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Ramos SI, Mussa Z, Giotti B, Tsankov A, Tsankova N. EPCO-25. MULTI-OMIC ANALYSIS OF THE GLIOBLASTOMA EPIGENOME AND TRANSCRIPTOME INFORMS OF MIGRATORY INTERNEURON-LIKE DEVELOPMENTAL REGULATORS. Neuro Oncol 2022. [PMCID: PMC9660401 DOI: 10.1093/neuonc/noac209.460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract
Recent studies have demonstrated that, despite their nomenclature, gliomas recapitulate an interneuron progenitor-like state that drives tumor progression. During human neurodevelopment, interneurons arise from the subcortical ganglionic eminences and migrate tangentially into the neocortex, settling in the cortical plate where they integrate local neurocircuitry. Analogously, malignant glioblastoma (GBM) cells migrate from the tumor core into the surrounding healthy tissue. This innate infiltrative property renders these malignant cells elusive to surgical resection, leading to tumor recurrence. To understand the regulatory networks that drive tumor infiltration from a neurodevelopmental perspective, we generated a single-nucleus Assay for Transposase-Accessible Chromatin sequencing (snATAC-seq) dataset of 41,000 nuclei from the core and infiltrative edge of surgically resected GBM specimens (n = 4). Concurrently, we sequenced 46,000 nuclei from non-pathological, postmortem samples of second- and third-trimester neocortices (n = 17). We integrated these datasets with paired single-nucleus RNA sequencing (snRNA-seq) data and identified candidate regulatory TFs that exhibit high correlation between motif enrichment and TF expression. Using single-trajectory inference and pseudo-time analyses, we identified TCF12 as a potential driver of interneuron lineage fate in developing cortical progenitors. Given its implication in projection neuron migration, we were intrigued to find that TCF12 activity is highest in GBM cells with a migratory interneuron signature, hinting at its putative role in tumor infiltration. To understand the significance of these findings, we will interrogate other genes in the TCF12 regulatory network with the ultimate goal of identifying therapeutic targets that inhibit GBM infiltration.
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Affiliation(s)
| | - Zarmeen Mussa
- Icahn School of Medicine at Mount Sinai , New York , USA
| | - Bruno Giotti
- Icahn School of Medicine at Mount Sinai , New York , USA
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Mussa Z, Ramos S, Beaumont K, Sebra R, Tsankov A, Tsankova N. EPCO-11. SINGLE-NUCLEI TRANSCRIPTOMICS RELATES GLIOBLASTOMA INFILTRATION TO DISTINCT GLIAL PROGENITOR STATES. Neuro Oncol 2021. [DOI: 10.1093/neuonc/noab196.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Our understanding of glioblastoma (GBM) intratumoral heterogeneity, particularly in the context of neurodevelopment, has thus far been primarily focused on the more surgically accessible tumor core niche. In contrast, the biology of GBM cells at the infiltrative edge, which evade surgical resection and drive tumor recurrence, remains poorly characterized. To this end, we microdissected and performed single-nuclei RNA sequencing (snRNA-seq) on approximately 62,000 nuclei taken from the tumor core and from the infiltrative edge of six GBM tumors with diverse genomic drivers, including IDH1, EGFR, PDGFRA, FGFR3, and NF1. Unbiased clustering reveals distinct neoplastic and non-neoplastic populations, further distinguished using copy number variation analysis. After projecting previously defined signatures taken from snRNA-seq analysis of human adult neocortex/subventricular zone and prenatal germinal matrix, we find that approximately 90% of tumor cells recapitulate a neurodevelopment-like molecular phenotype, reprising gene expression signatures of prenatal astrocytes and of a distinct glial intermediate progenitor cell population (g-IPC) that precedes both astrocyte and oligodendrocyte lineage differentiation. Examining the infiltrative edge of samples with the most confident microdissection (n=4), we see that while distinct populations of tumor cells in this niche express proneural and classical signatures, these cells are overall enriched for a g-IPC-like phenotype, relative to the tumor core, irrespective of the tumors’ genomic alterations. A subset of cells at the infiltrative edge, in particular, recapitulates the signature of an uncommitted g-IPC subtype, expressing both astroglial and oligodendroglial markers. Trajectory analyses also reveal distinct branches of core and edge tumor cells, which are predominantly astrocyte- and g-IPC-like, respectively. Differential gene expression analysis of GBM cells at the infiltrative edge vs. tumor core reveals a migration signature, dominated by EGFR, ERBB4, PCDH9, and PCDH15. Ultimately, this high resolution analysis of heterogeneity at the infiltrative edge allows us to uncover potentially targetable drivers of invasion in GBM.
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Affiliation(s)
- Zarmeen Mussa
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Susana Ramos
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Robert Sebra
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
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Barrette AM, Ronk H, Joshi T, Mussa Z, Mehrotra M, Bouras A, Nudelman G, Jesu Raj JG, Bozec D, Lam W, Houldsworth J, Yong R, Zaslavsky E, Hadjipanayis CG, Birtwistle MR, Tsankova NM. Anti-invasive efficacy and survival benefit of the YAP-TEAD inhibitor Verteporfin in preclinical glioblastoma models. Neuro Oncol 2021; 24:694-707. [PMID: 34657158 DOI: 10.1093/neuonc/noab244] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Glioblastoma (GBM) remains a largely incurable disease as current therapy fails to target the invasive nature of GBM growth in disease progression and recurrence. Here we use the FDA-approved drug and small molecule Hippo inhibitor Verteporfin to target YAP-TEAD activity, known to mediate convergent aspects of tumor invasion/metastasis, and assess the drug's efficacy and survival benefit in GBM models. METHODS Up to eight low-passage patient-derived GBM cell lines with distinct genomic drivers, including three primary/recurrent pairs, were treated with Verteporfin or vehicle to assess in-vitro effects on proliferation, migration, YAP-TEAD activity, and transcriptomics. Patient-derived orthotopic xenograft models (PDX) were used to assess Verteporfin's brain penetrance and effects on tumor burden and survival. RESULTS Verteporfin treatment disturbed YAP/TAZ-TEAD activity; disrupted transcriptome signatures related to invasion, epithelial-to-mesenchymal, and proneural-to-mesenchymal transition, phenocopying TEAD1-knockout effects; and impaired tumor migration/invasion dynamics across primary and recurrent GBM lines. In an aggressive orthotopic PDX GBM model, short-term Verteporfin treatment consistently diminished core and infiltrative tumor burden, which was associated with decreased tumor expression of Ki67, nuclear YAP, TEAD1, and TEAD-associated targets EGFR, CDH2 and ITGB1. Finally, long-term Verteporfin treatment appeared non-toxic and conferred survival benefit compared to vehicle in two PDX models: as monotherapy in primary (de-novo) GBM and in combination with Temozolomide chemoradiation in recurrent GBM, where VP treatment associated with increased MGMT methylation. CONCLUSIONS We demonstrate combined anti-invasive and anti-proliferative efficacy for Verteporfin with survival benefit in preclinical GBM models, indicating potential therapeutic value of this already FDA-approved drug if repurposed for glioblastoma patients.
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Affiliation(s)
- Anne Marie Barrette
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Neurosurgery, Stanford University, Stanford, CA, USA
| | - Halle Ronk
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tanvi Joshi
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zarmeen Mussa
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Meenakshi Mehrotra
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexandros Bouras
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - German Nudelman
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joe G Jesu Raj
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dominique Bozec
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - William Lam
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jane Houldsworth
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Raymund Yong
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elena Zaslavsky
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Marc R Birtwistle
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina, USA
| | - Nadejda M Tsankova
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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El Jamal SM, Pujadas E, Ramos I, Bryce C, Grimes ZM, Amanat F, Tsankova NM, Mussa Z, Olson S, Salem F, Miorin L, Aydillo T, Schotsaert M, Albrecht RA, Liu WC, Marjanovic N, Francoeur N, Sebra R, Sealfon SC, García-Sastre A, Fowkes M, Cordon-Cardo C, Westra WH. Tissue-based SARS-CoV-2 detection in fatal COVID-19 infections: Sustained direct viral-induced damage is not necessary to drive disease progression. Hum Pathol 2021; 114:110-119. [PMID: 33961839 PMCID: PMC8095022 DOI: 10.1016/j.humpath.2021.04.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/23/2021] [Accepted: 04/28/2021] [Indexed: 12/16/2022]
Abstract
Coronavirus disease 2019 (COVID-19) is an ongoing pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although viral infection is known to trigger inflammatory processes contributing to tissue injury and organ failure, it is unclear whether direct viral damage is needed to sustain cellular injury. An understanding of pathogenic mechanisms has been handicapped by the absence of optimized methods to visualize the presence and distribution of SARS-CoV-2 in damaged tissues. We first developed a positive control cell line (Vero E6) to validate SARS-CoV-2 detection assays. We then evaluated multiple organs (lungs, kidneys, heart, liver, brain, intestines, lymph nodes, and spleen) from fourteen COVID-19 autopsy cases using immunohistochemistry (IHC) for the spike and the nucleoprotein proteins, and RNA in situ hybridization (RNA ISH) for the spike protein mRNA. Tissue detection assays were compared with quantitative polymerase chain reaction (qPCR)-based detection. SARS-CoV-2 was histologically detected in the Vero E6 positive cell line control, 1 of 14 (7%) lungs, and none (0%) of the other 59 organs. There was perfect concordance between the IHC and RNA ISH results. qPCR confirmed high viral load in the SARS-CoV-2 ISH-positive lung tissue, and absent or low viral load in all ISH-negative tissues. In patients who die of COVID-19-related organ failure, SARS-CoV-2 is largely not detectable using tissue-based assays. Even in lungs showing widespread injury, SARS-CoV-2 viral RNA or proteins were detected in only a small minority of cases. This observation supports the concept that viral infection is primarily a trigger for multiple-organ pathogenic proinflammatory responses. Direct viral tissue damage is a transient phenomenon that is generally not sustained throughout disease progression.
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Affiliation(s)
- Siraj M El Jamal
- Departments of Pathology, Molecular and Cell-Based Medicine, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA.
| | - Elisabet Pujadas
- Departments of Pathology, Molecular and Cell-Based Medicine, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA
| | - Irene Ramos
- Department of Neurology, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029 USA
| | - Clare Bryce
- Departments of Pathology, Molecular and Cell-Based Medicine, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA
| | - Zachary M Grimes
- Departments of Pathology, Molecular and Cell-Based Medicine, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA
| | - Fatima Amanat
- Department of Microbiology, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA
| | - Nadejda M Tsankova
- Departments of Pathology, Molecular and Cell-Based Medicine, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA
| | - Zarmeen Mussa
- Departments of Pathology, Molecular and Cell-Based Medicine, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA
| | - Sara Olson
- Departments of Pathology, Molecular and Cell-Based Medicine, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA
| | - Fadi Salem
- Departments of Pathology, Molecular and Cell-Based Medicine, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA
| | - Lisa Miorin
- Department of Microbiology, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA; Global Health and Emerging Pathogens Institute, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA
| | - Teresa Aydillo
- Department of Microbiology, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA; Global Health and Emerging Pathogens Institute, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA
| | - Michael Schotsaert
- Department of Microbiology, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA; Global Health and Emerging Pathogens Institute, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA
| | - Randy A Albrecht
- Department of Microbiology, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA; Global Health and Emerging Pathogens Institute, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA
| | - Wen-Chun Liu
- Department of Microbiology, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA; Global Health and Emerging Pathogens Institute, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA; Biomedical Translation Research Center, Academia Sinica, Taipei, 11571, Taiwan
| | - Nada Marjanovic
- Department of Microbiology, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA
| | - Nancy Francoeur
- Department of Genetics and Genomic Sciences, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA; Sema4, Stamford, CT, 10029, USA
| | - Stuart C Sealfon
- Department of Neurology, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029 USA
| | - Adolfo García-Sastre
- Department of Microbiology, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA; Global Health and Emerging Pathogens Institute, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA; Department of Medicine, Division of Infectious Diseases, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA; The Tisch Cancer Institute, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA
| | - Mary Fowkes
- Departments of Pathology, Molecular and Cell-Based Medicine, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA
| | - Carlos Cordon-Cardo
- Departments of Pathology, Molecular and Cell-Based Medicine, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA
| | - William H Westra
- Departments of Pathology, Molecular and Cell-Based Medicine, The Icahn School of Medicine at Mount Sinai Hospital, New York, NY, 10029, USA.
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Mussa Z, Tome-Garcia J, Jiang Y, Akbarian S, Tsankova NM. Isolation of Adult Human Astrocyte Populations from Fresh-frozen Cortex using Fluorescence-Activated Nuclei Sorting. J Vis Exp 2021. [PMID: 33938880 DOI: 10.3791/62405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The complexity of human astrocytes remains poorly defined in primary human tissue, requiring better tools for their isolation and molecular characterization. Fluorescence-activated nuclei sorting (FANS) can be used to successfully isolate and study human neuronal nuclei (NeuN+) populations from frozen archival tissue, thereby avoiding problems associated with handling fresh tissue. However, efforts to similarly isolate astroglia from the non-neuronal (NeuN-) element are lacking. A recently developed and validated immunotagging strategy uses three transcription factor antibodies to simultaneously isolate enriched neuronal (NeuN+), astrocyte (paired box protein 6 (PAX6)+NeuN-), and oligodendrocyte progenitor (OLIG2+NeuN-) nuclei populations from non-diseased, fresh (unfixed) snap-frozen postmortem human temporal neocortex tissue. This technique was shown to be useful for the characterization of cell type-specific transcriptome alterations in primary pathological epilepsy neocortex. Transcriptomic analyses confirmed that PAX6+NeuN- sorted populations are robustly enriched for pan-astrocyte markers and capture astrocytes in both resting and reactive conditions. This paper describes the FANS methodology for the isolation of astrocyte-enriched nuclei populations from fresh-frozen human cortex, including tissue dissociation into single-nucleus (sn) suspension; immunotagging of nuclei with anti-NeuN and anti-PAX6 fluorescently conjugated antibodies; FANS gating strategies and quality control metrics for optimizing sensitivity and specificity during sorting and for confirming astrocyte enrichment; and recommended procurement for downstream transcriptome and chromatin accessibility sequencing at bulk or sn resolution. This protocol is applicable for non-necrotic, fresh-frozen, human cortical specimens with various pathologies and recommended postmortem tissue collection within 24 h.
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Affiliation(s)
- Zarmeen Mussa
- Department of Pathology, Icahn School of Medicine at Mount Sinai; Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai
| | - Jessica Tome-Garcia
- Department of Pathology, Icahn School of Medicine at Mount Sinai; Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai
| | - Yan Jiang
- Institutes of Brian Science, Fudan University
| | - Schahram Akbarian
- Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai; Department of Psychiatry, Icahn School of Medicine at Mount Sinai
| | - Nadejda M Tsankova
- Department of Pathology, Icahn School of Medicine at Mount Sinai; Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai;
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Barrette AM, Bouras A, Nudelman G, Mussa Z, Zaslavsky E, Hadjipanayis C, Birtwistle M, Tsankova N. EXTH-51. ANTI-INVASIVE EFFICACY AND SURVIVAL BENEFIT OF THE YAP-TEAD INHIBITOR VERTEPORFIN IN PRECLINICAL GLIOBLASTOMA MODELS. Neuro Oncol 2020. [DOI: 10.1093/neuonc/noaa215.405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Glioblastoma (GBM) remains an incurable disease, in large part due to its malignant infiltrative spread, and current clinical therapy fails to target the invasive nature of tumor cells in disease progression and recurrence. Here, we use the YAP-TEAD inhibitor Verteporfin to target a convergence point for regulating tumor invasion/metastasis and establish the robust anti-invasive therapeutic efficacy of this FDA-approved drug and its survival benefit across several preclinical glioma models. Using patient-derived GBM cells and orthotopic xenograft models (PDX), we show that Verteporfin treatment disrupts YAP/TAZ-TEAD activity and processes related to cell adhesion, migration and epithelial-mesenchymal transition. In-vitro, Verteporfin impairs tumor migration, invasion and motility dynamics. In-vivo, intraperitoneal administration of Verteporfin in mice with orthotopic PDX tumors shows consistent drug accumulation within the brain and decreased infiltrative tumor burden, across three independent experiments. Interestingly, PDX tumors with impaired invasion after Verteporfin treatment downregulate CDH2 and ITGB1 adhesion protein levels within the tumor microenvironment. Finally, Verteporfin treatment confers survival benefit in two independent PDX models: as monotherapy in de-novo GBM and in combination with standard-of-care chemoradiation in recurrent GBM. These findings indicate potential therapeutic value of this FDA-approved drug if repurposed for GBM patients.
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Affiliation(s)
| | | | | | - Zarmeen Mussa
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
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Mussa Z, Ramos S, Nabel E, Allette K, Hamid A, Cai M, Zhao W, Wang YC, Beaumont K, Sebra R, Tsankov A, Tsankova N. EPCO-20. RELATING GLIOBLASTOMA HETEROGENEITY TO HUMAN FETAL GLIAL DEVELOPMENT THROUGH HIGH RESOLUTION SINGLE NUCLEI TRANSCRIPTOMICS. Neuro Oncol 2020. [DOI: 10.1093/neuonc/noaa215.299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Glioblastoma (GBM) is thought to be driven by a therapy-resistant cancer stem cell population that recapitulates developmental phenotypes. Direct comparisons of GBM to glial states during human fetal development are limited due to paucity of data from late prenatal gestation, when gliogenesis is thought to occur. Here, we generated a comprehensive single nuclei RNA sequencing (snRNAseq) dataset of approximately 200,000 nuclei taken from the germinal matrix and the cortical plate of 16 fetal postmortem samples, ranging from 17 to 41 gestational weeks, enabling high spatiotemporal resolution of late neurogenesis and early-to-peak gliogenesis. We performed unbiased clustering to identify broad cell types within each sample and integrated all fetal samples to analyze evolving glial states and relationships across two regions and four developmental stages. Subclustering analysis of developing glia from the germinal matrix and cortical plate resolved developmental cell type signatures that are absent in the adult brain. Trajectory inference and pseudo-time analyses reconstructed relationships within these glial lineages and states, identifying a robust common glial progenitor population (GPC) with distinct signature, preceding both oligodendrocyte progenitor cell (OPC) and astrocyte lineage commitment during late prenatal development. We then performed snRNAseq on approximately 30,000 nuclei taken from the core and infiltrating edge of two surgically resected GBM samples with IDH-mutant and IDH-wildtype status and EGFR amplification. Uniform manifold approximation and projection (UMAP) dimensionality reduction revealed distinct neoplastic and non-neoplastic population clusters within each GBM sample. Projecting our previously defined neural stem cell / progenitor signatures onto each GBM UMAP identified notable predominance of the GPC-like developmental signature throughout both GBM tumors with focal minor contributions from the OPC-, transit amplifying-, and astrocyte-like signatures. The high spatial and temporal resolution of the generated roadmap dissolves GBM intratumoral heterogeneity into distinct developmental molecular states driven by potentially targetable regulatory networks.
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Affiliation(s)
- Zarmeen Mussa
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Susana Ramos
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elisa Nabel
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Ammar Hamid
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Maggie Cai
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Will Zhao
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ying-chih Wang
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Robert Sebra
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
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