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Dindot SV, Christian S, Murphy WJ, Berent A, Panagoulias J, Schlafer A, Ballard J, Radeva K, Robinson R, Myers L, Jepp T, Shaheen H, Hillman P, Konganti K, Hillhouse A, Bredemeyer KR, Black L, Douville J. An ASO therapy for Angelman syndrome that targets an evolutionarily conserved region at the start of the UBE3A-AS transcript. Sci Transl Med 2023; 15:eabf4077. [PMID: 36947593 DOI: 10.1126/scitranslmed.abf4077] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
Angelman syndrome is a devastating neurogenetic disorder for which there is currently no effective treatment. It is caused by mutations or epimutations affecting the expression or function of the maternally inherited allele of the ubiquitin-protein ligase E3A (UBE3A) gene. The paternal UBE3A allele is imprinted in neurons of the central nervous system (CNS) by the UBE3A antisense (UBE3A-AS) transcript, which represents the distal end of the small nucleolar host gene 14 (SNHG14) transcription unit. Reactivating the expression of the paternal UBE3A allele in the CNS has long been pursued as a therapeutic option for Angelman syndrome. Here, we described the development of an antisense oligonucleotide (ASO) therapy for Angelman syndrome that targets an evolutionarily conserved region demarcating the start of the UBE3A-AS transcript. We designed and chemically optimized gapmer ASOs targeting specific sequences at the start of the human UBE3A-AS transcript. We showed that ASOs targeting this region precisely and efficiently repress the transcription of UBE3A-AS, reactivating the expression of the paternal UBE3A allele in neurotypical and Angelman syndrome induced pluripotent stem cell-derived neurons. We further showed that human-targeted ASOs administered to the CNS of cynomolgus macaques by lumbar intrathecal injection repress UBE3A-AS and reactivate the expression of the paternal UBE3A allele throughout the CNS. These findings support the advancement of this investigational molecular therapy for Angelman syndrome into clinical development (ClinicalTrials.gov, NCT04259281).
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Affiliation(s)
- Scott V Dindot
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University, College Station, TX 77843, USA
- GeneTx Biotherapeutics LLC, Sarasota, FL 34233, USA
- Research Department, Ultragenyx Pharmaceutical, Novato, CA 94949, USA
| | - Sarah Christian
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
| | - William J Murphy
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
| | | | | | - Annalise Schlafer
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Johnathan Ballard
- Texas A&M Institute for Genomic Medicine (TIGM), Texas A&M University, College Station, TX 77843, USA
| | - Kamelia Radeva
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
- School of Biosciences and Medicine, University of Surrey, Guildford GU2 7XH, UK
| | - Ruth Robinson
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
- School of Biosciences and Medicine, University of Surrey, Guildford GU2 7XH, UK
| | - Luke Myers
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
- School of Biosciences and Medicine, University of Surrey, Guildford GU2 7XH, UK
| | - Thomas Jepp
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
- School of Biosciences and Medicine, University of Surrey, Guildford GU2 7XH, UK
| | - Hillary Shaheen
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Paul Hillman
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University, College Station, TX 77843, USA
| | - Kranti Konganti
- Texas A&M University Institute for Genome Sciences and Society (TIGSS), Texas A&M University, College Station, TX 77843, USA
| | - Andrew Hillhouse
- Texas A&M University Institute for Genome Sciences and Society (TIGSS), Texas A&M University, College Station, TX 77843, USA
| | - Kevin R Bredemeyer
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
| | | | - Julie Douville
- Charles River Laboratories, Montreal, Senneville, Quebec H9X 1C1, Canada
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St Jean SC, Jortner BS, Doan RN, Dindot SV, Johnson GS, Bullock G, Whitley DB, Levine JM, Hancock SK, Ambrus A, Porter BF. Pathologic characterization of canine multiple system degeneration in the Ibizan hound. Vet Pathol 2021; 59:132-137. [PMID: 34490804 DOI: 10.1177/03009858211043088] [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: 11/16/2022]
Abstract
Canine multiple system degeneration (CMSD) is a progressive hereditary neurodegenerative disorder commonly characterized by neuronal degeneration and loss in the cerebellum, olivary nuclei, substantia nigra, and caudate nuclei. In this article, we describe 3 cases of CMSD in Ibizan hounds. All patients exhibited marked cerebellar ataxia and had cerebellar atrophy on magnetic resonance imaging. At necropsy, all cases showed varying degrees of cerebellar atrophy, and 2 cases had gross cavitation of the caudate nuclei. Histologic findings included severe degeneration and loss of all layers of the cerebellum and neuronal loss and degeneration within the olivary nuclei, substantia nigra, and caudate nuclei. Pedigree analysis indicated an autosomal recessive mode of inheritance, but the causative gene in this breed is yet to be identified. CMSD resembles human multiple system atrophy and warrants further investigation.
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Affiliation(s)
| | | | - Ryan N Doan
- Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | | | | | | | - Sandra K Hancock
- Virginia-Maryland College of Veterinary Medicine, Blacksburg, VA, USA
| | - Andy Ambrus
- Texas A&M University, College Station, TX, USA
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3
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Kelly E, Meng F, Fujita H, Morgado F, Kazemi Y, Rice LC, Ren C, Escamilla CO, Gibson JM, Sajadi S, Pendry RJ, Tan T, Ellegood J, Basson MA, Blakely RD, Dindot SV, Golzio C, Hahn MK, Katsanis N, Robins DM, Silverman JL, Singh KK, Wevrick R, Taylor MJ, Hammill C, Anagnostou E, Pfeiffer BE, Stoodley CJ, Lerch JP, du Lac S, Tsai PT. Regulation of autism-relevant behaviors by cerebellar-prefrontal cortical circuits. Nat Neurosci 2020; 23:1102-1110. [PMID: 32661395 PMCID: PMC7483861 DOI: 10.1038/s41593-020-0665-z] [Citation(s) in RCA: 107] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 06/05/2020] [Indexed: 12/20/2022]
Abstract
Cerebellar dysfunction has been demonstrated in autism spectrum disorders (ASDs); however, the circuits underlying cerebellar contributions to ASD-relevant behaviors remain unknown. In this study, we demonstrated functional connectivity between the cerebellum and the medial prefrontal cortex (mPFC) in mice; showed that the mPFC mediates cerebellum-regulated social and repetitive/inflexible behaviors; and showed disruptions in connectivity between these regions in multiple mouse models of ASD-linked genes and in individuals with ASD. We delineated a circuit from cerebellar cortical areas Right crus 1 (Rcrus1) and posterior vermis through the cerebellar nuclei and ventromedial thalamus and culminating in the mPFC. Modulation of this circuit induced social deficits and repetitive behaviors, whereas activation of Purkinje cells (PCs) in Rcrus1 and posterior vermis improved social preference impairments and repetitive/inflexible behaviors, respectively, in male PC-Tsc1 mutant mice. These data raise the possibility that these circuits might provide neuromodulatory targets for the treatment of ASD.
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Affiliation(s)
- Elyza Kelly
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Fantao Meng
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Hirofumi Fujita
- Departments of Otolaryngology-Head and Neck Surgery, Neurology and Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Felipe Morgado
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Mouse Imaging Centre, Toronto Hospital for Sick Children, Toronto, ON, Canada
| | - Yasaman Kazemi
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Laura C Rice
- Department of Neuroscience, Center for Behavioral Neuroscience, American University, Washington, DC, USA
| | - Chongyu Ren
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Christine Ochoa Escamilla
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jennifer M Gibson
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sanaz Sajadi
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Robert J Pendry
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Tommy Tan
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jacob Ellegood
- Mouse Imaging Centre, Toronto Hospital for Sick Children, Toronto, ON, Canada
| | - M Albert Basson
- Centre for Craniofacial and Regenerative Biology and MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
| | - Randy D Blakely
- Department of Biomedical Science, Charles E. Schmidt College of Medicine and Brain Institute, Florida Atlantic University, Jupiter, Florida, USA
| | - Scott V Dindot
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Christelle Golzio
- Institut de Génétique et de Biologie Moléculaire et Cellulaire; Centre National de la Recherche Scientifique; Institut National de la Santé et de la Recherche Médicale; Université de Strasbourg, Illkirch, France
| | - Maureen K Hahn
- Department of Biomedical Science, Charles E. Schmidt College of Medicine and Brain Institute, Florida Atlantic University, Jupiter, Florida, USA
| | - Nicholas Katsanis
- ACT-GeM, Department of Human Genetics at Stanley Manne Children's Research Institute; Department of Pediatrics and Cellular and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Diane M Robins
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Jill L Silverman
- MIND Institute and Department of Psychiatry and Behavioral Sciences, University of California, Davis, Davis, CA, USA
| | - Karun K Singh
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Rachel Wevrick
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
| | - Margot J Taylor
- Department of Medical Imaging and Psychology, University of Toronto; Diagnostic Imaging, Hospital for Sick Children, Toronto, ON, USA
| | - Christopher Hammill
- Mouse Imaging Centre, Toronto Hospital for Sick Children, Toronto, ON, Canada
| | - Evdokia Anagnostou
- Department of Pediatrics, University of Toronto, Holland Bloorview Kids Rehabilitation Hospital, Toronto, ON, USA
| | - Brad E Pfeiffer
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Catherine J Stoodley
- Department of Neuroscience, Center for Behavioral Neuroscience, American University, Washington, DC, USA
| | - Jason P Lerch
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Mouse Imaging Centre, Toronto Hospital for Sick Children, Toronto, ON, Canada
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford, UK
| | - Sascha du Lac
- Departments of Otolaryngology-Head and Neck Surgery, Neurology and Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Peter T Tsai
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Departments of Psychiatry and Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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4
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Salazar-Medina AJ, Velazquez-Contreras EF, Sugich-Miranda R, Santacruz H, Navarro RE, Rocha-Alonzo F, Islas-Osuna MA, Chen PL, Christian SGB, Romoser AA, Dindot SV, Sayes CM, Sotelo-Mundo RR, Criscitiello MF. Immune response of human cultured cells towards macrocyclic Fe 2PO and Fe 2PC bioactive cyclophane complexes. PeerJ 2020; 8:e8956. [PMID: 32341898 PMCID: PMC7179565 DOI: 10.7717/peerj.8956] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 03/21/2020] [Indexed: 11/20/2022] Open
Abstract
Synthetic molecules that mimic the function of natural enzymes or molecules have untapped potential for use in the next generation of drugs. Cyclic compounds that contain aromatic rings are macrocyclic cyclophanes, and when they coordinate iron ions are of particular interest due to their antioxidant and biomimetic properties. However, little is known about the molecular responses at the cellular level. This study aims to evaluate the changes in immune gene expression in human cells exposed to the cyclophanes Fe2PO and Fe2PC. Confluent human embryonic kidney cells were exposed to either the cyclophane Fe2PO or Fe2PC before extraction of RNA. The expression of a panel of innate and adaptive immune genes was analyzed by quantitative real-time PCR. Evidence was found for an inflammatory response elicited by the cyclophane exposures. After 8 h of exposure, the cells increased the relative expression of inflammatory mediators such as interleukin 1; IRAK, which transduces signals between interleukin 1 receptors and the NFκB pathway; and the LPS pattern recognition receptor CD14. After 24 h of exposure, regulatory genes begin to counter the inflammation, as some genes involved in oxidative stress, apoptosis and non-inflammatory immune responses come into play. Both Fe2PO and Fe2PC induced similar immunogenetic changes in transcription profiles, but equal molar doses of Fe2PC resulted in more robust responses. These data suggest that further work in whole animal models may provide more insights into the extent of systemic physiological changes induced by these cyclophanes.
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Affiliation(s)
- Alex J Salazar-Medina
- Cátedra CONACYT-Departamento de Investigación en Polímeros y Materiales, Universidad de Sonora, Hermosillo, Sonora, Mexico
| | - Enrique F Velazquez-Contreras
- Departamento de Investigación en Polímeros y Materiales, Universidad de Sonora, Hermosillo, Sonora, Mexico.,Departamento de Ciencias Químico Biológicas, Universidad de Sonora, Hermosillo, Sonora, Mexico
| | - Rocio Sugich-Miranda
- Departamento de Ciencias Químico Biológicas, Universidad de Sonora, Hermosillo, Sonora, Mexico
| | - Hisila Santacruz
- Departamento de Investigación en Polímeros y Materiales, Universidad de Sonora, Hermosillo, Sonora, Mexico
| | - Rosa E Navarro
- Departamento de Investigación en Polímeros y Materiales, Universidad de Sonora, Hermosillo, Sonora, Mexico
| | - Fernando Rocha-Alonzo
- Departamento de Ciencias Químico Biológicas, Universidad de Sonora, Hermosillo, Sonora, Mexico
| | - Maria A Islas-Osuna
- Departamento de Investigación en Polímeros y Materiales, Universidad de Sonora, Hermosillo, Sonora, Mexico.,Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Sonora, Mexico
| | - Patricia L Chen
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, Texas A&M University, College Station, TX, USA
| | - Sarah G B Christian
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, Texas A&M University, College Station, TX, USA
| | - Amelia A Romoser
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX, USA
| | - Scott V Dindot
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX, USA
| | - Christie M Sayes
- Nanotoxicology and Nanopharmacology, RTI International, Research Triangle, MC, USA
| | - Rogerio R Sotelo-Mundo
- Biomolecular Structure Laboratory, Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Sonora, Mexico
| | - Michael F Criscitiello
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, Texas A&M University, College Station, TX, USA
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5
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Dodge A, Peters MM, Greene HE, Dietrick C, Botelho R, Chung D, Willman J, Nenninger AW, Ciarlone S, Kamath SG, Houdek P, Sumová A, Anderson AE, Dindot SV, Berg EL, O'Geen H, Segal DJ, Silverman JL, Weeber EJ, Nash KR. Generation of a Novel Rat Model of Angelman Syndrome with a Complete Ube3a Gene Deletion. Autism Res 2020; 13:397-409. [PMID: 31961493 PMCID: PMC7787396 DOI: 10.1002/aur.2267] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 01/02/2020] [Accepted: 01/06/2020] [Indexed: 11/08/2022]
Abstract
Angelman syndrome (AS) is a rare genetic disorder characterized by severe intellectual disability, seizures, lack of speech, and ataxia. The gene responsible for AS was identified as Ube3a and it encodes for E6AP, an E3 ubiquitin ligase. Currently, there is very little known about E6AP's mechanism of action in vivo or how the lack of this protein in neurons may contribute to the AS phenotype. Elucidating the mechanistic action of E6AP would enhance our understanding of AS and drive current research into new avenues that could lead to novel therapeutic approaches that target E6AP's various functions. To facilitate the study of AS, we have generated a novel rat model in which we deleted the rat Ube3a gene using CRISPR. The AS rat phenotypically mirrors human AS with loss of Ube3a expression in the brain and deficits in motor coordination as well as learning and memory. This model offers a new avenue for the study of AS. Autism Res 2020, 13: 397-409. © 2020 International Society for Autism Research,Wiley Periodicals, Inc. LAY SUMMARY: Angelman syndrome (AS) is a rare genetic disorder characterized by severe intellectual disability, seizures, difficulty speaking, and ataxia. The gene responsible for AS was identified as UBE3A, yet very little is known about its function in vivo or how the lack of this protein in neurons may contribute to the AS phenotype. To facilitate the study of AS, we have generated a novel rat model in which we deleted the rat Ube3a gene using CRISPR. The AS rat mirrors human AS with loss of Ube3a expression in the brain and deficits in motor coordination as well as learning and memory. This model offers a new avenue for the study of AS.
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Affiliation(s)
- Andie Dodge
- Department of Molecular Pharmacology and Physiology, University of South Florida, Tampa, Florida
| | - Melinda M Peters
- Department of Molecular Pharmacology and Physiology, University of South Florida, Tampa, Florida
| | - Hayden E Greene
- Department of Molecular Pharmacology and Physiology, University of South Florida, Tampa, Florida
| | - Clifton Dietrick
- Department of Molecular Pharmacology and Physiology, University of South Florida, Tampa, Florida
| | - Robert Botelho
- Department of Molecular Pharmacology and Physiology, University of South Florida, Tampa, Florida
| | - Diana Chung
- Department of Molecular Pharmacology and Physiology, University of South Florida, Tampa, Florida
| | - Jonathan Willman
- Department of Molecular Pharmacology and Physiology, University of South Florida, Tampa, Florida
| | - Austin W Nenninger
- Department of Molecular Pharmacology and Physiology, University of South Florida, Tampa, Florida
| | - Stephanie Ciarlone
- Department of Molecular Pharmacology and Physiology, University of South Florida, Tampa, Florida
- PTC Therapeutics Inc., Plainfield, 07080, New Jersey
| | - Siddharth G Kamath
- Department of Molecular Pharmacology and Physiology, University of South Florida, Tampa, Florida
| | - Pavel Houdek
- Department of Neurohumoral Regulations, Institute of Physiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Alena Sumová
- Department of Neurohumoral Regulations, Institute of Physiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Anne E Anderson
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Scott V Dindot
- Department of Veterinary Pathobiology, Texas A&M, College Station, Texas
| | - Elizabeth L Berg
- School of Medicine, MIND Institute, Department of Psychiatry and Behavioral Sciences, University of California - Davis, Sacramento, California
| | - Henriette O'Geen
- Genome Center and MIND Institute, University of California - Davis, Davis, California
| | - David J Segal
- Genome Center and MIND Institute, University of California - Davis, Davis, California
| | - Jill L Silverman
- School of Medicine, MIND Institute, Department of Psychiatry and Behavioral Sciences, University of California - Davis, Sacramento, California
| | - Edwin J Weeber
- Department of Molecular Pharmacology and Physiology, University of South Florida, Tampa, Florida
- PTC Therapeutics Inc., Plainfield, 07080, New Jersey
| | - Kevin R Nash
- Department of Molecular Pharmacology and Physiology, University of South Florida, Tampa, Florida
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6
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Berg EL, Pride MC, Petkova SP, Lee RD, Copping NA, Shen Y, Adhikari A, Fenton TA, Pedersen LR, Noakes LS, Nieman BJ, Lerch JP, Harris S, Born HA, Peters MM, Deng P, Cameron DL, Fink KD, Beitnere U, O'Geen H, Anderson AE, Dindot SV, Nash KR, Weeber EJ, Wöhr M, Ellegood J, Segal DJ, Silverman JL. Translational outcomes in a full gene deletion of ubiquitin protein ligase E3A rat model of Angelman syndrome. Transl Psychiatry 2020; 10:39. [PMID: 32066685 PMCID: PMC7026078 DOI: 10.1038/s41398-020-0720-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 12/17/2019] [Accepted: 01/02/2020] [Indexed: 12/17/2022] Open
Abstract
Angelman syndrome (AS) is a rare neurodevelopmental disorder characterized by developmental delay, impaired communication, motor deficits and ataxia, intellectual disabilities, microcephaly, and seizures. The genetic cause of AS is the loss of expression of UBE3A (ubiquitin protein ligase E6-AP) in the brain, typically due to a deletion of the maternal 15q11-q13 region. Previous studies have been performed using a mouse model with a deletion of a single exon of Ube3a. Since three splice variants of Ube3a exist, this has led to a lack of consistent reports and the theory that perhaps not all mouse studies were assessing the effects of an absence of all functional UBE3A. Herein, we report the generation and functional characterization of a novel model of Angelman syndrome by deleting the entire Ube3a gene in the rat. We validated that this resulted in the first comprehensive gene deletion rodent model. Ultrasonic vocalizations from newborn Ube3am-/p+ were reduced in the maternal inherited deletion group with no observable change in the Ube3am+/p- paternal transmission cohort. We also discovered Ube3am-/p+ exhibited delayed reflex development, motor deficits in rearing and fine motor skills, aberrant social communication, and impaired touchscreen learning and memory in young adults. These behavioral deficits were large in effect size and easily apparent in the larger rodent species. Low social communication was detected using a playback task that is unique to rats. Structural imaging illustrated decreased brain volume in Ube3am-/p+ and a variety of intriguing neuroanatomical phenotypes while Ube3am+/p- did not exhibit altered neuroanatomy. Our report identifies, for the first time, unique AS relevant functional phenotypes and anatomical markers as preclinical outcomes to test various strategies for gene and molecular therapies in AS.
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Affiliation(s)
- E L Berg
- MIND Institute and Department of Psychiatry and Behavioral Sciences, University of California Davis School of Medicine, Sacramento, CA, USA
| | - M C Pride
- MIND Institute and Department of Psychiatry and Behavioral Sciences, University of California Davis School of Medicine, Sacramento, CA, USA
| | - S P Petkova
- MIND Institute and Department of Psychiatry and Behavioral Sciences, University of California Davis School of Medicine, Sacramento, CA, USA
| | - R D Lee
- MIND Institute and Department of Psychiatry and Behavioral Sciences, University of California Davis School of Medicine, Sacramento, CA, USA
| | - N A Copping
- MIND Institute and Department of Psychiatry and Behavioral Sciences, University of California Davis School of Medicine, Sacramento, CA, USA
| | - Y Shen
- MIND Institute and Department of Psychiatry and Behavioral Sciences, University of California Davis School of Medicine, Sacramento, CA, USA
| | - A Adhikari
- MIND Institute and Department of Psychiatry and Behavioral Sciences, University of California Davis School of Medicine, Sacramento, CA, USA
| | - T A Fenton
- MIND Institute and Department of Psychiatry and Behavioral Sciences, University of California Davis School of Medicine, Sacramento, CA, USA
| | - L R Pedersen
- MIND Institute and Department of Psychiatry and Behavioral Sciences, University of California Davis School of Medicine, Sacramento, CA, USA
| | - L S Noakes
- Mouse Imaging Centre, Toronto Centre for Phenogenomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - B J Nieman
- Mouse Imaging Centre, Toronto Centre for Phenogenomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - J P Lerch
- Wellcome Centre for Integrative Neuroimaging, The University of Oxford, Oxford, UK
| | - S Harris
- Department of Pediatrics and Neurology, Baylor College of Medicine, Houston, TX, USA
| | - H A Born
- Department of Pediatrics and Neurology, Baylor College of Medicine, Houston, TX, USA
| | - M M Peters
- Department of Molecular Pharmacology and Physiology, University of South Florida, Tampa, FL, USA
| | - P Deng
- Stem Cell Program, Institute for Regenerative Cures, and Department of Neurology, University of California Davis School of Medicine, Sacramento, CA, USA
| | - D L Cameron
- Stem Cell Program, Institute for Regenerative Cures, and Department of Neurology, University of California Davis School of Medicine, Sacramento, CA, USA
| | - K D Fink
- Stem Cell Program, Institute for Regenerative Cures, and Department of Neurology, University of California Davis School of Medicine, Sacramento, CA, USA
| | - U Beitnere
- MIND Institute, Genome Center, and Department of Biochemistry and Molecular Medicine, University of California Davis, Davis, CA, USA
| | - H O'Geen
- MIND Institute, Genome Center, and Department of Biochemistry and Molecular Medicine, University of California Davis, Davis, CA, USA
| | - A E Anderson
- Department of Pediatrics and Neurology, Baylor College of Medicine, Houston, TX, USA
| | - S V Dindot
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - K R Nash
- Department of Molecular Pharmacology and Physiology, University of South Florida, Tampa, FL, USA
| | - E J Weeber
- Department of Molecular Pharmacology and Physiology, University of South Florida, Tampa, FL, USA
| | - M Wöhr
- Behavioral Neuroscience, Experimental and Biological Psychology, Philipps-University of Marburg, Marburg, Germany
| | - J Ellegood
- Mouse Imaging Centre, Toronto Centre for Phenogenomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - D J Segal
- MIND Institute, Genome Center, and Department of Biochemistry and Molecular Medicine, University of California Davis, Davis, CA, USA
| | - J L Silverman
- MIND Institute and Department of Psychiatry and Behavioral Sciences, University of California Davis School of Medicine, Sacramento, CA, USA.
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7
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Quist EM, Doan R, Pool RR, Porter BF, Bannasch DL, Dindot SV. Identification of a Candidate Mutation in the COL1A2 Gene of a Chow Chow With Osteogenesis Imperfecta. J Hered 2019; 109:308-314. [PMID: 29036614 DOI: 10.1093/jhered/esx074] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 09/18/2017] [Indexed: 01/08/2023] Open
Abstract
Osteogenesis imperfecta (OI) is a genetic disease that occurs in humans and animals. Individuals with OI exhibit signs of extreme bone fragility and osteopenia with frequent fractures and perinatal lethality in severe cases. In this study, we report the clinical diagnosis of OI in a dog and the use of targeted next-generation sequencing to identify a candidate autosomal dominant mutation in the COL1A2 gene. A 5-month-old male Chow Chow was examined with a fractured left humerus and resolving, bilateral femoral fractures. Radiographs revealed generalized osteopenia and bilateral humeral, radial, and femoral fractures. Targeted next-generation sequencing of genes associated with OI in humans (COL1A1, COL1A2, LEPRE1, SERPINH1, and CRTAP) revealed a G>A heterozygous mutation in the splice donor site of exon 18 of the COL1A2 gene (c.936 + 1G>A). The splice donor mutation was not detected among 91 control dogs representing 21 breeds. A comparative analysis of exon 18 and the exon-intron junction further showed that the mutated splice donor site is conserved among vertebrates. Altogether, these findings reveal a candidate autosomal splice donor site mutation causing OI in an individual Chow Chow.
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Affiliation(s)
- Erin M Quist
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX
| | - Ryan Doan
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX
| | - Roy R Pool
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX
| | - Brian F Porter
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX
| | - Danika L Bannasch
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA
| | - Scott V Dindot
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health Science Center, College Station, TX
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8
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Dindot SV, Doan RN, Kuskie KR, Hillman PR, Whitfield CM, McQueen CM, Bordin AI, Bourquin JR, Cohen ND. Postnatal changes in epigenetic modifications of neutrophils of foals are associated with increased ROS function and regulation of neutrophil function. Dev Comp Immunol 2018; 87:182-187. [PMID: 29958850 DOI: 10.1016/j.dci.2018.06.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 06/25/2018] [Accepted: 06/25/2018] [Indexed: 06/08/2023]
Abstract
Neonates of all species, including foals, are highly susceptible to infection, and neutrophils play a crucial role in innate immunity to infection. Evidence exists that neutrophils of neonatal foals are functionally deficient during the first weeks of life, including expression of cytokine genes such as IFNG. We hypothesized that postnatal epigenetic changes were likely to regulate the observed age-related changes in foal neutrophils. Using ChIP-Seq, we identified significant differences in trimethylated histone H3 lysine 4, an epigenetic modification associated with active promoters and enhancers, in neutrophils in foals at 30 days of age relative to 1 day of age. These chromatin changes were associated with genes implicated in immune responses and were consistent with age-related changes in neutrophil functional responses including ROS generation and IFN expression. Postnatal changes in epigenetic modifications suggest that environmentally-mediated cues help to promote maturation of neutrophil functional responses. Elucidating the environmental triggers and their signaling pathways could provide a means for improving innate immune responses of neonates to improve their ability to combat infectious diseases.
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Affiliation(s)
- Scott V Dindot
- Department of Veterinary Pathobiology, Texas A&M University College of Veterinary Medicine & Biomedical Sciences, College Station, TX, USA; Department of Molecular and Cellular Medicine, Texas A&M Health Science Center College of Medicine, College Station, TX, USA.
| | - Ryan N Doan
- Department of Veterinary Pathobiology, Texas A&M University College of Veterinary Medicine & Biomedical Sciences, College Station, TX, USA
| | - Kyle R Kuskie
- Department of Large Animal Clinical Sciences, Texas A&M University College of Veterinary Medicine & Biomedical Sciences, College Station, TX, USA
| | - Paul R Hillman
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center College of Medicine, College Station, TX, USA
| | - Canaan M Whitfield
- Department of Large Animal Clinical Sciences, Texas A&M University College of Veterinary Medicine & Biomedical Sciences, College Station, TX, USA
| | - Cole M McQueen
- Department of Large Animal Clinical Sciences, Texas A&M University College of Veterinary Medicine & Biomedical Sciences, College Station, TX, USA
| | - Angela I Bordin
- Department of Large Animal Clinical Sciences, Texas A&M University College of Veterinary Medicine & Biomedical Sciences, College Station, TX, USA
| | - Jessica R Bourquin
- Department of Large Animal Clinical Sciences, Texas A&M University College of Veterinary Medicine & Biomedical Sciences, College Station, TX, USA
| | - Noah D Cohen
- Department of Large Animal Clinical Sciences, Texas A&M University College of Veterinary Medicine & Biomedical Sciences, College Station, TX, USA.
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9
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Alves BRC, Cardoso RC, Doan R, Zhang Y, Dindot SV, Williams GL, Amstalden M. Nutritional programming of accelerated puberty in heifers: alterations in DNA methylation in the arcuate nucleus. Biol Reprod 2017; 96:174-184. [PMID: 28395339 DOI: 10.1095/biolreprod.116.144741] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 11/21/2016] [Indexed: 11/01/2022] Open
Abstract
High rates of body weight gain during the juvenile period appear to program molecular events within the hypothalamus, leading to advancement of puberty. Methylation of DNA, an epigenetic mechanism that controls gene expression, is associated with metabolic programming events and is proposed to play a role in the pubertal process. In this study, DNA methylation was assessed in genomic DNA obtained from the arcuate nucleus (ARC) of juvenile heifers fed to gain body weight at low (0.5 kg/d; low-gain, LG, n = 4) or high (1 kg/d; high-gain, HG, n = 4) rates from 4.5 to 8.5 mo of age (earliest puberty expected at 9 mo of age in HG heifers). Using a custom-designed oligonucleotide array targeted to imprinted genes and genes associated with nutritional inputs and the control of puberty, a comparative-genomic-hybridization array was used to identify differentially methylated regions between LG and HG heifers. Differential methylation of genomic regions associated with altered mRNA expression was observed for genes whose activity has been reported to be involved in the modulation of growth and metabolism (GHR) and puberty (HMGA2). Hence, increased rates of body weight gain during the juvenile period alter the methylation pattern of genomic DNA obtained from the ARC and these changes may be involved in programming the age at puberty in heifers.
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Affiliation(s)
- Bruna R C Alves
- Department of Animal Science, Texas A&M University, College Station, Texas, USA
| | - Rodolfo C Cardoso
- Department of Animal Science, Texas A&M University, College Station, Texas, USA.,Animal Reproduction Laboratory, Texas A&M AgriLife Research, Beeville, Texas, USA
| | - Ryan Doan
- Department of Veterinary Pathobiology, Texas A&M University, College Station, Texas, USA
| | - Youwen Zhang
- Department of Animal Science, Texas A&M University, College Station, Texas, USA.,Animal Reproduction Laboratory, Texas A&M AgriLife Research, Beeville, Texas, USA
| | - Scott V Dindot
- Department of Veterinary Pathobiology, Texas A&M University, College Station, Texas, USA
| | - Gary L Williams
- Department of Animal Science, Texas A&M University, College Station, Texas, USA.,Animal Reproduction Laboratory, Texas A&M AgriLife Research, Beeville, Texas, USA
| | - Marcel Amstalden
- Department of Animal Science, Texas A&M University, College Station, Texas, USA
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10
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Copping NA, Christian SGB, Ritter DJ, Islam MS, Buscher N, Zolkowska D, Pride MC, Berg EL, LaSalle JM, Ellegood J, Lerch JP, Reiter LT, Silverman JL, Dindot SV. Neuronal overexpression of Ube3a isoform 2 causes behavioral impairments and neuroanatomical pathology relevant to 15q11.2-q13.3 duplication syndrome. Hum Mol Genet 2017; 26:3995-4010. [PMID: 29016856 PMCID: PMC5886211 DOI: 10.1093/hmg/ddx289] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [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] [Received: 04/25/2017] [Revised: 06/21/2017] [Accepted: 07/10/2017] [Indexed: 01/07/2023] Open
Abstract
Maternally derived copy number gains of human chromosome 15q11.2-q13.3 (Dup15q syndrome or Dup15q) cause intellectual disability, epilepsy, developmental delay, hypotonia, speech impairments, and minor dysmorphic features. Dup15q syndrome is one of the most common and penetrant chromosomal abnormalities observed in individuals with autism spectrum disorder (ASD). Although ∼40 genes are located in the 15q11.2-q13.3 region, overexpression of the ubiquitin-protein E3A ligase (UBE3A) gene is thought to be the predominant molecular cause of the phenotypes observed in Dup15q syndrome. The UBE3A gene demonstrates maternal-specific expression in neurons and loss of maternal UBE3A causes Angelman syndrome, a neurodevelopmental disorder with some overlapping neurological features to Dup15q. To directly test the hypothesis that overexpression of UBE3A is an important underlying molecular cause of neurodevelopmental dysfunction, we developed and characterized a mouse overexpressing Ube3a isoform 2 in excitatory neurons. Ube3a isoform 2 is conserved between mouse and human and known to play key roles in neuronal function. Transgenic mice overexpressing Ube3a isoform 2 in excitatory forebrain neurons exhibited increased anxiety-like behaviors, learning impairments, and reduced seizure thresholds. However, these transgenic mice displayed normal social approach, social interactions, and repetitive motor stereotypies that are relevant to ASD. Reduced forebrain, hippocampus, striatum, amygdala, and cortical volume were also observed. Altogether, these findings show neuronal overexpression of Ube3a isoform 2 causes phenotypes translatable to neurodevelopmental disorders.
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Affiliation(s)
- Nycole A Copping
- MIND Institute, School of Medicine, University of California, Davis, Sacramento, CA, USA
| | | | - Dylan J Ritter
- MIND Institute, School of Medicine, University of California, Davis, Sacramento, CA, USA
- Texas A&M, College Station, TX, USA
| | - M Saharul Islam
- MIND Institute, School of Medicine, University of California, Davis, Sacramento, CA, USA
| | - Nathalie Buscher
- MIND Institute, School of Medicine, University of California, Davis, Sacramento, CA, USA
| | - Dorota Zolkowska
- MIND Institute, School of Medicine, University of California, Davis, Sacramento, CA, USA
| | - Michael C Pride
- MIND Institute, School of Medicine, University of California, Davis, Sacramento, CA, USA
| | - Elizabeth L Berg
- MIND Institute, School of Medicine, University of California, Davis, Sacramento, CA, USA
| | - Janine M LaSalle
- MIND Institute, School of Medicine, University of California, Davis, Sacramento, CA, USA
| | - Jacob Ellegood
- The Hospital for Sick Children, Mouse Imaging Centre, Toronto, ON, Canada
| | - Jason P Lerch
- The Hospital for Sick Children, Mouse Imaging Centre, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Lawrence T Reiter
- Departments of Neurology, Pediatrics and Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Jill L Silverman
- MIND Institute, School of Medicine, University of California, Davis, Sacramento, CA, USA
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11
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Hillman PR, Christian SGB, Doan R, Cohen ND, Konganti K, Douglas K, Wang X, Samollow PB, Dindot SV. Genomic imprinting does not reduce the dosage of UBE3A in neurons. Epigenetics Chromatin 2017; 10:27. [PMID: 28515788 PMCID: PMC5433054 DOI: 10.1186/s13072-017-0134-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 05/03/2017] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The ubiquitin protein E3A ligase gene (UBE3A) gene is imprinted with maternal-specific expression in neurons and biallelically expressed in all other cell types. Both loss-of-function and gain-of-function mutations affecting the dosage of UBE3A are associated with several neurodevelopmental syndromes and psychological conditions, suggesting that UBE3A is dosage-sensitive in the brain. The observation that loss of imprinting increases the dosage of UBE3A in brain further suggests that inactivation of the paternal UBE3A allele evolved as a dosage-regulating mechanism. To test this hypothesis, we examined UBE3A transcript and protein levels among cells, tissues, and species with different imprinting states of UBE3A. RESULTS Overall, we found no correlation between the imprinting status and dosage of UBE3A. Importantly, we found that maternal Ube3a protein levels increase in step with decreasing paternal Ube3a protein levels during neurogenesis in mouse, fully compensating for loss of expression of the paternal Ube3a allele in neurons. CONCLUSIONS Based on our findings, we propose that imprinting of UBE3A does not function to reduce the dosage of UBE3A in neurons but rather to regulate some other, as yet unknown, aspect of gene expression or protein function.
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Affiliation(s)
- Paul R Hillman
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77845 USA.,Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health Science Center, College Station, TX 77845 USA
| | - Sarah G B Christian
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77845 USA
| | - Ryan Doan
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77845 USA.,Interdisciplinary Genetics Program, College of Agriculture and Life Sciences, Texas A&M University, College Station, TX 77845 USA
| | - Noah D Cohen
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX USA
| | - Kranti Konganti
- Institute for Genome Science and Society, Texas A&M University, College Station, TX 77845 USA
| | - Kory Douglas
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX USA.,Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843 USA
| | - Xu Wang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853 USA
| | - Paul B Samollow
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843 USA
| | - Scott V Dindot
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77845 USA.,Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health Science Center, College Station, TX 77845 USA.,Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, 4467 TAMU, College Station, TX 77843 USA
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12
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McQueen CM, Whitfield-Cargile CM, Konganti K, Blodgett GP, Dindot SV, Cohen ND. TRPM2 SNP genotype previously associated with susceptibility to Rhodococcus equi pneumonia in Quarter Horse foals displays differential gene expression identified using RNA-Seq. BMC Genomics 2016; 17:993. [PMID: 27919223 PMCID: PMC5139010 DOI: 10.1186/s12864-016-3345-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 11/25/2016] [Indexed: 01/02/2023] Open
Abstract
Background Rhodococcus equi (R. equi) is an intracellular bacterium that affects young foals and immuno-compromised individuals causing severe pneumonia. Currently, the genetic mechanisms that confer susceptibility and/or resistance to R. equi are not fully understood. Previously, using a SNP-based genome-wide association study, we identified a region on equine chromosome 26 associated with culture-confirmed clinical pneumonia. To better characterize this region and understand the function of the SNP located within TRPM2 that was associated with R. equi pneumonia, we performed RNA-Seq on 12 horses representing the 3 genotypic forms of this SNP. Results We identified differentially expressed genes in the innate immune response pathway when comparing homozygous A allele horses with the AB and BB horses. Isoform analyses of the RNA-Seq data predicted the existence of multiple transcripts and provided evidence of differential expression at the TRPM2 locus. This finding is consistent with previously demonstrated work in human cell lines in which isoform-specific expression of TRPM2 was critical for cell viability. Conclusions This work demonstrates that SNPs in TRPM2 are associated with differences in gene expression, suggesting that modulation of expression of this innate immune gene contributes to susceptibility to R. equi pneumonia.
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Affiliation(s)
- Cole M McQueen
- Department of Large Animal Clinical Sciences, Texas A&M University College of Veterinary Medicine & Biomedical Sciences, College Station, TX, USA
| | - Canaan M Whitfield-Cargile
- Department of Large Animal Clinical Sciences, Texas A&M University College of Veterinary Medicine & Biomedical Sciences, College Station, TX, USA
| | - Kranti Konganti
- Texas A&M Institute for Genome Sciences and Society, Texas A&M University, College Station, TX, USA.,Department of Veterinary Pathobiology, Texas A&M University College of Veterinary Medicine & Biomedical Sciences, College Station, TX, USA
| | | | - Scott V Dindot
- Department of Veterinary Pathobiology, Texas A&M University College of Veterinary Medicine & Biomedical Sciences, College Station, TX, USA.
| | - Noah D Cohen
- Department of Large Animal Clinical Sciences, Texas A&M University College of Veterinary Medicine & Biomedical Sciences, College Station, TX, USA.
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13
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McQueen CM, Dindot SV, Foster MJ, Cohen ND. Genetic Susceptibility to Rhodococcus equi. J Vet Intern Med 2015; 29:1648-59. [PMID: 26340305 PMCID: PMC4895676 DOI: 10.1111/jvim.13616] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 06/29/2015] [Accepted: 08/10/2015] [Indexed: 02/02/2023] Open
Abstract
Rhodococcus equi pneumonia is a major cause of morbidity and mortality in neonatal foals. Much effort has been made to identify preventative measures and new treatments for R. equi with limited success. With a growing focus in the medical community on understanding the genetic basis of disease susceptibility, investigators have begun to evaluate the interaction of the genetics of the foal with R. equi. This review describes past efforts to understand the genetic basis underlying R. equi susceptibility and tolerance. It also highlights the genetic technology available to study horses and describes the use of this technology in investigating R. equi. This review provides readers with a foundational understanding of candidate gene approaches, single nucleotide polymorphism‐based, and copy number variant‐based genome‐wide association studies, and next generation sequencing (both DNA and RNA).
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Affiliation(s)
- C M McQueen
- Department of Large Animal Clinical Sciences, Texas A&M University, College Station, TX
| | - S V Dindot
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX
| | - M J Foster
- Medical Sciences Library, Texas A&M University, College Station, TX
| | - N D Cohen
- Department of Large Animal Clinical Sciences, Texas A&M University, College Station, TX
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14
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Ghaffari N, Sanchez-Flores A, Doan R, Garcia-Orozco KD, Chen PL, Ochoa-Leyva A, Lopez-Zavala AA, Carrasco JS, Hong C, Brieba LG, Rudiño-Piñera E, Blood PD, Sawyer JE, Johnson CD, Dindot SV, Sotelo-Mundo RR, Criscitiello MF. Novel transcriptome assembly and improved annotation of the whiteleg shrimp (Litopenaeus vannamei), a dominant crustacean in global seafood mariculture. Sci Rep 2014; 4:7081. [PMID: 25420880 PMCID: PMC4243063 DOI: 10.1038/srep07081] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 08/29/2014] [Indexed: 01/07/2023] Open
Abstract
We present a new transcriptome assembly of the Pacific whiteleg shrimp (Litopenaeus vannamei), the species most farmed for human consumption. Its functional annotation, a substantial improvement over previous ones, is provided freely. RNA-Seq with Illumina HiSeq technology was used to analyze samples extracted from shrimp abdominal muscle, hepatopancreas, gills and pleopods. We used the Trinity and Trinotate software suites for transcriptome assembly and annotation, respectively. The quality of this assembly and the affiliated targeted homology searches greatly enrich the curated transcripts currently available in public databases for this species. Comparison with the model arthropod Daphnia allows some insights into defining characteristics of decapod crustaceans. This large-scale gene discovery gives the broadest depth yet to the annotated transcriptome of this important species and should be of value to ongoing genomics and immunogenetic resistance studies in this shrimp of paramount global economic importance.
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Affiliation(s)
- Noushin Ghaffari
- Genomics and Bioinformatic Services, Texas A&M AgriLife Research, College Station, TX 77845 USA
| | - Alejandro Sanchez-Flores
- Unidad Universitaria de Apoyo Bioiformático, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Ryan Doan
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843 USA
| | - Karina D. Garcia-Orozco
- Centro de Investigación en Alimentación y Desarrollo (CIAD), Carretera a Ejido La Victoria, Km 0.6, Hermosillo, Sonora 83304 Mexico
| | - Patricia L. Chen
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843 USA
| | - Adrian Ochoa-Leyva
- Unidad de Genómica de Poblaciones Aplicada la Salud, Facultad de Química, UNAM, Instituto Nacional de Medicina Genómica (INMEGEN), México, D.F., 14610, Mexico
| | - Alonso A. Lopez-Zavala
- Centro de Investigación en Alimentación y Desarrollo (CIAD), Carretera a Ejido La Victoria, Km 0.6, Hermosillo, Sonora 83304 Mexico
| | - J. Salvador Carrasco
- Centro de Investigación en Alimentación y Desarrollo (CIAD), Carretera a Ejido La Victoria, Km 0.6, Hermosillo, Sonora 83304 Mexico
| | - Chris Hong
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843 USA
| | - Luis G. Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato Mexico
| | - Enrique Rudiño-Piñera
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnologia, Universidad Nacional Autónoma de Mexico, Cuernavaca, Morelos Mexico
| | | | - Jason E. Sawyer
- Department of Animal Sciences, Texas Agrilife Research, Texas A&M University, College Station, TX 77843 USA
| | - Charles D. Johnson
- Genomics and Bioinformatic Services, Texas A&M AgriLife Research, College Station, TX 77845 USA
| | - Scott V. Dindot
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843 USA
| | - Rogerio R. Sotelo-Mundo
- Centro de Investigación en Alimentación y Desarrollo (CIAD), Carretera a Ejido La Victoria, Km 0.6, Hermosillo, Sonora 83304 Mexico
| | - Michael F. Criscitiello
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843 USA
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843 USA
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health Sciences Center, Texas A&M University, College Station, TX 77843 USA
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15
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Wang J, Wu Z, Li D, Li N, Dindot SV, Satterfield MC, Bazer FW, Wu G. Nutrition, epigenetics, and metabolic syndrome. Antioxid Redox Signal 2012; 17:282-301. [PMID: 22044276 PMCID: PMC3353821 DOI: 10.1089/ars.2011.4381] [Citation(s) in RCA: 187] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Accepted: 11/01/2011] [Indexed: 01/21/2023]
Abstract
SIGNIFICANCE Epidemiological and animal studies have demonstrated a close link between maternal nutrition and chronic metabolic disease in children and adults. Compelling experimental results also indicate that adverse effects of intrauterine growth restriction on offspring can be carried forward to subsequent generations through covalent modifications of DNA and core histones. RECENT ADVANCES DNA methylation is catalyzed by S-adenosylmethionine-dependent DNA methyltransferases. Methylation, demethylation, acetylation, and deacetylation of histone proteins are performed by histone methyltransferase, histone demethylase, histone acetyltransferase, and histone deacetyltransferase, respectively. Histone activities are also influenced by phosphorylation, ubiquitination, ADP-ribosylation, sumoylation, and glycosylation. Metabolism of amino acids (glycine, histidine, methionine, and serine) and vitamins (B6, B12, and folate) plays a key role in provision of methyl donors for DNA and protein methylation. CRITICAL ISSUES Disruption of epigenetic mechanisms can result in oxidative stress, obesity, insulin resistance, diabetes, and vascular dysfunction in animals and humans. Despite a recognized role for epigenetics in fetal programming of metabolic syndrome, research on therapies is still in its infancy. Possible interventions include: 1) inhibition of DNA methylation, histone deacetylation, and microRNA expression; 2) targeting epigenetically disturbed metabolic pathways; and 3) dietary supplementation with functional amino acids, vitamins, and phytochemicals. FUTURE DIRECTIONS Much work is needed with animal models to understand the basic mechanisms responsible for the roles of specific nutrients in fetal and neonatal programming. Such new knowledge is crucial to design effective therapeutic strategies for preventing and treating metabolic abnormalities in offspring born to mothers with a previous experience of malnutrition.
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Affiliation(s)
- Junjun Wang
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing, China
| | - Zhenlong Wu
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing, China
| | - Defa Li
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing, China
| | - Ning Li
- State Key Laboratory of AgroBiotechnology, China Agricultural University, Beijing, China
| | - Scott V. Dindot
- Center for Animal Biotechnology and Genomics, Texas A&M University, College Station, Texas
- Department of Veterinary Pathobiology, Texas A&M University, College Station, Texas
- Department of Molecular and Cellular Medicine, Texas A&M University, College Station, Texas
| | - M. Carey Satterfield
- Center for Animal Biotechnology and Genomics, Texas A&M University, College Station, Texas
- Department of Animal Science, Texas A&M University, College Station, Texas
| | - Fuller W. Bazer
- Center for Animal Biotechnology and Genomics, Texas A&M University, College Station, Texas
- Department of Animal Science, Texas A&M University, College Station, Texas
| | - Guoyao Wu
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing, China
- Center for Animal Biotechnology and Genomics, Texas A&M University, College Station, Texas
- Department of Animal Science, Texas A&M University, College Station, Texas
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16
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Abstract
Copy number variants (CNVs) represent a substantial source of genetic variation in mammals. However, the occurrence of CNVs in horses and their subsequent impact on phenotypic variation is unknown. We performed a study to identify CNVs in 16 horses representing 15 distinct breeds (Equus caballus) and an individual gray donkey (Equus asinus) using a whole-exome tiling array and the array comparative genomic hybridization methodology. We identified 2368 CNVs ranging in size from 197 bp to 3.5 Mb. Merging identical CNVs from each animal yielded 775 CNV regions (CNVRs), involving 1707 protein- and RNA-coding genes. The number of CNVs per animal ranged from 55 to 347, with median and mean sizes of CNVs of 5.3 kb and 99.4 kb, respectively. Approximately 6% of the genes investigated were affected by a CNV. Biological process enrichment analysis indicated CNVs primarily affected genes involved in sensory perception, signal transduction, and metabolism. CNVs also were identified in genes regulating blood group antigens, coat color, fecundity, lactation, keratin formation, neuronal homeostasis, and height in other species. Collectively, these data are the first report of copy number variation in horses and suggest that CNVs are common in the horse genome and may modulate biological processes underlying different traits observed among horses and horse breeds.
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Affiliation(s)
- Ryan Doan
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
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Doan R, Cohen ND, Sawyer J, Ghaffari N, Johnson CD, Dindot SV. Whole-genome sequencing and genetic variant analysis of a Quarter Horse mare. BMC Genomics 2012; 13:78. [PMID: 22340285 PMCID: PMC3309927 DOI: 10.1186/1471-2164-13-78] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2011] [Accepted: 02/17/2012] [Indexed: 11/24/2022] Open
Abstract
Background The catalog of genetic variants in the horse genome originates from a few select animals, the majority originating from the Thoroughbred mare used for the equine genome sequencing project. The purpose of this study was to identify genetic variants, including single nucleotide polymorphisms (SNPs), insertion/deletion polymorphisms (INDELs), and copy number variants (CNVs) in the genome of an individual Quarter Horse mare sequenced by next-generation sequencing. Results Using massively parallel paired-end sequencing, we generated 59.6 Gb of DNA sequence from a Quarter Horse mare resulting in an average of 24.7X sequence coverage. Reads were mapped to approximately 97% of the reference Thoroughbred genome. Unmapped reads were de novo assembled resulting in 19.1 Mb of new genomic sequence in the horse. Using a stringent filtering method, we identified 3.1 million SNPs, 193 thousand INDELs, and 282 CNVs. Genetic variants were annotated to determine their impact on gene structure and function. Additionally, we genotyped this Quarter Horse for mutations of known diseases and for variants associated with particular traits. Functional clustering analysis of genetic variants revealed that most of the genetic variation in the horse's genome was enriched in sensory perception, signal transduction, and immunity and defense pathways. Conclusions This is the first sequencing of a horse genome by next-generation sequencing and the first genomic sequence of an individual Quarter Horse mare. We have increased the catalog of genetic variants for use in equine genomics by the addition of novel SNPs, INDELs, and CNVs. The genetic variants described here will be a useful resource for future studies of genetic variation regulating performance traits and diseases in equids.
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Affiliation(s)
- Ryan Doan
- Department of Veterinary Pathobiology, Texas A&M University College of Veterinary Medicine and Biomedical Sciences, College Station, TX, USA
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Dindot SV, Person R, Strivens M, Garcia R, Beaudet AL. Epigenetic profiling at mouse imprinted gene clusters reveals novel epigenetic and genetic features at differentially methylated regions. Genome Res 2009; 19:1374-83. [PMID: 19542493 DOI: 10.1101/gr.089185.108] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Genomic imprinting arises from allele-specific epigenetic modifications that are established during gametogenesis and that are maintained throughout somatic development. These parental-specific modifications include DNA methylation and post-translational modifications to histones, which create allele-specific active and repressive domains at imprinted regions. Through the use of a high-density genomic tiling array, we generated DNA and histone methylation profiles at 11 imprinted gene clusters in the mouse from DNA and from chromatin immunoprecipitated from sperm, heart, and cerebellum. Our analysis revealed that despite high levels of differential DNA methylation at non-CpG islands within these regions, imprinting control regions (ICRs) and secondary differentially methylated regions (DMRs) were identified by an overlapping pattern of H3K4 trimethylation (active chromatin) and H3K9 trimethylation (repressive chromatin) modifications in somatic tissue, and a sperm differentially methylated region (sDMR; sperm not equal somatic tissue). Using these features as a common signature of DMRs, we identified 11 unique regions that mapped to known imprinted genes, to uncharacterized genes, and to intergenic regions flanking known imprinted genes. A common feature among these regions was the presence of a CpG island and an array of tandem repeats. Collectively, this study provides a comprehensive analysis of DNA methylation and histone H3K4me3 and H3K9me3 modifications at imprinted gene clusters, and identifies common epigenetic and genetic features of regions regulating genomic imprinting.
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Affiliation(s)
- Scott V Dindot
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.
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Dindot SV, Antalffy BA, Bhattacharjee MB, Beaudet AL. The Angelman syndrome ubiquitin ligase localizes to the synapse and nucleus, and maternal deficiency results in abnormal dendritic spine morphology. Hum Mol Genet 2007; 17:111-8. [PMID: 17940072 DOI: 10.1093/hmg/ddm288] [Citation(s) in RCA: 280] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Loss of function of the maternally inherited allele for the UBE3A ubiquitin ligase gene causes Angelman syndrome (AS), which is characterized by severe neurological impairment and motor dysfunction. In addition, UBE3A lies within chromosome 15q11-q13 region, where maternal, but not paternal, duplications cause autism. The UBE3A gene product, E6-AP, has been shown to function both as an E3 ligase in the ubiquitin proteasome pathway and as a transcriptional coactivator. However, the specific role of E6-AP in the brain, or how loss of function of E6-AP results in AS, is unclear. Herein, we show, using a recombinant transgenic mouse expressing a Ube3a(YFP) fusion gene, that the maternal Ube3a(YFP) allele is upregulated and preferentially expressed in neurons, and that the fusion protein, E6-AP:YFP, is enriched in the nucleus and dendrites in vivo. We also show that E6-AP:YFP localizes to the nucleus and to presynaptic and postsynaptic compartments in cultured hippocampal neurons. Furthermore, we show that cerebellar Purkinje cell number and dendritic branching are not affected in Ube3a maternal-deficient mice, but that dendritic spine development, including spine morphology, number and length, is affected on cerebellar Purkinje cells and on pyramidal neurons in the hippocampus and cortex. Collectively, these data suggest that the neurological deficits observed in AS patients and in AS mice may result from specific abnormalities in synaptic development and/or plasticity.
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Affiliation(s)
- Scott V Dindot
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
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Dindot SV, Kent KC, Evers B, Loskutoff N, Womack J, Piedrahita JA. Conservation of genomic imprinting at the XIST, IGF2, and GTL2 loci in the bovine. Mamm Genome 2004; 15:966-74. [PMID: 15599555 DOI: 10.1007/s00335-004-2407-z] [Citation(s) in RCA: 56] [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] [Received: 04/07/2004] [Accepted: 08/20/2004] [Indexed: 10/24/2022]
Abstract
Genomic imprinting is theorized to exist in all placental mammals and some marsupials; however, extensive comparative analysis of animals aside from humans and mice remains incomplete. Here we report conservation of genomic imprinting in the bovine at the X chromosome inactivation-specific transcript (XIST), insulin-like growth factor 2 (IGF2), and gene trap locus 2 (GTL2) loci. Coding single nucleotide polymorphisms (SNPs) between Bos gaurus and Bos taurus were detected at the XIST, IGF2, and GTL2 loci, which have previously been identified as imprinted in either humans, mice, or sheep. Expression patterns of parental alleles in F1 hybrids indicated preferential paternal expression at the XIST locus solely in the chorion of females, whereas analysis of the IGF2 and GTL2 loci indicated preferential paternal and maternal expression of alleles, respectively, in both fetal and placental tissues. Comparative sequence analysis of the XIST locus and adjacent regions suggests that repression of the maternal allele in the bovine is controlled by a different mechanism than in mice, further reinforcing the importance of comparative analysis of imprinting.
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Affiliation(s)
- Scott V Dindot
- Department of Veterinary Anatomy and Public Health, College of Veterinary Medicine, Texas A&M University, College Station, Texas 77843, USA
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Dindot SV, Farin PW, Farin CE, Romano J, Walker S, Long C, Piedrahita JA. Epigenetic and genomic imprinting analysis in nuclear transfer derived Bos gaurus/Bos taurus hybrid fetuses. Biol Reprod 2004; 71:470-8. [PMID: 15044262 DOI: 10.1095/biolreprod.103.025775] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.9] [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: 12/14/2022] Open
Abstract
Somatic cell nuclear transfer (NT) in cattle is an inefficient process, whereby the production of calves is hindered by low pregnancy rates as well as fetal and placental abnormalities. Interspecies models have been previously used to facilitate the identification of single nucleotide polymorphisms (SNPs) within coding regions of genes to discriminate between parental alleles in the offspring. Here we report the use of a bovine interspecies model (Bos gaurus x Bos taurus) for the assessment and characterization of epigenetic modifications and genomic imprinting in Day 40-old female NT-derived fetuses and placenta. Analysis of NT and control pregnancies indicated disruption of genomic imprinting at the X inactivation-specific transcript (XIST) locus in the chorion, but not the fetus of clones, whereas proper allelic expression of the insulin-like growth factor II (IGF2) and gene trap locus 2 (GTL2) loci was maintained in both the fetus and placenta. Analysis of the XIST differentially methylated region (DMR) in clones indicated normal patterns of methylation; however, bisulfite sequencing of the satellite I repeat element and epidermal cytokeratin promoter indicated hypermethylation in the chorion of clones when compared with controls. No differences were detected in methylation levels in the fetus proper. These results indicate that the nuclear transfer process affects gene expression patterns in the trophectoderm- and inner cell mass-derived tissues to different extents.
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Affiliation(s)
- Scott V Dindot
- Department of Veterinary Anatomy and Public Health, College of Veterinary Medicine, Texas A&M University, College Station, TX 77840, USA
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