1
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Bonazzi S, Gray A, Thomsen NM, Biag J, Labbe-Giguere N, Keaney EP, Malik HA, Sun Y, Nunez J, Karki RG, Knapp M, Elling R, Fuller J, Pardee G, Craig L, Capre K, Salas S, Gorde A, Liang G, Lubicka D, McTighe SM, Goold C, Liu S, Deng L, Hong J, Fekete A, Stadelmann P, Frieauff W, Elhajouji A, Bauer D, Lerchner A, Radetich B, Furet P, Piizzi G, Burdette D, Wilson CJ, Peukert S, Hamann LG, Murphy LO, Curtis D. Identification of Brain-Penetrant ATP-Competitive mTOR Inhibitors for CNS Syndromes. J Med Chem 2023. [PMID: 37399505 DOI: 10.1021/acs.jmedchem.3c00705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2023]
Abstract
The allosteric inhibitor of the mechanistic target of rapamycin (mTOR) everolimus reduces seizures in tuberous sclerosis complex (TSC) patients through partial inhibition of mTOR functions. Due to its limited brain permeability, we sought to develop a catalytic mTOR inhibitor optimized for central nervous system (CNS) indications. We recently reported an mTOR inhibitor (1) that is able to block mTOR functions in the mouse brain and extend the survival of mice with neuronal-specific ablation of the Tsc1 gene. However, 1 showed the risk of genotoxicity in vitro. Through structure-activity relationship (SAR) optimization, we identified compounds 9 and 11 without genotoxicity risk. In neuronal cell-based models of mTOR hyperactivity, both corrected aberrant mTOR activity and significantly improved the survival rate of mice in the Tsc1 gene knockout model. Unfortunately, 9 and 11 showed limited oral exposures in higher species and dose-limiting toxicities in cynomolgus macaque, respectively. However, they remain optimal tools to explore mTOR hyperactivity in CNS disease models.
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Affiliation(s)
- Simone Bonazzi
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 181 Massachusetts Ave, Cambridge, Massachusetts 02139, United States
| | - Audrey Gray
- Neuroscience, Novartis Institutes for BioMedical Research, 22 Windsor Street, Cambridge, Massachusetts 02139, United States
| | - Noel M Thomsen
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 181 Massachusetts Ave, Cambridge, Massachusetts 02139, United States
| | - Jonathan Biag
- Neuroscience, Novartis Institutes for BioMedical Research, 22 Windsor Street, Cambridge, Massachusetts 02139, United States
| | - Nancy Labbe-Giguere
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 181 Massachusetts Ave, Cambridge, Massachusetts 02139, United States
| | - Erin P Keaney
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 181 Massachusetts Ave, Cambridge, Massachusetts 02139, United States
| | - Hasnain A Malik
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 181 Massachusetts Ave, Cambridge, Massachusetts 02139, United States
| | - Yingchuan Sun
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 181 Massachusetts Ave, Cambridge, Massachusetts 02139, United States
| | - Jill Nunez
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 181 Massachusetts Ave, Cambridge, Massachusetts 02139, United States
| | - Rajeshri G Karki
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 181 Massachusetts Ave, Cambridge, Massachusetts 02139, United States
| | - Mark Knapp
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5959 Horton St, Emeryville, California 94608, United States
| | - Robert Elling
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5959 Horton St, Emeryville, California 94608, United States
| | - John Fuller
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, 5959 Horton St, Emeryville, California 94608, United States
| | - Gwynn Pardee
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, 5959 Horton St, Emeryville, California 94608, United States
| | - Lucas Craig
- Neuroscience, Novartis Institutes for BioMedical Research, 22 Windsor Street, Cambridge, Massachusetts 02139, United States
| | - Ketthsy Capre
- Neuroscience, Novartis Institutes for BioMedical Research, 22 Windsor Street, Cambridge, Massachusetts 02139, United States
| | - Sarah Salas
- Neuroscience, Novartis Institutes for BioMedical Research, 22 Windsor Street, Cambridge, Massachusetts 02139, United States
| | - Aakruti Gorde
- Neuroscience, Novartis Institutes for BioMedical Research, 22 Windsor Street, Cambridge, Massachusetts 02139, United States
| | - Guiqing Liang
- Pharmacokinetic Sciences, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Danuta Lubicka
- Global Drug Development/Technical Research and Development, Novartis Institutes for BioMedical Research, 700 Main Street, Cambridge, Massachusetts 02139, United States
| | - Stephanie M McTighe
- Neuroscience, Novartis Institutes for BioMedical Research, 22 Windsor Street, Cambridge, Massachusetts 02139, United States
| | - Carleton Goold
- Neuroscience, Novartis Institutes for BioMedical Research, 22 Windsor Street, Cambridge, Massachusetts 02139, United States
| | - Shanming Liu
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, 181 Massachusetts Ave, Cambridge, Massachusetts 02139, United States
| | - Lin Deng
- Pharmacokinetic Sciences, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Jin Hong
- Preclinical Safety, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Alexander Fekete
- Preclinical Safety, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Pascal Stadelmann
- Preclinical Safety, Novartis Institutes for BioMedical Research, Fabrikstrasse 28, 4056 Basel, Switzerland
| | - Wilfried Frieauff
- Preclinical Safety, Novartis Institutes for BioMedical Research, Fabrikstrasse 28, 4056 Basel, Switzerland
| | - Azeddine Elhajouji
- Preclinical Safety, Novartis Institutes for BioMedical Research, Fabrikstrasse 28, 4056 Basel, Switzerland
| | - Daniel Bauer
- Preclinical Safety, Novartis Institutes for BioMedical Research, Fabrikstrasse 28, 4056 Basel, Switzerland
| | - Andreas Lerchner
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Fabrikstrasse 22, 4056 Basel, Switzerland
| | - Branko Radetich
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 181 Massachusetts Ave, Cambridge, Massachusetts 02139, United States
| | - Pascal Furet
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Fabrikstrasse 22, 4056 Basel, Switzerland
| | - Grazia Piizzi
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 181 Massachusetts Ave, Cambridge, Massachusetts 02139, United States
| | - Doug Burdette
- Pharmacokinetic Sciences, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Christopher J Wilson
- Neuroscience, Novartis Institutes for BioMedical Research, 22 Windsor Street, Cambridge, Massachusetts 02139, United States
| | - Stefan Peukert
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 181 Massachusetts Ave, Cambridge, Massachusetts 02139, United States
| | - Lawrence G Hamann
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 181 Massachusetts Ave, Cambridge, Massachusetts 02139, United States
| | - Leon O Murphy
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, 181 Massachusetts Ave, Cambridge, Massachusetts 02139, United States
| | - Daniel Curtis
- Neuroscience, Novartis Institutes for BioMedical Research, 22 Windsor Street, Cambridge, Massachusetts 02139, United States
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2
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Iourov IY, Vorsanova SG, Kurinnaia OS, Kutsev SI, Yurov YB. Somatic mosaicism in the diseased brain. Mol Cytogenet 2022; 15:45. [PMID: 36266706 PMCID: PMC9585840 DOI: 10.1186/s13039-022-00624-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/05/2022] [Accepted: 10/07/2022] [Indexed: 11/10/2022] Open
Abstract
It is hard to believe that all the cells of a human brain share identical genomes. Indeed, single cell genetic studies have demonstrated intercellular genomic variability in the normal and diseased brain. Moreover, there is a growing amount of evidence on the contribution of somatic mosaicism (the presence of genetically different cell populations in the same individual/tissue) to the etiology of brain diseases. However, brain-specific genomic variations are generally overlooked during the research of genetic defects associated with a brain disease. Accordingly, a review of brain-specific somatic mosaicism in disease context seems to be required. Here, we overview gene mutations, copy number variations and chromosome abnormalities (aneuploidy, deletions, duplications and supernumerary rearranged chromosomes) detected in the neural/neuronal cells of the diseased brain. Additionally, chromosome instability in non-cancerous brain diseases is addressed. Finally, theoretical analysis of possible mechanisms for neurodevelopmental and neurodegenerative disorders indicates that a genetic background for formation of somatic (chromosomal) mosaicism in the brain is likely to exist. In total, somatic mosaicism affecting the central nervous system seems to be a mechanism of brain diseases.
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Affiliation(s)
- Ivan Y Iourov
- Yurov's Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia. .,Vorsanova's Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics and Pediatric Surgery of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow, Russia. .,Department of Medical Biological Disciplines, Belgorod State University, Belgorod, Russia.
| | - Svetlana G Vorsanova
- Yurov's Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia.,Vorsanova's Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics and Pediatric Surgery of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow, Russia
| | - Oxana S Kurinnaia
- Yurov's Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia.,Vorsanova's Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics and Pediatric Surgery of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow, Russia
| | | | - Yuri B Yurov
- Yurov's Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia.,Vorsanova's Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics and Pediatric Surgery of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow, Russia
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3
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Whitlock JH, Soelter TM, Williams AS, Hardigan AA, Lasseigne BN. Liquid biopsies in epilepsy: biomarkers for etiology, diagnosis, prognosis, and therapeutics. Hum Cell 2022; 35:15-22. [PMID: 34694568 PMCID: PMC8732818 DOI: 10.1007/s13577-021-00624-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 09/29/2021] [Indexed: 01/19/2023]
Abstract
Epilepsy is one of the most common diseases of the central nervous system, impacting nearly 50 million people around the world. Heterogeneous in nature, epilepsy presents in children and adults alike. Currently, surgery is one treatment approach that can completely cure epilepsy. However, not all individuals are eligible for surgical procedures or have successful outcomes. In addition to surgical approaches, antiepileptic drugs (AEDs) have also allowed individuals with epilepsy to achieve freedom from seizures. Others have found treatment through nonpharmacologic approaches such as vagus nerve stimulation, or responsive neurostimulation. Difficulty in accessing samples of human brain tissue along with advances in sequencing technology have driven researchers to investigate sampling liquid biopsies in blood, serum, plasma, and cerebrospinal fluid within the context of epilepsy. Liquid biopsies provide minimal or non-invasive sample collection approaches and can be assayed relatively easily across multiple time points, unlike tissue-based sampling. Various efforts have investigated circulating nucleic acids from these samples including microRNAs, cell-free DNA, transfer RNAs, and long non-coding RNAs. Here, we review nucleic acid-based liquid biopsies in epilepsy to improve understanding of etiology, diagnosis, prediction, and therapeutic monitoring.
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Affiliation(s)
- Jordan H Whitlock
- Cell, Developmental and Integrative Biology, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Tabea M Soelter
- Cell, Developmental and Integrative Biology, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Avery S Williams
- Cell, Developmental and Integrative Biology, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Andrew A Hardigan
- Cell, Developmental and Integrative Biology, The University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Brittany N Lasseigne
- Cell, Developmental and Integrative Biology, The University of Alabama at Birmingham, Birmingham, AL, USA.
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4
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Bizzotto S, Dou Y, Ganz J, Doan RN, Kwon M, Bohrson CL, Kim SN, Bae T, Abyzov A, Park PJ, Walsh CA. Landmarks of human embryonic development inscribed in somatic mutations. Science 2021; 371:1249-1253. [PMID: 33737485 DOI: 10.1126/science.abe1544] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 02/09/2021] [Indexed: 12/13/2022]
Abstract
Although cell lineage information is fundamental to understanding organismal development, very little direct information is available for humans. We performed high-depth (250×) whole-genome sequencing of multiple tissues from three individuals to identify hundreds of somatic single-nucleotide variants (sSNVs). Using these variants as "endogenous barcodes" in single cells, we reconstructed early embryonic cell divisions. Targeted sequencing of clonal sSNVs in different organs (about 25,000×) and in more than 1000 cortical single cells, as well as single-nucleus RNA sequencing and single-nucleus assay for transposase-accessible chromatin sequencing of ~100,000 cortical single cells, demonstrated asymmetric contributions of early progenitors to extraembryonic tissues, distinct germ layers, and organs. Our data suggest onset of gastrulation at an effective progenitor pool of about 170 cells and about 50 to 100 founders for the forebrain. Thus, mosaic mutations provide a permanent record of human embryonic development at very high resolution.
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Affiliation(s)
- Sara Bizzotto
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA.,Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yanmei Dou
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Javier Ganz
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA.,Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ryan N Doan
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Minseok Kwon
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Craig L Bohrson
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Sonia N Kim
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA.,Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,PhD Program in Biological and Biomedical Sciences, Harvard University, Boston, MA 02115, USA
| | - Taejeong Bae
- Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Alexej Abyzov
- Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | | | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA. .,Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA. .,Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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5
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Doan RN, Miller MB, Kim SN, Rodin RE, Ganz J, Bizzotto S, Morillo KS, Huang AY, Digumarthy R, Zemmel Z, Walsh CA. MIPP-Seq: ultra-sensitive rapid detection and validation of low-frequency mosaic mutations. BMC Med Genomics 2021; 14:47. [PMID: 33579278 PMCID: PMC7881461 DOI: 10.1186/s12920-021-00893-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 02/03/2021] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Mosaic mutations contribute to numerous human disorders. As such, the identification and precise quantification of mosaic mutations is essential for a wide range of research applications, clinical diagnoses, and early detection of cancers. Currently, the low-throughput nature of single allele assays (e.g., allele-specific ddPCR) commonly used for genotyping known mutations at very low alternate allelic fractions (AAFs) have limited the integration of low-level mosaic analyses into clinical and research applications. The growing importance of mosaic mutations requires a more rapid, low-cost solution for mutation detection and validation. METHODS To overcome these limitations, we developed Multiple Independent Primer PCR Sequencing (MIPP-Seq) which combines the power of ultra-deep sequencing and truly independent assays. The accuracy of MIPP-seq to quantifiable detect and measure extremely low allelic fractions was assessed using a combination of SNVs, insertions, and deletions at known allelic fractions in blood and brain derived DNA samples. RESULTS The Independent amplicon analyses of MIPP-Seq markedly reduce the impact of allelic dropout, amplification bias, PCR-induced, and sequencing artifacts. Using low DNA inputs of either 25 ng or 50 ng of DNA, MIPP-Seq provides sensitive and quantitative assessments of AAFs as low as 0.025% for SNVs, insertion, and deletions. CONCLUSIONS MIPP-Seq provides an ultra-sensitive, low-cost approach for detecting and validating known and novel mutations in a highly scalable system with broad utility spanning both research and clinical diagnostic testing applications. The scalability of MIPP-Seq allows for multiplexing mutations and samples, which dramatically reduce costs of variant validation when compared to methods like ddPCR. By leveraging the power of individual analyses of multiple unique and independent reactions, MIPP-Seq can validate and precisely quantitate extremely low AAFs across multiple tissues and mutational categories including both indels and SNVs. Furthermore, using Illumina sequencing technology, MIPP-seq provides a robust method for accurate detection of novel mutations at an extremely low AAF.
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Affiliation(s)
- Ryan N Doan
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Center for Life Sciences 15062, 300 Longwood Avenue, BCH3150, Boston, MA, 02115, USA.
- Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
- Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA.
| | - Michael B Miller
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Center for Life Sciences 15062, 300 Longwood Avenue, BCH3150, Boston, MA, 02115, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Sonia N Kim
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Center for Life Sciences 15062, 300 Longwood Avenue, BCH3150, Boston, MA, 02115, USA
- Program in Biological and Biomedical Sciences, Harvard University, Boston, MA, USA
| | - Rachel E Rodin
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Center for Life Sciences 15062, 300 Longwood Avenue, BCH3150, Boston, MA, 02115, USA
| | - Javier Ganz
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Center for Life Sciences 15062, 300 Longwood Avenue, BCH3150, Boston, MA, 02115, USA
| | - Sara Bizzotto
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Center for Life Sciences 15062, 300 Longwood Avenue, BCH3150, Boston, MA, 02115, USA
| | - Katherine S Morillo
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Center for Life Sciences 15062, 300 Longwood Avenue, BCH3150, Boston, MA, 02115, USA
| | - August Yue Huang
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Center for Life Sciences 15062, 300 Longwood Avenue, BCH3150, Boston, MA, 02115, USA
| | - Reethika Digumarthy
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Center for Life Sciences 15062, 300 Longwood Avenue, BCH3150, Boston, MA, 02115, USA
| | - Zachary Zemmel
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Center for Life Sciences 15062, 300 Longwood Avenue, BCH3150, Boston, MA, 02115, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Center for Life Sciences 15062, 300 Longwood Avenue, BCH3150, Boston, MA, 02115, USA.
- Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
- Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA.
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6
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LaSarge CL, Pun RYK, Gu Z, Riccetti MR, Namboodiri DV, Tiwari D, Gross C, Danzer SC. mTOR-driven neural circuit changes initiate an epileptogenic cascade. Prog Neurobiol 2020; 200:101974. [PMID: 33309800 DOI: 10.1016/j.pneurobio.2020.101974] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/22/2020] [Accepted: 12/05/2020] [Indexed: 11/29/2022]
Abstract
Mutations in genes regulating mTOR pathway signaling are now recognized as a significant cause of epilepsy. Interestingly, these mTORopathies are often caused by somatic mutations, affecting variable numbers of neurons. To better understand how this variability affects disease phenotype, we developed a mouse model in which the mTOR pathway inhibitor Pten can be deleted from 0 to 40 % of hippocampal granule cells. In vivo, low numbers of knockout cells caused focal seizures, while higher numbers led to generalized seizures. Generalized seizures coincided with the loss of local circuit interneurons. In hippocampal slices, low knockout cell loads produced abrupt reductions in population spike threshold, while spontaneous excitatory postsynaptic currents and circuit level recurrent activity increased gradually with rising knockout cell load. Findings demonstrate that knockout cells load is a critical variable regulating disease phenotype, progressing from subclinical circuit abnormalities to electrobehavioral seizures with secondary involvement of downstream neuronal populations.
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Affiliation(s)
- Candi L LaSarge
- Department of Anesthesia, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, United States; Center for Pediatric Neuroscience, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, United States
| | - Raymund Y K Pun
- Department of Anesthesia, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, United States; Center for Pediatric Neuroscience, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, United States
| | - Zhiqing Gu
- Department of Anesthesia, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, United States; Shanghai Children's Hospital, Shanghai, 200062, China
| | - Matthew R Riccetti
- Molecular and Developmental Biology Graduate Program, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, United States
| | - Devi V Namboodiri
- Department of Anesthesia, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, United States
| | - Durgesh Tiwari
- Division of Neurology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, United States; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Christina Gross
- Center for Pediatric Neuroscience, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, United States; Division of Neurology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, United States; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Steve C Danzer
- Department of Anesthesia, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, United States; Center for Pediatric Neuroscience, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, United States; Molecular and Developmental Biology Graduate Program, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, United States; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States; Department of Anesthesia, University of Cincinnati, Cincinnati, OH, 45267, United States.
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7
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Gavrilovici C, Jiang Y, Kiroski I, Teskey GC, Rho JM, Nguyen MD. Postnatal Role of the Cytoskeleton in Adult Epileptogenesis. Cereb Cortex Commun 2020; 1:tgaa024. [PMID: 32864616 PMCID: PMC7446231 DOI: 10.1093/texcom/tgaa024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 06/08/2020] [Accepted: 06/11/2020] [Indexed: 02/07/2023] Open
Abstract
Mutations in cytoskeletal proteins can cause early infantile and childhood epilepsies by misplacing newly born neurons and altering neuronal connectivity. In the adult epileptic brain, cytoskeletal disruption is often viewed as being secondary to aberrant neuronal activity and/or death, and hence simply represents an epiphenomenon. Here, we review the emerging evidence collected in animal models and human studies implicating the cytoskeleton as a potential causative factor in adult epileptogenesis. Based on the emerging evidence, we propose that cytoskeletal disruption may be an important pathogenic mechanism in the mature epileptic brain.
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Affiliation(s)
- Cezar Gavrilovici
- Departments of Neurosciences & Pediatrics, University of California San Diego, Rady Children’s Hospital San Diego, San Diego, CA 92123, USA
| | - Yulan Jiang
- Departments of Clinical Neurosciences, Cell Biology & Anatomy, and Biochemistry & Molecular Biology, Hotchkiss Brain Institute, Alberta Children Hospital Research Institute, University of Calgary, Calgary T2N 4N1, Canada
| | - Ivana Kiroski
- Departments of Clinical Neurosciences, Cell Biology & Anatomy, and Biochemistry & Molecular Biology, Hotchkiss Brain Institute, Alberta Children Hospital Research Institute, University of Calgary, Calgary T2N 4N1, Canada
| | - G Campbell Teskey
- Department of Cell Biology & Anatomy, Hotchkiss Brain Institute, Alberta Children Hospital Research Institute, University of Calgary, Calgary T2N 4N1, Canada
| | - Jong M Rho
- Departments of Neurosciences & Pediatrics, University of California San Diego, Rady Children’s Hospital San Diego, San Diego, CA 92123, USA
| | - Minh Dang Nguyen
- Departments of Clinical Neurosciences, Cell Biology & Anatomy, and Biochemistry & Molecular Biology, Hotchkiss Brain Institute, Alberta Children Hospital Research Institute, University of Calgary, Calgary T2N 4N1, Canada
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8
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Heinzen EL. Somatic variants in epilepsy - advancing gene discovery and disease mechanisms. Curr Opin Genet Dev 2020; 65:1-7. [PMID: 32422520 DOI: 10.1016/j.gde.2020.04.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 04/15/2020] [Indexed: 01/03/2023]
Abstract
In the past ten years, there has been increasing recognition that cells can acquire genetic variants during cortical development that can give rise to brain malformations as well as nonlesional focal epilepsy. These often brain tissue-specific, de novo variants can result in highly variable phenotypes based on the burden of a variant in specific tissues and cells. By discovering these variants, shared pathophysiological mechanisms are being revealed between clinically distinct disorders. Beyond informing disease mechanisms, mosaic variants also offer a powerful research tool to trace cellular lineages, to study the roles of specialized cell types in disease presentation, and to establish the cell-type specific genomic consequences of a variant.
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Affiliation(s)
- Erin L Heinzen
- Eshelman School of Pharmacy, Division of Pharmacotherapy and Experimental Therapeutics, University of North Carolina, Chapel Hill, NC, United States; Department of Genetics, School of Medicine, University of North Carolina, Chapel Hill, NC, United States.
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9
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Hwang SH, Bang S, Kim W, Chung J. Von Hippel-Lindau tumor suppressor (VHL) stimulates TOR signaling by interacting with phosphoinositide 3-kinase (PI3K). J Biol Chem 2020; 295:2336-2347. [PMID: 31959630 DOI: 10.1074/jbc.ra119.011596] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 01/08/2020] [Indexed: 12/11/2022] Open
Abstract
Cell growth is positively controlled by the phosphoinositide 3-kinase (PI3K)-target of rapamycin (TOR) signaling pathway under conditions of abundant growth factors and nutrients. To discover additional mechanisms that regulate cell growth, here we performed RNAi-based mosaic analyses in the Drosophila fat body, the primary metabolic organ in the fly. Unexpectedly, the knockdown of the Drosophila von Hippel-Lindau (VHL) gene markedly decreased cell size and body size. These cell growth phenotypes induced by VHL loss of function were recovered by activation of TOR signaling in Drosophila Consistent with the genetic interactions between VHL and the signaling components of PI3K-TOR pathway in Drosophila, we observed that VHL loss of function in mammalian cells causes decreased phosphorylation of ribosomal protein S6 kinase and Akt, which represent the main activities of this pathway. We further demonstrate that VHL activates TOR signaling by directly interacting with the p110 catalytic subunit of PI3K. On the basis of the evolutionarily conserved regulation of PI3K-TOR signaling by VHL observed here, we propose that VHL plays an important role in the regulation and maintenance of proper cell growth in metazoans.
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Affiliation(s)
- Sun-Hong Hwang
- School of Biological Sciences, Seoul National University, Gwanak-Gu, Seoul 08826, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Gwanak-Gu, Seoul 08826, Republic of Korea
| | - Sunhoe Bang
- School of Biological Sciences, Seoul National University, Gwanak-Gu, Seoul 08826, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Gwanak-Gu, Seoul 08826, Republic of Korea
| | - Wonho Kim
- Institute of Molecular Biology and Genetics, Seoul National University, Gwanak-Gu, Seoul 08826, Republic of Korea
| | - Jongkyeong Chung
- School of Biological Sciences, Seoul National University, Gwanak-Gu, Seoul 08826, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Gwanak-Gu, Seoul 08826, Republic of Korea.
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10
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Bonazzi S, Goold CP, Gray A, Thomsen NM, Nunez J, Karki RG, Gorde A, Biag JD, Malik HA, Sun Y, Liang G, Lubicka D, Salas S, Labbe-Giguere N, Keaney EP, McTighe S, Liu S, Deng L, Piizzi G, Lombardo F, Burdette D, Dodart JC, Wilson CJ, Peukert S, Curtis D, Hamann LG, Murphy LO. Discovery of a Brain-Penetrant ATP-Competitive Inhibitor of the Mechanistic Target of Rapamycin (mTOR) for CNS Disorders. J Med Chem 2020; 63:1068-1083. [PMID: 31955578 DOI: 10.1021/acs.jmedchem.9b01398] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Recent clinical evaluation of everolimus for seizure reduction in patients with tuberous sclerosis complex (TSC), a disease with overactivated mechanistic target of rapamycin (mTOR) signaling, has demonstrated the therapeutic value of mTOR inhibitors for central nervous system (CNS) indications. Given that everolimus is an incomplete inhibitor of the mTOR function, we sought to develop a new mTOR inhibitor that has improved properties and is suitable for CNS disorders. Starting from an in-house purine-based compound, optimization of the physicochemical properties of a thiazolopyrimidine series led to the discovery of the small molecule 7, a potent and selective brain-penetrant ATP-competitive mTOR inhibitor. In neuronal cell-based models of mTOR hyperactivity, 7 corrected the mTOR pathway activity and the resulting neuronal overgrowth phenotype. The new mTOR inhibitor 7 showed good brain exposure and significantly improved the survival rate of mice with neuronal-specific ablation of the Tsc1 gene. These results demonstrate the potential utility of this tool compound to test therapeutic hypotheses that depend on mTOR hyperactivity in the CNS.
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Affiliation(s)
- Simone Bonazzi
- Global Discovery Chemistry , Novartis Institutes for BioMedical Research , 181 Massachusetts Ave , Cambridge , Massachusetts 02139 , United States
| | - Carleton P Goold
- Neuroscience , Novartis Institutes for BioMedical Research , 22 Windsor Street , Cambridge , Massachusetts 02139 , United States
| | - Audrey Gray
- Neuroscience , Novartis Institutes for BioMedical Research , 22 Windsor Street , Cambridge , Massachusetts 02139 , United States
| | - Noel M Thomsen
- Global Discovery Chemistry , Novartis Institutes for BioMedical Research , 181 Massachusetts Ave , Cambridge , Massachusetts 02139 , United States
| | - Jill Nunez
- Global Discovery Chemistry , Novartis Institutes for BioMedical Research , 181 Massachusetts Ave , Cambridge , Massachusetts 02139 , United States
| | - Rajeshri G Karki
- Global Discovery Chemistry , Novartis Institutes for BioMedical Research , 181 Massachusetts Ave , Cambridge , Massachusetts 02139 , United States
| | - Aakruti Gorde
- Neuroscience , Novartis Institutes for BioMedical Research , 22 Windsor Street , Cambridge , Massachusetts 02139 , United States
| | - Jonathan D Biag
- Neuroscience , Novartis Institutes for BioMedical Research , 22 Windsor Street , Cambridge , Massachusetts 02139 , United States
| | - Hasnain A Malik
- Global Discovery Chemistry , Novartis Institutes for BioMedical Research , 181 Massachusetts Ave , Cambridge , Massachusetts 02139 , United States
| | - Yingchuan Sun
- Global Discovery Chemistry , Novartis Institutes for BioMedical Research , 181 Massachusetts Ave , Cambridge , Massachusetts 02139 , United States
| | - Guiqing Liang
- Pharmacokinetic Sciences , Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Danuta Lubicka
- Global Drug Development/Technical Research and Development , Novartis Institutes for BioMedical Research , 700 Main Street , Cambridge , Massachusetts 02139 , United States
| | - Sarah Salas
- Neuroscience , Novartis Institutes for BioMedical Research , 22 Windsor Street , Cambridge , Massachusetts 02139 , United States
| | - Nancy Labbe-Giguere
- Global Discovery Chemistry , Novartis Institutes for BioMedical Research , 181 Massachusetts Ave , Cambridge , Massachusetts 02139 , United States
| | - Erin P Keaney
- Global Discovery Chemistry , Novartis Institutes for BioMedical Research , 181 Massachusetts Ave , Cambridge , Massachusetts 02139 , United States
| | - Stephanie McTighe
- Neuroscience , Novartis Institutes for BioMedical Research , 22 Windsor Street , Cambridge , Massachusetts 02139 , United States
| | - Shanming Liu
- Chemical Biology and Therapeutics , Novartis Institutes for BioMedical Research , 181 Massachusetts Ave , Cambridge , Massachusetts 02139 , United States
| | - Lin Deng
- Pharmacokinetic Sciences , Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Grazia Piizzi
- Global Discovery Chemistry , Novartis Institutes for BioMedical Research , 181 Massachusetts Ave , Cambridge , Massachusetts 02139 , United States
| | - Franco Lombardo
- Pharmacokinetic Sciences , Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Doug Burdette
- Pharmacokinetic Sciences , Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Jean-Cosme Dodart
- Neuroscience , Novartis Institutes for BioMedical Research , 22 Windsor Street , Cambridge , Massachusetts 02139 , United States
| | - Christopher J Wilson
- Neuroscience , Novartis Institutes for BioMedical Research , 22 Windsor Street , Cambridge , Massachusetts 02139 , United States
| | - Stefan Peukert
- Global Discovery Chemistry , Novartis Institutes for BioMedical Research , 181 Massachusetts Ave , Cambridge , Massachusetts 02139 , United States
| | - Daniel Curtis
- Neuroscience , Novartis Institutes for BioMedical Research , 22 Windsor Street , Cambridge , Massachusetts 02139 , United States
| | - Lawrence G Hamann
- Global Discovery Chemistry , Novartis Institutes for BioMedical Research , 181 Massachusetts Ave , Cambridge , Massachusetts 02139 , United States
| | - Leon O Murphy
- Chemical Biology and Therapeutics , Novartis Institutes for BioMedical Research , 181 Massachusetts Ave , Cambridge , Massachusetts 02139 , United States
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11
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Berkowitz A. Playing the genome card. J Neurogenet 2019; 34:189-197. [PMID: 31872788 DOI: 10.1080/01677063.2019.1706093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
In the 1990s, prominent biologists and journalists predicted that by 2020 each of us would carry a genome card, which would allow physicians to access our entire genome sequence and routinely use this information to diagnose and treat common and debilitating conditions. This is not yet the case. Why not? Common and debilitating diseases are rarely caused by single-gene mutations, and this was recognized before these genome card predictions had been made. Debilitating conditions, including common psychiatric disorders, are typically caused either by rare mutations or by complex interactions of many genes, each having a small effect, and epigenetic, environmental, and microbial factors. In such cases, having a complete genome sequence may have limited utility in diagnosis and treatment. Genome sequencing technologies have transformed biological research in many ways, but had a much smaller effect than expected on treatments of common diseases. Thus, early proponents of genome sequencing effectively "mis-promised" its benefits. One reason may be that there are incentives for both biologists and journalists to tell simple stories, including the idea of relatively simple genetic causation of common, debilitating diseases. These incentives may have led to misleading predictions, which to some extent continue today. Although the Human Genome Project has facilitated biological research generally, the mis-promising of medical benefits, at least for treating common and debilitating disorders, could undermine support for scientific research over the long term.
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Affiliation(s)
- Ari Berkowitz
- Department of Biology and Cellular & Behavioral Neurobiology Graduate Program, University of Oklahoma, Norman, OK, USA
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