Weighted gene co-expression network analysis (WGCNA) was used for screening A3C-related genes. Comprehensive bioinformation analyses were performed and multiple levels of expression, survival rate, and biological functions were assessed to explore the functions of A3C. RESULTS A3C expression was significantly higher in LGGs than in normal tissues but lower than in glioblastoma (GBM), indicating its role as an independent prognosis predictor for LGGs. Twenty-eight A3C-related genes were found with WGCNA for unsupervised clustering analysis and three modification patterns with different outcomes and immune cell infiltration were identified. A3C and the A3C score were also correlated with immune cell infiltration and the expression of immune checkpoints. In addition, the A3C score was correlated with increased sensitivity to chemotherapy. Single-cell RNA (scRNA) analysis indicated that A3C most probably expresses on immune cells, such as T cells, B cells and macrophage. CONCLUSIONS A3C is an immune-related prognostic biomarker in LGGs. Developing drugs to block A3C could enhance the efficiency of immunotherapy and improve disease survival.Abbreviation: A3C: Apolipoprotein B mRNA editing catalytic polypeptide-like (APOBEC) type 3C; LGGs: lower-grade gliomas; CGGA: Chinese Glioma Genome Atlas; WGCNA: Weighted gene co-expression network analysis; scRNA: Single-cell RNA; HGG: higher-grade glioma; OS: overall survival; TME: tumor microenvironment; KM: Kaplan-Meier; PFI: progression-free interval; IDH: isocitrate dehydrogenase; ROC: receiver operating characteristic; GS: gene significance; MM: module membership; TIMER: Tumor IMmune Estimation Resource; GSVA: gene set variation analysis; ssGSEA: single-sample gene-set enrichment analysis; PCA: principal component analysis; AUC: area under ROC curve; HAVCR2: hepatitis A virus cellular receptor 2; PDCD1: programmed cell death 1; PDCD1LG2: PDCD1 ligand 2; PTPRC: protein tyrosine phosphatase receptor type C; ACC: Adrenocortical carcinoma; BLCA: Bladder Urothelial Carcinoma;BRCA: Breast invasive carcinoma; CESC: Cervical squamous cell carcinoma and endocervical adenocarcinoma; CHOLCholangiocarcinoma; COADColon adenocarcinoma; DLBC: Lymphoid Neoplasm Diffuse Large B-cell Lymphoma; ESCA: Esophageal carcinoma; GBM: Glioblastoma multiforme; HNSC: Head and Neck squamous cell carcinoma; KICH: Kidney Chromophobe; KIRC: Kidney renal clear cell carcinoma; KIRP: Kidney renal papillary cell carcinoma; LAML: Acute Myeloid Leukemia; LGG: Brain Lower Grade Glioma; LIHC: Liver hepatocellular carcinoma; LUAD: Lung adenocarcinoma; LUSC: Lung squamous cell carcinoma; MESO: Mesothelioma; OV: Ovarian serous cystadenocarcinoma; PAAD: Pancreatic adenocarcinoma; PCPG: Pheochromocytoma and Paraganglioma; PRAD: Prostate adenocarcinoma; READ: Rectum adenocarcinoma; SARC: Sarcoma; SKCM: Skin Cutaneous Melanoma; STAD: Stomach adenocarcinoma; TGCT: Testicular Germ Cell Tumors; THCA: Thyroid carcinoma; THYM: Thymoma; UCEC: Uterine Corpus Endometrial Carcinoma; UCS: Uterine Carcinosarcoma; UVM: Uveal Melanoma.
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Affiliation(s)
- Shufa Zhao
- Department of Neurosurgery, Huzhou Cent Hospital, Affiliated Cent Hospital Huzhou University, Huzhou, Zhejiang, China
| | - Yuntao Li
- Department of Neurosurgery, Huzhou Cent Hospital, Affiliated Cent Hospital Huzhou University, Huzhou, Zhejiang, China
| | - Jie Xu
- Department of Neurosurgery, Huzhou Cent Hospital, Affiliated Cent Hospital Huzhou University, Huzhou, Zhejiang, China
| | - Liang Shen
- Department of Neurosurgery, The affiliated Changzhou Second People's Hospital of Nanjing Medical University, Changzhou, Jiangsu, China
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Gödicke S, Kresbach C, Ehlert M, Obrecht D, Altendorf L, Hack K, von Hoff K, Carén H, Melcher V, Kerl K, Englinger B, Filbin M, Pajtler KW, Gojo J, Pietsch T, Rutkowski S, Schüller U. Clinically relevant molecular hallmarks of PFA ependymomas display intratumoral heterogeneity and correlate with tumor morphology. Acta Neuropathol 2024; 147:23. [PMID: 38265527 PMCID: PMC10808473 DOI: 10.1007/s00401-023-02682-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 12/05/2023] [Accepted: 12/30/2023] [Indexed: 01/25/2024]
Abstract
Posterior fossa type A (PF-EPN-A, PFA) ependymoma are aggressive tumors that mainly affect children and have a poor prognosis. Histopathology shows significant intratumoral heterogeneity, ranging from loose tissue to often sharply demarcated, extremely cell-dense tumor areas. To determine molecular differences in morphologically different areas and to understand their clinical significance, we analyzed 113 PF-EPN-A samples, including 40 corresponding relapse samples. Cell-dense areas ranged from 0 to 100% of the tumor area and displayed a higher proportion of proliferating tumor cells (p < 0.01). Clinically, cell density was associated with poor progression-free and overall survival (pPFS = 0.0026, pOS < 0.01). Molecularly, tumor areas with low and high cell density showed diverging DNA methylation profiles regarding their similarity to distinct previously discovered PF-EPN-A subtypes in 9/21 cases. Prognostically relevant chromosomal changes at 1q and 6q showed spatial heterogeneity within single tumors and were significantly enriched in cell-dense tumor areas as shown by single-cell RNA (scRNA)-sequencing as well as copy number profiling and fluorescence in situ hybridization (FISH) analyses of different tumor areas. Finally, spatial transcriptomics revealed cell-dense areas of different tumors to be more similar than various different areas of the same tumor. High-density areas distinctly overexpressed genes encoding histone proteins, WNT5A, TGFB1, or IGF2. Relapsing tumors displayed a higher proportion of cell-dense areas (p = 0.036), a change in PF-EPN-A methylation subtypes (13/32 patients), and novel chromosome 1q gains and 6q losses (12/32 cases) compared to corresponding primary tumors. Our data suggest that PF-EPN-A ependymomas habor a previously unrecognized intratumoral heterogeneity with clinical implications, which has to be accounted for when selecting diagnostic material, inter alia, by histological evaluation of the proportion of cell-dense areas.
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Affiliation(s)
- Swenja Gödicke
- Department of Pediatric Hematolgoy and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center, Hamburg-Eppendorf, Hamburg, Germany
| | - Catena Kresbach
- Department of Pediatric Hematolgoy and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center, Hamburg-Eppendorf, Hamburg, Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
| | - Max Ehlert
- Department of Pediatric Hematolgoy and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center, Hamburg-Eppendorf, Hamburg, Germany
| | - Denise Obrecht
- Department of Pediatric Hematolgoy and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Lea Altendorf
- Department of Pediatric Hematolgoy and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center, Hamburg-Eppendorf, Hamburg, Germany
| | - Karoline Hack
- Department of Pediatric Hematolgoy and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center, Hamburg-Eppendorf, Hamburg, Germany
| | - Katja von Hoff
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, Berlin Institute of Health, Berlin, Germany
- Department of Pediatrics and Adolescent Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Helena Carén
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Center for Cancer Research, Sahlgrenska Academy, University of Gothenburg, Göteborg, Sweden
| | - Viktoria Melcher
- Department of Pediatric Hematology and Oncology, University Children's Hospital Münster, 48149, Münster, Germany
| | - Kornelius Kerl
- Department of Pediatric Hematology and Oncology, University Children's Hospital Münster, 48149, Münster, Germany
| | - Bernhard Englinger
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Department of Urology, Comprehensive Cancer Center, Medical University of Vienna, 1090, Vienna, Austria
- Center for Cancer Research and Comprehensive Cancer Center, Medical University Vienna, 1090, Vienna, Austria
| | - Mariella Filbin
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Kristian W Pajtler
- Hopp Children's Cancer Center Heidelberg (KiTZ), 69120, Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120, Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, 69120, Heidelberg, Germany
| | - Johannes Gojo
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics and Comprehensive Cancer Center, Medical University of Vienna, 1090, Vienna, Austria
| | - Torsten Pietsch
- Institute of Neuropathology, DGNN Brain Tumor Reference Center, University of Bonn Medical Center, Bonn, Germany
| | - Stefan Rutkowski
- Department of Pediatric Hematolgoy and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ulrich Schüller
- Department of Pediatric Hematolgoy and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
- Research Institute Children's Cancer Center, Hamburg-Eppendorf, Hamburg, Germany.
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany.
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9
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Lago C, Federico A, Leva G, Mack NL, Schwalm B, Ballabio C, Gianesello M, Abballe L, Giovannoni I, Reddel S, Rossi S, Leone N, Carai A, Mastronuzzi A, Bisio A, Soldano A, Quintarelli C, Locatelli F, Kool M, Miele E, Tiberi L. Patient- and xenograft-derived organoids recapitulate pediatric brain tumor features and patient treatments. EMBO Mol Med 2023; 15:e18199. [PMID: 38037472 DOI: 10.15252/emmm.202318199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 10/19/2023] [Accepted: 10/24/2023] [Indexed: 12/02/2023] Open
Abstract
Brain tumors are the leading cause of cancer-related death in children. Experimental in vitro models that faithfully capture the hallmarks and tumor heterogeneity of pediatric brain cancers are limited and hard to establish. We present a protocol that enables efficient generation, expansion, and biobanking of pediatric brain cancer organoids. Utilizing our protocol, we have established patient-derived organoids (PDOs) from ependymomas, medulloblastomas, low-grade glial tumors, and patient-derived xenograft organoids (PDXOs) from medulloblastoma xenografts. PDOs and PDXOs recapitulate histological features, DNA methylation profiles, and intratumor heterogeneity of the tumors from which they were derived. We also showed that PDOs can be xenografted. Most interestingly, when subjected to the same routinely applied therapeutic regimens, PDOs respond similarly to the patients. Taken together, our study highlights the potential of PDOs and PDXOs for research and translational applications for personalized medicine.
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Affiliation(s)
- Chiara Lago
- Armenise-Harvard Laboratory of Brain Disorders and Cancer, CIBIO, Trento, Italy
| | - Aniello Federico
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Paediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Gloria Leva
- Armenise-Harvard Laboratory of Brain Disorders and Cancer, CIBIO, Trento, Italy
| | - Norman L Mack
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Paediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Benjamin Schwalm
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Paediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Claudio Ballabio
- Armenise-Harvard Laboratory of Brain Disorders and Cancer, CIBIO, Trento, Italy
| | - Matteo Gianesello
- Armenise-Harvard Laboratory of Brain Disorders and Cancer, CIBIO, Trento, Italy
| | - Luana Abballe
- Department of Onco-Hematology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, Scientific Institute for Research, Hospitalization and Healthcare (IRCCS), Rome, Italy
| | | | - Sofia Reddel
- Department of Onco-Hematology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, Scientific Institute for Research, Hospitalization and Healthcare (IRCCS), Rome, Italy
| | - Sabrina Rossi
- Pathology Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Nicolas Leone
- Pathology Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Andrea Carai
- Neurosurgery Unit, Department of Neurosciences, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Angela Mastronuzzi
- Department of Onco-Hematology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, Scientific Institute for Research, Hospitalization and Healthcare (IRCCS), Rome, Italy
| | - Alessandra Bisio
- Laboratory of Radiobiology, CIBIO, Trento, Italy
- Trento Institute for Fundamental Physics and Application, TIFPA, Trento, Italy
| | - Alessia Soldano
- Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
| | - Concetta Quintarelli
- Department of Onco-Hematology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, Scientific Institute for Research, Hospitalization and Healthcare (IRCCS), Rome, Italy
| | - Franco Locatelli
- Department of Onco-Hematology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, Scientific Institute for Research, Hospitalization and Healthcare (IRCCS), Rome, Italy
- Catholic University of the Sacred Heart, Rome, Italy
| | - Marcel Kool
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Paediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Evelina Miele
- Department of Onco-Hematology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, Scientific Institute for Research, Hospitalization and Healthcare (IRCCS), Rome, Italy
| | - Luca Tiberi
- Armenise-Harvard Laboratory of Brain Disorders and Cancer, CIBIO, Trento, Italy
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10
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Donson AM, Bertrand KC, Riemondy KA, Gao D, Zhuang Y, Sanford B, Norris GA, Chapman RJ, Fu R, Willard N, Griesinger AM, Ribeiro de Sousa G, Amani V, Grimaldo E, Hankinson TC, Booker F, Sill M, Grundy RG, Pajtler KW, Ellison DW, Foreman NK, Ritzmann TA. Significant increase of high-risk chromosome 1q gain and 6q loss at recurrence in posterior fossa group A ependymoma: A multicenter study. Neuro Oncol 2023; 25:1854-1867. [PMID: 37246777 PMCID: PMC10547517 DOI: 10.1093/neuonc/noad096] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Indexed: 05/30/2023] Open
Abstract
BACKGROUND Ependymoma (EPN) posterior fossa group A (PFA) has the highest rate of recurrence and the worst prognosis of all EPN molecular groups. At relapse, it is typically incurable even with re-resection and re-irradiation. The biology of recurrent PFA remains largely unknown; however, the increasing use of surgery at first recurrence has now provided access to clinical samples to facilitate a better understanding of this. METHODS In this large longitudinal international multicenter study, we examined matched samples of primary and recurrent disease from PFA patients to investigate the biology of recurrence. RESULTS DNA methylome derived copy number variants (CNVs) revealed large-scale chromosome gains and losses at recurrence in PFA. CNV changes were dominated by chromosome 1q gain and/or 6q loss, both previously identified as high-risk factors in PFA, which were present in 23% at presentation but increased to 61% at first recurrence. Multivariate survival analyses of this cohort showed that cases with 1q gain or 6q loss at first recurrence were significantly more likely to recur again. Predisposition to 1q+/6q- CNV changes at recurrence correlated with hypomethylation of heterochromatin-associated DNA at presentation. Cellular and molecular analyses revealed that 1q+/6q- PFA had significantly higher proportions of proliferative neuroepithelial undifferentiated progenitors and decreased differentiated neoplastic subpopulations. CONCLUSIONS This study provides clinically and preclinically actionable insights into the biology of PFA recurrence. The hypomethylation predisposition signature in PFA is a potential risk-classifier for trial stratification. We show that the cellular heterogeneity of PFAs evolves largely because of genetic evolution of neoplastic cells.
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Affiliation(s)
- Andrew M Donson
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, Colorado, USA
| | | | - Kent A Riemondy
- RNA Biosciences Initiative, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Dexiang Gao
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- University of Colorado Cancer Center Biostatistics and Bioinformatics Shared Resource, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Yonghua Zhuang
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- University of Colorado Cancer Center Biostatistics and Bioinformatics Shared Resource, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Bridget Sanford
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Gregory A Norris
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Rebecca J Chapman
- Children’s Brain Tumor Research Centre, University of Nottingham, Nottingham, UK
| | - Rui Fu
- Computational Biology, New York Genome Center, New York, New York, USA
| | - Nicholas Willard
- Department of Pathology, University of Colorado Denver, Aurora, Colorado, USA
| | - Andrea M Griesinger
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Graziella Ribeiro de Sousa
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Vladimir Amani
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Enrique Grimaldo
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Todd C Hankinson
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, Colorado, USA
- Department of Neurosurgery, University of Colorado Denver, Aurora, Colorado, USA
| | - Ffyona Booker
- Children’s Brain Tumor Research Centre, University of Nottingham, Nottingham, UK
| | - Martin Sill
- Hopp-Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Richard G Grundy
- Children’s Brain Tumor Research Centre, University of Nottingham, Nottingham, UK
| | - Kristian W Pajtler
- Hopp-Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Nicholas K Foreman
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Timothy A Ritzmann
- Children’s Brain Tumor Research Centre, University of Nottingham, Nottingham, UK
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11
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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: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [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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12
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Amani V, Riemondy KA, Fu R, Griesinger AM, Grimaldo E, De Sousa GR, Gilani A, Hemenway M, Foreman NK, Donson AM, Willard N. Integration of single-nuclei RNA-sequencing, spatial transcriptomics and histochemistry defines the complex microenvironment of NF1-associated plexiform neurofibromas. Acta Neuropathol Commun 2023; 11:158. [PMID: 37770931 PMCID: PMC10537467 DOI: 10.1186/s40478-023-01639-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/17/2023] [Indexed: 09/30/2023] Open
Abstract
Plexiform neurofibroma (PN) is a leading cause of morbidity in children with the genetic condition Neurofibromatosis Type 1 (NF1), often disfiguring or threatening vital structures. During formation of PN, a complex tumor microenvironment (TME) develops, with recruitment of neoplastic and non-neoplastic cell types being critical for growth and progression. Due to the cohesive cellularity of PN, single-cell RNA-sequencing is difficult and may result in a loss of detection of critical cellular subpopulations. To bypass this barrier, we performed single-nuclei RNA-sequencing (snRNA-seq) on 8 frozen PN samples, and integrated this with spatial transcriptomics (ST) in 4 PN samples and immunohistochemistry to provide morphological context to transcriptomic data. SnRNA-seq analysis definitively charted the heterogeneous cellular subpopulations in the PN TME, with the predominant fraction being fibroblast subtypes. PN showed a remarkable amount of inter-sample homogeneity regarding cellular subpopulation proportions despite being resected from a variety of anatomical locations. ST analysis identified distinct cellular subpopulations which were annotated using snRNA-seq data and correlated with histological features. Schwann cell/fibroblast interactions were identified by receptor/ligand interaction analysis demonstrating a high probability of Neurexin 1/Neuroligin 1 (NRXN1/NLGN1) receptor-ligand cross-talk predicted between fibroblasts and non-myelinated Schwann cells (NM-SC) and subtypes, respectively. We observed aberrant expression of NRXN1 and NLGN1 in our PN snRNA-seq data compared to a normal mouse sciatic nerve single-cell RNA-seq dataset. This pathway has never been described in PN and may indicate a clear and direct communication pathway between putative NM-SC cells of origin and surrounding fibroblasts, potentially driving disease progression. SnRNA-seq integrated with spatial transcriptomics advances our understanding of the complex cellular heterogeneity of PN TME and identify potential novel communication pathways that may drive disease progression, a finding that could provide translational therapy options for patients with these devastating tumors of childhood and early adulthood.
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Affiliation(s)
- Vladimir Amani
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, USA.
| | - Kent A Riemondy
- RNA Biosciences Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Rui Fu
- Computational Biology, New York Genome Center, New York, NY, USA
| | - Andrea M Griesinger
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, USA
| | - Enrique Grimaldo
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, USA
| | - Graziella Ribeiro De Sousa
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, USA
| | - Ahmed Gilani
- Department of Pathology, University of Colorado Denver, Aurora, CO, USA
| | - Molly Hemenway
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, USA
| | - Nicholas K Foreman
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, USA
| | - Andrew M Donson
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, USA
| | - Nicholas Willard
- Department of Pathology, University of Colorado Denver, Aurora, CO, USA
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13
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Griesinger AM, Riemondy K, Eswaran N, Donson AM, Willard N, Prince EW, Paine SM, Bowes G, Rheaume J, Chapman RJ, Ramage J, Jackson A, Grundy RG, Foreman NK, Ritzmann TA. Multi-omic approach identifies hypoxic tumor-associated myeloid cells that drive immunobiology of high-risk pediatric ependymoma. iScience 2023; 26:107585. [PMID: 37694144 PMCID: PMC10484966 DOI: 10.1016/j.isci.2023.107585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 05/01/2023] [Accepted: 08/04/2023] [Indexed: 09/12/2023] Open
Abstract
Ependymoma (EPN) is a devastating childhood brain tumor. Single-cell analyses have illustrated the cellular heterogeneity of EPN tumors, identifying multiple neoplastic cell states including a mesenchymal-differentiated subpopulation which characterizes the PFA1 subtype. Here, we characterize the EPN immune environment, in the context of both tumor subtypes and tumor cell subpopulations using single-cell sequencing (scRNAseq, n = 27), deconvolution of bulk tumor gene expression (n = 299), spatial proteomics (n = 54), and single-cell cytokine release assays (n = 12). We identify eight distinct myeloid-derived subpopulations from which a group of cells, termed hypoxia myeloid cells, demonstrate features of myeloid-derived suppressor cells, including IL6/STAT3 pathway activation and wound healing ontologies. In PFA tumors, hypoxia myeloid cells colocalize with mesenchymal-differentiated cells in necrotic and perivascular niches and secrete IL-8, which we hypothesize amplifies the EPN immunosuppressive microenvironment. This myeloid cell-driven immunosuppression will need to be targeted for immunotherapy to be effective in this difficult-to-cure childhood brain tumor.
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Affiliation(s)
- Andrea M. Griesinger
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, CO 80045, USA
- Department of Pediatrics, University of Colorado Denver, Aurora, CO 80045, USA
- Colorado Clinical and Translational Sciences Institute, University of Colorado Denver, Aurora, CO 80045, USA
| | - Kent Riemondy
- RNA Bioscience Initiative, University of Colorado Denver, Aurora, CO 80045, USA
| | - Nithyashri Eswaran
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, CO 80045, USA
- Department of Pediatrics, University of Colorado Denver, Aurora, CO 80045, USA
| | - Andrew M. Donson
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, CO 80045, USA
- Department of Pediatrics, University of Colorado Denver, Aurora, CO 80045, USA
| | - Nicholas Willard
- Department of Pathology, University of Colorado Denver, Aurora, CO 80045, USA
| | - Eric W. Prince
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, CO 80045, USA
- Department of Neurosurgery, University of Colorado Denver, Aurora, CO 80045, USA
| | - Simon M.L. Paine
- Children’s Brain Tumour Research Centre, University of Nottingham Biodiscovery Institute, Nottingham, UK
- Nottingham University Hospitals NHS Trust, Queen’s Medical Centre, Derby Road, Nottingham NG7 2UH, UK
| | - Georgia Bowes
- Children’s Brain Tumour Research Centre, University of Nottingham Biodiscovery Institute, Nottingham, UK
| | | | - Rebecca J. Chapman
- Children’s Brain Tumour Research Centre, University of Nottingham Biodiscovery Institute, Nottingham, UK
- University of Nottingham Biodiscovery Institute, Nottingham, UK
| | - Judith Ramage
- University of Nottingham Biodiscovery Institute, Nottingham, UK
| | - Andrew Jackson
- University of Nottingham Biodiscovery Institute, Nottingham, UK
| | - Richard G. Grundy
- Children’s Brain Tumour Research Centre, University of Nottingham Biodiscovery Institute, Nottingham, UK
- Nottingham University Hospitals NHS Trust, Queen’s Medical Centre, Derby Road, Nottingham NG7 2UH, UK
| | - Nicholas K. Foreman
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, CO 80045, USA
- Department of Pediatrics, University of Colorado Denver, Aurora, CO 80045, USA
- Colorado Clinical and Translational Sciences Institute, University of Colorado Denver, Aurora, CO 80045, USA
- Department of Neurosurgery, University of Colorado Denver, Aurora, CO 80045, USA
| | - Timothy A. Ritzmann
- Children’s Brain Tumour Research Centre, University of Nottingham Biodiscovery Institute, Nottingham, UK
- Nottingham University Hospitals NHS Trust, Queen’s Medical Centre, Derby Road, Nottingham NG7 2UH, UK
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14
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Nabbi A, Beck P, Delaidelli A, Oldridge DA, Sudhaman S, Zhu K, Yang SYC, Mulder DT, Bruce JP, Paulson JN, Raman P, Zhu Y, Resnick AC, Sorensen PH, Sill M, Brabetz S, Lambo S, Malkin D, Johann PD, Kool M, Jones DTW, Pfister SM, Jäger N, Pugh TJ. Transcriptional immunogenomic analysis reveals distinct immunological clusters in paediatric nervous system tumours. Genome Med 2023; 15:67. [PMID: 37679810 PMCID: PMC10486055 DOI: 10.1186/s13073-023-01219-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 08/07/2023] [Indexed: 09/09/2023] Open
Abstract
BACKGROUND Cancer immunotherapies including immune checkpoint inhibitors and Chimeric Antigen Receptor (CAR) T-cell therapy have shown variable response rates in paediatric patients highlighting the need to establish robust biomarkers for patient selection. While the tumour microenvironment in adults has been widely studied to delineate determinants of immune response, the immune composition of paediatric solid tumours remains relatively uncharacterized calling for investigations to identify potential immune biomarkers. METHODS To inform immunotherapy approaches in paediatric cancers with embryonal origin, we performed an immunogenomic analysis of RNA-seq data from 925 treatment-naïve paediatric nervous system tumours (pedNST) spanning 12 cancer types from three publicly available data sets. RESULTS Within pedNST, we uncovered four broad immune clusters: Paediatric Inflamed (10%), Myeloid Predominant (30%), Immune Neutral (43%) and Immune Desert (17%). We validated these clusters using immunohistochemistry, methylation immune inference and segmentation analysis of tissue images. We report shared biology of these immune clusters within and across cancer types, and characterization of specific immune cell frequencies as well as T- and B-cell repertoires. We found no associations between immune infiltration levels and tumour mutational burden, although molecular cancer entities were enriched within specific immune clusters. CONCLUSIONS Given the heterogeneity of immune infiltration within pedNST, our findings suggest personalized immunogenomic profiling is needed to guide selection of immunotherapeutic strategies.
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Affiliation(s)
- Arash Nabbi
- Princess Margaret Cancer Centre, University Health Network, Princess Margaret Cancer Research Tower, Room 9-305, MaRS Centre, 101 College Street, Toronto, M5G 1L7, Canada
| | - Pengbo Beck
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology and German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), B062, Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Alberto Delaidelli
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Derek A Oldridge
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Sumedha Sudhaman
- Division of Hematology/Oncology, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Kelsey Zhu
- Princess Margaret Cancer Centre, University Health Network, Princess Margaret Cancer Research Tower, Room 9-305, MaRS Centre, 101 College Street, Toronto, M5G 1L7, Canada
| | - S Y Cindy Yang
- Princess Margaret Cancer Centre, University Health Network, Princess Margaret Cancer Research Tower, Room 9-305, MaRS Centre, 101 College Street, Toronto, M5G 1L7, Canada
| | - David T Mulder
- Princess Margaret Cancer Centre, University Health Network, Princess Margaret Cancer Research Tower, Room 9-305, MaRS Centre, 101 College Street, Toronto, M5G 1L7, Canada
| | - Jeffrey P Bruce
- Princess Margaret Cancer Centre, University Health Network, Princess Margaret Cancer Research Tower, Room 9-305, MaRS Centre, 101 College Street, Toronto, M5G 1L7, Canada
| | - Joseph N Paulson
- Department of Biostatistics, Genentech Inc, San Francisco, CA, USA
| | - Pichai Raman
- Division of Neurosurgery, Center for Childhood Cancer Research, Department of Biomedical and Health Informatics and Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Yuankun Zhu
- Division of Neurosurgery, Center for Childhood Cancer Research, Department of Biomedical and Health Informatics and Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Adam C Resnick
- Division of Neurosurgery, Center for Childhood Cancer Research, Department of Biomedical and Health Informatics and Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Poul H Sorensen
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Martin Sill
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology and German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), B062, Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Sebastian Brabetz
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology and German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), B062, Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Sander Lambo
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology and German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), B062, Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - David Malkin
- Division of Hematology/Oncology, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Pascal D Johann
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology and German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), B062, Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Marcel Kool
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology and German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), B062, Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - 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
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology and German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), B062, Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Natalie Jäger
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
- Division of Pediatric Neurooncology and German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), B062, Im Neuenheimer Feld 580, 69120, Heidelberg, Germany.
| | - Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network, Princess Margaret Cancer Research Tower, Room 9-305, MaRS Centre, 101 College Street, Toronto, M5G 1L7, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, Canada.
- Ontario Institute for Cancer Research, Toronto, Canada.
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15
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Nualart F, Cifuentes M, Ramírez E, Martínez F, Barahona MJ, Ferrada L, Saldivia N, Bongarzone ER, Thorens B, Salazar K. Hyperglycemia increases SCO-spondin and Wnt5a secretion into the cerebrospinal fluid to regulate ependymal cell beating and glucose sensing. PLoS Biol 2023; 21:e3002308. [PMID: 37733692 PMCID: PMC10513282 DOI: 10.1371/journal.pbio.3002308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 08/22/2023] [Indexed: 09/23/2023] Open
Abstract
Hyperglycemia increases glucose concentrations in the cerebrospinal fluid (CSF), activating glucose-sensing mechanisms and feeding behavior in the hypothalamus. Here, we discuss how hyperglycemia temporarily modifies ependymal cell ciliary beating to increase hypothalamic glucose sensing. A high level of glucose in the rat CSF stimulates glucose transporter 2 (GLUT2)-positive subcommissural organ (SCO) cells to release SCO-spondin into the dorsal third ventricle. Genetic inactivation of mice GLUT2 decreases hyperglycemia-induced SCO-spondin secretion. In addition, SCO cells secrete Wnt5a-positive vesicles; thus, Wnt5a and SCO-spondin are found at the apex of dorsal ependymal cilia to regulate ciliary beating. Frizzled-2 and ROR2 receptors, as well as specific proteoglycans, such as glypican/testican (essential for the interaction of Wnt5a with its receptors) and Cx43 coupling, were also analyzed in ependymal cells. Finally, we propose that the SCO-spondin/Wnt5a/Frizzled-2/Cx43 axis in ependymal cells regulates ciliary beating, a cyclic and adaptive signaling mechanism to control glucose sensing.
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Affiliation(s)
- Francisco Nualart
- Laboratory of Neurobiology and Stem Cells, NeuroCellT, Department of Cellular Biology, Faculty of Biological Sciences, University of Concepcion, Concepcion, Chile
- Center for Advanced Microscopy CMA BIO BIO, University of Concepcion, Concepcion, Chile
| | - Manuel Cifuentes
- Department of Cell Biology, Genetics and Physiology, University of Malaga, Málaga Biomedical Research Institute and Nanomedicine Platform (IBIMA-BIONAND Platform), Malaga, Spain
| | - Eder Ramírez
- Center for Advanced Microscopy CMA BIO BIO, University of Concepcion, Concepcion, Chile
| | - Fernando Martínez
- Laboratory of Neurobiology and Stem Cells, NeuroCellT, Department of Cellular Biology, Faculty of Biological Sciences, University of Concepcion, Concepcion, Chile
| | - María José Barahona
- Center for Advanced Microscopy CMA BIO BIO, University of Concepcion, Concepcion, Chile
| | - Luciano Ferrada
- Center for Advanced Microscopy CMA BIO BIO, University of Concepcion, Concepcion, Chile
| | - Natalia Saldivia
- Laboratory of Neurobiology and Stem Cells, NeuroCellT, Department of Cellular Biology, Faculty of Biological Sciences, University of Concepcion, Concepcion, Chile
| | - Ernesto R. Bongarzone
- Department of Anatomy and Cell Biology, College of Medicine, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Bernard Thorens
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Katterine Salazar
- Laboratory of Neurobiology and Stem Cells, NeuroCellT, Department of Cellular Biology, Faculty of Biological Sciences, University of Concepcion, Concepcion, Chile
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16
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de Sousa GR, Salomão KB, Nagano LFP, Riemondy KA, Chagas PS, Veronez LC, Saggioro FP, Marie SKN, Yunes JA, Cardinalli IA, Brandalise SR, de Paula Queiroz RG, Scrideli CA, Donson AM, Foreman NK, Tone LG, Valera ET. Identification of HDAC4 as a potential therapeutic target and prognostic biomarker for ZFTA-fused ependymomas. Cancer Gene Ther 2023; 30:1105-1113. [PMID: 37041276 DOI: 10.1038/s41417-023-00616-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/21/2023] [Accepted: 03/28/2023] [Indexed: 04/13/2023]
Abstract
Members of the HDAC family are predictive biomarkers and regulate the tumorigenesis in several cancers. However, the role of these genes in the biology of intracranial ependymomas (EPNs) remains unexplored. Here, an analysis of eighteen HDACs genes in an EPN transcriptomic dataset, revealed significantly higher levels of HDAC4 in supratentorial ZFTA fusion (ST-ZFTA) compared with ST-YAP1 fusion and posterior fossa EPNs, while HDAC7 and SIRT2 were downregulated in ST-ZFTA. HDAC4 was also overexpressed in ST-ZFTA as measured by single-cell RNA-Seq, quantitative real time-polymerase chain reaction, and immunohistochemistry. Survival analyses showed a significantly worse outcome for EPNs with higher HDAC4 and SIRT1 mRNA levels. Ontology enrichment analysis showed an HDAC4-high signature consistent with viral processes while collagen-containing extracellular matrix and cell-cell junction were enriched in those with an HDAC4-low signature. Immune gene analysis demonstrated a correlation between HDAC4 expression and low levels of NK resting cells. Several small molecules compounds targeting HDAC4 and ABCG2, were predicted by in silico analysis to be effective against HDAC4-high ZFTA. Our results provide novel insights into the biology of the HDAC family in intracranial ependymomas and reveal HDAC4 as a prognostic marker and potential therapeutic target in ST-ZFTA.
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Affiliation(s)
- Graziella R de Sousa
- Department of Genetics, Ribeirão Preto Medical School, 3900, Bandeirantes Avenue, Ribeirão Preto, SP, 14049-900, Brazil.
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.
| | - Karina B Salomão
- Department of Pediatrics, Ribeirão Preto Medical School, 3900, Bandeirantes Avenue, Ribeirão Preto, SP, 14049-900, Brazil
| | - Luis F P Nagano
- Department of Genetics, Ribeirão Preto Medical School, 3900, Bandeirantes Avenue, Ribeirão Preto, SP, 14049-900, Brazil
| | - Kent A Riemondy
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Pablo S Chagas
- Department of Genetics, Ribeirão Preto Medical School, 3900, Bandeirantes Avenue, Ribeirão Preto, SP, 14049-900, Brazil
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Luciana C Veronez
- Department of Pediatrics, Ribeirão Preto Medical School, 3900, Bandeirantes Avenue, Ribeirão Preto, SP, 14049-900, Brazil
| | - Fabiano P Saggioro
- Department of Pathology, Ribeirão Preto Medical School, 3900, Bandeirantes Avenue, Ribeirão Preto, SP, 14049-900, Brazil
| | - Suely K N Marie
- Laboratory of Molecular and Cellular Biology (LIM 15), Department of Neurology, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo, 01246-903, SP, Brazil
| | | | | | | | - Rosane G de Paula Queiroz
- Department of Pediatrics, Ribeirão Preto Medical School, 3900, Bandeirantes Avenue, Ribeirão Preto, SP, 14049-900, Brazil
| | - Carlos A Scrideli
- Department of Genetics, Ribeirão Preto Medical School, 3900, Bandeirantes Avenue, Ribeirão Preto, SP, 14049-900, Brazil
- Department of Pediatrics, Ribeirão Preto Medical School, 3900, Bandeirantes Avenue, Ribeirão Preto, SP, 14049-900, Brazil
| | - Andrew M Donson
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, 80045, USA
| | - Nicholas K Foreman
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, 80045, USA
| | - Luiz G Tone
- Department of Genetics, Ribeirão Preto Medical School, 3900, Bandeirantes Avenue, Ribeirão Preto, SP, 14049-900, Brazil
- Department of Pediatrics, Ribeirão Preto Medical School, 3900, Bandeirantes Avenue, Ribeirão Preto, SP, 14049-900, Brazil
| | - Elvis T Valera
- Department of Pediatrics, Ribeirão Preto Medical School, 3900, Bandeirantes Avenue, Ribeirão Preto, SP, 14049-900, Brazil
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17
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de Koning W, Feenstra FF, Calkoen FGJ, van der Lugt J, Kester LA, Mustafa DAM. Characterizing the tumor immune microenvironment of ependymomas using targeted gene expression profiles and RNA sequencing. Cancer Immunol Immunother 2023; 72:2659-2670. [PMID: 37072536 PMCID: PMC10361846 DOI: 10.1007/s00262-023-03450-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 04/07/2023] [Indexed: 04/20/2023]
Abstract
BACKGROUND Defining the tumor immune microenvironment (TIME) of patients using transcriptome analysis is gaining more popularity. Here, we examined and discussed the pros and cons of using RNA sequencing for fresh frozen samples and targeted gene expression immune profiles (NanoString) for formalin-fixed, paraffin-embedded (FFPE) samples to characterize the TIME of ependymoma samples. RESULTS Our results showed a stable expression of the 40 housekeeping genes throughout all samples. The Pearson correlation of the endogenous genes was high. To define the TIME, we first checked the expression of the PTPRC gene, known as CD45, and found it was above the detection limit in all samples by both techniques. T cells were identified consistently using the two types of data. In addition, both techniques showed that the immune landscape was heterogeneous in the 6 ependymoma samples used for this study. CONCLUSIONS The low-abundant genes were detected in higher quantities using the NanoString technique, even when FFPE samples were used. RNA sequencing is better suited for biomarker discovery, fusion gene detection, and getting a broader overview of the TIME. The technique that was used to measure the samples had a considerable effect on the type of immune cells that were identified. The limited number of tumor-infiltrating immune cells compared to the high density of tumor cells in ependymoma can limit the sensitivity of RNA expression techniques regarding the identification of the infiltrating immune cells.
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Affiliation(s)
- W. de Koning
- Tumor Immuno-Pathology Laboratory, Department of Pathology and Clinical Bioinformatics, Erasmus University Medical Centre, Rotterdam, The Netherlands
- Clinical Bioinformatics Unit, Department of Pathology and Clinical Bioinformatics, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - F. F. Feenstra
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - F. G. J. Calkoen
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - J. van der Lugt
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - L. A. Kester
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - D. A. M. Mustafa
- Tumor Immuno-Pathology Laboratory, Department of Pathology and Clinical Bioinformatics, Erasmus University Medical Centre, Rotterdam, The Netherlands
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18
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Han YP, Lin HW, Li H. Cancer Stem Cells in Tumours of the Central Nervous System in Children: A Comprehensive Review. Cancers (Basel) 2023; 15:3154. [PMID: 37370764 DOI: 10.3390/cancers15123154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/30/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
Cancer stem cells (CSCs) are a subgroup of cells found in various kinds of tumours with stem cell characteristics, such as self-renewal, induced differentiation, and tumourigenicity. The existence of CSCs is regarded as a major source of tumour recurrence, metastasis, and resistance to conventional chemotherapy and radiation treatment. Tumours of the central nervous system (CNS) are the most common solid tumours in children, which have many different types including highly malignant embryonal tumours and midline gliomas, and low-grade gliomas with favourable prognoses. Stem cells from the CNS tumours have been largely found and reported by researchers in the last decade and their roles in tumour biology have been deeply studied. However, the cross-talk of CSCs among different CNS tumour types and their clinical impacts have been rarely discussed. This article comprehensively reviews the achievements in research on CSCs in paediatric CNS tumours. Biological functions, diagnostic values, and therapeutic perspectives are reviewed in detail. Further investigations into CSCs are warranted to improve the clinical practice in treating children with CNS tumours.
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Affiliation(s)
- Yi-Peng Han
- Department of Neurosurgery, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Hou-Wei Lin
- Department of Paediatric Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
- Department of Paediatric Surgery, Jiaxing Women and Children Hospital Affiliated to Jiaxing University, Jiaxing 314001, China
| | - Hao Li
- Department of Neurosurgery, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
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19
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Wei H, Wu X, Withrow J, Cuevas-Diaz Duran R, Singh S, Chaboub LS, Rakshit J, Mejia J, Rolfe A, Herrera JJ, Horner PJ, Wu JQ. Glial progenitor heterogeneity and key regulators revealed by single-cell RNA sequencing provide insight to regeneration in spinal cord injury. Cell Rep 2023; 42:112486. [PMID: 37149868 PMCID: PMC10511029 DOI: 10.1016/j.celrep.2023.112486] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 02/12/2023] [Accepted: 04/22/2023] [Indexed: 05/09/2023] Open
Abstract
Recent studies have revealed the heterogeneous nature of astrocytes; however, how diverse constituents of astrocyte-lineage cells are regulated in adult spinal cord after injury and contribute to regeneration remains elusive. We perform single-cell RNA sequencing of GFAP-expressing cells from sub-chronic spinal cord injury models and identify and compare with the subpopulations in acute-stage data. We find subpopulations with distinct functional enrichment and their identities defined by subpopulation-specific transcription factors and regulons. Immunohistochemistry, RNAscope experiments, and quantification by stereology verify the molecular signature, location, and morphology of potential resident neural progenitors or neural stem cells in the adult spinal cord before and after injury and uncover the populations of the intermediate cells enriched in neuronal genes that could potentially transition into other subpopulations. This study has expanded the knowledge of the heterogeneity and cell state transition of glial progenitors in adult spinal cord before and after injury.
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Affiliation(s)
- Haichao Wei
- The Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX 77030, USA; Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX 77030, USA
| | - Xizi Wu
- The Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX 77030, USA; Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX 77030, USA
| | - Joseph Withrow
- The Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX 77030, USA
| | - Raquel Cuevas-Diaz Duran
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Nuevo León 64710, Mexico
| | - Simranjit Singh
- The Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX 77030, USA; Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX 77030, USA
| | - Lesley S Chaboub
- Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Jyotirmoy Rakshit
- The Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX 77030, USA; Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX 77030, USA
| | - Julio Mejia
- Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Andrew Rolfe
- The Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX 77030, USA; Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX 77030, USA
| | - Juan J Herrera
- Department of Diagnostic and Interventional Imaging, McGovern Medical School, UTHealth, Houston, TX 77030, USA
| | - Philip J Horner
- Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA.
| | - Jia Qian Wu
- The Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX 77030, USA; Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX 77030, USA; MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA.
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20
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Fu R, Norris GA, Willard N, Griesinger AM, Riemondy KA, Amani V, Grimaldo E, Harris F, Hankinson TC, Mitra S, Ritzmann TA, Grundy RR, Foreman NK, Donson AM. Spatial transcriptomic analysis delineates epithelial and mesenchymal subpopulations and transition stages in childhood ependymoma. Neuro Oncol 2023; 25:786-798. [PMID: 36215273 PMCID: PMC10076949 DOI: 10.1093/neuonc/noac219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND The diverse cellular constituents of childhood brain tumor ependymoma, recently revealed by single cell RNA-sequencing, may underly therapeutic resistance. Here we use spatial transcriptomics to further advance our understanding of the tumor microenvironment, mapping cellular subpopulations to the tumor architecture of ependymoma posterior fossa subgroup A (PFA), the commonest and most deadly childhood ependymoma variant. METHODS Spatial transcriptomics data from intact PFA sections was deconvoluted to resolve the histological arrangement of neoplastic and non-neoplastic cell types. Key findings were validated using immunohistochemistry, in vitro functional assays and outcome analysis in clinically-annotated PFA bulk transcriptomic data. RESULTS PFA are comprised of epithelial and mesenchymal histological zones containing a diversity of cellular states, each zone including co-existing and spatially distinct undifferentiated progenitor-like cells; a quiescent mesenchymal zone population, and a second highly mitotic progenitor population that is restricted to hypercellular epithelial zones and that is more abundant in progressive tumors. We show that myeloid cell interaction is the leading cause of mesenchymal transition in PFA, occurring in zones spatially distinct from hypoxia-induced mesenchymal transition, and these distinct EMT-initiating processes were replicated using in vitro models of PFA. CONCLUSIONS These insights demonstrate the utility of spatial transcriptomics to advance our understanding of ependymoma biology, revealing a clearer picture of the cellular constituents of PFA, their interactions and influence on tumor progression.
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Affiliation(s)
- Rui Fu
- RNA Biosciences Initiative, University of Colorado Denver, Aurora, Colorado, USA
| | - Gregory A Norris
- Department of Pediatrics, University of Colorado Denver, Aurora, Colorado, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Nicholas Willard
- Department of Pathology, University of Colorado Denver, Aurora, Colorado, USA
| | - Andrea M Griesinger
- Department of Pediatrics, University of Colorado Denver, Aurora, Colorado, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Kent A Riemondy
- RNA Biosciences Initiative, University of Colorado Denver, Aurora, Colorado, USA
| | - Vladimir Amani
- Department of Pediatrics, University of Colorado Denver, Aurora, Colorado, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Enrique Grimaldo
- Department of Pediatrics, University of Colorado Denver, Aurora, Colorado, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Faith Harris
- Department of Pediatrics, University of Colorado Denver, Aurora, Colorado, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Todd C Hankinson
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, Colorado, USA
- Department of Neurosurgery, University of Colorado Denver, Aurora, Colorado, USA
| | - Siddhartha Mitra
- Department of Pediatrics, University of Colorado Denver, Aurora, Colorado, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Timothy A Ritzmann
- Children’s Brain Tumor Research Centre, School of Medicine, University of Nottingham, Nottingham, UK
| | - Richard R Grundy
- Children’s Brain Tumor Research Centre, School of Medicine, University of Nottingham, Nottingham, UK
| | - Nicholas K Foreman
- Department of Pediatrics, University of Colorado Denver, Aurora, Colorado, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Andrew M Donson
- Department of Pediatrics, University of Colorado Denver, Aurora, Colorado, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, Colorado, USA
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21
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Hwang EI, Hanson D, Filbin MG, Mack SC. Why haven't we solved intracranial pediatric ependymoma? Current questions and barriers to treatment advances. Neoplasia 2023; 39:100895. [PMID: 36944298 PMCID: PMC10036929 DOI: 10.1016/j.neo.2023.100895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/20/2023] [Accepted: 02/28/2023] [Indexed: 03/22/2023]
Abstract
Pediatric intracranial ependymoma has seen a recent exponential expansion of biological findings, rapidly dividing the diagnosis into several subgroups, each with specific molecular and clinical characteristics. While such subdivision may complicate clinical conclusions from historical trials, this knowledge also provides an opportunity for interrogating the major clinical and biological questions preventing near-term translation into effective therapy for children with ependymoma. In this article, we briefly review some of the most critical clinical questions facing both patient management and the construct of future trials in childhood ependymoma, as well as explore some of the current barriers to efficient translation of preclinical discovery to the clinic.
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22
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Lee MK, Azizgolshani N, Zhang Z, Perreard L, Kolling FW, Nguyen LN, Zanazzi GJ, Salas LA, Christensen BC. Hydroxymethylation alterations in progenitor-like cell types of pediatric central nervous system tumors are associated with cell type-specific transcriptional changes. RESEARCH SQUARE 2023:rs.3.rs-2517758. [PMID: 36909536 PMCID: PMC10002842 DOI: 10.21203/rs.3.rs-2517758/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
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 utilized 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 identified a preponderance differential CpG hydroxymethylation rather than methylation. Genes with differential hydroxymethylation, like HDAC4 and IGF1R, were 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 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 Cardiothoracic 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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23
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Lee MK, Azizgolshani N, Shapiro JA, Nguyen LN, Kolling FW, Zanazzi GJ, Frost HR, Christensen BC. Tumor type and cell type-specific gene expression alterations in diverse pediatric central nervous system tumors identified using single nuclei RNA-seq. RESEARCH SQUARE 2023:rs.3.rs-2517703. [PMID: 36865335 PMCID: PMC9980204 DOI: 10.21203/rs.3.rs-2517703/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
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 collected single nuclei RNA-seq data from 35 pediatric CNS tumors and three non-tumoral pediatric brain tissues (84,700 nuclei) and characterized tumor heterogeneity and transcriptomic alterations. We distinguished cell subpopulations associated with specific tumor types including radial glial cells in ependymomas and oligodendrocyte precursor cells in astrocytomas. In tumors, we observed pathways important in neural stem cell-like populations, a cell type previously associated with therapy resistance. Lastly, we identified 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. In this study, we address current gaps in understanding single nuclei gene expression profiles of previously uninvestigated 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 Cardiothoracic 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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24
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Pun M, Pratt D, Nano PR, Joshi PK, Jiang L, Englinger B, Rao A, Cieslik M, Chinnaiyan AM, Aldape K, Pfister S, Filbin MG, Bhaduri A, Venneti S. Common molecular features of H3K27M DMGs and PFA ependymomas map to hindbrain developmental pathways. Acta Neuropathol Commun 2023; 11:25. [PMID: 36759899 PMCID: PMC9912509 DOI: 10.1186/s40478-023-01514-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/11/2023] [Indexed: 02/11/2023] Open
Abstract
Globally decreased histone 3, lysine 27 tri-methylation (H3K27me3) is a hallmark of H3K27-altered diffuse midline gliomas (DMGs) and group-A posterior fossa ependymomas (PFAs). H3K27-altered DMGs are largely characterized by lysine-to-methionine mutations in histone 3 at position 27 (H3K27M). Most PFAs overexpress EZH inhibitory protein (EZHIP), which possesses a region of similarity to the mutant H3K27M. Both H3K27M and EZHIP inhibit the function of the polycomb repressive complex 2 (PRC2) responsible for H3K27me3 deposition. These tumors often arise in neighboring regions of the brainstem and posterior fossa. In rare cases PFAs harbor H3K27M mutations, and DMGs overexpress EZHIP. These findings together raise the possibility that certain cell populations in the developing hindbrain/posterior fossa are especially sensitive to modulation of H3K27me3 states. We identified shared molecular features by comparing genomic, bulk transcriptomic, chromatin-based profiles, and single-cell RNA-sequencing (scRNA-seq) data from the two tumor classes. Our approach demonstrated that 1q gain, a key biomarker in PFAs, is prognostic in H3.1K27M, but not H3.3K27M gliomas. Conversely, Activin A Receptor Type 1 (ACVR1), which is associated with mutations in H3.1K27M gliomas, is overexpressed in a subset of PFAs with poor outcome. Despite diffuse H3K27me3 reduction, previous work shows that both tumors maintain genomic H3K27me3 deposition at select sites. We demonstrate heterogeneity in shared patterns of residual H3K27me3 for both tumors that largely segregated with inferred anatomic tumor origins and progenitor populations of tumor cells. In contrast, analysis of genes linked to H3K27 acetylation (H3K27ac)-marked enhancers showed higher expression in astrocytic-like tumor cells. Finally, common H3K27me3-marked genes mapped closely to expression patterns in the human developing hindbrain. Overall, our data demonstrate developmentally relevant molecular similarities between PFAs and H3K27M DMGs and support the overall hypothesis that deregulated mechanisms of hindbrain development are central to the biology of both tumors.
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Affiliation(s)
- Matthew Pun
- Laboratory of Brain Tumor Metabolism and Epigenetics, Department of Pathology, University of Michigan, 3520E MSRB 1, 1150 W. Medical Center, Ann Arbor, MI, 41804, USA
- Chad Carr Pediatric Tumor Center, Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Medical Scientist Training Program, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Drew Pratt
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Dr., Room 2S235, Bethesda, MD, 20892, USA
| | - Patricia R Nano
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Piyush K Joshi
- Hopp Children's Cancer Center (KiTZ) Heidelberg, Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Li Jiang
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02115, USA
| | - Bernhard Englinger
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Department of Urology, Comprehensive Cancer Center, Medical University of Vienna, 1090, Vienna, Austria
- Center for Cancer Research and Comprehensive Cancer Center, Medical University Vienna, 1090, Vienna, Austria
| | - Arvind Rao
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Marcin Cieslik
- Michigan Center for Translational Pathology, Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Howard Hughes Medical Institute, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Kenneth Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Dr., Room 2S235, Bethesda, MD, 20892, USA
| | - Stefan Pfister
- Hopp Children's Cancer Center (KiTZ) Heidelberg, Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120, Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, 69120, Heidelberg, Germany
| | - Mariella G Filbin
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Aparna Bhaduri
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Sriram Venneti
- Laboratory of Brain Tumor Metabolism and Epigenetics, Department of Pathology, University of Michigan, 3520E MSRB 1, 1150 W. Medical Center, Ann Arbor, MI, 41804, USA.
- Chad Carr Pediatric Tumor Center, Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA.
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
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25
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Aubin RG, Montelongo J, Hu R, Camara PG. Clustering-independent estimation of cell abundances in bulk tissues using single-cell RNA-seq data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.06.527318. [PMID: 36798206 PMCID: PMC9934539 DOI: 10.1101/2023.02.06.527318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Single-cell RNA-sequencing has transformed the study of biological tissues by enabling transcriptomic characterizations of their constituent cell states. Computational methods for gene expression deconvolution use this information to infer the cell composition of related tissues profiled at the bulk level. However, current deconvolution methods are restricted to discrete cell types and have limited power to make inferences about continuous cellular processes like cell differentiation or immune cell activation. We present ConDecon, a clustering-independent method for inferring the likelihood for each cell in a single-cell dataset to be present in a bulk tissue. ConDecon represents an improvement in functionality and accuracy with respect to current deconvolution methods. Using ConDecon, we discover the implication of neurodegenerative microglial inflammatory pathways in the mesenchymal transformation of ependymoma, recapitulate spatial patterns of cell differentiation during zebrafish embryogenesis, and make temporal inferences from bulk ATAC-seq data. Overall, ConDecon significantly enhances our understanding of dynamic cellular processes within bulk tissue samples.
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Affiliation(s)
- Rachael G Aubin
- Department of Genetics and Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, 3700 Hamilton Walk, Philadelphia, PA 19104
| | - Javier Montelongo
- Department of Genetics and Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, 3700 Hamilton Walk, Philadelphia, PA 19104
| | - Robert Hu
- Department of Genetics and Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, 3700 Hamilton Walk, Philadelphia, PA 19104
| | - Pablo G Camara
- Department of Genetics and Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, 3700 Hamilton Walk, Philadelphia, PA 19104
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26
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Rodrigo Albors A, Singer GA, Llorens-Bobadilla E, Frisén J, May AP, Ponting CP, Storey KG. An ependymal cell census identifies heterogeneous and ongoing cell maturation in the adult mouse spinal cord that changes dynamically on injury. Dev Cell 2023; 58:239-255.e10. [PMID: 36706756 DOI: 10.1016/j.devcel.2023.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 10/14/2022] [Accepted: 01/04/2023] [Indexed: 01/27/2023]
Abstract
The adult spinal cord stem cell potential resides within the ependymal cell population and declines with age. Ependymal cells are, however, heterogeneous, and the biological diversity this represents and how it changes with age remain unknown. Here, we present a single-cell transcriptomic census of spinal cord ependymal cells from adult and aged mice, identifying not only all known ependymal cell subtypes but also immature as well as mature cell states. By comparing transcriptomes of spinal cord and brain ependymal cells, which lack stem cell abilities, we identify immature cells as potential spinal cord stem cells. Following spinal cord injury, these cells re-enter the cell cycle, which is accompanied by a short-lived reversal of ependymal cell maturation. We further analyze ependymal cells in the human spinal cord and identify widespread cell maturation and altered cell identities. This in-depth characterization of spinal cord ependymal cells provides insight into their biology and informs strategies for spinal cord repair.
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Affiliation(s)
- Aida Rodrigo Albors
- Division of Molecular, Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.
| | - Gail A Singer
- Division of Molecular, Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | | | - Jonas Frisén
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Andrew P May
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Tornado Bio, Inc., South San Francisco, CA 94080, USA
| | - Chris P Ponting
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Kate G Storey
- Division of Molecular, Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.
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27
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Single-cell technologies uncover intra-tumor heterogeneity in childhood cancers. Semin Immunopathol 2023; 45:61-69. [PMID: 36625902 DOI: 10.1007/s00281-022-00981-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 12/11/2022] [Indexed: 01/11/2023]
Abstract
Childhood cancer is the second leading cause of death in children aged 1 to 14. Although survival rates have vastly improved over the past 40 years, cancer resistance and relapse remain a significant challenge. Advances in single-cell technologies enable dissection of tumors to unprecedented resolution. This facilitates unraveling the heterogeneity of childhood cancers to identify cell subtypes that are prone to treatment resistance. The rapid accumulation of single-cell data from different modalities necessitates the development of novel computational approaches for processing, visualizing, and analyzing single-cell data. Here, we review single-cell approaches utilized or under development in the context of childhood cancers. We review computational methods for analyzing single-cell data and discuss best practices for their application. Finally, we review the impact of several studies of childhood tumors analyzed with these approaches and future directions to implement single-cell studies into translational cancer research in pediatric oncology.
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28
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Vegliante R, Pastushenko I, Blanpain C. Deciphering functional tumor states at single-cell resolution. EMBO J 2022; 41:e109221. [PMID: 34918370 PMCID: PMC8762559 DOI: 10.15252/embj.2021109221] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/07/2021] [Accepted: 11/10/2021] [Indexed: 01/19/2023] Open
Abstract
Within a tumor, cancer cells exist in different states that are associated with distinct tumor functions, including proliferation, differentiation, invasion, metastasis, and resistance to anti-cancer therapy. The identification of the gene regulatory networks underpinning each state is essential for better understanding functional tumor heterogeneity and revealing tumor vulnerabilities. Here, we review the different studies identifying tumor states by single-cell sequencing approaches and the mechanisms that promote and sustain these functional states and regulate their transitions. We also describe how different tumor states are spatially distributed and interact with the specific stromal cells that compose the tumor microenvironment. Finally, we discuss how the understanding of tumor plasticity and transition states can be used to develop new strategies to improve cancer therapy.
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Affiliation(s)
- Rolando Vegliante
- Laboratory of Stem Cells and CancerUniversité Libre de BruxellesBrusselsBelgium
| | | | - Cédric Blanpain
- Laboratory of Stem Cells and CancerUniversité Libre de BruxellesBrusselsBelgium
- WELBIOUniversité Libre de BruxellesBrusselsBelgium
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29
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Is IIIG9 a New Protein with Exclusive Ciliary Function? Analysis of Its Potential Role in Cancer and Other Pathologies. Cells 2022; 11:cells11203327. [PMID: 36291193 PMCID: PMC9600092 DOI: 10.3390/cells11203327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/23/2022] [Accepted: 10/03/2022] [Indexed: 11/16/2022] Open
Abstract
The identification of new proteins that regulate the function of one of the main cellular phosphatases, protein phosphatase 1 (PP1), is essential to find possible pharmacological targets to alter phosphatase function in various cellular processes, including the initiation and development of multiple diseases. IIIG9 is a regulatory subunit of PP1 initially identified in highly polarized ciliated cells. In addition to its ciliary location in ependymal cells, we recently showed that IIIG9 has extraciliary functions that regulate the integrity of adherens junctions. In this review, we perform a detailed analysis of the expression, localization, and function of IIIG9 in adult and developing normal brains. In addition, we provide a 3D model of IIIG9 protein structure for the first time, verifying that the classic structural and conformational characteristics of the PP1 regulatory subunits are maintained. Our review is especially focused on finding evidence linking IIIG9 dysfunction with the course of some pathologies, such as ciliopathies, drug dependence, diseases based on neurological development, and the development of specific high-malignancy and -frequency brain tumors in the pediatric population. Finally, we propose that IIIG9 is a relevant regulator of PP1 function in physiological and pathological processes in the CNS.
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30
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Gonzalez Castro LN, Liu I, Filbin M. Characterizing the biology of primary brain tumors and their microenvironment via single-cell profiling methods. Neuro Oncol 2022; 25:234-247. [PMID: 36197833 PMCID: PMC9925698 DOI: 10.1093/neuonc/noac211] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Genomic and transcriptional heterogeneity is prevalent among the most common and aggressive primary brain tumors in children and adults. Over the past 20 years, advances in bioengineering, biochemistry and bioinformatics have enabled the development of an array of techniques to study tumor biology at single-cell resolution. The application of these techniques to study primary brain tumors has helped advance our understanding of their intra-tumoral heterogeneity and uncover new insights regarding their co-option of developmental programs and signaling from their microenvironment to promote tumor proliferation and invasion. These insights are currently being harnessed to develop new therapeutic approaches. Here we provide an overview of current single-cell techniques and discuss relevant biology and therapeutic insights uncovered by their application to primary brain tumors in children and adults.
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Affiliation(s)
- L Nicolas Gonzalez Castro
- Corresponding Author: L. Nicolas Gonzalez Castro, MD, PhD, Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA ()
| | | | - Mariella Filbin
- Pediatric Neuro-Oncology Program, Dana-Farber/Boston Children’s and Blood Disorders Center, Boston, MA, USA
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31
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Christensen E, Naidas A, Chen D, Husic M, Shooshtari P. TMExplorer: A tumour microenvironment single-cell RNAseq database and search tool. PLoS One 2022; 17:e0272302. [PMID: 36084081 PMCID: PMC9462821 DOI: 10.1371/journal.pone.0272302] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 07/17/2022] [Indexed: 02/01/2023] Open
Abstract
MOTIVATION The tumour microenvironment (TME) contains various cells including stromal fibroblasts, immune and malignant cells, and its composition can be elucidated using single-cell RNA sequencing (scRNA-seq). scRNA-seq datasets from several cancer types are available, yet we lack a comprehensive database to collect and present related TME data in an easily accessible format. RESULTS We therefore built a TME scRNA-seq database, and created the R package TMExplorer to facilitate investigation of the TME. TMExplorer provides an interface to easily access all available datasets and their metadata. The users can search for datasets using a thorough range of characteristics. The TMExplorer allows for examination of the TME using scRNA-seq in a way that is streamlined and allows for easy integration into already existing scRNA-seq analysis pipelines.
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Affiliation(s)
- Erik Christensen
- Department of Computer Science, University of Western Ontario, London, ON, Canada
- Children Health Research Institute, Victoria Research Labs, London, ON, Canada
| | - Alaine Naidas
- Children Health Research Institute, Victoria Research Labs, London, ON, Canada
- Department of Pathology and Lab Medicine, University of Western Ontario, London, ON, Canada
| | - David Chen
- Children Health Research Institute, Victoria Research Labs, London, ON, Canada
- Department of Pathology and Lab Medicine, University of Western Ontario, London, ON, Canada
| | - Mia Husic
- Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada
| | - Parisa Shooshtari
- Department of Computer Science, University of Western Ontario, London, ON, Canada
- Children Health Research Institute, Victoria Research Labs, London, ON, Canada
- Department of Pathology and Lab Medicine, University of Western Ontario, London, ON, Canada
- Lawson Health Research Institute, London, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
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32
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Gimple RC, Yang K, Halbert ME, Agnihotri S, Rich JN. Brain cancer stem cells: resilience through adaptive plasticity and hierarchical heterogeneity. Nat Rev Cancer 2022; 22:497-514. [PMID: 35710946 DOI: 10.1038/s41568-022-00486-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/03/2022] [Indexed: 02/07/2023]
Abstract
Malignant brain tumours are complex ecosystems containing neoplastic and stromal components that generate adaptive and evolutionarily driven aberrant tissues in the central nervous system. Brain cancers are cultivated by a dynamic population of stem-like cells that enforce intratumoural heterogeneity and respond to intrinsic microenvironment or therapeutically guided insults through proliferation, plasticity and restructuring of neoplastic and stromal components. Far from a rigid hierarchy, heterogeneous neoplastic populations transition between cellular states with differential self-renewal capacities, endowing them with powerful resilience. Here we review the biological machinery used by brain tumour stem cells to commandeer tissues in the intracranial space, evade immune responses and resist chemoradiotherapy. Through recent advances in single-cell sequencing, improved models to investigate the role of the tumour microenvironment and a deeper understanding of the fundamental role of the immune system in cancer biology, we are now better equipped to explore mechanisms by which these processes can be exploited for therapeutic benefit.
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Affiliation(s)
- Ryan C Gimple
- Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
| | - Kailin Yang
- Department of Radiation Oncology, Taussig Cancer Center, Cleveland Clinic, Cleveland, OH, USA
| | - Matthew E Halbert
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sameer Agnihotri
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jeremy N Rich
- University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, PA, USA.
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA, USA.
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33
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Aubin RG, Troisi EC, Montelongo J, Alghalith AN, Nasrallah MP, Santi M, Camara PG. Pro-inflammatory cytokines mediate the epithelial-to-mesenchymal-like transition of pediatric posterior fossa ependymoma. Nat Commun 2022; 13:3936. [PMID: 35803925 PMCID: PMC9270322 DOI: 10.1038/s41467-022-31683-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 06/28/2022] [Indexed: 12/13/2022] Open
Abstract
Pediatric ependymoma is a devastating brain cancer marked by its relapsing pattern and lack of effective chemotherapies. This shortage of treatments is due to limited knowledge about ependymoma tumorigenic mechanisms. By means of single-nucleus chromatin accessibility and gene expression profiling of posterior fossa primary tumors and distal metastases, we reveal key transcription factors and enhancers associated with the differentiation of ependymoma tumor cells into tumor-derived cell lineages and their transition into a mesenchymal-like state. We identify NFκB, AP-1, and MYC as mediators of this transition, and show that the gene expression profiles of tumor cells and infiltrating microglia are consistent with abundant pro-inflammatory signaling between these populations. In line with these results, both TGF-β1 and TNF-α induce the expression of mesenchymal genes on a patient-derived cell model, and TGF-β1 leads to an invasive phenotype. Altogether, these data suggest that tumor gliosis induced by inflammatory cytokines and oxidative stress underlies the mesenchymal phenotype of posterior fossa ependymoma.
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Affiliation(s)
- Rachael G Aubin
- Department of Genetics and Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Emma C Troisi
- Department of Genetics and Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Javier Montelongo
- Department of Genetics and Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Adam N Alghalith
- Department of Genetics and Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Maclean P Nasrallah
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Mariarita Santi
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Pathology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Pablo G Camara
- Department of Genetics and Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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Wu H, Fu R, Zhang YH, Liu Z, Chen ZH, Xu J, Tian Y, Jin W, Wong SZH, Wu QF. Single-Cell RNA Sequencing Unravels Upregulation of Immune Cell Crosstalk in Relapsed Pediatric Ependymoma. Front Immunol 2022; 13:903246. [PMID: 35844565 PMCID: PMC9281506 DOI: 10.3389/fimmu.2022.903246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 06/01/2022] [Indexed: 11/13/2022] Open
Abstract
Ependymoma (EPN) is a malignant glial tumor occurring throughout central nervous system, which commonly presents in children. Although recent studies have characterized EPN samples at both the bulk and single-cell level, intratumoral heterogeneity across subclones remains a confounding factor that impedes understanding of EPN biology. In this study, we generated a high-resolution single-cell dataset of pediatric ependymoma with a particular focus on the comparison of subclone differences within tumors and showed upregulation of cilium-associated genes in more highly differentiated subclone populations. As a proxy to traditional pseudotime analysis, we applied a novel trajectory scoring method to reveal cellular compositions associated with poor survival outcomes across primary and relapsed patients. Furthermore, we identified putative cell–cell communication features between relapsed and primary samples and showed upregulation of pathways associated with immune cell crosstalk. Our results revealed both inter- and intratumoral heterogeneity in EPN and provided a framework for studying transcriptomic signatures of individual subclones at single-cell resolution.
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Affiliation(s)
- Haoda Wu
- State Key Laboratory of Molecular Development Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- *Correspondence: Haoda Wu, ; Samuel Zheng Hao Wong, ; Wenfei Jin, ; Yongji Tian,
| | - Ruiqing Fu
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yu-Hong Zhang
- State Key Laboratory of Molecular Development Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhiming Liu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Zhen-Hua Chen
- State Key Laboratory of Molecular Development Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jingkai Xu
- Department of Dermatology, China–Japan Friendship Hospital, Beijing, China
| | - Yongji Tian
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- *Correspondence: Haoda Wu, ; Samuel Zheng Hao Wong, ; Wenfei Jin, ; Yongji Tian,
| | - Wenfei Jin
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
- *Correspondence: Haoda Wu, ; Samuel Zheng Hao Wong, ; Wenfei Jin, ; Yongji Tian,
| | - Samuel Zheng Hao Wong
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, United States
- *Correspondence: Haoda Wu, ; Samuel Zheng Hao Wong, ; Wenfei Jin, ; Yongji Tian,
| | - Qing-Feng Wu
- State Key Laboratory of Molecular Development Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Beijing, China
- Chinese Institute for Brain Research, Beijing, China
- Beijing Children Hospital, Capital Medical University, Beijing, China
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Batchu S, Patel K, Yu S, Mohamed AT, Karsy M. Single cell transcriptomics reveals unique metabolic profiles of ependymoma subgroups. Gene X 2022; 820:146278. [PMID: 35143938 DOI: 10.1016/j.gene.2022.146278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 01/15/2022] [Accepted: 02/03/2022] [Indexed: 11/28/2022] Open
Abstract
OBJECTIVE Ependymomas are biologically diverse tumors with five major genomic subgroups. However, intratumor heterogeneity continues to be poorly understood. The present study characterized the metabolic landscapes of ependymoma subgroups at the single-cell level. METHODS Expression profiles from 11,200 ependymoma single cells derived from the five major subgroups and 7,200 ependymoma-derived non-neoplastic cells were computationally analyzed using a robust workflow to elucidate relative differences in metabolic pathway activities. RESULTS Dimensionality reduction using metabolic expression profiles exhibited clustering corresponding to each tumor subgroup, but non-neoplastic cells exhibited no discernable differences between subgroups. From the 80 metabolic pathways examined, over 75 pathways had significantly different activity scores between ependymoma subgroups. Further analysis of metabolic heterogeneity suggests that mitochondrial oxidative phosphorylation accounts for considerable metabolic variation within tumor subgroups and non-neoplastic cells of the same cell type. Drug metabolism pathways, specifically those involving cytochromes P450, were also found to be major contributors to heterogeneity. CONCLUSIONS Ependymoma subgroups display distinct metabolic differences as evaluated through gene expression profiles with certain pathways contributing greatly to intra-subgroup variation. These results may account for variation in tumor metabolism, treatment response, and potential targeting approaches that disrupt metabolic signalling.
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Affiliation(s)
| | - Karan Patel
- Cooper Medical School, Camden, NJ, United States
| | - Siyuan Yu
- Cooper Medical School, Camden, NJ, United States
| | | | - Michael Karsy
- Thomas Jefferson University Hospital, Department of Neurosurgery, Philadelphia, PA, United States
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Saleh AH, Samuel N, Juraschka K, Saleh MH, Taylor MD, Fehlings MG. The biology of ependymomas and emerging novel therapies. Nat Rev Cancer 2022; 22:208-222. [PMID: 35031778 DOI: 10.1038/s41568-021-00433-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/01/2021] [Indexed: 12/20/2022]
Abstract
Ependymomas are rare central nervous system tumours that can arise in the brain's supratentorial region or posterior fossa, or in the spinal cord. In 1924, Percival Bailey published the first comprehensive study of ependymomas. Since then, and especially over the past 10 years, our understanding of ependymomas has grown exponentially. In this Review, we discuss the evolution in knowledge regarding ependymoma subgroups and the resultant clinical implications. We also discuss key oncogenic and tumour suppressor signalling pathways that regulate tumour growth, the role of epigenetic dysregulation in the biology of ependymomas, and the various biological features of ependymoma tumorigenesis, including cell immortalization, stem cell-like properties, the tumour microenvironment and metastasis. We further review the limitations of current therapies such as relapse, radiation-induced cognitive deficits and chemotherapy resistance. Finally, we highlight next-generation therapies that are actively being explored, including tyrosine kinase inhibitors, telomerase inhibitors, anti-angiogenesis agents and immunotherapy.
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Affiliation(s)
- Amr H Saleh
- MD Program, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Nardin Samuel
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, ON, Canada
| | - Kyle Juraschka
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, ON, Canada
| | - Mohammad H Saleh
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada
| | - Michael D Taylor
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, ON, Canada
- Division of Neurosurgery, Department of Surgery, The Hospital for Sick Children, Toronto, ON, Canada
| | - Michael G Fehlings
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, ON, Canada.
- Division of Neurosurgery, University Health Network, Toronto Western Hospital, Toronto, ON, Canada.
- Krembil Neuroscience Centre, University Health Network, Toronto, ON, Canada.
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Riemondy KA, Venkataraman S, Willard N, Nellan A, Sanford B, Griesinger AM, Amani V, Mitra S, Hankinson TC, Handler MH, Sill M, Ocasio J, Weir SJ, Malawsky DS, Gershon TR, Garancher A, Wechsler-Reya RJ, Hesselberth JR, Foreman NK, Donson AM, Vibhakar R. Neoplastic and immune single-cell transcriptomics define subgroup-specific intra-tumoral heterogeneity of childhood medulloblastoma. Neuro Oncol 2022; 24:273-286. [PMID: 34077540 PMCID: PMC8804892 DOI: 10.1093/neuonc/noab135] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Medulloblastoma (MB) is a heterogeneous disease in which neoplastic cells and associated immune cells contribute to disease progression. We aimed to determine the influence of neoplastic and immune cell diversity on MB biology in patient samples and animal models. METHODS To better characterize cellular heterogeneity in MB we used single-cell RNA sequencing, immunohistochemistry, and deconvolution of transcriptomic data to profile neoplastic and immune populations in patient samples and animal models across childhood MB subgroups. RESULTS Neoplastic cells cluster primarily according to individual sample of origin which is influenced by chromosomal copy number variance. Harmony alignment reveals novel MB subgroup/subtype-associated subpopulations that recapitulate neurodevelopmental processes, including photoreceptor and glutamatergic neuron-like cells in molecular subgroups GP3 and GP4, and a specific nodule-associated neuronally differentiated subpopulation in the sonic hedgehog subgroup. We definitively chart the spectrum of MB immune cell infiltrates, which include subpopulations that recapitulate developmentally related neuron-pruning and antigen-presenting myeloid cells. MB cellular diversity matching human samples is mirrored in subgroup-specific mouse models of MB. CONCLUSIONS These findings provide a clearer understanding of the diverse neoplastic and immune cell subpopulations that constitute the MB microenvironment.
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Affiliation(s)
- Kent A Riemondy
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Sujatha Venkataraman
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, Colorado, USA
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Nicholas Willard
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Anandani Nellan
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, Colorado, USA
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Bridget Sanford
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Andrea M Griesinger
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, Colorado, USA
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Vladimir Amani
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, Colorado, USA
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Siddhartha Mitra
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, Colorado, USA
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Todd C Hankinson
- Department of Neurosurgery, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Michael H Handler
- Department of Neurosurgery, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Martin Sill
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jennifer Ocasio
- Department of Neurology, UNC School of Medicine, Chapel Hill, North Carolina, USA
| | - Seth J Weir
- Department of Neurology, UNC School of Medicine, Chapel Hill, North Carolina, USA
| | - Daniel S Malawsky
- Department of Neurology, UNC School of Medicine, Chapel Hill, North Carolina, USA
| | - Timothy R Gershon
- Department of Neurology, UNC School of Medicine, Chapel Hill, North Carolina, USA
| | - Alexandra Garancher
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Robert J Wechsler-Reya
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Jay R Hesselberth
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Nicholas K Foreman
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, Colorado, USA
- Department of Neurosurgery, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Andrew M Donson
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, Colorado, USA
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Rajeev Vibhakar
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, Colorado, USA
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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38
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Cell-of-Origin and Genetic, Epigenetic, and Microenvironmental Factors Contribute to the Intra-Tumoral Heterogeneity of Pediatric Intracranial Ependymoma. Cancers (Basel) 2021; 13:cancers13236100. [PMID: 34885210 PMCID: PMC8657076 DOI: 10.3390/cancers13236100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/24/2021] [Accepted: 12/01/2021] [Indexed: 02/07/2023] Open
Abstract
Intra-tumoral heterogeneity (ITH) is a complex multifaceted phenomenon that posits major challenges for the clinical management of cancer patients. Genetic, epigenetic, and microenvironmental factors are concurrent drivers of diversity among the distinct populations of cancer cells. ITH may also be installed by cancer stem cells (CSCs), that foster unidirectional hierarchy of cellular phenotypes or, alternatively, shift dynamically between distinct cellular states. Ependymoma (EPN), a molecularly heterogeneous group of tumors, shows a specific spatiotemporal distribution that suggests a link between ependymomagenesis and alterations of the biological processes involved in embryonic brain development. In children, EPN most often arises intra-cranially and is associated with an adverse outcome. Emerging evidence shows that EPN displays large intra-patient heterogeneity. In this review, after touching on EPN inter-tumoral heterogeneity, we focus on the sources of ITH in pediatric intra-cranial EPN in the framework of the CSC paradigm. We also examine how single-cell technology has shed new light on the complexity and developmental origins of EPN and the potential impact that this understanding may have on the therapeutic strategies against this deadly pediatric malignancy.
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Zhang Q, Cheng S, Wang Y, Wang M, Lu Y, Wen Z, Ge Y, Ma Q, Chen Y, Zhang Y, Cao R, Li M, Liu W, Wang B, Wu Q, Jia W, Wang X. Interrogation of the microenvironmental landscape in spinal ependymomas reveals dual functions of tumor-associated macrophages. Nat Commun 2021; 12:6867. [PMID: 34824203 PMCID: PMC8617028 DOI: 10.1038/s41467-021-27018-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 11/01/2021] [Indexed: 02/01/2023] Open
Abstract
Spinal ependymomas are the most common spinal cord tumors in adults, but their intratumoral cellular heterogeneity has been less studied, and how spinal microglia are involved in tumor progression is still unknown. Here, our single-cell RNA-sequencing analyses of three spinal ependymoma subtypes dissect the microenvironmental landscape of spinal ependymomas and reveal tumor-associated macrophage (TAM) subsets with distinct functional phenotypes. CCL2+ TAMs are related to the immune response and exhibit a high capacity for apoptosis, while CD44+ TAMs are associated with tumor angiogenesis. By combining these results with those of single-cell ATAC-sequencing data analysis, we reveal that TEAD1 and EGR3 play roles in regulating the functional diversity of TAMs. We further identify diverse characteristics of both malignant cells and TAMs that might underlie the different malignant degrees of each subtype. Finally, assessment of cell-cell interactions reveal that stromal cells act as extracellular factors that mediate TAM diversity. Overall, our results reveal dual functions of TAMs in tumor progression, providing valuable insights for TAM-targeting immunotherapy.
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Affiliation(s)
- Qianqian Zhang
- State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Brain-Intelligence Technology (Shanghai), Bioland Laboratory (Guangzhou), Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Sijin Cheng
- State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Brain-Intelligence Technology (Shanghai), Bioland Laboratory (Guangzhou), Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Yongzhi Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, 100070, Beijing, China
- China National Clinical Research Center for Neurological Diseases, 100070, Beijing, China
| | - Mengdi Wang
- State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Brain-Intelligence Technology (Shanghai), Bioland Laboratory (Guangzhou), Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Yufeng Lu
- State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Brain-Intelligence Technology (Shanghai), Bioland Laboratory (Guangzhou), Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Zengqi Wen
- State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Brain-Intelligence Technology (Shanghai), Bioland Laboratory (Guangzhou), Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Yuxin Ge
- State Key Laboratory of Cognitive Neuroscience and Learning, IDG/McGovern Institute for Brain Research, Beijing Normal University, 100875, Beijing, China
| | - Qiang Ma
- State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Brain-Intelligence Technology (Shanghai), Bioland Laboratory (Guangzhou), Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Youqiao Chen
- State Key Laboratory of Cognitive Neuroscience and Learning, IDG/McGovern Institute for Brain Research, Beijing Normal University, 100875, Beijing, China
| | - Yaowu Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, 100070, Beijing, China
- China National Clinical Research Center for Neurological Diseases, 100070, Beijing, China
| | - Ren Cao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, 100070, Beijing, China
- China National Clinical Research Center for Neurological Diseases, 100070, Beijing, China
| | - Min Li
- State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Brain-Intelligence Technology (Shanghai), Bioland Laboratory (Guangzhou), Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Weihao Liu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, 100070, Beijing, China
- China National Clinical Research Center for Neurological Diseases, 100070, Beijing, China
| | - Bo Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, 100070, Beijing, China
- China National Clinical Research Center for Neurological Diseases, 100070, Beijing, China
| | - Qian Wu
- State Key Laboratory of Cognitive Neuroscience and Learning, IDG/McGovern Institute for Brain Research, Beijing Normal University, 100875, Beijing, China.
- Chinese Institute for Brain Research, 102206, Beijing, China.
| | - Wenqing Jia
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, 100070, Beijing, China.
- China National Clinical Research Center for Neurological Diseases, 100070, Beijing, China.
| | - Xiaoqun Wang
- State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Brain-Intelligence Technology (Shanghai), Bioland Laboratory (Guangzhou), Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
- Chinese Institute for Brain Research, 102206, Beijing, China.
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University & Capital Medical University, 100069, Beijing, China.
- Advanced Innovation Center for Human Brain Protection, Beijing Institute for Brain Disorders, Capital Medical University, 100069, Beijing, China.
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40
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Panwalkar P, Tamrazi B, Dang D, Chung C, Sweha S, Natarajan SK, Pun M, Bayliss J, Ogrodzinski MP, Pratt D, Mullan B, Hawes D, Yang F, Lu C, Sabari BR, Achreja A, Heon J, Animasahun O, Cieslik M, Dunham C, Yip S, Hukin J, Phillips JJ, Bornhorst M, Griesinger AM, Donson AM, Foreman NK, Garton HJ, Heth J, Muraszko K, Nazarian J, Koschmann C, Jiang L, Filbin MG, Nagrath D, Kool M, Korshunov A, Pfister SM, Gilbertson RJ, Allis CD, Chinnaiyan A, Lunt SY, Blüml S, Judkins AR, Venneti S. Targeting integrated epigenetic and metabolic pathways in lethal childhood PFA ependymomas. Sci Transl Med 2021; 13:eabc0497. [PMID: 34613815 PMCID: PMC8762577 DOI: 10.1126/scitranslmed.abc0497] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Childhood posterior fossa group A ependymomas (PFAs) have limited treatment options and bear dismal prognoses compared to group B ependymomas (PFBs). PFAs overexpress the oncohistone-like protein EZHIP (enhancer of Zeste homologs inhibitory protein), causing global reduction of repressive histone H3 lysine 27 trimethylation (H3K27me3), similar to the oncohistone H3K27M. Integrated metabolic analyses in patient-derived cells and tumors, single-cell RNA sequencing of tumors, and noninvasive metabolic imaging in patients demonstrated enhanced glycolysis and tricarboxylic acid (TCA) cycle metabolism in PFAs. Furthermore, high glycolytic gene expression in PFAs was associated with a poor outcome. PFAs demonstrated high EZHIP expression associated with poor prognosis and elevated activating mark histone H3 lysine 27 acetylation (H3K27ac). Genomic H3K27ac was enriched in PFAs at key glycolytic and TCA cycle–related genes including hexokinase-2 and pyruvate dehydrogenase. Similarly, mouse neuronal stem cells (NSCs) expressing wild-type EZHIP (EZHIP-WT) versus catalytically attenuated EZHIP-M406K demonstrated H3K27ac enrichment at hexokinase-2 and pyruvate dehydrogenase, accompanied by enhanced glycolysis and TCA cycle metabolism. AMPKα-2, a key component of the metabolic regulator AMP-activated protein kinase (AMPK), also showed H3K27ac enrichment in PFAs and EZHIP-WT NSCs. The AMPK activator metformin lowered EZHIP protein concentrations, increased H3K27me3, suppressed TCA cycle metabolism, and showed therapeutic efficacy in vitro and in vivo in patient-derived PFA xenografts in mice. Our data indicate that PFAs and EZHIP-WT–expressing NSCs are characterized by enhanced glycolysis and TCA cycle metabolism. Repurposing the antidiabetic drug metformin lowered pathogenic EZHIP, increased H3K27me3, and suppressed tumor growth, suggesting that targeting integrated metabolic/epigenetic pathways is a potential therapeutic strategy for treating childhood ependymomas.
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Affiliation(s)
- Pooja Panwalkar
- Laboratory of Brain Tumor Metabolism and Epigenetics, Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Benita Tamrazi
- Department of Radiology, Children’s Hospital Los Angeles, Keck School of Medicine University of Southern California, Los Angeles, CA, 90027, USA
| | - Derek Dang
- Laboratory of Brain Tumor Metabolism and Epigenetics, Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Chan Chung
- Laboratory of Brain Tumor Metabolism and Epigenetics, Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
- Current address- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea
| | - Stefan Sweha
- Laboratory of Brain Tumor Metabolism and Epigenetics, Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Siva Kumar Natarajan
- Laboratory of Brain Tumor Metabolism and Epigenetics, Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Matthew Pun
- Laboratory of Brain Tumor Metabolism and Epigenetics, Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jill Bayliss
- Laboratory of Brain Tumor Metabolism and Epigenetics, Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Martin P. Ogrodzinski
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48823, USA
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, 48823, USA
- Department of Physiology, Michigan State University, East Lansing, MI, 48823, USA
| | - Drew Pratt
- Laboratory of Brain Tumor Metabolism and Epigenetics, Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Brendan Mullan
- Department of Pediatrics, Michigan Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Debra Hawes
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Keck School of Medicine University of Southern California, Los Angeles, CA, 90027, USA
| | - Fusheng Yang
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Keck School of Medicine University of Southern California, Los Angeles, CA, 90027, USA
| | - Chao Lu
- Department of Genetics and Development and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Benjamin R. Sabari
- Laboratory of Chromatin Biology & Epigenetics, The Rockefeller University, New York, NY, 10065, USA
| | - Abhinav Achreja
- Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jin Heon
- Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Olamide Animasahun
- Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Marcin Cieslik
- Laboratory of Brain Tumor Metabolism and Epigenetics, Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Christopher Dunham
- Division of Anatomic Pathology, British Columbia Children's Hospital, Vancouver, British Columbia, V6H 3N1, Canada
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Stephen Yip
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Juliette Hukin
- Division of Hematology and Oncology, Children's and Women's Health Centre of B.C, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Joanna J. Phillips
- Department of Pathology, University of California, San Francisco, CA, 94132, USA
- Department of Neurological Surgery, University of California, San Francisco, CA, USA. 94132
| | - Miriam Bornhorst
- Research Center for Genetic Medicine, Children's National Health System, Washington DC, 20012, USA
- Brain Tumor Institute, Children's National Health System, Washington, DC 20012, USA
| | - Andrea M Griesinger
- Department of Pediatrics, University of Colorado Denver, Aurora, 80045, Colorado
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, 80045, Colorado
| | - Andrew M Donson
- Department of Pediatrics, University of Colorado Denver, Aurora, 80045, Colorado
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, 80045, Colorado
| | - Nicholas K Foreman
- Department of Pediatrics, University of Colorado Denver, Aurora, 80045, Colorado
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, 80045, Colorado
| | - Hugh J.L. Garton
- Department of Neurosurgery, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jason Heth
- Department of Neurosurgery, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Karin Muraszko
- Department of Neurosurgery, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Javad Nazarian
- Research Center for Genetic Medicine, Children's National Health System, Washington DC, 20012, USA
- Brain Tumor Institute, Children's National Health System, Washington, DC 20012, USA
- DMG Research Center Department of Oncology University Children's Hospital, CH-8032 Zürich
| | - Carl Koschmann
- Department of Pediatrics, Michigan Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Li Jiang
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02115, USA
| | - Mariella G. Filbin
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02115, USA
| | - Deepak Nagrath
- Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Marcel Kool
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, 69120, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, 69120, Germany
- Princess Máxima Center for Pediatric Oncology, Utrecht, 3584, the Netherlands
| | - Andrey Korshunov
- Department of Neuropathology, German Cancer Research Center (DKFZ), University Hospital Heidelberg and CCU Neuropathology, Heidelberg, 69120, Germany
| | - Stefan M. Pfister
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, 69120, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, 69120, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, 69120, Germany
| | | | - C. David Allis
- Laboratory of Chromatin Biology & Epigenetics, The Rockefeller University, New York, NY, 10065, USA
| | - Arul Chinnaiyan
- Laboratory of Brain Tumor Metabolism and Epigenetics, Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Sophia Y. Lunt
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48823, USA
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, 48823, USA
| | - Stefan Blüml
- Department of Radiology, Children’s Hospital Los Angeles, Keck School of Medicine University of Southern California, Los Angeles, CA, 90027, USA
| | - Alexander R. Judkins
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Keck School of Medicine University of Southern California, Los Angeles, CA, 90027, USA
| | - Sriram Venneti
- Laboratory of Brain Tumor Metabolism and Epigenetics, Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Pediatrics, Michigan Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
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Lötsch D, Kirchhofer D, Englinger B, Jiang L, Okonechnikov K, Senfter D, Laemmerer A, Gabler L, Pirker C, Donson AM, Bannauer P, Korbel P, Jaunecker CN, Hübner JM, Mayr L, Madlener S, Schmook MT, Ricken G, Maaß K, Grusch M, Holzmann K, Grasl-Kraupp B, Spiegl-Kreinecker S, Hsu J, Dorfer C, Rössler K, Azizi AA, Foreman NK, Peyrl A, Haberler C, Czech T, Slavc I, Filbin MG, Pajtler KW, Kool M, Berger W, Gojo J. Targeting fibroblast growth factor receptors to combat aggressive ependymoma. Acta Neuropathol 2021; 142:339-360. [PMID: 34046693 PMCID: PMC8270873 DOI: 10.1007/s00401-021-02327-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 04/10/2021] [Accepted: 05/10/2021] [Indexed: 12/16/2022]
Abstract
Ependymomas (EPN) are central nervous system tumors comprising both aggressive and more benign molecular subtypes. However, therapy of the high-risk subtypes posterior fossa group A (PF-A) and supratentorial RELA-fusion positive (ST-RELA) is limited to gross total resection and radiotherapy, as effective systemic treatment concepts are still lacking. We have recently described fibroblast growth factor receptors 1 and 3 (FGFR1/FGFR3) as oncogenic drivers of EPN. However, the underlying molecular mechanisms and their potential as therapeutic targets have not yet been investigated in detail. Making use of transcriptomic data across 467 EPN tissues, we found that FGFR1 and FGFR3 were both widely expressed across all molecular groups. FGFR3 mRNA levels were enriched in ST-RELA showing the highest expression among EPN as well as other brain tumors. We further identified high expression levels of fibroblast growth factor 1 and 2 (FGF1, FGF2) across all EPN subtypes while FGF9 was elevated in ST-EPN. Interrogation of our EPN single-cell RNA-sequencing data revealed that FGFR3 was further enriched in cycling and progenitor-like cell populations. Corroboratively, we found FGFR3 to be predominantly expressed in radial glia cells in both mouse embryonal and human brain datasets. Moreover, we detected alternative splicing of the FGFR1/3-IIIc variant, which is known to enhance ligand affinity and FGFR signaling. Dominant-negative interruption of FGFR1/3 activation in PF-A and ST-RELA cell models demonstrated inhibition of key oncogenic pathways leading to reduced cell growth and stem cell characteristics. To explore the feasibility of therapeutically targeting FGFR, we tested a panel of FGFR inhibitors in 12 patient-derived EPN cell models revealing sensitivity in the low-micromolar to nano-molar range. Finally, we gain the first clinical evidence for the activity of the FGFR inhibitor nintedanib in the treatment of a patient with recurrent ST-RELA. Together, these preclinical and clinical data suggest FGFR inhibition as a novel and feasible approach to combat aggressive EPN.
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MESH Headings
- Animals
- Central Nervous System Neoplasms/genetics
- Central Nervous System Neoplasms/pathology
- Ependymoma/genetics
- Ependymoma/pathology
- Humans
- Mice
- Neoplasm Recurrence, Local/genetics
- Neoplasm Recurrence, Local/metabolism
- Neoplasm Recurrence, Local/pathology
- Receptor, Fibroblast Growth Factor, Type 1/genetics
- Receptor, Fibroblast Growth Factor, Type 1/metabolism
- Receptor, Fibroblast Growth Factor, Type 3/metabolism
- Receptors, Fibroblast Growth Factor/genetics
- Receptors, Fibroblast Growth Factor/metabolism
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Affiliation(s)
- Daniela Lötsch
- Department of Neurosurgery, Medical University of Vienna, Vienna, Austria
- Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Dominik Kirchhofer
- Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Bernhard Englinger
- Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, USA
| | - Li Jiang
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, USA
| | - Konstantin Okonechnikov
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Daniel Senfter
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Anna Laemmerer
- Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Lisa Gabler
- Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Christine Pirker
- Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Andrew M Donson
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, USA
- Department of Pediatrics, University of Colorado Denver, Aurora, CO, USA
| | - Peter Bannauer
- Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Pia Korbel
- Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Carola N Jaunecker
- Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Jens-Martin Hübner
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Lisa Mayr
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Sibylle Madlener
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Maria T Schmook
- Department of Biomedical Imaging and Image-Guided Therapy, Medical University of Vienna, Vienna, Austria
| | - Gerda Ricken
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Kendra Maaß
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Michael Grusch
- Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Klaus Holzmann
- Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Bettina Grasl-Kraupp
- Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Sabine Spiegl-Kreinecker
- Department of Neurosurgery, Kepler University Hospital GmbH, Johannes Kepler University, Linz, Austria
| | - Jennifer Hsu
- Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Christian Dorfer
- Department of Neurosurgery, Medical University of Vienna, Vienna, Austria
| | - Karl Rössler
- Department of Neurosurgery, Medical University of Vienna, Vienna, Austria
| | - Amedeo A Azizi
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Nicholas K Foreman
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, USA
- Department of Pediatrics, University of Colorado Denver, Aurora, CO, USA
| | - Andreas Peyrl
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Christine Haberler
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Thomas Czech
- Department of Neurosurgery, Medical University of Vienna, Vienna, Austria
| | - Irene Slavc
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Mariella G Filbin
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, USA
| | - Kristian W Pajtler
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Haematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Marcel Kool
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Walter Berger
- Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Johannes Gojo
- Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria.
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria.
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany.
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Affiliation(s)
- Timothy A Ritzmann
- The Children's Brain Tumour Research Centre, University of Nottingham, Nottingham, UK
| | - John-Paul Kilday
- Children's Brain Tumour Research Network (CBTRN), Royal Manchester Children's Hospital, University of Manchester, Manchester, UK
| | - Richard G Grundy
- The Children's Brain Tumour Research Centre, University of Nottingham, Nottingham, UK
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Ozawa T, Kaneko S, Szulzewsky F, Qiao Z, Takadera M, Narita Y, Kondo T, Holland EC, Hamamoto R, Ichimura K. C11orf95-RELA fusion drives aberrant gene expression through the unique epigenetic regulation for ependymoma formation. Acta Neuropathol Commun 2021; 9:36. [PMID: 33685520 PMCID: PMC7941712 DOI: 10.1186/s40478-021-01135-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 02/21/2021] [Indexed: 12/13/2022] Open
Abstract
Recurrent C11orf95-RELA fusions (RELAFUS) are the hallmark of supratentorial ependymomas. The presence of RELA as the fusion partner indicates a close association of aberrant NF-κB activity with tumorigenesis. However, the oncogenic role of the C11orf95 has not been determined. Here, we performed ChIP-seq analyses to explore genomic regions bound by RELAFUS and H3K27ac proteins in human 293T and mouse ependymoma cells. We then utilized published RNA-Seq data from human and mouse RELAFUS tumors and identified target genes that were directly regulated by RELAFUS in these tumors. Subsequent transcription factor motif analyses of RELAFUS target genes detected a unique GC-rich motif recognized by the C11orf95 moiety, that is present in approximately half of RELAFUS target genes. Luciferase assays confirmed that a promoter carrying this motif is sufficient to drive RELAFUS-dependent gene expression. Further, the RELAFUS target genes were found to be overlapped with Rela target genes primarily via non-canonical NF-κB binding sites. Using a series of truncation and substitution mutants of RELAFUS, we also show that the activation domain in the RELAFUS moiety is necessary for the regulation of gene expression of these RELAFUS target genes. Lastly, we performed an anti-cancer drug screening with mouse ependymoma cells and identified potential anti-ependymoma drugs that are related to the oncogenic mechanism of RELAFUS. These findings suggested that RELAFUS might induce ependymoma formation through oncogenic pathways orchestrated by both C11orf95 and RELA target genes. Thus, our study unveils a complex gene function of RELAFUS as an oncogenic transcription factor in RELAFUS positive ependymomas.
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Servidei T, Meco D, Martini M, Battaglia A, Granitto A, Buzzonetti A, Babini G, Massimi L, Tamburrini G, Scambia G, Ruggiero A, Riccardi R. The BET Inhibitor OTX015 Exhibits In Vitro and In Vivo Antitumor Activity in Pediatric Ependymoma Stem Cell Models. Int J Mol Sci 2021; 22:ijms22041877. [PMID: 33668642 PMCID: PMC7918371 DOI: 10.3390/ijms22041877] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 02/02/2021] [Accepted: 02/10/2021] [Indexed: 12/28/2022] Open
Abstract
Childhood ependymomas are heterogenous chemoresistant neoplasms arising from aberrant stem-like cells. Epigenome deregulation plays a pivotal role in ependymoma pathogenesis, suggesting that epigenetic modifiers hold therapeutic promise against this disease. Bromodomain and extraterminal domain (BET) proteins are epigenome readers of acetylated signals in histones and coactivators for oncogenic and stemness-related transcriptional networks, including MYC/MYCN (Proto-Oncogene, BHLH Transcritpion Factor)-regulated genes. We explored BET inhibition as an anticancer strategy in a panel of pediatric patient-derived ependymoma stem cell models by OTX015-mediated suppression of BET/acetylated histone binding. We found that ependymoma tissues and lines express BET proteins and their targets MYC and MYCN. In vitro, OTX015 reduced cell proliferation by inducing G0/G1-phase accumulation and apoptosis at clinically tolerable doses. Mechanistically, inhibitory p21 and p27 increased in a p53-independent manner, whereas the proliferative driver, phospho-signal transducer and activator of transcription 3 (STAT3), decreased. Upregulation of apoptosis-related proteins and survivin downregulation were correlated with cell line drug sensitivity. Minor alterations of MYC/MYCN expression were reported. In vivo, OTX015 significantly improved survival in 2/3 orthotopic ependymoma models. BET proteins represent promising targets for pharmaceutical intervention with OTX015 against ependymoma. The identification of predictive determinants of sensitivity may help identify ependymoma molecular subsets more likely to benefit from BET inhibitor therapies.
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Affiliation(s)
- Tiziana Servidei
- UOC Pediatric Oncology, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (D.M.); (A.R.); (R.R.)
- Correspondence: ; Tel.: +39-06-30155165
| | - Daniela Meco
- UOC Pediatric Oncology, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (D.M.); (A.R.); (R.R.)
| | - Maurizio Martini
- Department of Pathology, Fondazione Policlinico Universitario A. Gemelli IRCCS, Catholic University of Sacred Heart, 00168 Rome, Italy; (M.M.); (A.G.)
| | - Alessandra Battaglia
- Department of Life Sciences and Public Health, Section of Gynecology and Obstetrics, Catholic University of Sacred Heart, 00168 Rome, Italy;
| | - Alessia Granitto
- Department of Pathology, Fondazione Policlinico Universitario A. Gemelli IRCCS, Catholic University of Sacred Heart, 00168 Rome, Italy; (M.M.); (A.G.)
| | - Alexia Buzzonetti
- UOC Oncological Gynecology, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (A.B.); (G.B.); (G.S.)
| | - Gabriele Babini
- UOC Oncological Gynecology, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (A.B.); (G.B.); (G.S.)
| | - Luca Massimi
- UOC Neurochirurgia Infantile, Dipartimento di Scienze Dell’Invecchiamento, Neurologiche, Ortopediche e della Testa-Collo, Fondazione Policlinico Universitario A. Gemelli—IRCCS, Università Cattolica del Sacro Cuore, 00168 Roma, Italy; (L.M.); (G.T.)
| | - Gianpiero Tamburrini
- UOC Neurochirurgia Infantile, Dipartimento di Scienze Dell’Invecchiamento, Neurologiche, Ortopediche e della Testa-Collo, Fondazione Policlinico Universitario A. Gemelli—IRCCS, Università Cattolica del Sacro Cuore, 00168 Roma, Italy; (L.M.); (G.T.)
| | - Giovanni Scambia
- UOC Oncological Gynecology, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (A.B.); (G.B.); (G.S.)
| | - Antonio Ruggiero
- UOC Pediatric Oncology, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (D.M.); (A.R.); (R.R.)
| | - Riccardo Riccardi
- UOC Pediatric Oncology, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (D.M.); (A.R.); (R.R.)
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Decreased content of ascorbic acid (vitamin C) in the brain of knockout mouse models of Na+,K+-ATPase-related neurologic disorders. PLoS One 2021; 16:e0246678. [PMID: 33544780 PMCID: PMC7864419 DOI: 10.1371/journal.pone.0246678] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 01/23/2021] [Indexed: 12/21/2022] Open
Abstract
Na+,K+-ATPase is a crucial protein responsible for maintaining the electrochemical gradients across the cell membrane. The Na+,K+-ATPase is comprised of catalytic α, β, and γ subunits. In adult brains, the α3 subunit, encoded by ATP1A3, is predominantly expressed in neurons, whereas the α2 subunit, encoded by ATP1A2, is expressed in glial cells. In foetal brains, the α2 is expressed in neurons as well. Mutations in α subunits cause a variety of neurologic disorders. Notably, the onset of symptoms in ATP1A2- and ATP1A3-related neurologic disorders is usually triggered by physiological or psychological stressors. To gain insight into the distinct roles of the α2 and α3 subunits in the developing foetal brain, whose developmental dysfunction may be a predisposing factor of neurologic disorders, we compared the phenotypes of mouse foetuses with double homozygous knockout of Atp1a2 and Atp1a3 (α2α3-dKO) to those with single knockout. The brain haemorrhage phenotype of α2α3-dKO was similar to that of homozygous knockout of the gene encoding ascorbic acid (ASC or vitamin C) transporter, SVCT2. The α2α3-dKO brain showed significantly decreased level of ASC compared with the wild-type (WT) and single knockout. We found that the ASC content in the basal ganglia and cerebellum was significantly lower in the adult Atp1a3 heterozygous knockout mouse (α3-HT) than in the WT. Interestingly, we observed a significant decrease in the ASC level in the basal ganglia and cerebellum of α3-HT in the peripartum period, during which mice are under physiological stress. These observations indicate that the α2 and α3 subunits independently contribute to the ASC level in the foetal brain and that the α3 subunit contributes to ASC transport in the adult basal ganglia and cerebellum. We propose that decreases in ASC levels may affect neural network development and are linked to the pathophysiology of ATP1A2- and ATP1A3-related neurologic disorders.
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