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Hadad S, Gupta R, Oberheim Bush NA, Taylor JW, Villanueva-Meyer JE, Young JS, Wu J, Ravindranathan A, Zhang Y, Warrier G, McCoy L, Shai A, Pekmezci M, Perry A, Bollen AW, Phillips JJ, Braunstein SE, Raleigh DR, Theodosopoulos P, Aghi MK, Chang EF, Hervey-Jumper SL, Costello JF, de Groot J, Butowski NA, Clarke JL, Chang SM, Berger MS, Molinaro AM, Solomon DA. "De novo replication repair deficient glioblastoma, IDH-wildtype" is a distinct glioblastoma subtype in adults that may benefit from immune checkpoint blockade. Acta Neuropathol 2023; 147:3. [PMID: 38079020 PMCID: PMC10713691 DOI: 10.1007/s00401-023-02654-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/24/2023] [Accepted: 10/24/2023] [Indexed: 12/18/2023]
Abstract
Glioblastoma is a clinically and molecularly heterogeneous disease, and new predictive biomarkers are needed to identify those patients most likely to respond to specific treatments. Through prospective genomic profiling of 459 consecutive primary treatment-naïve IDH-wildtype glioblastomas in adults, we identified a unique subgroup (2%, 9/459) defined by somatic hypermutation and DNA replication repair deficiency due to biallelic inactivation of a canonical mismatch repair gene. The deleterious mutations in mismatch repair genes were often present in the germline in the heterozygous state with somatic inactivation of the remaining allele, consistent with glioblastomas arising due to underlying Lynch syndrome. A subset of tumors had accompanying proofreading domain mutations in the DNA polymerase POLE and resultant "ultrahypermutation". The median age at diagnosis was 50 years (range 27-78), compared with 63 years for the other 450 patients with conventional glioblastoma (p < 0.01). All tumors had histologic features of the giant cell variant of glioblastoma. They lacked EGFR amplification, lacked combined trisomy of chromosome 7 plus monosomy of chromosome 10, and only rarely had TERT promoter mutation or CDKN2A homozygous deletion, which are hallmarks of conventional IDH-wildtype glioblastoma. Instead, they harbored frequent inactivating mutations in TP53, NF1, PTEN, ATRX, and SETD2 and recurrent activating mutations in PDGFRA. DNA methylation profiling revealed they did not align with known reference adult glioblastoma methylation classes, but instead had unique globally hypomethylated epigenomes and mostly classified as "Diffuse pediatric-type high grade glioma, RTK1 subtype, subclass A". Five patients were treated with immune checkpoint blockade, four of whom survived greater than 3 years. The median overall survival was 36.8 months, compared to 15.5 months for the other 450 patients (p < 0.001). We conclude that "De novo replication repair deficient glioblastoma, IDH-wildtype" represents a biologically distinct subtype in the adult population that may benefit from prospective identification and treatment with immune checkpoint blockade.
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Affiliation(s)
- Sara Hadad
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Rohit Gupta
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Nancy Ann Oberheim Bush
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Jennie W Taylor
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Javier E Villanueva-Meyer
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, CA, USA
| | - Jacob S Young
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Jasper Wu
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Ajay Ravindranathan
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Yalan Zhang
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Gayathri Warrier
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Lucie McCoy
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Anny Shai
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Melike Pekmezci
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Arie Perry
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Andrew W Bollen
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Joanna J Phillips
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Steve E Braunstein
- Department of Radiation Oncology, University of California, San Francisco, CA, USA
| | - David R Raleigh
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
- Department of Radiation Oncology, University of California, San Francisco, CA, USA
| | - Philip Theodosopoulos
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Manish K Aghi
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Edward F Chang
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Shawn L Hervey-Jumper
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Joseph F Costello
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - John de Groot
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Nicholas A Butowski
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Jennifer L Clarke
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Susan M Chang
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Mitchel S Berger
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Annette M Molinaro
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA.
| | - David A Solomon
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA.
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2
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Williams EA, Ravindranathan A, Gupta R, Stevers NO, Suwala AK, Hong C, Kim S, Yuan JB, Wu J, Barreto J, Lucas CHG, Chan E, Pekmezci M, LeBoit PE, Mully T, Perry A, Bollen A, Van Ziffle J, Devine WP, Reddy AT, Gupta N, Basnet KM, Macaulay RJB, Malafronte P, Lee H, Yong WH, Williams KJ, Juratli TA, Mata DA, Huang RSP, Hiemenz MC, Pavlick DC, Frampton GM, Janovitz T, Ross JS, Chang SM, Berger MS, Jacques L, Song JS, Costello JF, Solomon DA. Novel SOX10 indel mutations drive schwannomas through impaired transactivation of myelination gene programs. Neuro Oncol 2023; 25:2221-2236. [PMID: 37436963 PMCID: PMC10708934 DOI: 10.1093/neuonc/noad121] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Indexed: 07/14/2023] Open
Abstract
BACKGROUND Schwannomas are common peripheral nerve sheath tumors that can cause severe morbidity given their stereotypic intracranial and paraspinal locations. Similar to many solid tumors, schwannomas and other nerve sheath tumors are primarily thought to arise due to aberrant hyperactivation of the RAS growth factor signaling pathway. Here, we sought to further define the molecular pathogenesis of schwannomas. METHODS We performed comprehensive genomic profiling on a cohort of 96 human schwannomas, as well as DNA methylation profiling on a subset. Functional studies including RNA sequencing, chromatin immunoprecipitation-DNA sequencing, electrophoretic mobility shift assay, and luciferase reporter assays were performed in a fetal glial cell model following transduction with wildtype and tumor-derived mutant isoforms of SOX10. RESULTS We identified that nearly one-third of sporadic schwannomas lack alterations in known nerve sheath tumor genes and instead harbor novel recurrent in-frame insertion/deletion mutations in SOX10, which encodes a transcription factor responsible for controlling Schwann cell differentiation and myelination. SOX10 indel mutations were highly enriched in schwannomas arising from nonvestibular cranial nerves (eg facial, trigeminal, vagus) and were absent from vestibular nerve schwannomas driven by NF2 mutation. Functional studies revealed these SOX10 indel mutations have retained DNA binding capacity but impaired transactivation of glial differentiation and myelination gene programs. CONCLUSIONS We thus speculate that SOX10 indel mutations drive a unique subtype of schwannomas by impeding proper differentiation of immature Schwann cells.
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Affiliation(s)
- Erik A Williams
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Ajay Ravindranathan
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Rohit Gupta
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Nicholas O Stevers
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
| | - Abigail K Suwala
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
| | - Chibo Hong
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
| | - Somang Kim
- Department of Physics and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Jimmy Bo Yuan
- Department of Physics and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Jasper Wu
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Jairo Barreto
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Calixto-Hope G Lucas
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Emily Chan
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Melike Pekmezci
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Philip E LeBoit
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Thaddeus Mully
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Arie Perry
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
| | - Andrew Bollen
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Jessica Van Ziffle
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - W Patrick Devine
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Alyssa T Reddy
- Departments of Neurology and Pediatrics, University of California, San Francisco, San Francisco, California, USA
| | - Nalin Gupta
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
| | | | | | | | - Han Lee
- Department of Pathology, University of California, Davis, Sacramento, California, USA
| | - William H Yong
- Department of Pathology and Laboratory Medicine, University of California, Irvine, Irvine, California, USA
| | - Kevin Jon Williams
- Departments of Physiology and Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania, USA
| | - Tareq A Juratli
- Department of Neurosurgery, Division of Neuro-Oncology, Faculty of Medicine and Carl Gustav Carus University Hospital, Dresden, Germany
| | - Douglas A Mata
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA
| | | | | | - Dean C Pavlick
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA
| | | | - Tyler Janovitz
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA
| | - Jeffrey S Ross
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA
- Department of Pathology, State University of New York Upstate Medical University, Syracuse, New York, USA
| | - Susan M Chang
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
| | - Mitchel S Berger
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
| | - Line Jacques
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
| | - Jun S Song
- Department of Physics and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Joseph F Costello
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
| | - David A Solomon
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
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3
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Terry M, Gupta R, Ravindranathan A, Wu J, Chan E, Bollen AW, Chang SM, Berger MS, Jacques L, Solomon DA. Somatic mosaic SOX10 indel mutations underlie a form of segmental schwannomatosis. Acta Neuropathol 2023; 146:857-860. [PMID: 37821623 PMCID: PMC10627975 DOI: 10.1007/s00401-023-02641-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/29/2023] [Accepted: 09/29/2023] [Indexed: 10/13/2023]
Affiliation(s)
- Merryl Terry
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Rohit Gupta
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Ajay Ravindranathan
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Jasper Wu
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Emily Chan
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Andrew W Bollen
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Susan M Chang
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Mitchel S Berger
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Line Jacques
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA.
| | - David A Solomon
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA.
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4
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Lucas CHG, Sloan EA, Gupta R, Wu J, Pratt D, Vasudevan HN, Ravindranathan A, Barreto J, Williams EA, Shai A, Whipple NS, Bruggers CS, Maher O, Nabors B, Rodriguez M, Samuel D, Brown M, Carmichael J, Lu R, Mirchia K, Sullivan DV, Pekmezci M, Tihan T, Bollen AW, Perry A, Banerjee A, Mueller S, Gupta N, Hervey-Jumper SL, Oberheim Bush NA, Daras M, Taylor JW, Butowski NA, de Groot J, Clarke JL, Raleigh DR, Costello JF, Phillips JJ, Reddy AT, Chang SM, Berger MS, Solomon DA. Multiplatform molecular analyses refine classification of gliomas arising in patients with neurofibromatosis type 1. Acta Neuropathol 2022; 144:747-765. [PMID: 35945463 PMCID: PMC9468105 DOI: 10.1007/s00401-022-02478-5] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 07/29/2022] [Accepted: 07/30/2022] [Indexed: 01/28/2023]
Abstract
Gliomas arising in the setting of neurofibromatosis type 1 (NF1) are heterogeneous, occurring from childhood through adulthood, can be histologically low-grade or high-grade, and follow an indolent or aggressive clinical course. Comprehensive profiling of genetic alterations beyond NF1 inactivation and epigenetic classification of these tumors remain limited. Through next-generation sequencing, copy number analysis, and DNA methylation profiling of gliomas from 47 NF1 patients, we identified 2 molecular subgroups of NF1-associated gliomas. The first harbored biallelic NF1 inactivation only, occurred primarily during childhood, followed a more indolent clinical course, and had a unique epigenetic signature for which we propose the terminology "pilocytic astrocytoma, arising in the setting of NF1". The second subgroup harbored additional oncogenic alterations including CDKN2A homozygous deletion and ATRX mutation, occurred primarily during adulthood, followed a more aggressive clinical course, and was epigenetically diverse, with most tumors aligning with either high-grade astrocytoma with piloid features or various subclasses of IDH-wildtype glioblastoma. Several patients were treated with small molecule MEK inhibitors that resulted in stable disease or tumor regression when used as a single agent, but only in the context of those tumors with NF1 inactivation lacking additional oncogenic alterations. Together, these findings highlight recurrently altered pathways in NF1-associated gliomas and help inform targeted therapeutic strategies for this patient population.
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Affiliation(s)
- Calixto-Hope G Lucas
- Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA, 94143, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Emily A Sloan
- Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA, 94143, USA
- Department of Pathology, Medstar Georgetown University Hospital, Washington, DC, USA
| | - Rohit Gupta
- Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA, 94143, USA
| | - Jasper Wu
- Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA, 94143, USA
| | - Drew Pratt
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Harish N Vasudevan
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Ajay Ravindranathan
- Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA, 94143, USA
| | - Jairo Barreto
- Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA, 94143, USA
| | - Erik A Williams
- Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA, 94143, USA
| | - Anny Shai
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Nicholas S Whipple
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Utah, Salt Lake City, UT, USA
| | - Carol S Bruggers
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Utah, Salt Lake City, UT, USA
| | - Ossama Maher
- Department of Oncology, Nicklaus Children's Hospital, Miami, FL, USA
| | - Burt Nabors
- Division of Neuro-Oncology, Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - David Samuel
- Department of Hematology/Oncology, Valley Children's Hospital, Madera, CA, USA
| | - Melandee Brown
- Department of Neurosurgery, Valley Children's Hospital, Madera, CA, USA
| | - Jason Carmichael
- Department of Medical Genetics and Metabolism, Valley Children's Hospital, Madera, CA, USA
| | - Rufei Lu
- Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA, 94143, USA
| | - Kanish Mirchia
- Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA, 94143, USA
| | - Daniel V Sullivan
- Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA, 94143, USA
| | - Melike Pekmezci
- Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA, 94143, USA
| | - Tarik Tihan
- Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA, 94143, USA
| | - Andrew W Bollen
- Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA, 94143, USA
| | - Arie Perry
- Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA, 94143, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Anuradha Banerjee
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Sabine Mueller
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Nalin Gupta
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Shawn L Hervey-Jumper
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Nancy Ann Oberheim Bush
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
- Division of Neuro-Oncology, Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Mariza Daras
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
- Division of Neuro-Oncology, Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Jennie W Taylor
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
- Division of Neuro-Oncology, Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Nicholas A Butowski
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
- Division of Neuro-Oncology, Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - John de Groot
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
- Division of Neuro-Oncology, Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Jennifer L Clarke
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
- Division of Neuro-Oncology, Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - David R Raleigh
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Joseph F Costello
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Joanna J Phillips
- Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA, 94143, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Alyssa T Reddy
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Susan M Chang
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
- Division of Neuro-Oncology, Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Mitchel S Berger
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - David A Solomon
- Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA, 94143, USA.
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5
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Lucas CHG, Gupta R, Wu J, Shah K, Ravindranathan A, Barreto J, Gener M, Ginn KF, Prall OWJ, Xu H, Kee D, Ko HS, Yaqoob N, Zia N, Florez A, Cha S, Perry A, Clarke JL, Chang SM, Berger MS, Solomon DA. EWSR1-BEND2 fusion defines an epigenetically distinct subtype of astroblastoma. Acta Neuropathol 2022; 143:109-113. [PMID: 34825267 PMCID: PMC8732961 DOI: 10.1007/s00401-021-02388-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/05/2021] [Accepted: 11/17/2021] [Indexed: 11/02/2022]
Affiliation(s)
- Calixto-Hope G Lucas
- Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA, 94143, USA
| | - Rohit Gupta
- Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA, 94143, USA
| | - Jasper Wu
- Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA, 94143, USA
| | - Kathan Shah
- Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA, 94143, USA
| | - Ajay Ravindranathan
- Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA, 94143, USA
| | - Jairo Barreto
- Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA, 94143, USA
| | - Melissa Gener
- Department of Pathology, Children's Mercy Hospital, Kansas City, MO, USA
| | - Kevin F Ginn
- Department of Pediatric Hematology and Oncology, Children's Mercy Hospital, Kansas City, MO, USA
| | - Owen W J Prall
- Department of Pathology, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, VIC, Australia
| | - Huiling Xu
- Department of Pathology, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, VIC, Australia
| | - Damien Kee
- Department of Medical Oncology, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, VIC, Australia
| | - Hyun S Ko
- Department of Cancer Imaging, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, VIC, Australia
| | - Nausheen Yaqoob
- Department of Histopathology, Indus Hospital and Health Network, Karachi, Pakistan
| | - Nida Zia
- Department of Pediatric Hematology and Oncology, Indus Hospital and Health Network, Karachi, Pakistan
| | - Adriana Florez
- Department of Pathology, Fundación Santafé de Bogotá, Bogota, Colombia
| | - Soonmee Cha
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, CA, USA
| | - Arie Perry
- Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA, 94143, USA
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Jennifer L Clarke
- Division of Neuro-Oncology, Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Susan M Chang
- Division of Neuro-Oncology, Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Mitchel S Berger
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - David A Solomon
- Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA, 94143, USA.
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6
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Mondal G, Lee JC, Ravindranathan A, Villanueva-Meyer JE, Tran QT, Allen SJ, Barreto J, Gupta R, Doo P, Van Ziffle J, Onodera C, Devine P, Grenert JP, Samuel D, Li R, Metrock LK, Jin LW, Antony R, Alashari M, Cheshier S, Whipple NS, Bruggers C, Raffel C, Gupta N, Kline CN, Reddy A, Banerjee A, Hall MD, Mehta MP, Khatib Z, Maher OM, Brathwaite C, Pekmezci M, Phillips JJ, Bollen AW, Tihan T, Lucas JT, Broniscer A, Berger MS, Perry A, Orr BA, Solomon DA. Pediatric bithalamic gliomas have a distinct epigenetic signature and frequent EGFR exon 20 insertions resulting in potential sensitivity to targeted kinase inhibition. Acta Neuropathol 2020; 139:1071-1088. [PMID: 32303840 DOI: 10.1007/s00401-020-02155-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 04/03/2020] [Accepted: 04/04/2020] [Indexed: 10/24/2022]
Abstract
Brain tumors are the most common solid tumors of childhood, and the genetic drivers and optimal therapeutic strategies for many of the different subtypes remain unknown. Here, we identify that bithalamic gliomas harbor frequent mutations in the EGFR oncogene, only rare histone H3 mutation (in contrast to their unilateral counterparts), and a distinct genome-wide DNA methylation profile compared to all other glioma subtypes studied to date. These EGFR mutations are either small in-frame insertions within exon 20 (intracellular tyrosine kinase domain) or missense mutations within exon 7 (extracellular ligand-binding domain) that occur in the absence of accompanying gene amplification. We find these EGFR mutations are oncogenic in primary astrocyte models and confer sensitivity to specific tyrosine kinase inhibitors dependent on location within the kinase domain or extracellular domain. We initiated treatment with targeted kinase inhibitors in four children whose tumors harbor EGFR mutations with encouraging results. This study identifies a promising genomically-tailored therapeutic strategy for bithalamic gliomas, a lethal and genetically distinct brain tumor of childhood.
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Chen F, Jimenez RJ, Sharma K, Luu HY, Hsu BY, Ravindranathan A, Stohr BA, Willenbring H. Broad Distribution of Hepatocyte Proliferation in Liver Homeostasis and Regeneration. Cell Stem Cell 2019; 26:27-33.e4. [PMID: 31866223 DOI: 10.1016/j.stem.2019.11.001] [Citation(s) in RCA: 125] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 09/06/2019] [Accepted: 11/07/2019] [Indexed: 12/30/2022]
Abstract
Hepatocyte proliferation is the principal mechanism for generating new hepatocytes in liver homeostasis and regeneration. Recent studies have suggested that this ability is not equally distributed among hepatocytes but concentrated in a small subset of hepatocytes acting like stem cells, located around the central vein or distributed throughout the liver lobule and exhibiting active WNT signaling or high telomerase activity, respectively. These findings were obtained by utilizing components of these growth regulators as markers for genetic lineage tracing. Here, we used random lineage tracing to localize and quantify clonal expansion of hepatocytes in normal and injured liver. We found that modest proliferation of hepatocytes distributed throughout the lobule maintains the hepatocyte mass and that most hepatocytes proliferate to regenerate it, with diploidy providing a growth advantage over polyploidy. These results show that the ability to proliferate is broadly distributed among hepatocytes rather than limited to a rare stem cell-like population.
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Affiliation(s)
- Feng Chen
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA.
| | - Robert J Jimenez
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Khushbu Sharma
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; College of Arts and Sciences, University of San Francisco, San Francisco, CA 94117, USA
| | - Hubert Y Luu
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Division of General Surgery, Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Bernadette Y Hsu
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ajay Ravindranathan
- Division of Surgical Pathology, Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Bradley A Stohr
- Division of Surgical Pathology, Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Holger Willenbring
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Division of Transplant Surgery, Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Liver Center, University of California, San Francisco, San Francisco, CA 94143, USA.
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Ravindranathan A, Diolaiti ME, Cimini BA, Stohr BA. In Situ Visualization of Telomere Length, Telomere Elongation, and TERT Expression in Single Cells. ACTA ACUST UNITED AC 2019; 85:e97. [PMID: 31763768 DOI: 10.1002/cpcb.97] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Telomerase plays a critical role in cancer and aging by adding hexa-nucleotide repeats to the ends of telomeres and extending the cellular proliferative lifespan. The very low level of telomerase expression in most cell populations and the difficulty of detecting telomere elongation in single cells have limited the study of telomerase expression and function in individual cells of a heterogeneous population. The method described in this article combines single-molecule detection (RNAscope) of telomerase reverse transcriptase (TERT) with our previously described TSQ1 assay for in situ monitoring of telomere extension, thereby enabling detection of TERT expression, telomere length, and telomere elongation in single cells and providing a unique approach for studying the factors that regulate telomere elongation by telomerase. © 2019 by John Wiley & Sons, Inc. Basic Protocol 1: TSQ1 lentivirus production Basic Protocol 2: TSQ1 lentiviral infection and plating Basic Protocol 3: RNAscope analysis Basic Protocol 4: TSQ1 PNA-FISH detection.
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Affiliation(s)
- Ajay Ravindranathan
- Department of Pathology, University of California, San Francisco, California
| | - Morgan E Diolaiti
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | | | - Bradley A Stohr
- Department of Pathology, University of California, San Francisco, California
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Ravindranathan A, Cimini B, Diolaiti ME, Stohr BA. Preliminary development of an assay for detection of TERT expression, telomere length, and telomere elongation in single cells. PLoS One 2018; 13:e0206525. [PMID: 30517099 PMCID: PMC6281304 DOI: 10.1371/journal.pone.0206525] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 10/15/2018] [Indexed: 02/06/2023] Open
Abstract
The telomerase enzyme enables unlimited proliferation of most human cancer cells by elongating telomeres and preventing replicative senescence. Despite the critical importance of telomerase in cancer biology, challenges detecting telomerase activity and expression in individual cells have hindered the ability to study patterns of telomerase expression and function across heterogeneous cell populations. While sensitive assays to ascertain telomerase expression and function exist, these approaches have proven difficult to implement at the single cell level. Here, we validate in situ RNAscope detection of the telomerase TERT mRNA and couple this assay with our recently described TSQ1 method for in situ detection of telomere elongation. This approach enables detection of TERT expression, telomere length, and telomere elongation within individual cells of the population. Using this assay, we show that the heterogeneous telomere elongation observed across a HeLa cell population is in part driven by variable expression of the TERT gene. Furthermore, we show that the absence of detectable telomere elongation in some TERT-positive cells is the result of inhibition by the telomeric shelterin complex. This combined assay provides a new approach for understanding the integrated expression, function, and regulation of telomerase at the single cell level.
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Affiliation(s)
- Ajay Ravindranathan
- Department of Pathology, University of California, San Francisco, California, United States of America
| | - Beth Cimini
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, United States of America
| | - Morgan E Diolaiti
- Department of Pathology, University of California, San Francisco, California, United States of America
| | - Bradley A Stohr
- Department of Pathology, University of California, San Francisco, California, United States of America
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10
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Liu SY, Joseph NM, Ravindranathan A, Stohr BA, Greenland NY, Vohra P, Hosfield E, Yeh I, Talevich E, Onodera C, Van Ziffle JA, Grenert JP, Bastian BC, Chen YY, Krings G. Genomic profiling of malignant phyllodes tumors reveals aberrations in FGFR1 and PI-3 kinase/RAS signaling pathways and provides insights into intratumoral heterogeneity. Mod Pathol 2016; 29:1012-27. [PMID: 27255162 DOI: 10.1038/modpathol.2016.97] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 04/18/2016] [Accepted: 04/22/2016] [Indexed: 12/16/2022]
Abstract
Malignant phyllodes tumors of the breast are poorly understood rare neoplasms with potential for aggressive behavior. Few efficacious treatment options exist for progressed or metastatic disease. The molecular features of malignant phyllodes tumors are poorly defined, and a deeper understanding of the genetics of these tumors may shed light on pathogenesis and progression and potentially identify novel treatment approaches. We sequenced 510 cancer-related genes in 10 malignant phyllodes tumors, including 5 tumors with liposarcomatous differentiation and 1 with myxoid chondrosarcoma-like differentiation. Intratumoral heterogeneity was assessed by sequencing two separate areas in 7 tumors, including non-heterologous and heterologous components of tumors with heterologous differentiation. Activating hotspot mutations in FGFR1 were identified in 2 tumors. Additional recurrently mutated genes included TERT promoter (6/10), TP53 (4/10), PIK3CA (3/10), MED12 (3/10), SETD2 (2/10) and KMT2D (2/10). Together, genomic aberrations in FGFR/EGFR PI-3 kinase and RAS pathways were identified in 8 (80%) tumors and included mutually exclusive and potentially actionable activating FGFR1, PIK3CA and BRAF V600E mutations, inactivating TSC2 mutation, EGFR amplification and PTEN loss. Seven (70%) malignant phyllodes tumors harbored TERT aberrations (six promoter mutations, one amplification). For comparison, TERT promoter mutations were identified by Sanger sequencing in 33% borderline (n=12) and no (0%, n=8) benign phyllodes tumors (P=0.391 and P=0.013 vs malignant tumors, respectively). Genetic features specific to liposarcoma, including CDK4/MDM2 amplification, were not identified. Copy number analysis revealed intratumoral heterogeneity and evidence for divergent tumor evolution in malignant phyllodes tumors with and without heterologous differentiation. Tumors with liposarcomatous differentiation revealed more chromosomal aberrations in non-heterologous components compared with liposarcomatous components. EGFR amplification was heterogeneous and present only in the non-heterologous component of one tumor with liposarcomatous differentiation. The results identify novel pathways involved in the pathogenesis of malignant phyllodes tumors, which significantly increase our understanding of tumor biology and have potential clinical impact.
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Affiliation(s)
- Su-Yang Liu
- Department of Pathology, University of California San Francisco (UCSF), San Francisco, CA, USA
| | - Nancy M Joseph
- Department of Pathology, University of California San Francisco (UCSF), San Francisco, CA, USA
| | - Ajay Ravindranathan
- Department of Pathology, University of California San Francisco (UCSF), San Francisco, CA, USA
| | - Bradley A Stohr
- Department of Pathology, University of California San Francisco (UCSF), San Francisco, CA, USA
| | - Nancy Y Greenland
- Department of Pathology, University of California San Francisco (UCSF), San Francisco, CA, USA
| | - Poonam Vohra
- Department of Pathology, University of California San Francisco (UCSF), San Francisco, CA, USA.,Department of Pathology, San Francisco General Hospital, San Francisco, CA, USA
| | | | - Iwei Yeh
- Department of Dermatology, University of California San Francisco (UCSF), San Francisco, CA, USA
| | - Eric Talevich
- Department of Pathology, University of California San Francisco (UCSF), San Francisco, CA, USA
| | - Courtney Onodera
- Department of Pathology, University of California San Francisco (UCSF), San Francisco, CA, USA
| | - Jessica A Van Ziffle
- Department of Pathology, University of California San Francisco (UCSF), San Francisco, CA, USA
| | - James P Grenert
- Department of Pathology, University of California San Francisco (UCSF), San Francisco, CA, USA
| | - Boris C Bastian
- Department of Pathology, University of California San Francisco (UCSF), San Francisco, CA, USA.,Department of Dermatology, University of California San Francisco (UCSF), San Francisco, CA, USA
| | - Yunn-Yi Chen
- Department of Pathology, University of California San Francisco (UCSF), San Francisco, CA, USA
| | - Gregor Krings
- Department of Pathology, University of California San Francisco (UCSF), San Francisco, CA, USA
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11
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Joslyn G, Ravindranathan A, Brush G, Schuckit M, White RL. Human Variation in Alcohol Response Is Influenced by Variation in Neuronal Signaling Genes. Alcohol Clin Exp Res 2010; 34:800-12. [DOI: 10.1111/j.1530-0277.2010.01152.x] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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12
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Kerns RT, Ravindranathan A, Hassan S, Cage MP, York T, Sikela JM, Williams RW, Miles MF. Ethanol-responsive brain region expression networks: implications for behavioral responses to acute ethanol in DBA/2J versus C57BL/6J mice. J Neurosci 2006; 25:2255-66. [PMID: 15745951 PMCID: PMC6726093 DOI: 10.1523/jneurosci.4372-04.2005] [Citation(s) in RCA: 189] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Activation of the mesolimbic dopamine reward pathway by acute ethanol produces reinforcement and changes in gene expression that appear to be crucial to the molecular basis for adaptive behaviors and addiction. The inbred mouse strains DBA/2J and C57BL/6J exhibit contrasting acute behavioral responses to ethanol. We used oligonucleotide microarrays and bioinformatics methods to characterize patterns of gene expression in three brain regions of the mesolimbic reward pathway of these strains. Expression profiling included examination of both differences in gene expression 4 h after saline injection or acute ethanol (2 g/kg). Using a rigorous stepwise method for microarray analysis, we identified 788 genes differentially expressed in control DBA/2J versus C57BL/6J mice and 307 ethanol-regulated genes in the nucleus accumbens, prefrontal cortex, and ventral tegmental area. There were strikingly divergent patterns of ethanol-responsive gene expression in the two strains. Ethanol-responsive genes also showed clustering at discrete chromosomal regions, suggesting local chromatin effects in regulation. Ethanol-regulated genes were generally related to neuroplasticity, but regulation of discrete functional groups and pathways was brain region specific: glucocorticoid signaling, neurogenesis, and myelination in the prefrontal cortex; neuropeptide signaling and developmental genes, including factor Bdnf, in the nucleus accumbens; and retinoic acid signaling in the ventral tegmental area. Bioinformatics analysis identified several potential candidate genes for quantitative trait loci linked to ethanol behaviors, further supporting a role for expression profiling in identifying genes for complex traits. Brain region-specific changes in signaling and neuronal plasticity may be critical components in development of lasting ethanol behavioral phenotypes such as dependence, sensitization, and craving.
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Affiliation(s)
- Robnet T Kerns
- Department of Pharmacology/Toxicology and the Center for Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia 23298, USA
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13
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He DY, McGough NNH, Ravindranathan A, Jeanblanc J, Logrip ML, Phamluong K, Janak PH, Ron D. Glial cell line-derived neurotrophic factor mediates the desirable actions of the anti-addiction drug ibogaine against alcohol consumption. J Neurosci 2005; 25:619-28. [PMID: 15659598 PMCID: PMC1193648 DOI: 10.1523/jneurosci.3959-04.2005] [Citation(s) in RCA: 137] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Alcohol addiction manifests as uncontrolled drinking despite negative consequences. Few medications are available to treat the disorder. Anecdotal reports suggest that ibogaine, a natural alkaloid, reverses behaviors associated with addiction including alcoholism; however, because of side effects, ibogaine is not used clinically. In this study, we first characterized the actions of ibogaine on ethanol self-administration in rodents. Ibogaine decreased ethanol intake by rats in two-bottle choice and operant self-administration paradigms. Ibogaine also reduced operant self-administration of ethanol in a relapse model. Next, we identified a molecular mechanism that mediates the desirable activities of ibogaine on ethanol intake. Microinjection of ibogaine into the ventral tegmental area (VTA), but not the substantia nigra, reduced self-administration of ethanol, and systemic administration of ibogaine increased the expression of glial cell line-derived neurotrophic factor (GDNF) in a midbrain region that includes the VTA. In dopaminergic neuron-like SHSY5Y cells, ibogaine treatment upregulated the GDNF pathway as indicated by increases in phosphorylation of the GDNF receptor, Ret, and the downstream kinase, ERK1 (extracellular signal-regulated kinase 1). Finally, the ibogaine-mediated decrease in ethanol self-administration was mimicked by intra-VTA microinjection of GDNF and was reduced by intra-VTA delivery of anti-GDNF neutralizing antibodies. Together, these results suggest that GDNF in the VTA mediates the action of ibogaine on ethanol consumption. These findings highlight the importance of GDNF as a new target for drug development for alcoholism that may mimic the effect of ibogaine against alcohol consumption but avoid the negative side effects.
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Affiliation(s)
- Dao-Yao He
- Ernest Gallo Research Center, University of California, San Francisco, Emeryville, California 94608, USA
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14
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Zhang L, Wang L, Ravindranathan A, Miles MF. A new algorithm for analysis of oligonucleotide arrays: application to expression profiling in mouse brain regions. J Mol Biol 2002; 317:225-35. [PMID: 11902839 DOI: 10.1006/jmbi.2001.5350] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Oligonucleotide arrays are a powerful technology for measuring the expression of thousands of genes simultaneously. Improvements in the sensitivity and precision of the measurements, which often pose a challenge to users, would assist the practical application of the technology. Here, we describe a new analysis algorithm for assessing changes in gene expression using oligonucleotide arrays. Changes in expression are detected in terms of the statistical significance (S-score) of change, which combines signals detected by multiple probe pairs according to an error model characteristic of oligonucleotide arrays. We show that the S-score is sensitive and reliable, enabling us to obtain more consistent results than with existing methods. Cluster analysis of S-score data of four brain regions exhibits patterns that are more distinctive because of improved data quality. In our case study of two mouse brain regions, over 200 genes were identified to have detectable changes between the ventral tegmental area and the prefrontal cortex. The genes with the most distinctive changes are found to be related to myelin or neurofilament synthesis, calcium signaling, and transcription factors. Many of these findings are in agreement with previous studies, using other techniques, such as in situ hybridization. Overall, our findings suggest that this new algorithm may have broad applicability for improving the analysis of oligonucleotide array data.
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Affiliation(s)
- Li Zhang
- The Ernest Gallo Clinic and Research Center and Department of Neurology, University of California at San Francisco, 5858 Horton Street Suite 200 Emeryville, CA 94608, USA
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15
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Kesner RP, Ravindranathan A, Jackson P, Giles R, Chiba AA. A neural circuit analysis of visual recognition memory: role of perirhinal, medial, and lateral entorhinal cortex. Learn Mem 2001; 8:87-95. [PMID: 11274254 PMCID: PMC311369 DOI: 10.1101/lm.29401] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Using a continuous recognition memory procedure for visual object information, we sequentially presented rats with eight novel objects and four repeated objects (chosen from the 8). These were selected from 120 different three-dimensional objects of varying sizes, shapes, textures, and degree of brightness. Repeated objects had lags ranging from 0 to 4 (from 0 to 4 different objects between the first and repeated presentation). An object was presented on one side of a long table divided in half by an opaque Plexiglas guillotine door, and the latency between opening the door and the rat moving the object was measured. The first presentation of an object resulted in reinforcement, but repeated presentations did not result in a reinforcement. After completion of acquisition training (significantly longer latencies for repeated presentation compared with the first presentation of an object), rats received lesions of the perirhinal, medial, or lateral entorhinal cortex or served as sham operated controls. On the basis of postsurgery testing and additional tests, the results indicated that rats with perirhinal cortex lesions had a sustained impairment in performing the task. There were no sustained deficits with medial or lateral entorhinal cortex lesions. The data suggest that recognition memory for visual object information is mediated primarily by the perirhinal cortex but not by the medial or lateral entorhinal cortex.
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Affiliation(s)
- R P Kesner
- Department of Psychology, University of Utah, Salt Lake City, Utah 84112, USA.
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16
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Ravindranathan A, Donevan SD, Sugden SG, Greig A, Rao MS, Parks TN. Contrasting molecular composition and channel properties of AMPA receptors on chick auditory and brainstem motor neurons. J Physiol 2000; 523 Pt 3:667-84. [PMID: 10718746 PMCID: PMC2269838 DOI: 10.1111/j.1469-7793.2000.00667.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
1. Neurons in the brainstem auditory pathway exhibit a number of specializations for transmitting signals reliably at high rates, notably synaptic AMPA receptors with very rapid kinetics. Previous work has not revealed a common structural pattern shared by the AMPA receptors of auditory neurons that could account for their distinct functional properties. 2. We have used whole-cell patch-clamp recordings, mRNA analysis, immunofluorescence, Western blots and agonist-evoked cobalt uptake to compare AMPA receptors on the first-, second- and third-order neurons in the chick ascending auditory pathway with those on brainstem motor neurons of the glossopharyngeal/vagal nucleus, which have been shown to have very slow desensitization kinetics. 3. The results indicate that the AMPA receptors of the cochlear ganglion, nucleus magnocellularis and nucleus laminaris share a number of structural and functional properties that distinguish them from the AMPA receptors of brainstem motor neurons, namely a lower relative abundance of glutamate receptor (GluR)2 transcript and much lower levels of GluR2 immunoreactivity, higher relative levels of GluR3 flop and GluR4 flop, lower relative abundance of the C-terminal splice variants GluR4c and 4d, less R/G editing of GluR2 and 3, greater permeability to calcium, predominantly inwardly rectifying I-V relationships, and greater susceptibility to block by Joro spider toxin. 4. We conclude that the AMPA receptors of auditory neurons acquire rapid kinetics from their high content of GluR3 flop and GluR4 flop subunits and their high permeability to Ca2+ from selective post-transcriptional suppression of GluR2 expression.
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Affiliation(s)
- A Ravindranathan
- Department of Neurobiology and Anatomy and Department of Neurology and Anticonvulsant Drug Development Program, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
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17
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Lee JC, Greig A, Ravindranathan A, Parks TN, Rao MS. Molecular analysis of AMPA-specific receptors: subunit composition, editing, and calcium influx determination in small amounts of tissue. Brain Res Brain Res Protoc 1998; 3:142-54. [PMID: 9813290 DOI: 10.1016/s1385-299x(98)00035-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Glutamate activates three distinct classes of ionotropic receptors: AMPA, kainate and NMDA. AMPA receptors (AMPARs) are of particular importance as they mediate the majority of fast excitatory synaptic transmission and are implicated in a variety of neurological disorders [B. Bettler, C. Mulle, AMPA and kainate receptors, Neuropharmacology 34 (1995) 123-139]. Functional AMPARs are believed to be a heteromer comprising a combination of four closely related subunits, GluRs1-4 [B. Bettler, C. Mulle, AMPA and kainate receptors, Neuropharmacology 34 (1995) 123-139]. Diversity of AMPARs is obtained through multiple combinations of AMPAR subunits, by alternative splicing of subunits at the flip/flop and/or C-terminal sites, and by mRNA editing of a single amino acid at multiple sites [M. Hollmann, M. Hartley, S. Heinemann, Ca2+ permeability of KA-AMPA-gated glutamate receptor channel depends on subunit composition, Science 252 (1991) 851-853; B. Sommer, K. Keinanen, T.A. Verdoorn, W. Wisden, N. Burhashev, A. Herb, M. Kohler, T. Takagi, B. Sakmann, P.H. Seeburg, Flip and flop: a cell-specific functional switch in glutamate-operated channels in the CNS, Science 249 (1990) 1580-1585; B. Sommer, M. Kohler, R. Sprengel, P.H. Seeburg, RNA editing in brain controls a determinant of ion flow in glutamate-gated channels, Cell 67 (1991)]. The subunit combination, editing status, and splice variant expression have profound effects on channel kinetics and can serve as predictors of the channel's properties [M. Hollmann, M. Hartley, S. Heinemann, Ca2+ permeability of KA-AMPA-gated glutamate receptor channel depends on subunit composition, Science 252 (1991) 851-853; B. Sommer, K. Keinanen, T.A. Verdoorn, W. Wisden, N. Burhashev, A. Herb, M. Kohler, T. Takagi, B. Sakmann, P.H. Seeburg, Flip and flop: a cell-specific functional switch in glutamate-operated channels in the CNS, Science 249 (1990) 1580-1585; B. Sommer, M. Kohler, R. Sprengel, P.H. Seeburg, RNA editing in brain controls a determinant of ion flow in glutamate-gated channels, Cell 67 (1991)]. In this manuscript, we detail procedures for profiling AMPAR composition, namely: relative subunit ratios, expression of flip/flop isoforms, Q/R and R/G editing status, and Ca2+ permeability using small amounts of cDNA from identified cell populations.
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Affiliation(s)
- J C Lee
- Department of Neurobiology and Anatomy, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
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18
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Ravindranathan A, Parks TN, Rao MS. New isoforms of the chick glutamate receptor subunit GluR4: molecular cloning, regional expression and developmental analysis. Brain Res Mol Brain Res 1997; 50:143-53. [PMID: 9406929 DOI: 10.1016/s0169-328x(97)00179-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
To identify chick GluR4 isoforms, we used PCR to amplify a C-terminal region that is the site of alternative splicing in rat. We report here the cloning of three novel chick GluR4 isoforms. GluR4c has a 113-bp insert in the C-terminus, is expressed in flip and flop isoforms, is most strongly expressed in the cerebellum, midbrain and forebrain, and appears from embryonic day (E) 2.5 through at least post-hatching day (P) 2, with a peak of expression at E17. GluR4d has a 184-bp segment inserted at the 4c splice site, occurs as flip and flop isoforms, is expressed most strongly in cerebellum, hindbrain and forebrain, and is present from E11 through P2, with peak expression at E17. GluR4s is a shortened form that lacks the nominal 4th transmembrane and flip/flop domains and shares a common C-terminal region with GluR4. GluR4s is expressed most strongly in the hindbrain and cerebellum and its expression increases from E11 through P2. Experiments on purified cerebellar cells show that glia express GluR4c and GluR4d at combined levels nearly twice that of GluR4 and that flip isoforms predominate. In contrast, granule cells express GluR4c and GluR4d at a level comparable to GluR4 and express GluR4s at a level less than half that in cerebellar glia. Thus, the independence of alternative splicing at the flip/flop and C-terminal splice sites allows seven alternatively spliced forms of GluR4 to exist in chick CNS. This structural diversity increases the potential for functional diversity in neuronal and glial GluRs incorporating GluR4.
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Affiliation(s)
- A Ravindranathan
- Department of Neurobiology and Anatomy, University of Utah School of Medicine, Salt Lake City 84132, USA
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Abstract
Using oligonucleotide primers, we have amplified and sequenced the alpha-amino-3-hydroxy-5-methylisoxazole-4-propionic acid (AMPA) receptors from the brain of 17-day-old chick embryos. Both flip and flop isoforms of each of these glutamate receptors (GluR) were identified and cloned. Nucleotide comparisons showed that the two isoforms for each chick receptor subtype were 71-78% identical, whereas homologous chick and rat isoforms were 94-98% identical. Reverse transcriptase-polymerase chain reaction and restriction enzyme analysis were employed to identify regional variation in flip and flop levels of each AMPA receptor. Flip isoforms of GluR 1-3 predominated in forebrain, while flop variants of GluR 1-4 were more prevalent in the cerebellum. This differential regional expression suggests that alternative splicing of AMPA receptor subunits contributes importantly to synaptic diversity in chick central nervous systems.
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Affiliation(s)
- A Ravindranathan
- Department of Neurobiology and Anatomy, University of Utah School of Medicine, Salt Lake City 84132, USA
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Ravindranathan A, Coon H, DeLisi L, Holik J, Hoff M, Brown A, Shields G, Crow T, Byerley W. Linkage analysis between schizophrenia and a microsatellite polymorphism for the D5 dopamine receptor gene. Psychiatr Genet 1994; 4:77-80. [PMID: 8055250 DOI: 10.1097/00041444-199422000-00002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Using 23 multiplex pedigrees we tested for linkage between schizophrenia and a microsatellite polymorphism for the D5 dopamine receptor gene (DRD5). Assuming autosomal dominant inheritance and a maximum penetrance of 0.6, an overall lod score of -4.54 was derived at 0% recombination. For recessive transmission the summary lod score was -8.37 at 0% recombination. These data suggest that mutations of the D5 dopamine receptor gene are unlikely to be of major etiological importance in the pathogeneses of schizophrenia in the families studied. However, our study does not exclude the D5 dopamine receptor gene as a candidate gene for schizophrenia because some of our families were not informative for linkage and because of the likelihood of genetic heterogeneity.
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Affiliation(s)
- A Ravindranathan
- Department of Neuroscience, University of Utah School of Medicine, Salt Lake City 84132
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