1
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Miller TE, El Farran CA, Couturier CP, Chen Z, D’Antonio JP, Verga J, Villanueva MA, Castro LNG, Tong YE, Saadi TA, Chiocca AN, Fischer DS, Heiland DH, Guerriero JL, Petrecca K, Suva ML, Shalek AK, Bernstein BE. Programs, Origins, and Niches of Immunomodulatory Myeloid Cells in Gliomas. bioRxiv 2023:2023.10.24.563466. [PMID: 37961527 PMCID: PMC10634776 DOI: 10.1101/2023.10.24.563466] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Gliomas are incurable malignancies notable for an immunosuppressive microenvironment with abundant myeloid cells whose immunomodulatory properties remain poorly defined. Here, utilizing scRNA-seq data for 183,062 myeloid cells from 85 human tumors, we discover that nearly all glioma-associated myeloid cells express at least one of four immunomodulatory activity programs: Scavenger Immunosuppressive, C1Q Immunosuppressive, CXCR4 Inflammatory, and IL1B Inflammatory. All four programs are present in IDH1 mutant and wild-type gliomas and are expressed in macrophages, monocytes, and microglia whether of blood or resident myeloid cell origins. Integrating our scRNA-seq data with mitochondrial DNA-based lineage tracing, spatial transcriptomics, and organoid explant systems that model peripheral monocyte infiltration, we show that these programs are driven by microenvironmental cues and therapies rather than myeloid cell type, origin, or mutation status. The C1Q Immunosuppressive program is driven by routinely administered dexamethasone. The Scavenger Immunosuppressive program includes ligands with established roles in T-cell suppression, is induced in hypoxic regions, and is associated with immunotherapy resistance. Both immunosuppressive programs are less prevalent in lower-grade gliomas, which are instead enriched for the CXCR4 Inflammatory program. Our study provides a framework to understand immunomodulatory myeloid cells in glioma, and a foundation to develop more effective immunotherapies.
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Affiliation(s)
- Tyler E. Miller
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA
- Department of Cell Biology and Pathology, Harvard Medical School, Boston, MA 02215, USA
- Ludwig Center at Harvard Medical School, Boston, MA, USA
| | - Chadi A. El Farran
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA
- Department of Cell Biology and Pathology, Harvard Medical School, Boston, MA 02215, USA
- Ludwig Center at Harvard Medical School, Boston, MA, USA
| | - Charles P. Couturier
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA
- Institute for Medical Engineering and Sciences and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Neurosurgery, Brigham and Women’s Hospital, Boston, MA 02115 USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Zeyu Chen
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA
- Department of Cell Biology and Pathology, Harvard Medical School, Boston, MA 02215, USA
| | - Joshua P. D’Antonio
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA
- Department of Cell Biology and Pathology, Harvard Medical School, Boston, MA 02215, USA
| | - Julia Verga
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA
| | - Martin A. Villanueva
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Institute for Medical Engineering and Sciences and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - L. Nicolas Gonzalez Castro
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Center for Neuro-Oncology, Dana-Farber Cancer Institute; Department of Neurology, Brigham and Women’s Hospital, Boston, MA 02115 USA
| | - Yuzhou Evelyn Tong
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Institute for Medical Engineering and Sciences and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Tariq Al Saadi
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, Quebec, Canada
| | - Andrew N. Chiocca
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA
| | | | - Dieter Henrik Heiland
- Microenvironment and Immunology Research Laboratory, Medical Center - University of Freiburg, Freiburg, Germany. Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, USA
| | - Jennifer L. Guerriero
- Ludwig Center at Harvard Medical School, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Cancer Institute; Division of Breast Surgery, Department of Surgery, Brigham and Women’s Hospital, Boston, MA, USA
| | - Kevin Petrecca
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, Quebec, Canada
| | - Mario L. Suva
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Alex K. Shalek
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Institute for Medical Engineering and Sciences and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Bradley E. Bernstein
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA
- Department of Cell Biology and Pathology, Harvard Medical School, Boston, MA 02215, USA
- Ludwig Center at Harvard Medical School, Boston, MA, USA
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2
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Takahashi M, Chong HB, Zhang S, Lazarov MJ, Harry S, Maynard M, White R, Murrey HE, Hilbert B, Neil JR, Gohar M, Ge M, Zhang J, Durr BR, Kryukov G, Tsou CC, Brooijmans N, Alghali ASO, Rubio K, Vilanueva A, Harrison D, Koglin AS, Ojeda S, Karakyriakou B, Healy A, Assaad J, Makram F, Rachman I, Khandelwal N, Tien PC, Popoola G, Chen N, Vordermark K, Richter M, Patel H, Yang TY, Griesshaber H, Hosp T, van den Ouweland S, Hara T, Bussema L, Dong R, Shi L, Rasmussen MQ, Domingues AC, Lawless A, Fang J, Yoda S, Nguyen LP, Reeves SM, Wakefield FN, Acker A, Clark SE, Dubash T, Fisher DE, Maheswaran S, Haber DA, Boland G, Sade-Feldman M, Jenkins R, Hata A, Bardeesy N, Suva ML, Martin B, Liau B, Ott C, Rivera MN, Lawrence MS, Bar-Peled L. DrugMap: A quantitative pan-cancer analysis of cysteine ligandability. bioRxiv 2023:2023.10.20.563287. [PMID: 37961514 PMCID: PMC10634688 DOI: 10.1101/2023.10.20.563287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Cysteine-focused chemical proteomic platforms have accelerated the clinical development of covalent inhibitors of a wide-range of targets in cancer. However, how different oncogenic contexts influence cysteine targeting remains unknown. To address this question, we have developed DrugMap , an atlas of cysteine ligandability compiled across 416 cancer cell lines. We unexpectedly find that cysteine ligandability varies across cancer cell lines, and we attribute this to differences in cellular redox states, protein conformational changes, and genetic mutations. Leveraging these findings, we identify actionable cysteines in NFκB1 and SOX10 and develop corresponding covalent ligands that block the activity of these transcription factors. We demonstrate that the NFκB1 probe blocks DNA binding, whereas the SOX10 ligand increases SOX10-SOX10 interactions and disrupts melanoma transcriptional signaling. Our findings reveal heterogeneity in cysteine ligandability across cancers, pinpoint cell-intrinsic features driving cysteine targeting, and illustrate the use of covalent probes to disrupt oncogenic transcription factor activity.
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3
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Chanoch-Myers R, Wider A, Suva ML, Tirosh I. Correction: Elucidating the diversity of malignant mesenchymal states in glioblastoma by integrative analysis. Genome Med 2022; 14:117. [PMID: 36224665 PMCID: PMC9559008 DOI: 10.1186/s13073-022-01122-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Affiliation(s)
- Rony Chanoch-Myers
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Adi Wider
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Mario L Suva
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Itay Tirosh
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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4
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Chanoch-Myers R, Wider A, Suva ML, Tirosh I. Elucidating the diversity of malignant mesenchymal states in glioblastoma by integrative analysis. Genome Med 2022; 14:106. [PMID: 36123598 PMCID: PMC9484143 DOI: 10.1186/s13073-022-01109-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 08/31/2022] [Indexed: 12/15/2022] Open
Abstract
Background Multiple glioblastoma studies have described a mesenchymal (MES) state, with each study defining the MES program by distinct sets of genes and highlighting distinct functional associations, including both immune activation and suppression. These variable descriptions complicate our understanding of the MES state and its implications. Here, we hypothesize that there is a range of glioma MES states, possibly reflecting distinct prior states in which a MES program can be induced, and/or distinct mechanisms that induce the MES states in those cells. Methods We integrated multiple published single-cell and bulk RNA sequencing datasets and MES signatures to define a core MES program that recurs across studies, as well as multiple function-specific MES signatures that vary across MES cells. We then examined the co-occurrence of these signatures and their associations with genetic and microenvironmental features. Results Based on co-occurrence of MES signatures, we found three main variants of MES states: hypoxia-related (MES-Hyp), astrocyte-related (MES-Ast), and an intermediate state. Notably, the MES states are differentially associated with genetic and microenvironmental features. MES-Hyp is preferentially associated with NF1 deletion, overall macrophage abundance, a high macrophage/microglia ratio, and M2-related macrophages, consistent with previous studies that associated MES with immune suppression. In contrast, MES-Ast is associated with T cell abundance and cytotoxicity, consistent with immune activation through expression of MHC-I/II. Conclusions Diverse MES states occur in glioblastoma. These states share a subset of core genes but differ primarily in their association with hypoxia vs. astrocytic expression programs, and with immune suppression vs. activation, respectively. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-022-01109-8.
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Affiliation(s)
- Rony Chanoch-Myers
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Adi Wider
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Mario L Suva
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Itay Tirosh
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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5
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Natsumeda M, Miyahara H, Yoshimura J, Nakata S, Nozawa T, Ito J, Kanemaru Y, Watanabe J, Tsukamoto Y, Okada M, Oishi M, Hirato J, Wataya T, Ahsan S, Tateishi K, Yamamoto T, Rodriguez FJ, Takahashi H, Hovestadt V, Suva ML, Taylor MD, Eberhart CG, Fujii Y, Kakita A. GLI3 Is Associated With Neuronal Differentiation in SHH-Activated and WNT-Activated Medulloblastoma. J Neuropathol Exp Neurol 2021; 80:129-136. [PMID: 33249504 DOI: 10.1093/jnen/nlaa141] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Glioma-associated oncogene homolog 3 (GLI3), whose main function is to inhibit GLI1, has been associated with neuronal differentiation in medulloblastoma. However, it is not clear what molecular subtype(s) show increased GLI3 expression. GLI3 levels were assessed by immunohistochemistry in 2 independent cohorts, including a total of 88 cases, and found to be high in both WNT- and SHH-activated medulloblastoma. Analysis of bulk mRNA expression data and single cell RNA sequencing studies confirmed that GLI1 and GLI3 are highly expressed in SHH-activated medulloblastoma, whereas GLI3 but not GLI1 is highly expressed in WNT-activated medulloblastoma. Immunohistochemical analysis has shown that GLI3 is expressed inside the neuronal differentiated nodules of SHH-activated medulloblastoma, whereas GLI1/2 are expressed in desmoplastic areas. In contrast, GLI3 is diffusely expressed in WNT-activated medulloblastoma, whereas GLI1 is suppressed. Our data suggest that GLI3 may be a master regulator of neuronal differentiation and morphology in these subgroups.
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Affiliation(s)
- Manabu Natsumeda
- From the Department of Neurosurgery, Brain Research Institute, Niigata University, Niigata, Japan
| | - Hiroaki Miyahara
- Department of Pediatrics, Oita University Faculty of Medicine, Yufu, Japan.,Department of Neuropathology, Institute for Medical Science of Aging, Aichi Medical University, Japan
| | - Junichi Yoshimura
- From the Department of Neurosurgery, Brain Research Institute, Niigata University, Niigata, Japan
| | - Satoshi Nakata
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Takanori Nozawa
- From the Department of Neurosurgery, Brain Research Institute, Niigata University, Niigata, Japan
| | - Junko Ito
- From the Department of Neurosurgery, Brain Research Institute, Niigata University, Niigata, Japan.,Department of Pathology, Brain Research Institute, Niigata University
| | - Yu Kanemaru
- From the Department of Neurosurgery, Brain Research Institute, Niigata University, Niigata, Japan
| | - Jun Watanabe
- From the Department of Neurosurgery, Brain Research Institute, Niigata University, Niigata, Japan
| | - Yoshihiro Tsukamoto
- From the Department of Neurosurgery, Brain Research Institute, Niigata University, Niigata, Japan
| | - Masayasu Okada
- From the Department of Neurosurgery, Brain Research Institute, Niigata University, Niigata, Japan
| | - Makoto Oishi
- From the Department of Neurosurgery, Brain Research Institute, Niigata University, Niigata, Japan
| | - Junko Hirato
- Department of Pathology, Public Tomioka General Hospital, Tomioka, Japan.,Department of Human Pathology, Gunma University, Maebashi, Japan
| | - Takafumi Wataya
- Department of Human Pathology, Gunma University, Maebashi, Japan
| | - Sama Ahsan
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Kensuke Tateishi
- Department of Neurosurgery, Yokohama City University, Yokohama, Japan
| | - Tetsuya Yamamoto
- Department of Neurosurgery, Yokohama City University, Yokohama, Japan
| | - Fausto J Rodriguez
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Hitoshi Takahashi
- Department of Pathology, Brain Research Institute, Niigata University
| | - Volker Hovestadt
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusettes.,Broad Institute of Harvard and MIT, Cambridge, Massachusettes
| | - Mario L Suva
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusettes.,Broad Institute of Harvard and MIT, Cambridge, Massachusettes
| | - Michael D Taylor
- Department of Neurosurgery, Hospital for Sick Children, Toronto, Canada
| | | | - Yukihiko Fujii
- From the Department of Neurosurgery, Brain Research Institute, Niigata University, Niigata, Japan
| | - Akiyoshi Kakita
- Department of Pathology, Brain Research Institute, Niigata University
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6
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Nduom EK, Gephart MH, Chheda MG, Suva ML, Amankulor N, Battiste JD, Campian JL, Dacey RG, Das S, Fecci PE, Hadjipanayis CG, Hoang KB, Jalali A, Orringer D, Patel AJ, Placantonakis D, Rodriguez A, Yang I, Yu JS, Zipfel GJ, Dunn GP, Leuthardt EC, Kim AH. Re-evaluating Biopsy for Recurrent Glioblastoma: A Position Statement by the Christopher Davidson Forum Investigators. Neurosurgery 2021; 89:129-132. [PMID: 33862619 DOI: 10.1093/neuros/nyab063] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 01/05/2021] [Indexed: 11/15/2022] Open
Abstract
Patients with glioblastoma (GBM) need bold new approaches to their treatment, yet progress has been hindered by a relative inability to dynamically track treatment response, mechanisms of resistance, evolution of targetable mutations, and changes in mutational burden. We are writing on behalf of a multidisciplinary group of academic neuro-oncology professionals who met at the collaborative Christopher Davidson Forum at Washington University in St Louis in the fall of 2019. We propose a dramatic but necessary change to the routine management of patients with GBM to advance the field: to routinely biopsy recurrent GBM at the time of presumed recurrence. Data derived from these samples will identify true recurrence vs treatment effect, avoid treatments with little chance of success, enable clinical trial access, and aid in the scientific advancement of our understanding of GBM.
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Affiliation(s)
- Edjah K Nduom
- Department of Neurological Surgery, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Melanie Hayden Gephart
- Department of Neurological Surgery, Stanford University School of Medicine, Palo Alto, California, USA
| | - Milan G Chheda
- Departments of Medicine and Neurology, Washington University School of Medicine, St Louis, Missouri, USA
| | - Mario L Suva
- Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| | - Nduka Amankulor
- Department of Neurological Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - James D Battiste
- Department of Neurology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Jian L Campian
- Department of Medicine, Washington University School of Medicine, St Louis, Missouri, USA
| | - Ralph G Dacey
- Department of Neurological Surgery, Washington University School of Medicine, St Louis, Missouri, USA
| | - Sunit Das
- Division of Neurosurgery, University of Toronto, Toronto, Canada
| | - Peter E Fecci
- Department of Neurosurgery, Duke University Medical Center, Durham, North Carolina, USA
| | | | - Kimberly B Hoang
- Department of Neurological Surgery, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Ali Jalali
- Department of Neurosurgery, Baylor College of Medicine, Houston, Texas, USA
| | - Daniel Orringer
- Department of Neurosurgery, NYU Grossman School of Medicine, New York, New York, USA
| | - Akash J Patel
- Department of Neurosurgery, Baylor College of Medicine, Houston, Texas, USA
| | | | - Analiz Rodriguez
- Department of Neurosurgery, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Isaac Yang
- Department of Neurosurgery, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Jennifer S Yu
- Department of Radiation Oncology and Cancer Biology, Cleveland Clinic, Cleveland, Ohio, USA
| | - Greg J Zipfel
- Department of Neurological Surgery, Washington University School of Medicine, St Louis, Missouri, USA
| | - Gavin P Dunn
- Department of Neurological Surgery, Washington University School of Medicine, St Louis, Missouri, USA
| | - Eric C Leuthardt
- Department of Neurological Surgery, Washington University School of Medicine, St Louis, Missouri, USA
| | - Albert H Kim
- Department of Neurological Surgery, Washington University School of Medicine, St Louis, Missouri, USA
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7
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Englinger B, Gojo J, Jiang L, Hübner JM, Shaw ML, Hack OA, Madlener S, Kirchhofer D, Liu I, Pyrdol J, Hovestadt V, Mazzola E, Mathewson ND, Trissal M, Lötsch D, Berger W, Dorfer C, Haberler C, Halfmann A, Mayr L, Peyrl A, Geyeregger R, Pajtler KW, Milde T, Geduldig JE, Pelton K, Czech T, Ashenberg O, Wucherpfennig KW, Rozenblatt-Rosen O, Alexandrescu S, Ligon KL, Pfister SM, Regev A, Slavc I, Suva ML, Kool M, Filbin M. EPEN-21. IMPAIRED NEURONAL-GLIAL FATE SPECIFICATION IN PEDIATRIC EPENDYMOMA REVEALED BY SINGLE-CELL RNA-SEQ. Neuro Oncol 2020. [PMCID: PMC7715721 DOI: 10.1093/neuonc/noaa222.158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Ependymoma represents a heterogeneous disease affecting the entire neuraxis. Extensive molecular profiling efforts have identified molecular ependymoma subgroups based on DNA methylation. However, the intratumoral heterogeneity and developmental origins of these groups are only partially understood, and effective treatments are still lacking for about 50% of patients with high-risk tumors. We interrogated the cellular architecture of ependymoma using single cell/nucleus RNA-sequencing to analyze 24 tumor specimens across major molecular subgroups and anatomic locations. We additionally analyzed ten patient-derived ependymoma cell models and two patient-derived xenografts (PDXs). Interestingly, we identified an analogous cellular hierarchy across all ependymoma groups, originating from undifferentiated neural stem cell-like populations towards different degrees of impaired differentiation states comprising neuronal precursor-like, astro-glial-like, and ependymal-like tumor cells. While prognostically favorable ependymoma groups predominantly harbored differentiated cell populations, aggressive groups were enriched for undifferentiated subpopulations. Projection of transcriptomic signatures onto an independent bulk RNA-seq cohort stratified patient survival even within known molecular groups, thus refining the prognostic power of DNA methylation-based profiling. Furthermore, we identified novel potentially druggable targets including IGF- and FGF-signaling within poorly prognostic transcriptional programs. Ependymoma-derived cell models/PDXs widely recapitulated the transcriptional programs identified within fresh tumors and are leveraged to validate identified target genes in functional follow-up analyses. Taken together, our analyses reveal a developmental hierarchy and transcriptomic context underlying the biologically and clinically distinct behavior of ependymoma groups. The newly characterized cellular states and underlying regulatory networks could serve as basis for future therapeutic target identification and reveal biomarkers for clinical trials.
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Affiliation(s)
- Bernhard Englinger
- Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Johannes Gojo
- Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Vienna, Austria
| | - Li Jiang
- Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jens M Hübner
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, BW, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, BW, Germany
| | - McKenzie L Shaw
- Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Olivia A Hack
- Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Sibylle Madlener
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Vienna, Austria
| | - Dominik Kirchhofer
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Vienna, Austria
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Vienna, Vienna, Austria
| | - Ilon Liu
- Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jason Pyrdol
- Department of Cancer Immunology and Virology, Department of Microbiology and Immunobiology, Department of Neurology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Volker Hovestadt
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Emanuele Mazzola
- Department of Biostatistics & Computational Biology, Boston, MA, USA
| | - Nathan D Mathewson
- Department of Cancer Immunology and Virology, Department of Microbiology and Immunobiology, Department of Neurology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Maria Trissal
- Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Daniela Lötsch
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Vienna, Austria
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Vienna, Vienna, Austria
| | - Walter Berger
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Vienna, Vienna, Austria
| | - Christian Dorfer
- Department of Neurosurgery, Medical University of Vienna, Vienna, Vienna, Austria
| | - Christine Haberler
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, Vienna, Vienna, Austria
| | - Angela Halfmann
- Clinical Cell Biology, Children’s Cancer Research Institute (CCRI), St Anna Kinderkrebsforschung, Vienna, Vienna, Austria
| | - Lisa Mayr
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Vienna, Austria
| | - Andreas Peyrl
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Vienna, Austria
| | - Rene Geyeregger
- Clinical Cell Biology, Children’s Cancer Research Institute (CCRI), St Anna Kinderkrebsforschung, Vienna, Vienna, Austria
| | - Kristian W Pajtler
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, BW, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, BW, Germany
| | - Till Milde
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, BW, Germany
- Department of Paediatric Haematology and Oncology, Heidelberg University Hospital, Heidelberg, BW, Germany
| | - Jack E Geduldig
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kristine Pelton
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Thomas Czech
- Department of Neurosurgery, Medical University of Vienna, Vienna, Vienna, Austria
| | - Orr Ashenberg
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Kai W Wucherpfennig
- Department of Cancer Immunology and Virology, Department of Microbiology and Immunobiology, Department of Neurology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | | | | | - Keith L Ligon
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Oncologic Pathology, Brigham and Women’s Hospital, Boston Children’s Hospital, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Stefan M Pfister
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, BW, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, BW, Germany
| | - Aviv Regev
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute and Koch Institute of Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Irene Slavc
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Vienna, Austria
| | - Mario L Suva
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Marcel Kool
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, BW, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, BW, Germany
| | - Mariella Filbin
- Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
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8
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Kim GB, Pacheco DRF, Saxon D, Yang A, Sabat S, Dutra-Clarke M, Levy R, Watkins A, Park H, Akhtar AA, Linesch PW, Kobritz N, Shandra SS, Grausam K, Ayala-Sarmiento A, Molina J, Sedivakova K, Gareau DS, Filbin MG, Bannykh S, Tang J, Suva ML, Chen B, Danielpour M, Breunig JJ. Abstract NG01: MADR: Rapid generation of somatic mosaics to model cancer in mice and human organoids. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-ng01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
In situ transgenesis methods such as virus and electroporation can create somatic transgenic mice quickly, but they lack the exquisite control over copy number, zygosity, and locus specificity. We have recently established mosaic analysis by dual recombinase-mediated cassette exchange (MADR), which permits stable labeling of mutant cells expressing transgenic elements from precisely-defined chromosomal loci. MADR provides a toolkit of elements for combinatorial labeling, inducible/reversible transgene manipulation, VCre recombinase expression, and genetic manipulation of human cells. Further, we have demonstrated the versatility of MADR by creating glioma models with mixed, reporter-identified zygosity or with “personalized” driver mutations from pediatric glioma. For example, introducing H3f3a mutation variants with MADR regulates the spatiotemporal profile of glioma, and single-cell RNA and ATAC sequencing analysis demonstrates a recapitulation of developmental hierarchy seen in K27M-mutant human glioma. Moreover, we have generated novel models of supratentorial ependymoma using patient-derived oncofusion transgenes. These models display a high degree of fidelity and we now compare these models on a single-cell level with our previous models and human tumor cell transcriptomes. In addition, we now demonstrate the ability to generalize the MADR technology to other non-CNS tissues using local plasmid delivery. Finally, we have engineered human cells to allow for MADR transgenesis and somatic transgenic organoids. These combined approaches will enable researchers to discovery disease mechanisms and test therapeutics in more physiologically relevant cancer models.MADR is extensible to thousands of existing mouse lines and can be adapted to human cells, providing a flexible platform to democratize the generation of somatic transgenic disease models.
Citation Format: Gi Bum Kim, David Rincon Fernandez Pacheco, David Saxon, Amy Yang, Sara Sabat, Marina Dutra-Clarke, Rachelle Levy, Ashley Watkins, Hannah Park, Aslam Abbasi Akhtar, Paul W. Linesch, Naomi Kobritz, Swasty S. Shandra, Katie Grausam, Alberto Ayala-Sarmiento, Jessica Molina, Kristyna Sedivakova, Daniel S. Gareau, Mariella G. Filbin, Serguei Bannykh, Jie Tang, Mario L. Suva, Bin Chen, Moise Danielpour, Joshua J. Breunig. MADR: Rapid generation of somatic mosaics to model cancer in mice and human organoids [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr NG01.
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Affiliation(s)
- Gi Bum Kim
- Cedars-Sinai Medical Center, Los Angeles, CA, Rockefeller University, New York, NY, Dana Farber Boston Children's Cancer and Blood Disorder Center, Boston, MA, Broad Institute of MIT and Harvard, Cambridge, MA, University of California Santa Cruz, Santa Cruz, CA
| | - David Rincon Fernandez Pacheco
- Cedars-Sinai Medical Center, Los Angeles, CA, Rockefeller University, New York, NY, Dana Farber Boston Children's Cancer and Blood Disorder Center, Boston, MA, Broad Institute of MIT and Harvard, Cambridge, MA, University of California Santa Cruz, Santa Cruz, CA
| | - David Saxon
- Cedars-Sinai Medical Center, Los Angeles, CA, Rockefeller University, New York, NY, Dana Farber Boston Children's Cancer and Blood Disorder Center, Boston, MA, Broad Institute of MIT and Harvard, Cambridge, MA, University of California Santa Cruz, Santa Cruz, CA
| | - Amy Yang
- Cedars-Sinai Medical Center, Los Angeles, CA, Rockefeller University, New York, NY, Dana Farber Boston Children's Cancer and Blood Disorder Center, Boston, MA, Broad Institute of MIT and Harvard, Cambridge, MA, University of California Santa Cruz, Santa Cruz, CA
| | - Sara Sabat
- Cedars-Sinai Medical Center, Los Angeles, CA, Rockefeller University, New York, NY, Dana Farber Boston Children's Cancer and Blood Disorder Center, Boston, MA, Broad Institute of MIT and Harvard, Cambridge, MA, University of California Santa Cruz, Santa Cruz, CA
| | - Marina Dutra-Clarke
- Cedars-Sinai Medical Center, Los Angeles, CA, Rockefeller University, New York, NY, Dana Farber Boston Children's Cancer and Blood Disorder Center, Boston, MA, Broad Institute of MIT and Harvard, Cambridge, MA, University of California Santa Cruz, Santa Cruz, CA
| | - Rachelle Levy
- Cedars-Sinai Medical Center, Los Angeles, CA, Rockefeller University, New York, NY, Dana Farber Boston Children's Cancer and Blood Disorder Center, Boston, MA, Broad Institute of MIT and Harvard, Cambridge, MA, University of California Santa Cruz, Santa Cruz, CA
| | - Ashley Watkins
- Cedars-Sinai Medical Center, Los Angeles, CA, Rockefeller University, New York, NY, Dana Farber Boston Children's Cancer and Blood Disorder Center, Boston, MA, Broad Institute of MIT and Harvard, Cambridge, MA, University of California Santa Cruz, Santa Cruz, CA
| | - Hannah Park
- Cedars-Sinai Medical Center, Los Angeles, CA, Rockefeller University, New York, NY, Dana Farber Boston Children's Cancer and Blood Disorder Center, Boston, MA, Broad Institute of MIT and Harvard, Cambridge, MA, University of California Santa Cruz, Santa Cruz, CA
| | - Aslam Abbasi Akhtar
- Cedars-Sinai Medical Center, Los Angeles, CA, Rockefeller University, New York, NY, Dana Farber Boston Children's Cancer and Blood Disorder Center, Boston, MA, Broad Institute of MIT and Harvard, Cambridge, MA, University of California Santa Cruz, Santa Cruz, CA
| | - Paul W. Linesch
- Cedars-Sinai Medical Center, Los Angeles, CA, Rockefeller University, New York, NY, Dana Farber Boston Children's Cancer and Blood Disorder Center, Boston, MA, Broad Institute of MIT and Harvard, Cambridge, MA, University of California Santa Cruz, Santa Cruz, CA
| | - Naomi Kobritz
- Cedars-Sinai Medical Center, Los Angeles, CA, Rockefeller University, New York, NY, Dana Farber Boston Children's Cancer and Blood Disorder Center, Boston, MA, Broad Institute of MIT and Harvard, Cambridge, MA, University of California Santa Cruz, Santa Cruz, CA
| | - Swasty S. Shandra
- Cedars-Sinai Medical Center, Los Angeles, CA, Rockefeller University, New York, NY, Dana Farber Boston Children's Cancer and Blood Disorder Center, Boston, MA, Broad Institute of MIT and Harvard, Cambridge, MA, University of California Santa Cruz, Santa Cruz, CA
| | - Katie Grausam
- Cedars-Sinai Medical Center, Los Angeles, CA, Rockefeller University, New York, NY, Dana Farber Boston Children's Cancer and Blood Disorder Center, Boston, MA, Broad Institute of MIT and Harvard, Cambridge, MA, University of California Santa Cruz, Santa Cruz, CA
| | - Alberto Ayala-Sarmiento
- Cedars-Sinai Medical Center, Los Angeles, CA, Rockefeller University, New York, NY, Dana Farber Boston Children's Cancer and Blood Disorder Center, Boston, MA, Broad Institute of MIT and Harvard, Cambridge, MA, University of California Santa Cruz, Santa Cruz, CA
| | - Jessica Molina
- Cedars-Sinai Medical Center, Los Angeles, CA, Rockefeller University, New York, NY, Dana Farber Boston Children's Cancer and Blood Disorder Center, Boston, MA, Broad Institute of MIT and Harvard, Cambridge, MA, University of California Santa Cruz, Santa Cruz, CA
| | - Kristyna Sedivakova
- Cedars-Sinai Medical Center, Los Angeles, CA, Rockefeller University, New York, NY, Dana Farber Boston Children's Cancer and Blood Disorder Center, Boston, MA, Broad Institute of MIT and Harvard, Cambridge, MA, University of California Santa Cruz, Santa Cruz, CA
| | - Daniel S. Gareau
- Cedars-Sinai Medical Center, Los Angeles, CA, Rockefeller University, New York, NY, Dana Farber Boston Children's Cancer and Blood Disorder Center, Boston, MA, Broad Institute of MIT and Harvard, Cambridge, MA, University of California Santa Cruz, Santa Cruz, CA
| | - Mariella G. Filbin
- Cedars-Sinai Medical Center, Los Angeles, CA, Rockefeller University, New York, NY, Dana Farber Boston Children's Cancer and Blood Disorder Center, Boston, MA, Broad Institute of MIT and Harvard, Cambridge, MA, University of California Santa Cruz, Santa Cruz, CA
| | - Serguei Bannykh
- Cedars-Sinai Medical Center, Los Angeles, CA, Rockefeller University, New York, NY, Dana Farber Boston Children's Cancer and Blood Disorder Center, Boston, MA, Broad Institute of MIT and Harvard, Cambridge, MA, University of California Santa Cruz, Santa Cruz, CA
| | - Jie Tang
- Cedars-Sinai Medical Center, Los Angeles, CA, Rockefeller University, New York, NY, Dana Farber Boston Children's Cancer and Blood Disorder Center, Boston, MA, Broad Institute of MIT and Harvard, Cambridge, MA, University of California Santa Cruz, Santa Cruz, CA
| | - Mario L. Suva
- Cedars-Sinai Medical Center, Los Angeles, CA, Rockefeller University, New York, NY, Dana Farber Boston Children's Cancer and Blood Disorder Center, Boston, MA, Broad Institute of MIT and Harvard, Cambridge, MA, University of California Santa Cruz, Santa Cruz, CA
| | - Bin Chen
- Cedars-Sinai Medical Center, Los Angeles, CA, Rockefeller University, New York, NY, Dana Farber Boston Children's Cancer and Blood Disorder Center, Boston, MA, Broad Institute of MIT and Harvard, Cambridge, MA, University of California Santa Cruz, Santa Cruz, CA
| | - Moise Danielpour
- Cedars-Sinai Medical Center, Los Angeles, CA, Rockefeller University, New York, NY, Dana Farber Boston Children's Cancer and Blood Disorder Center, Boston, MA, Broad Institute of MIT and Harvard, Cambridge, MA, University of California Santa Cruz, Santa Cruz, CA
| | - Joshua J. Breunig
- Cedars-Sinai Medical Center, Los Angeles, CA, Rockefeller University, New York, NY, Dana Farber Boston Children's Cancer and Blood Disorder Center, Boston, MA, Broad Institute of MIT and Harvard, Cambridge, MA, University of California Santa Cruz, Santa Cruz, CA
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9
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Kim GB, Rincon Fernandez Pacheco D, Saxon D, Yang A, Sabet S, Dutra-Clarke M, Levy R, Watkins A, Park H, Abbasi Akhtar A, Linesch PW, Kobritz N, Chandra SS, Grausam K, Ayala-Sarmiento A, Molina J, Sedivakova K, Hoang K, Tsyporin J, Gareau DS, Filbin MG, Bannykh S, Santiskulvong C, Wang Y, Tang J, Suva ML, Chen B, Danielpour M, Breunig JJ. Rapid Generation of Somatic Mouse Mosaics with Locus-Specific, Stably Integrated Transgenic Elements. Cell 2020; 179:251-267.e24. [PMID: 31539496 DOI: 10.1016/j.cell.2019.08.013] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 05/24/2019] [Accepted: 08/06/2019] [Indexed: 12/11/2022]
Abstract
In situ transgenesis methods such as viruses and electroporation can rapidly create somatic transgenic mice but lack control over copy number, zygosity, and locus specificity. Here we establish mosaic analysis by dual recombinase-mediated cassette exchange (MADR), which permits stable labeling of mutant cells expressing transgenic elements from precisely defined chromosomal loci. We provide a toolkit of MADR elements for combination labeling, inducible and reversible transgene manipulation, VCre recombinase expression, and transgenesis of human cells. Further, we demonstrate the versatility of MADR by creating glioma models with mixed reporter-identified zygosity or with "personalized" driver mutations from pediatric glioma. MADR is extensible to thousands of existing mouse lines, providing a flexible platform to democratize the generation of somatic mosaic mice. VIDEO ABSTRACT.
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Affiliation(s)
- Gi Bum Kim
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | | | - David Saxon
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Amy Yang
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Sara Sabet
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Marina Dutra-Clarke
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Rachelle Levy
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Ashley Watkins
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Hannah Park
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Aslam Abbasi Akhtar
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Paul W Linesch
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Naomi Kobritz
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Swasty S Chandra
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Katie Grausam
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Alberto Ayala-Sarmiento
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jessica Molina
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Kristyna Sedivakova
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Kendy Hoang
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, 1156 High St., Santa Cruz, CA 95064, USA
| | - Jeremiah Tsyporin
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, 1156 High St., Santa Cruz, CA 95064, USA
| | - Daniel S Gareau
- Laboratory for Investigative Dermatology, The Rockefeller University, New York, NY 10065, USA
| | - Mariella G Filbin
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Serguei Bannykh
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Chintda Santiskulvong
- Center for Neural Sciences in Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Yizhou Wang
- Center for Neural Sciences in Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jie Tang
- Center for Neural Sciences in Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Mario L Suva
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Bin Chen
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, 1156 High St., Santa Cruz, CA 95064, USA
| | - Moise Danielpour
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Neurosurgery, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Joshua J Breunig
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Center for Neural Sciences in Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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10
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Ahmed R, Omidian Z, Giwa A, Cornwell B, Majety N, Bell DR, Lee S, Zhang H, Michels A, Desiderio S, Sadegh-Nasseri S, Rabb H, Gritsch S, Suva ML, Cahan P, Zhou R, Jie C, Donner T, Hamad ARA. A Public BCR Present in a Unique Dual-Receptor-Expressing Lymphocyte from Type 1 Diabetes Patients Encodes a Potent T Cell Autoantigen. Cell 2020; 177:1583-1599.e16. [PMID: 31150624 DOI: 10.1016/j.cell.2019.05.007] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 12/10/2018] [Accepted: 05/02/2019] [Indexed: 12/17/2022]
Abstract
T and B cells are the two known lineages of adaptive immune cells. Here, we describe a previously unknown lymphocyte that is a dual expresser (DE) of TCR and BCR and key lineage markers of both B and T cells. In type 1 diabetes (T1D), DEs are predominated by one clonotype that encodes a potent CD4 T cell autoantigen in its antigen binding site. Molecular dynamics simulations revealed that this peptide has an optimal binding register for diabetogenic HLA-DQ8. In concordance, a synthetic version of the peptide forms stable DQ8 complexes and potently stimulates autoreactive CD4 T cells from T1D patients, but not healthy controls. Moreover, mAbs bearing this clonotype are autoreactive against CD4 T cells and inhibit insulin tetramer binding to CD4 T cells. Thus, compartmentalization of adaptive immune cells into T and B cells is not absolute, and violators of this paradigm are likely key drivers of autoimmune diseases.
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Affiliation(s)
- Rizwan Ahmed
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Zahra Omidian
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Adebola Giwa
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Benjamin Cornwell
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Neha Majety
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - David R Bell
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, USA
| | - Sangyun Lee
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, USA
| | - Hao Zhang
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Aaron Michels
- Barbara Davis Center for Diabetes, University of Colorado, Aurora, CO 80045, USA
| | - Stephen Desiderio
- Department of Molecular Biology and Genetics and Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | - Hamid Rabb
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Simon Gritsch
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Mario L Suva
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Patrick Cahan
- Department of Molecular Biology and Genetics and Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ruhong Zhou
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, USA; Department of Chemistry, Columbia University, New York, NY 10027, USA.
| | - Chunfa Jie
- Department of Biochemistry and Nutrition, Des Moines University, Des Moines, IA 50312, USA
| | - Thomas Donner
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Abdel Rahim A Hamad
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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11
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Anastas JN, Zee BM, Kalin JH, Kim M, Guo R, Alexandrescu S, Blanco MA, Giera S, Gillespie SM, Das J, Wu M, Nocco S, Bonal DM, Nguyen QD, Suva ML, Bernstein BE, Alani R, Golub TR, Cole PA, Filbin MG, Shi Y. Re-programing Chromatin with a Bifunctional LSD1/HDAC Inhibitor Induces Therapeutic Differentiation in DIPG. Cancer Cell 2019; 36:528-544.e10. [PMID: 31631026 DOI: 10.1016/j.ccell.2019.09.005] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 08/02/2019] [Accepted: 09/12/2019] [Indexed: 02/01/2023]
Abstract
H3K27M mutations resulting in epigenetic dysfunction are frequently observed in diffuse intrinsic pontine glioma (DIPGs), an incurable pediatric cancer. We conduct a CRISPR screen revealing that knockout of KDM1A encoding lysine-specific demethylase 1 (LSD1) sensitizes DIPG cells to histone deacetylase (HDAC) inhibitors. Consistently, Corin, a bifunctional inhibitor of HDACs and LSD1, potently inhibits DIPG growth in vitro and in xenografts. Mechanistically, Corin increases H3K27me3 levels suppressed by H3K27M histones, and simultaneously increases HDAC-targeted H3K27ac and LSD1-targeted H3K4me1 at differentiation-associated genes. Corin treatment induces cell death, cell-cycle arrest, and a cellular differentiation phenotype and drives transcriptional changes correlating with increased survival time in DIPG patients. These data suggest a strategy for treating DIPG by simultaneously inhibiting LSD1 and HDACs.
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Affiliation(s)
- Jamie N Anastas
- Division of Newborn Medicine and Epigenetics Program, Department of Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Barry M Zee
- Division of Newborn Medicine and Epigenetics Program, Department of Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Jay H Kalin
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Division of Genetics, Department of Medicine, Brigham and Womens Hospital, Boston, MA 02115, USA
| | - Mirhee Kim
- NYU Medical School, New York, NY 10016, USA
| | - Robyn Guo
- Duke University, Durham, NC 27708, USA
| | - Sanda Alexandrescu
- Department of Pathology Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute and Children's Hospital Cancer Center, Boston, MA 02215, USA
| | - Mario Andres Blanco
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Shawn M Gillespie
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Jayanta Das
- Eshelman School of Pharmacy, UNC Chapel Hill, Chapel Hill, NC 27599, USA
| | - Muzhou Wu
- Department of Dermatology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Sarah Nocco
- Department of Dermatology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Dennis M Bonal
- Lurie Family Imaging Center, Center for Biomedical Imaging in Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Quang-De Nguyen
- Lurie Family Imaging Center, Center for Biomedical Imaging in Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Mario L Suva
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Bradley E Bernstein
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Rhoda Alani
- Department of Dermatology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Todd R Golub
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, 20815 MD, USA
| | - Philip A Cole
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Division of Genetics, Department of Medicine, Brigham and Womens Hospital, Boston, MA 02115, USA
| | - Mariella G Filbin
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Children's Hospital Cancer Center, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
| | - Yang Shi
- Division of Newborn Medicine and Epigenetics Program, Department of Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
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12
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Nagaraja S, Quezada MA, Gillespie SM, Arzt M, Lennon JJ, Woo PJ, Hovestadt V, Kambhampati M, Filbin MG, Suva ML, Nazarian J, Monje M. Histone Variant and Cell Context Determine H3K27M Reprogramming of the Enhancer Landscape and Oncogenic State. Mol Cell 2019; 76:965-980.e12. [PMID: 31588023 DOI: 10.1016/j.molcel.2019.08.030] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 08/06/2019] [Accepted: 08/29/2019] [Indexed: 01/03/2023]
Abstract
Development of effective targeted cancer therapies is fundamentally limited by our molecular understanding of disease pathogenesis. Diffuse intrinsic pontine glioma (DIPG) is a fatal malignancy of the childhood pons characterized by a unique substitution to methionine in histone H3 at lysine 27 (H3K27M) that results in globally altered epigenetic marks and oncogenic transcription. Through primary DIPG tumor characterization and isogenic oncohistone expression, we show that the same H3K27M mutation displays distinct modes of oncogenic reprogramming and establishes distinct enhancer architecture depending upon both the variant of histone H3 and the cell context in which the mutation occurs. Compared with non-malignant pediatric pontine tissue, we identify and functionally validate both shared and variant-specific pathophysiology. Altogether, we provide a powerful resource of epigenomic data in 25 primary DIPG samples and 5 rare normal pediatric pontine tissue samples, revealing clinically relevant functional distinctions previously unidentified in DIPG.
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Affiliation(s)
- Surya Nagaraja
- Department of Neurology, Stanford University School of Medicine, Stanford, CA, USA; Stanford Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael A Quezada
- Department of Neurology, Stanford University School of Medicine, Stanford, CA, USA
| | - Shawn M Gillespie
- Department of Neurology, Stanford University School of Medicine, Stanford, CA, USA
| | - Marlene Arzt
- Department of Neurology, Stanford University School of Medicine, Stanford, CA, USA
| | - James J Lennon
- Department of Neurology, Stanford University School of Medicine, Stanford, CA, USA
| | - Pamelyn J Woo
- Department of Neurology, Stanford University School of Medicine, Stanford, CA, USA
| | - Volker Hovestadt
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Klarman Cell Observatory, Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA 02142, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Madhuri Kambhampati
- Research Center for Genetic Medicine, Children's National Health System, Washington, DC, USA
| | - Mariella G Filbin
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorder Center and Harvard Medical School, Boston, MA, USA
| | - Mario L Suva
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Klarman Cell Observatory, Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA 02142, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Javad Nazarian
- Research Center for Genetic Medicine, Children's National Health System, Washington, DC, USA; Department of Integrative Systems Biology, George Washington University School of Medicine and Health Sciences, Washington, DC, USA; Department of Oncology, University Children's Hospital, Zurich, Switzerland
| | - Michelle Monje
- Department of Neurology, Stanford University School of Medicine, Stanford, CA, USA; Stanford Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA; Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA; Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
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13
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Reitman ZJ, Paolella B, Bergthold G, Pelton K, Jones R, Becker S, Sinai CE, Malkin H, Huang Y, Grimmett L, Herbert ZT, Sun Y, Weatherbee J, Alberta J, Daley J, Rozenblatt-Rosen O, Segal R, Haas-Kogan D, Filbin MG, Suva ML, Regev A, Stiles C, Kieran MW, Goumnerova L, Ligon KL, Shalek AK, Bandopadhayay P, Beroukhim R. Abstract 3647: Single cell RNA sequencing reveals mitogenic and progenitor gene programs inBRAF-rearranged pilocytic astrocytomas. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-3647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Single-cell RNA sequencing (scRNAseq) has been performed across a range of intermediate to high-grade gliomas that each harbor multiple driver mutations. Pilocytic astrocytoma (PA), the most common childhood brain tumor, is a low-grade glioma. PAs frequently harbor oncogenic KIAA1549-BRAF fusions, and exhibit low rates of other driver mutations. While PAs exhibit a favorable prognosis compared to the higher-grade gliomas, treatment morbidity and tumor recurrence can represent major challenges for some PA patients. We performed scRNAseq of both tumor and non-tumor cells in newly-diagnosed PAs that contained KIAA1549-BRAF rearrangements. To confidently distinguish tumor cells from nontumor cells, we sorted cells by glial progenitor marker A2B5 status and profiled KIAA1549-BRAF fusion status of cells using a sensitive quantitative PCR-based assay. Results were validated using RNA in situ hybridization. When compared to higher-grade gliomas, a higher proportion of the PA tumor cells exhibited a differentiated, astrocyte-like phenotype. A smaller proportion of cells exhibited a progenitor-like phenotype with evidence of proliferation. These progenitor-like tumor cells expressed a mitogen-activated protein kinase (MAPK) program that was absent from higher-grade gliomas. Similar patterns of expression of genes associated with the astrocyte-like and MAPK gene programs were also seen in formalin fixed, paraffin embedded PA tissues using RNA in situ hybridization. Immune cells, especially microglia, comprised almost half of all cells in the PAs and accounted for differences in bulk expression profiles between tumor locations and subtypes. These single cell transcriptional data reveal a transcriptional developmental hierarchy in a pediatric low grade glioma that is skewed towards more mature brain cells compared to higher-grade gliomas. The results indicate that future analyses of bulk PA tissues should attempt to account for considerable infiltration by nontumor cells. Finally, the finding that a MAPK gene program is not uniformly expressed in PA tumor cells has implications for ongoing clinical investigations of therapies directed at the MAPK pathway for the treatment of PA.
Citation Format: Zachary J. Reitman, Brenton Paolella, Guillaume Bergthold, Kristine Pelton, Robert Jones, Sarah Becker, Claire E. Sinai, Haley Malkin, Ying Huang, Leslie Grimmett, Zachary T. Herbert, Yu Sun, Jessica Weatherbee, John Alberta, John Daley, Orit Rozenblatt-Rosen, Rosalind Segal, Daphne Haas-Kogan, Mariella G. Filbin, Mario L. Suva, Aviv Regev, Charles Stiles, Mark W. Kieran, Liliana Goumnerova, Keith L. Ligon, Alex K. Shalek, Pratiti Bandopadhayay, Rameen Beroukhim. Single cell RNA sequencing reveals mitogenic and progenitor gene programs inBRAF-rearranged pilocytic astrocytomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3647.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Ying Huang
- 1Dana-Farber Cancer Institute, Boston, MA
| | | | | | - Yu Sun
- 1Dana-Farber Cancer Institute, Boston, MA
| | | | | | - John Daley
- 1Dana-Farber Cancer Institute, Boston, MA
| | | | | | | | | | | | - Aviv Regev
- 2Broad Institute of Harvard and MIT, Cambridge, MA
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14
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Hovestadt V, Filbin MG, Bihannic L, Shaw ML, DeWitt JM, Groves A, Smith KS, Hadley J, Gajjar A, Robinson GW, Mayr L, Slavc I, Goumnerova L, Ligon KL, Suva ML, Northcott PA, Bernstein BE. MBRS-28. SINGLE-CELL TRANSCRIPTOME ANALYSIS OF MEDULLOBLASTOMA. Neuro Oncol 2018. [DOI: 10.1093/neuonc/noy059.473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Volker Hovestadt
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Mariella G Filbin
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
| | - Laure Bihannic
- Department of Developmental Neurobiology, St Jude Children’s Research Hospital, Memphis, TN, USA
| | - McKenzie L Shaw
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - John M DeWitt
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Andrew Groves
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Kyle S Smith
- Department of Developmental Neurobiology, St Jude Children’s Research Hospital, Memphis, TN, USA
| | - Jennifer Hadley
- Department of Developmental Neurobiology, St Jude Children’s Research Hospital, Memphis, TN, USA
| | - Amar Gajjar
- Department of Oncology, St Jude Children’s Research Hospital, Memphis, TN, USA
| | - Giles W Robinson
- Department of Oncology, St Jude Children’s Research Hospital, Memphis, TN, USA
| | - Lisa Mayr
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | - Irene Slavc
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | - Liliana Goumnerova
- Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
| | - Keith L Ligon
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
| | - Mario L Suva
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Paul A Northcott
- Department of Developmental Neurobiology, St Jude Children’s Research Hospital, Memphis, TN, USA
| | - Bradley E Bernstein
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
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15
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Brastianos PK, Nayyar N, Rosebrock D, Leshchiner I, Gill CM, Livitz D, Bertalan MS, D'Andrea M, Hoang K, Aquilanti E, Chukwueke UN, Kaneb A, Chi A, Plotkin S, Gerstner ER, Frosch MP, Suva ML, Cahill DP, Getz G, Batchelor TT. Resolving the phylogenetic origin of glioblastoma via multifocal genomic analysis of pre-treatment and treatment-resistant autopsy specimens. NPJ Precis Oncol 2017; 1:33. [PMID: 29872714 PMCID: PMC5871833 DOI: 10.1038/s41698-017-0035-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 08/01/2017] [Accepted: 08/02/2017] [Indexed: 12/13/2022] Open
Abstract
Glioblastomas are malignant neoplasms composed of diverse cell populations. This intratumoral diversity has an underlying architecture, with a hierarchical relationship through clonal evolution from a common ancestor. Therapies are limited by emergence of resistant subclones from this phylogenetic reservoir. To characterize this clonal ancestral origin of recurrent tumors, we determined phylogenetic relationships using whole exome sequencing of pre-treatment IDH1/2 wild-type glioblastoma specimens, matched to post-treatment autopsy samples (n = 9) and metastatic extracranial post-treatment autopsy samples (n = 3). We identified “truncal” genetic events common to the evolutionary ancestry of the initial specimen and later recurrences, thereby inferring the identity of the precursor cell population. Mutations were identified in a subset of cases in known glioblastoma genes such as NF1(n = 3), TP53(n = 4) and EGFR(n = 5). However, by phylogenetic analysis, there were no protein-coding mutations as recurrent truncal events across the majority of cases. In contrast, whole copy-loss of chromosome 10 (12 of 12 cases), copy-loss of chromosome 9p21 (11 of 12 cases) and copy-gain in chromosome 7 (10 of 12 cases) were identified as shared events in the majority of cases. Strikingly, mutations in the TERT promoter were also identified as shared events in all evaluated pairs (9 of 9). Thus, we define four truncal non-coding genomic alterations that represent early genomic events in gliomagenesis, that identify the persistent cellular reservoir from which glioblastoma recurrences emerge. Therapies to target these key early genomic events are needed. These findings offer an evolutionary explanation for why precision therapies that target protein-coding mutations lack efficacy in GBM. Non-coding and structural alterations may be early drivers of brain cancer development. A team led by Priscilla Brastianos and Tracy Batchelor from Massachusetts General Hospital, Boston, USA, analyzed the genetic landscape of glioblastoma by comparing pre-treatment and autopsy tumor specimens from 12 patients who died of the aggressive brain cancer. They identified a common set of four genetic events that occurred early in the evolution of nearly every patient’s cancer: three losses or gains of chromosome regions or entire chromosomes, and mutations in the gene-activating promoter of TERT, which encodes an enzyme implicated in the cancer’s growth. The findings help explain why therapies that target protein-coding mutations don’t work in brain cancer when they do in other tumor types. They also point to new drug targets.
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Affiliation(s)
- Priscilla K Brastianos
- 1Division of Hematology/Oncology, Massachusetts General Hospital, Boston, Massachusetts USA.,2Broad Institute of MIT and Harvard, Boston, Massachusetts USA.,3Harvard Medical School, Boston, Massachusetts USA.,4Division of Neuro-Oncology, Massachusetts General Hospital, Boston, Massachusetts USA.,5Cancer Center, Massachusetts General Hospital, Boston, Massachusetts USA
| | - Naema Nayyar
- 2Broad Institute of MIT and Harvard, Boston, Massachusetts USA.,4Division of Neuro-Oncology, Massachusetts General Hospital, Boston, Massachusetts USA.,5Cancer Center, Massachusetts General Hospital, Boston, Massachusetts USA
| | | | | | - Corey M Gill
- 4Division of Neuro-Oncology, Massachusetts General Hospital, Boston, Massachusetts USA.,5Cancer Center, Massachusetts General Hospital, Boston, Massachusetts USA
| | - Dimitri Livitz
- 2Broad Institute of MIT and Harvard, Boston, Massachusetts USA
| | - Mia S Bertalan
- 4Division of Neuro-Oncology, Massachusetts General Hospital, Boston, Massachusetts USA.,5Cancer Center, Massachusetts General Hospital, Boston, Massachusetts USA
| | - Megan D'Andrea
- 4Division of Neuro-Oncology, Massachusetts General Hospital, Boston, Massachusetts USA.,5Cancer Center, Massachusetts General Hospital, Boston, Massachusetts USA
| | - Kaitlin Hoang
- 4Division of Neuro-Oncology, Massachusetts General Hospital, Boston, Massachusetts USA.,5Cancer Center, Massachusetts General Hospital, Boston, Massachusetts USA
| | - Elisa Aquilanti
- 1Division of Hematology/Oncology, Massachusetts General Hospital, Boston, Massachusetts USA.,2Broad Institute of MIT and Harvard, Boston, Massachusetts USA.,3Harvard Medical School, Boston, Massachusetts USA.,4Division of Neuro-Oncology, Massachusetts General Hospital, Boston, Massachusetts USA.,5Cancer Center, Massachusetts General Hospital, Boston, Massachusetts USA
| | - Ugonma N Chukwueke
- 4Division of Neuro-Oncology, Massachusetts General Hospital, Boston, Massachusetts USA.,5Cancer Center, Massachusetts General Hospital, Boston, Massachusetts USA
| | - Andrew Kaneb
- 4Division of Neuro-Oncology, Massachusetts General Hospital, Boston, Massachusetts USA.,5Cancer Center, Massachusetts General Hospital, Boston, Massachusetts USA
| | - Andrew Chi
- 6Laura and Isaac Perlmutter Cancer Center, NYU Langone Medical Center, New York, NY USA
| | - Scott Plotkin
- 1Division of Hematology/Oncology, Massachusetts General Hospital, Boston, Massachusetts USA.,3Harvard Medical School, Boston, Massachusetts USA.,4Division of Neuro-Oncology, Massachusetts General Hospital, Boston, Massachusetts USA.,5Cancer Center, Massachusetts General Hospital, Boston, Massachusetts USA
| | - Elizabeth R Gerstner
- 1Division of Hematology/Oncology, Massachusetts General Hospital, Boston, Massachusetts USA.,3Harvard Medical School, Boston, Massachusetts USA.,4Division of Neuro-Oncology, Massachusetts General Hospital, Boston, Massachusetts USA.,5Cancer Center, Massachusetts General Hospital, Boston, Massachusetts USA
| | - Mathew P Frosch
- 3Harvard Medical School, Boston, Massachusetts USA.,7Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts USA
| | - Mario L Suva
- 3Harvard Medical School, Boston, Massachusetts USA.,7Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts USA
| | - Daniel P Cahill
- 3Harvard Medical School, Boston, Massachusetts USA.,5Cancer Center, Massachusetts General Hospital, Boston, Massachusetts USA.,8Department of Neurosurgery, Massachusetts General Hospital, Boston, Massachusetts USA
| | - Gad Getz
- 2Broad Institute of MIT and Harvard, Boston, Massachusetts USA.,3Harvard Medical School, Boston, Massachusetts USA.,5Cancer Center, Massachusetts General Hospital, Boston, Massachusetts USA.,7Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts USA
| | - Tracy T Batchelor
- 1Division of Hematology/Oncology, Massachusetts General Hospital, Boston, Massachusetts USA.,3Harvard Medical School, Boston, Massachusetts USA.,4Division of Neuro-Oncology, Massachusetts General Hospital, Boston, Massachusetts USA.,5Cancer Center, Massachusetts General Hospital, Boston, Massachusetts USA
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16
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Tang Q, Iyer S, Lobbardi R, Moore JC, Chen H, Lareau C, Hebert C, Shaw ML, Neftel C, Suva ML, Ceol CJ, Bernards A, Aryee M, Pinello L, Drummond IA, Langenau DM. Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single-cell resolution using RNA sequencing. J Exp Med 2017; 214:2875-2887. [PMID: 28878000 PMCID: PMC5626406 DOI: 10.1084/jem.20170976] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 07/18/2017] [Accepted: 07/26/2017] [Indexed: 01/01/2023] Open
Abstract
The work by Tang et al. provides a comprehensive, single-cell, transcriptomic analysis of kidney and blood cells from the adult zebrafish, identifying novel cell types, including two classes of NK immune cells, classically defined and erythroid-primed hematopoietic stem and progenitor cells, mucin-secreting kidney cells, and kidney stem/progenitor cells. Recent advances in single-cell, transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. In this study, we used massively parallel, single-cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow, constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner, our approach was useful in characterizing immune-cell deficiencies within DNA–protein kinase catalytic subunit (prkdc), interleukin-2 receptor γ a (il2rga), and double-homozygous–mutant fish, identifying blood cell losses in T, B, and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types, including two classes of natural killer immune cells, classically defined and erythroid-primed hematopoietic stem and progenitor cells, mucin-secreting kidney cells, and kidney stem/progenitor cells. In total, our work provides the first, comprehensive, single-cell, transcriptomic analysis of kidney and marrow cells in the adult zebrafish.
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Affiliation(s)
- Qin Tang
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA.,Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA.,Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA.,Harvard Stem Cell Institute, Harvard University, Cambridge, MA
| | - Sowmya Iyer
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA
| | - Riadh Lobbardi
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA.,Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA.,Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA.,Harvard Stem Cell Institute, Harvard University, Cambridge, MA
| | - John C Moore
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA.,Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA.,Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA.,Harvard Stem Cell Institute, Harvard University, Cambridge, MA
| | - Huidong Chen
- Department of Biostatistics, T.H. Chan School of Public Health, Harvard University, Boston, MA.,Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA.,Department of Computer Science and Technology, Tongji University, Shanghai, China
| | - Caleb Lareau
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA.,Department of Biostatistics, T.H. Chan School of Public Health, Harvard University, Boston, MA
| | - Christine Hebert
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA.,Broad Institute, Cambridge, MA
| | - McKenzie L Shaw
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA.,Broad Institute, Cambridge, MA
| | - Cyril Neftel
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA.,Broad Institute, Cambridge, MA
| | - Mario L Suva
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA.,Broad Institute, Cambridge, MA
| | - Craig J Ceol
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA
| | - Andre Bernards
- Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA
| | - Martin Aryee
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA.,Department of Biostatistics, T.H. Chan School of Public Health, Harvard University, Boston, MA
| | - Luca Pinello
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA.,Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA
| | - Iain A Drummond
- Division of Nephrology, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - David M Langenau
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA .,Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA.,Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA.,Harvard Stem Cell Institute, Harvard University, Cambridge, MA
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17
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Filbin MG, Tirosh I, Escalante LE, Venteicher AS, Goumnerova L, Pelton K, Bandopadhayay P, Mount C, Slavc I, Czech T, Gojo J, Lavarino C, Mora J, Monje M, Kieran MW, Ligon KL, Golub T, Regev A, Suva ML. HG-110SINGLE-CELL TRANSCRIPTOME ANALYSIS IN PEDIATRIC HEMISPHERIC AND MIDLINE HIGH-GRADE GLIOMAS. Neuro Oncol 2016. [DOI: 10.1093/neuonc/now073.106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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18
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Wright KD, Bandopadhayay P, Gourmnerova L, Chi SN, Manley P, Marcus K, Kannan G, Banerjee A, Becher O, Bendel A, Bowers D, Bredlau AL, Cohen K, Comito M, Elster JD, Etzl M, Fisher PG, Gardner S, Goldman S, Gururangan S, Handler MH, Jabado N, Karajannis M, Khatib Z, Leary SE, MacDonald TJ, Monje M, Nazemi K, Robison NJ, Rubin J, Sandler ES, Snuderl M, Wang ZJ, Sinai CE, Greenspan L, Lawler K, Neuberg D, Filbin M, Segal R, Suva ML, Beroukhim R, Ligon K, Gupta N, Prados M, Kieran MW. HG-73SAFETY AND FEASIBILITY OF A MULTI-INSTITUTIONAL PHASE II TRIAL INCOPORATING BIOPSY AND MOLECULARLY DETERMINED TREATMENT OF CHILDREN AND YOUNG ADULTS WITH NEWLY DIAGNOSED DIFFUSE INTRINSIC PONTINE GLIOMAS (DIPG). Neuro Oncol 2016. [DOI: 10.1093/neuonc/now073.69] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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19
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Filbin MG, Tirosh I, Escalante LE, Venteicher AS, Hebert C, Goumnerova L, Ligon KL, Golub T, Regev A, Suva ML. PTPS-06SINGLE-CELL TRANSCRIPTOME ANALYSIS IN PEDIATRIC HIGH-GRADE GLIOMA. Neuro Oncol 2015. [DOI: 10.1093/neuonc/nov228.06] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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