1
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San Roman AK, Skaletsky H, Godfrey AK, Bokil NV, Teitz L, Singh I, Blanton LV, Bellott DW, Pyntikova T, Lange J, Koutseva N, Hughes JF, Brown L, Phou S, Buscetta A, Kruszka P, Banks N, Dutra A, Pak E, Lasutschinkow PC, Keen C, Davis SM, Lin AE, Tartaglia NR, Samango-Sprouse C, Muenke M, Page DC. The human Y and inactive X chromosomes similarly modulate autosomal gene expression. Cell Genom 2024; 4:100462. [PMID: 38190107 PMCID: PMC10794785 DOI: 10.1016/j.xgen.2023.100462] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/15/2023] [Accepted: 11/14/2023] [Indexed: 01/09/2024]
Abstract
Somatic cells of human males and females have 45 chromosomes in common, including the "active" X chromosome. In males the 46th chromosome is a Y; in females it is an "inactive" X (Xi). Through linear modeling of autosomal gene expression in cells from individuals with zero to three Xi and zero to four Y chromosomes, we found that Xi and Y impact autosomal expression broadly and with remarkably similar effects. Studying sex chromosome structural anomalies, promoters of Xi- and Y-responsive genes, and CRISPR inhibition, we traced part of this shared effect to homologous transcription factors-ZFX and ZFY-encoded by Chr X and Y. This demonstrates sex-shared mechanisms by which Xi and Y modulate autosomal expression. Combined with earlier analyses of sex-linked gene expression, our studies show that 21% of all genes expressed in lymphoblastoid cells or fibroblasts change expression significantly in response to Xi or Y chromosomes.
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Affiliation(s)
| | - Helen Skaletsky
- Whitehead Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA
| | - Alexander K Godfrey
- Whitehead Institute, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Neha V Bokil
- Whitehead Institute, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Levi Teitz
- Whitehead Institute, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Isani Singh
- Whitehead Institute, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA
| | | | | | | | - Julian Lange
- Whitehead Institute, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | | | - Laura Brown
- Whitehead Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA
| | - Sidaly Phou
- Whitehead Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA
| | - Ashley Buscetta
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paul Kruszka
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicole Banks
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA; Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amalia Dutra
- Cytogenetics and Microscopy Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Evgenia Pak
- Cytogenetics and Microscopy Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | | | - Shanlee M Davis
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Angela E Lin
- Medical Genetics, Massachusetts General for Children, Boston, MA 02114, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Nicole R Tartaglia
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA; Developmental Pediatrics, eXtraOrdinarY Kids Program, Children's Hospital Colorado, Aurora, CO 80011, USA
| | - Carole Samango-Sprouse
- Focus Foundation, Davidsonville, MD 21035, USA; Department of Pediatrics, George Washington University, Washington, DC 20052, USA; Department of Human and Molecular Genetics, Florida International University, Miami, FL 33199, USA
| | - Maximilian Muenke
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David C Page
- Whitehead Institute, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA.
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2
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Detera-Wadleigh SD, Kassem L, Besancon E, Lopes F, Akula N, Sung H, Blattner M, Sheridan L, Lacbawan LN, Garcia J, Gordovez F, Hosey K, Donner C, Salvini C, Schulze T, Chen DTW, England B, Cross J, Jiang X, Corona W, Russ J, Mallon B, Dutra A, Pak E, Steiner J, Malik N, de Guzman T, Horato N, Mallmann MB, Mendes V, Dűck AL, Nardi AE, McMahon FJ. A resource of induced pluripotent stem cell (iPSC) lines including clinical, genomic, and cellular data from genetically isolated families with mood and psychotic disorders. Transl Psychiatry 2023; 13:397. [PMID: 38104115 PMCID: PMC10725500 DOI: 10.1038/s41398-023-02641-w] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 10/05/2023] [Accepted: 10/30/2023] [Indexed: 12/19/2023] Open
Abstract
Genome-wide (GWAS) and copy number variant (CNV) association studies have reproducibly identified numerous risk alleles associated with bipolar disorder (BD), major depressive disorder (MDD), and schizophrenia (SCZ), but biological characterization of these alleles lags gene discovery, owing to the inaccessibility of live human brain cells and inadequate animal models for human psychiatric conditions. Human-derived induced pluripotent stem cells (iPSCs) provide a renewable cellular reagent that can be differentiated into living, disease-relevant cells and 3D brain organoids carrying the full complement of genetic variants present in the donor germline. Experimental studies of iPSC-derived cells allow functional characterization of risk alleles, establishment of causal relationships between genes and neurobiology, and screening for novel therapeutics. Here we report the creation and availability of an iPSC resource comprising clinical, genomic, and cellular data obtained from genetically isolated families with BD and related conditions. Results from the first 324 study participants, 61 of whom have validated pluripotent clones, show enrichment of rare single nucleotide variants and CNVs overlapping many known risk genes and pathogenic CNVs. This growing iPSC resource is available to scientists pursuing functional genomic studies of BD and related conditions.
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Affiliation(s)
- Sevilla D Detera-Wadleigh
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA.
| | - Layla Kassem
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA.
| | - Emily Besancon
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - Fabiana Lopes
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
- Laboratorio de Panico e Respiracao, Instituto de Psiquiatria, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 22410-003, Brazil
- Department of Psychiatry and Human Behavior, Alpert Medical School of Brown University, Providence, RI, 02903, USA
| | - Nirmala Akula
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - Heejong Sung
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - Meghan Blattner
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - Laura Sheridan
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - Ley Nadine Lacbawan
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - Joshua Garcia
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - Francis Gordovez
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - Katherine Hosey
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - Cassandra Donner
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - Claudio Salvini
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
- Laboratorio de Panico e Respiracao, Instituto de Psiquiatria, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 22410-003, Brazil
| | - Thomas Schulze
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
- Institute of Psychiatric Phenomics and Genomics, LMU Munich, 80336, München, Germany
- Department of Psychiatry and Behavioral Sciences, Upstate University Hospital, Syracuse, NY, 13210, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - David T W Chen
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - Bryce England
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - Joanna Cross
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - Xueying Jiang
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - Winston Corona
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - Jill Russ
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - Barbara Mallon
- Center for Scientific Review, Neurotechnology and Vision Branch, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Amalia Dutra
- Cytogenetics and Microscopy Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Evgenia Pak
- Cytogenetics and Microscopy Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Joe Steiner
- Neurotherapeutics Development Unit, NINDS, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Nasir Malik
- Neurotherapeutics Development Unit, NINDS, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Theresa de Guzman
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - Natia Horato
- Laboratorio de Panico e Respiracao, Instituto de Psiquiatria, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 22410-003, Brazil
| | - Mariana B Mallmann
- Laboratorio de Panico e Respiracao, Instituto de Psiquiatria, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 22410-003, Brazil
| | - Victoria Mendes
- Laboratorio de Panico e Respiracao, Instituto de Psiquiatria, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 22410-003, Brazil
| | - Amanda L Dűck
- Laboratorio de Panico e Respiracao, Instituto de Psiquiatria, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 22410-003, Brazil
| | - Antonio E Nardi
- Laboratorio de Panico e Respiracao, Instituto de Psiquiatria, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 22410-003, Brazil
| | - Francis J McMahon
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
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3
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Makova KD, Pickett BD, Harris RS, Hartley GA, Cechova M, Pal K, Nurk S, Yoo D, Li Q, Hebbar P, McGrath BC, Antonacci F, Aubel M, Biddanda A, Borchers M, Bomberg E, Bouffard GG, Brooks SY, Carbone L, Carrel L, Carroll A, Chang PC, Chin CS, Cook DE, Craig SJ, de Gennaro L, Diekhans M, Dutra A, Garcia GH, Grady PG, Green RE, Haddad D, Hallast P, Harvey WT, Hickey G, Hillis DA, Hoyt SJ, Jeong H, Kamali K, Kosakovsky Pond SL, LaPolice TM, Lee C, Lewis AP, Loh YHE, Masterson P, McCoy RC, Medvedev P, Miga KH, Munson KM, Pak E, Paten B, Pinto BJ, Potapova T, Rhie A, Rocha JL, Ryabov F, Ryder OA, Sacco S, Shafin K, Shepelev VA, Slon V, Solar SJ, Storer JM, Sudmant PH, Sweetalana, Sweeten A, Tassia MG, Thibaud-Nissen F, Ventura M, Wilson MA, Young AC, Zeng H, Zhang X, Szpiech ZA, Huber CD, Gerton JL, Yi SV, Schatz MC, Alexandrov IA, Koren S, O’Neill RJ, Eichler E, Phillippy AM. The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes. bioRxiv 2023:2023.11.30.569198. [PMID: 38077089 PMCID: PMC10705393 DOI: 10.1101/2023.11.30.569198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
Apes possess two sex chromosomes-the male-specific Y and the X shared by males and females. The Y chromosome is crucial for male reproduction, with deletions linked to infertility. The X chromosome carries genes vital for reproduction and cognition. Variation in mating patterns and brain function among great apes suggests corresponding differences in their sex chromosome structure and evolution. However, due to their highly repetitive nature and incomplete reference assemblies, ape sex chromosomes have been challenging to study. Here, using the state-of-the-art experimental and computational methods developed for the telomere-to-telomere (T2T) human genome, we produced gapless, complete assemblies of the X and Y chromosomes for five great apes (chimpanzee, bonobo, gorilla, Bornean and Sumatran orangutans) and a lesser ape, the siamang gibbon. These assemblies completely resolved ampliconic, palindromic, and satellite sequences, including the entire centromeres, allowing us to untangle the intricacies of ape sex chromosome evolution. We found that, compared to the X, ape Y chromosomes vary greatly in size and have low alignability and high levels of structural rearrangements. This divergence on the Y arises from the accumulation of lineage-specific ampliconic regions and palindromes (which are shared more broadly among species on the X) and from the abundance of transposable elements and satellites (which have a lower representation on the X). Our analysis of Y chromosome genes revealed lineage-specific expansions of multi-copy gene families and signatures of purifying selection. In summary, the Y exhibits dynamic evolution, while the X is more stable. Finally, mapping short-read sequencing data from >100 great ape individuals revealed the patterns of diversity and selection on their sex chromosomes, demonstrating the utility of these reference assemblies for studies of great ape evolution. These complete sex chromosome assemblies are expected to further inform conservation genetics of nonhuman apes, all of which are endangered species.
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Affiliation(s)
| | - Brandon D. Pickett
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Monika Cechova
- University of California Santa Cruz, Santa Cruz, CA, USA
| | - Karol Pal
- Penn State University, University Park, PA, USA
| | - Sergey Nurk
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - DongAhn Yoo
- University of Washington School of Medicine, Seattle, WA, USA
| | - Qiuhui Li
- Johns Hopkins University, Baltimore, MD, USA
| | - Prajna Hebbar
- University of California Santa Cruz, Santa Cruz, CA, USA
| | | | | | | | | | | | - Erich Bomberg
- University of Münster, Münster, Germany
- MPI for Developmental Biology, Tübingen, Germany
| | - Gerard G. Bouffard
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Shelise Y. Brooks
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lucia Carbone
- Oregon Health & Science University, Portland, OR, USA
- Oregon National Primate Research Center, Hillsboro, OR, USA
| | - Laura Carrel
- Penn State University School of Medicine, Hershey, PA, USA
| | | | | | - Chen-Shan Chin
- Foundation of Biological Data Sciences, Belmont, CA, USA
| | | | | | | | - Mark Diekhans
- University of California Santa Cruz, Santa Cruz, CA, USA
| | - Amalia Dutra
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gage H. Garcia
- University of Washington School of Medicine, Seattle, WA, USA
| | | | | | - Diana Haddad
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Pille Hallast
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Glenn Hickey
- University of California Santa Cruz, Santa Cruz, CA, USA
| | - David A. Hillis
- University of California Santa Barbara, Santa Barbara, CA, USA
| | | | - Hyeonsoo Jeong
- University of Washington School of Medicine, Seattle, WA, USA
| | | | | | | | - Charles Lee
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | | | - Patrick Masterson
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Karen H. Miga
- University of California Santa Cruz, Santa Cruz, CA, USA
| | | | - Evgenia Pak
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Benedict Paten
- University of California Santa Cruz, Santa Cruz, CA, USA
| | | | | | - Arang Rhie
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Fedor Ryabov
- Masters Program in National Research University Higher School of Economics, Moscow, Russia
| | | | - Samuel Sacco
- University of California Santa Cruz, Santa Cruz, CA, USA
| | | | | | | | - Steven J. Solar
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Sweetalana
- Penn State University, University Park, PA, USA
| | - Alex Sweeten
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Johns Hopkins University, Baltimore, MD, USA
| | | | - Françoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Alice C. Young
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Xinru Zhang
- Penn State University, University Park, PA, USA
| | | | | | | | - Soojin V. Yi
- University of California Santa Barbara, Santa Barbara, CA, USA
| | | | | | - Sergey Koren
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Evan Eichler
- University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Adam M. Phillippy
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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4
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Sendell-Price AT, Tulenko FJ, Pettersson M, Kang D, Montandon M, Winkler S, Kulb K, Naylor GP, Phillippy A, Fedrigo O, Mountcastle J, Balacco JR, Dutra A, Dale RE, Haase B, Jarvis ED, Myers G, Burgess SM, Currie PD, Andersson L, Schartl M. Low mutation rate in epaulette sharks is consistent with a slow rate of evolution in sharks. Nat Commun 2023; 14:6628. [PMID: 37857613 PMCID: PMC10587355 DOI: 10.1038/s41467-023-42238-x] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 10/03/2023] [Indexed: 10/21/2023] Open
Abstract
Sharks occupy diverse ecological niches and play critical roles in marine ecosystems, often acting as apex predators. They are considered a slow-evolving lineage and have been suggested to exhibit exceptionally low cancer rates. These two features could be explained by a low nuclear mutation rate. Here, we provide a direct estimate of the nuclear mutation rate in the epaulette shark (Hemiscyllium ocellatum). We generate a high-quality reference genome, and resequence the whole genomes of parents and nine offspring to detect de novo mutations. Using stringent criteria, we estimate a mutation rate of 7×10-10 per base pair, per generation. This represents one of the lowest directly estimated mutation rates for any vertebrate clade, indicating that this basal vertebrate group is indeed a slowly evolving lineage whose ability to restore genetic diversity following a sustained population bottleneck may be hampered by a low mutation rate.
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Affiliation(s)
- Ashley T Sendell-Price
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE75123, Uppsala, Sweden
- Bioinformatics Research Technology Platform, University of Warwick, Coventry, UK
| | - Frank J Tulenko
- Australian Regenerative Medicine Institute, Monash University, Victoria, 3800, Australia
| | - Mats Pettersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE75123, Uppsala, Sweden
| | - Du Kang
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX, 78666, USA
| | - Margo Montandon
- Australian Regenerative Medicine Institute, Monash University, Victoria, 3800, Australia
| | - Sylke Winkler
- Max-Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
| | - Kathleen Kulb
- Max-Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
| | - Gavin P Naylor
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Adam Phillippy
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health Bethesda, Bethesda, MD, 20892, USA
| | - Olivier Fedrigo
- Vertebrate Genome Laboratory, Rockefeller University, New York, NY, 10065, USA
| | - Jacquelyn Mountcastle
- Research Center for Genomic and Computational Biology, Duke University, Durham, NC, 27708, USA
| | - Jennifer R Balacco
- Research Center for Genomic and Computational Biology, Duke University, Durham, NC, 27708, USA
| | - Amalia Dutra
- Cytogenetics and Microscopy Core, National Human Genome Research Institute, National Institutes of Health Bethesda, Bethesda, MD, 20892, USA
| | - Rebecca E Dale
- Australian Regenerative Medicine Institute, Monash University, Victoria, 3800, Australia
| | - Bettina Haase
- Vertebrate Genome Laboratory, Rockefeller University, New York, NY, 10065, USA
| | - Erich D Jarvis
- Vertebrate Genome Laboratory, Rockefeller University, New York, NY, 10065, USA
| | - Gene Myers
- Max-Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
- Center of Systems Biology Dresden, 01307, Dresden, Germany
| | - Shawn M Burgess
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health Bethesda, Bethesda, MD, 20892, USA.
| | - Peter D Currie
- Australian Regenerative Medicine Institute, Monash University, Victoria, 3800, Australia.
- EMBL Australia, Victorian Node, Monash University, Clayton, Victoria, 3800, Australia.
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE75123, Uppsala, Sweden.
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX77483, USA.
| | - Manfred Schartl
- Developmental Biochemistry, Theodor-Boveri Institute, Biocenter, University of Würzburg, 97074, Würzburg, Germany.
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5
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San Roman AK, Skaletsky H, Godfrey AK, Bokil NV, Teitz L, Singh I, Blanton LV, Bellott DW, Pyntikova T, Lange J, Koutseva N, Hughes JF, Brown L, Phou S, Buscetta A, Kruszka P, Banks N, Dutra A, Pak E, Lasutschinkow PC, Keen C, Davis SM, Lin AE, Tartaglia NR, Samango-Sprouse C, Muenke M, Page DC. The human Y and inactive X chromosomes similarly modulate autosomal gene expression. bioRxiv 2023:2023.06.05.543763. [PMID: 37333288 PMCID: PMC10274745 DOI: 10.1101/2023.06.05.543763] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Somatic cells of human males and females have 45 chromosomes in common, including the "active" X chromosome. In males the 46th chromosome is a Y; in females it is an "inactive" X (Xi). Through linear modeling of autosomal gene expression in cells from individuals with zero to three Xi and zero to four Y chromosomes, we found that Xi and Y impact autosomal expression broadly and with remarkably similar effects. Studying sex-chromosome structural anomalies, promoters of Xi- and Y-responsive genes, and CRISPR inhibition, we traced part of this shared effect to homologous transcription factors - ZFX and ZFY - encoded by Chr X and Y. This demonstrates sex-shared mechanisms by which Xi and Y modulate autosomal expression. Combined with earlier analyses of sex-linked gene expression, our studies show that 21% of all genes expressed in lymphoblastoid cells or fibroblasts change expression significantly in response to Xi or Y chromosomes.
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Affiliation(s)
| | - Helen Skaletsky
- Whitehead Institute; Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Whitehead Institute; Cambridge, MA 02142, USA
| | - Alexander K. Godfrey
- Whitehead Institute; Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Neha V. Bokil
- Whitehead Institute; Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Levi Teitz
- Whitehead Institute; Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Isani Singh
- Whitehead Institute; Cambridge, MA 02142, USA
- Harvard Medical School, Boston, MA 02115, USA
| | | | | | | | - Julian Lange
- Whitehead Institute; Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | | | | | - Laura Brown
- Whitehead Institute; Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Whitehead Institute; Cambridge, MA 02142, USA
| | - Sidaly Phou
- Whitehead Institute; Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Whitehead Institute; Cambridge, MA 02142, USA
| | - Ashley Buscetta
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda; MD 20892, USA
| | - Paul Kruszka
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda; MD 20892, USA
| | - Nicole Banks
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda; MD 20892, USA
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health; Bethesda, MD 20892 USA
| | - Amalia Dutra
- Cytogenetics and Microscopy Core, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD 20892 USA
| | - Evgenia Pak
- Cytogenetics and Microscopy Core, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD 20892 USA
| | | | | | - Shanlee M. Davis
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Angela E. Lin
- Medical Genetics, Massachusetts General for Children, Boston, MA 02114, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Nicole R. Tartaglia
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Developmental Pediatrics, eXtraOrdinarY Kids Program, Children’s Hospital Colorado, Aurora, CO 80011, USA
| | - Carole Samango-Sprouse
- Focus Foundation, Davidsonville, MD 21035, USA
- Department of Pediatrics, George Washington University, Washington, DC 20052, USA; Department of Human and Molecular Genetics, Florida International University, Miami, FL 33199, USA
| | - Maximilian Muenke
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda; MD 20892, USA
| | - David C. Page
- Whitehead Institute; Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, Whitehead Institute; Cambridge, MA 02142, USA
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6
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Martinez NJ, Braisted JC, Dranchak PK, Moran JJ, Larson H, Queme B, Pak E, Dutra A, Rai G, Cheng KCC, Svaren J, Inglese J. Genome-Edited Coincidence and PMP22-HiBiT Fusion Reporter Cell Lines Enable an Artifact-Suppressive Quantitative High-Throughput Screening Strategy for PMP22 Gene-Dosage Disorder Drug Discovery. ACS Pharmacol Transl Sci 2021; 4:1422-1436. [PMID: 34423274 DOI: 10.1021/acsptsci.1c00110] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Indexed: 12/23/2022]
Abstract
Charcot-Marie-Tooth 1A (CMT1A) is the most common form of hereditary peripheral neuropathies, characterized by genetic duplication of the critical myelin gene Peripheral Myelin Protein 22 (PMP22). PMP22 overexpression results in abnormal Schwann cell differentiation, leading to axonal loss and muscle wasting. Since regulation of PMP22 expression is a major target of therapeutic discovery for CMT1A, we sought to establish unbiased approaches that allow the identification of therapeutic agents for this disease. Using genome editing, we generated a coincidence reporter assay that accurately monitors Pmp22 transcript levels in the S16 rat Schwann cell line, while reducing reporter-based false positives. A quantitative high-throughput screen (qHTS) of 42 577 compounds using this assay revealed diverse novel chemical classes that reduce endogenous Pmp22 transcript levels. Moreover, some of these classes show pharmacological specificity in reducing Pmp22 over another major myelin-associated gene, Mpz (Myelin protein zero). Finally, to investigate whether compound-mediated reduction of Pmp22 transcripts translates to reduced PMP22 protein levels, we edited the S16 genome to generate a reporter assay that expresses a PMP22-HiBiT fusion protein using CRISPR/Cas9. Overall, we present a screening platform that combines genome edited cell lines encoding reporters that monitor transcriptional and post-translational regulation of PMP22 with titration-based screening (e.g., qHTS), which could be efficiently incorporated into drug discovery campaigns for CMT1A.
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Affiliation(s)
- Natalia J Martinez
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - John C Braisted
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Patricia K Dranchak
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - John J Moran
- Department of Comparative Biosciences, and Waisman Center, University of Wisconsin, Madison, Wisconsin 53705, United States
| | - Hunter Larson
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Bryan Queme
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Evgenia Pak
- National Human Genome Research Institute, National Institute of Health, Bethesda, Maryland 20817, United States
| | - Amalia Dutra
- National Human Genome Research Institute, National Institute of Health, Bethesda, Maryland 20817, United States
| | - Ganesha Rai
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Ken Chih-Chien Cheng
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - John Svaren
- Department of Comparative Biosciences, and Waisman Center, University of Wisconsin, Madison, Wisconsin 53705, United States
| | - James Inglese
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States.,National Human Genome Research Institute, National Institute of Health, Bethesda, Maryland 20817, United States
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7
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Miga KH, Koren S, Rhie A, Vollger MR, Gershman A, Bzikadze A, Brooks S, Howe E, Porubsky D, Logsdon GA, Schneider VA, Potapova T, Wood J, Chow W, Armstrong J, Fredrickson J, Pak E, Tigyi K, Kremitzki M, Markovic C, Maduro V, Dutra A, Bouffard GG, Chang AM, Hansen NF, Wilfert AB, Thibaud-Nissen F, Schmitt AD, Belton JM, Selvaraj S, Dennis MY, Soto DC, Sahasrabudhe R, Kaya G, Quick J, Loman NJ, Holmes N, Loose M, Surti U, Risques RA, Graves Lindsay TA, Fulton R, Hall I, Paten B, Howe K, Timp W, Young A, Mullikin JC, Pevzner PA, Gerton JL, Sullivan BA, Eichler EE, Phillippy AM. Telomere-to-telomere assembly of a complete human X chromosome. Nature 2020; 585:79-84. [PMID: 32663838 PMCID: PMC7484160 DOI: 10.1038/s41586-020-2547-7] [Citation(s) in RCA: 390] [Impact Index Per Article: 97.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 05/29/2020] [Indexed: 12/15/2022]
Abstract
After two decades of improvements, the current human reference genome (GRCh38) is the most accurate and complete vertebrate genome ever produced. However, no single chromosome has been finished end to end, and hundreds of unresolved gaps persist1,2. Here we present a human genome assembly that surpasses the continuity of GRCh382, along with a gapless, telomere-to-telomere assembly of a human chromosome. This was enabled by high-coverage, ultra-long-read nanopore sequencing of the complete hydatidiform mole CHM13 genome, combined with complementary technologies for quality improvement and validation. Focusing our efforts on the human X chromosome3, we reconstructed the centromeric satellite DNA array (approximately 3.1 Mb) and closed the 29 remaining gaps in the current reference, including new sequences from the human pseudoautosomal regions and from cancer-testis ampliconic gene families (CT-X and GAGE). These sequences will be integrated into future human reference genome releases. In addition, the complete chromosome X, combined with the ultra-long nanopore data, allowed us to map methylation patterns across complex tandem repeats and satellite arrays. Our results demonstrate that finishing the entire human genome is now within reach, and the data presented here will facilitate ongoing efforts to complete the other human chromosomes.
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Affiliation(s)
- Karen H Miga
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA.
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mitchell R Vollger
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Ariel Gershman
- Department of Molecular Biology and Genetics, Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Andrey Bzikadze
- Graduate Program in Bioinformatics and Systems Biology, University of California San Diego, San Diego, CA, USA
| | - Shelise Brooks
- NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Rockville, MD, USA
| | - Edmund Howe
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Glennis A Logsdon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Valerie A Schneider
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Tamara Potapova
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | | | | | - Joel Armstrong
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | | | - Evgenia Pak
- Cytogenetic and Microscopy Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kristof Tigyi
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Milinn Kremitzki
- McDonnell Genome Institute at Washington University, St Louis, MO, USA
| | | | - Valerie Maduro
- Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Amalia Dutra
- Cytogenetic and Microscopy Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gerard G Bouffard
- NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Rockville, MD, USA
| | - Alexander M Chang
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Nancy F Hansen
- Comparative Genomics Analysis Unit, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Amy B Wilfert
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Françoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | | | | | | | - Megan Y Dennis
- Department of Biochemistry and Molecular Medicine, Genome Center, MIND Institute, University of California Davis, Davis, CA, USA
| | - Daniela C Soto
- Department of Biochemistry and Molecular Medicine, Genome Center, MIND Institute, University of California Davis, Davis, CA, USA
| | - Ruta Sahasrabudhe
- DNA Technologies Core, Genome Center, University of California Davis, Davis, CA, USA
| | - Gulhan Kaya
- Department of Biochemistry and Molecular Medicine, Genome Center, MIND Institute, University of California Davis, Davis, CA, USA
| | - Josh Quick
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Nicholas J Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Nadine Holmes
- DeepSeq, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Matthew Loose
- DeepSeq, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Urvashi Surti
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Rosa Ana Risques
- Department of Pathology, University of Washington, Seattle, WA, USA
| | | | - Robert Fulton
- McDonnell Genome Institute at Washington University, St Louis, MO, USA
| | - Ira Hall
- McDonnell Genome Institute at Washington University, St Louis, MO, USA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | | | - Winston Timp
- Department of Molecular Biology and Genetics, Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Alice Young
- NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Rockville, MD, USA
| | - James C Mullikin
- NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Rockville, MD, USA
| | - Pavel A Pevzner
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | | | - Beth A Sullivan
- Department of Molecular Genetics and Microbiology, Division of Human Genetics, Duke University Medical Center, Durham, NC, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
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8
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Serra-Vinardell J, Sandler MB, Pak E, Zheng W, Dutra A, Introne W, Gahl WA, Malicdan MC. Generation and characterization of four Chediak-Higashi Syndrome (CHS) induced pluripotent stem cell (iPSC) lines. Stem Cell Res 2020; 47:101883. [PMID: 32619719 DOI: 10.1016/j.scr.2020.101883] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/08/2020] [Accepted: 06/16/2020] [Indexed: 11/29/2022] Open
Abstract
Chediak-Higashi Syndrome (CHS) is a lysosome-related organelle (LRO) disorder caused by biallelic mutations in the lysosomal trafficking regulator gene, LYST. The clinical features of CHS include oculocutaneous albinism, primary immunodeficiency, bleeding diathesis, risk for development of hemophagocyticlymphohistiocytosis,and progressive neurological problems. The pathophysiological mechanisms underlying this disease are unknown, so developing therapeutic options remains challenging. In this study,four induced pluripotent stem (iPSC) lines from unrelated CHS patients have been generated and successfully characterized for exploring the role of LYST in health and disease in diversecell types.
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Affiliation(s)
- Jenny Serra-Vinardell
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Maxwell B Sandler
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Evgenia Pak
- Cytogenetics Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wei Zheng
- National Center for Advancing Translational Science, NIH, Rockville, MD 20850, USA
| | - Amalia Dutra
- Cytogenetics Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wendy Introne
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - William A Gahl
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA; Undiagnosed Diseases Program, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Common Fund, Office of the Director, NIH, Bethesda, MD 20892, USA
| | - May Christine Malicdan
- Undiagnosed Diseases Program, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Common Fund, Office of the Director, NIH, Bethesda, MD 20892, USA.
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9
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Lawlor N, Márquez EJ, Orchard P, Narisu N, Shamim MS, Thibodeau A, Varshney A, Kursawe R, Erdos MR, Kanke M, Gu H, Pak E, Dutra A, Russell S, Li X, Piecuch E, Luo O, Chines PS, Fuchbserger C, Sethupathy P, Aiden AP, Ruan Y, Aiden EL, Collins FS, Ucar D, Parker SCJ, Stitzel ML. Multiomic Profiling Identifies cis-Regulatory Networks Underlying Human Pancreatic β Cell Identity and Function. Cell Rep 2020; 26:788-801.e6. [PMID: 30650367 PMCID: PMC6389269 DOI: 10.1016/j.celrep.2018.12.083] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [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: 08/07/2018] [Revised: 10/26/2018] [Accepted: 12/18/2018] [Indexed: 12/22/2022] Open
Abstract
EndoC-βH1 is emerging as a critical human β cell model to study the genetic and environmental etiologies of β cell (dys)function and diabetes. Comprehensive knowledge of its molecular landscape is lacking, yet required, for effective use of this model. Here, we report chromosomal (spectral karyotyping), genetic (genotyping), epigenomic (ChIP-seq and ATAC-seq), chromatin interaction (Hi-C and Pol2 ChIA-PET), and transcriptomic (RNA-seq and miRNA-seq) maps of EndoC-βH1. Analyses of these maps define known (e.g., PDX1 and ISL1) and putative (e.g., PCSK1 and mir-375) β cell-specific transcriptional cis-regulatory networks and identify allelic effects on cis-regulatory element use. Importantly, comparison with maps generated in primary human islets and/or β cells indicates preservation of chromatin looping but also highlights chromosomal aberrations and fetal genomic signatures in EndoC-βH1. Together, these maps, and a web application we created for their exploration, provide important tools for the design of experiments to probe and manipulate the genetic programs governing β cell identity and (dys)function in diabetes. EndoC-βH1 is becoming an important cellular model to study genes and pathways governing human β cell identity and function, but its (epi)genomic similarity to primary human islets is unknown. Lawlor et al. complete and compare extensive EndoC and primary human islet multiomic maps to identify shared and distinct genomic circuitry.
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Affiliation(s)
- Nathan Lawlor
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Eladio J Márquez
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Peter Orchard
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Narisu Narisu
- National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Muhammad Saad Shamim
- Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA; Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Asa Thibodeau
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Arushi Varshney
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Romy Kursawe
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Michael R Erdos
- National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Matt Kanke
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Huiya Gu
- Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Evgenia Pak
- National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Amalia Dutra
- National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Sheikh Russell
- Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA
| | - Xingwang Li
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Emaly Piecuch
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Department of Genetics and Genome Sciences, University of Connecticut, Farmington, CT 06032, USA
| | - Oscar Luo
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Peter S Chines
- National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Christian Fuchbserger
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Praveen Sethupathy
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Aviva Presser Aiden
- Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Bioengineering, Rice University, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yijun Ruan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Erez Lieberman Aiden
- Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA; Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Francis S Collins
- National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Duygu Ucar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Department of Genetics and Genome Sciences, University of Connecticut, Farmington, CT 06032, USA; Institute for Systems Genomics, University of Connecticut, Farmington, CT 06032, USA
| | - Stephen C J Parker
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Michael L Stitzel
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Department of Genetics and Genome Sciences, University of Connecticut, Farmington, CT 06032, USA; Institute for Systems Genomics, University of Connecticut, Farmington, CT 06032, USA.
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10
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Pantera H, Moran JJ, Hung HA, Pak E, Dutra A, Svaren J. Regulation of the neuropathy-associated Pmp22 gene by a distal super-enhancer. Hum Mol Genet 2019; 27:2830-2839. [PMID: 29771329 DOI: 10.1093/hmg/ddy191] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 05/09/2018] [Indexed: 12/27/2022] Open
Abstract
Peripheral nerve myelination is adversely affected in the most common form of the hereditary peripheral neuropathy called Charcot-Marie-Tooth Disease. This form, classified as CMT1A, is caused by a 1.4 Mb duplication on chromosome 17, which includes the abundantly expressed Schwann cell myelin gene, Peripheral Myelin Protein 22 (PMP22). This is one of the most common copy number variants causing neurological disease. Overexpression of Pmp22 in rodent models recapitulates several aspects of neuropathy, and reduction of Pmp22 in such models results in amelioration of the neuropathy phenotype. Recently we identified a potential super-enhancer approximately 90-130 kb upstream of the Pmp22 transcription start sites. This super-enhancer encompasses a cluster of individual enhancers that have the acetylated histone H3K27 active enhancer mark, and coincides with smaller duplications identified in patients with milder CMT1A-like symptoms, where the PMP22 coding region itself was not part of the duplication. In this study, we have utilized genome editing to create a deletion of this super-enhancer to determine its role in Pmp22 regulation. Our data show a significant decrease in Pmp22 transcript expression using allele-specific internal controls. Moreover, the P2 promoter of the Pmp22 gene, which is used in other cell types, is affected, but we find that the Schwann cell-specific P1 promoter is disproportionately more sensitive to loss of the super-enhancer. These data show for the first time the requirement of these upstream enhancers for full Pmp22 expression.
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Affiliation(s)
- Harrison Pantera
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA.,Molecular and Cellular Pharmacology Graduate Program, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - John J Moran
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Holly A Hung
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Evgenia Pak
- Cytogenetics and Microscopy Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Amalia Dutra
- Cytogenetics and Microscopy Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - John Svaren
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA.,Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, WI 53705, USA
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11
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Westbroek W, Nguyen M, Siebert M, Lindstrom T, Burnett RA, Aflaki E, Jung O, Tamargo R, Rodriguez-Gil JL, Acosta W, Hendrix A, Behre B, Tayebi N, Fujiwara H, Sidhu R, Renvoise B, Ginns EI, Dutra A, Pak E, Cramer C, Ory DS, Pavan WJ, Sidransky E. A new glucocerebrosidase-deficient neuronal cell model provides a tool to probe pathophysiology and therapeutics for Gaucher disease. Dis Model Mech 2016; 9:769-78. [PMID: 27482815 PMCID: PMC4958308 DOI: 10.1242/dmm.024588] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 05/12/2016] [Indexed: 12/30/2022] Open
Abstract
Glucocerebrosidase is a lysosomal hydrolase involved in the breakdown of glucosylceramide. Gaucher disease, a recessive lysosomal storage disorder, is caused by mutations in the gene GBA1. Dysfunctional glucocerebrosidase leads to accumulation of glucosylceramide and glycosylsphingosine in various cell types and organs. Mutations in GBA1 are also a common genetic risk factor for Parkinson disease and related synucleinopathies. In recent years, research on the pathophysiology of Gaucher disease, the molecular link between Gaucher and Parkinson disease, and novel therapeutics, have accelerated the need for relevant cell models with GBA1 mutations. Although induced pluripotent stem cells, primary rodent neurons, and transfected neuroblastoma cell lines have been used to study the effect of glucocerebrosidase deficiency on neuronal function, these models have limitations because of challenges in culturing and propagating the cells, low yield, and the introduction of exogenous mutant GBA1. To address some of these difficulties, we established a high yield, easy-to-culture mouse neuronal cell model with nearly complete glucocerebrosidase deficiency representative of Gaucher disease. We successfully immortalized cortical neurons from embryonic null allele gba−/− mice and the control littermate (gba+/+) by infecting differentiated primary cortical neurons in culture with an EF1α-SV40T lentivirus. Immortalized gba−/− neurons lack glucocerebrosidase protein and enzyme activity, and exhibit a dramatic increase in glucosylceramide and glucosylsphingosine accumulation, enlarged lysosomes, and an impaired ATP-dependent calcium-influx response; these phenotypical characteristics were absent in gba+/+ neurons. This null allele gba−/− mouse neuronal model provides a much-needed tool to study the pathophysiology of Gaucher disease and to evaluate new therapies. Summary: This work describes the generation of a novel immortalized glucocerebrosidase-deficient neuronal cell model with utility for pathophysiology research and therapeutic development in Gaucher disease.
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Affiliation(s)
- Wendy Westbroek
- Section on Molecular Neurogenetics, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Matthew Nguyen
- Section on Molecular Neurogenetics, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Marina Siebert
- Section on Molecular Neurogenetics, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA Postgraduate Program in Cellular and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91501-970, Brazil
| | - Taylor Lindstrom
- Section on Molecular Neurogenetics, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Robert A Burnett
- Section on Molecular Neurogenetics, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Elma Aflaki
- Section on Molecular Neurogenetics, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Olive Jung
- Section on Molecular Neurogenetics, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rafael Tamargo
- Section on Molecular Neurogenetics, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jorge L Rodriguez-Gil
- Genomics, Development, and Disease Section, Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - An Hendrix
- Laboratory of Experimental Cancer Research, Department of Radiation Oncology and Experimental Cancer Research, Ghent University Hospital, Ghent 9000, Belgium
| | - Bahafta Behre
- Section on Molecular Neurogenetics, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nahid Tayebi
- Section on Molecular Neurogenetics, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hideji Fujiwara
- Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Rohini Sidhu
- Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Benoit Renvoise
- Cell Biology Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Edward I Ginns
- Lysosomal Disorders Treatment and Research Program, Clinical Labs, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Amalia Dutra
- Cytogenetics Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Evgenia Pak
- Cytogenetics Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Daniel S Ory
- Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - William J Pavan
- Genomics, Development, and Disease Section, Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ellen Sidransky
- Section on Molecular Neurogenetics, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
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12
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Pathak A, Pemov A, McMaster ML, Dewan R, Ravichandran S, Pak E, Dutra A, Lee HJ, Vogt A, Zhang X, Yeager M, Anderson S, Kirby M, Caporaso N, Greene MH, Goldin LR, Stewart DR. Juvenile myelomonocytic leukemia due to a germline CBL Y371C mutation: 35-year follow-up of a large family. Hum Genet 2015; 134:775-87. [PMID: 25939664 DOI: 10.1007/s00439-015-1550-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 04/05/2015] [Indexed: 12/11/2022]
Abstract
Juvenile myelomonocytic leukemia (JMML) is a pediatric myeloproliferative neoplasm that arises from malignant transformation of the stem cell compartment and results in increased production of myeloid cells. Somatic and germline variants in CBL (Casitas B-lineage lymphoma proto-oncogene) have been associated with JMML. We report an incompletely penetrant CBL Y371C mutation discovered by whole-exome sequencing in three individuals with JMML in a large pedigree with 35 years of follow-up. The Y371 residue is highly evolutionarily conserved among CBL orthologs and paralogs. In silico bioinformatics prediction programs suggested that the Y371C mutation is highly deleterious. Protein structural modeling revealed that the Y371C mutation abrogated the ability of the CBL protein to adopt a conformation that is required for ubiquitination. Clinically, the three mutation-positive JMML individuals exhibited variable clinical courses; in two out of three, primary hematologic abnormalities persisted into adulthood with minimal clinical symptoms. The penetrance of the CBL Y371C mutation was 30% for JMML and 40% for all leukemia. Of the 8 mutation carriers in the family with available photographs, only one had significant dysmorphic features; we found no evidence of a clinical phenotype consistent with a "CBL syndrome". Although CBL Y371C has been previously reported in familial JMML, we are the first group to follow a complete pedigree harboring this mutation for an extended period, revealing additional information about this variant's penetrance, function and natural history.
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Affiliation(s)
- Anand Pathak
- Division of Cancer Epidemiology and Genetics, Clinical Genetics Branch, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive Rm 6E450, Bethesda, MD, 20892, USA,
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13
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Aflaki E, Stubblefield BK, Maniwang E, Lopez G, Moaven N, Goldin E, Marugan J, Patnaik S, Dutra A, Southall N, Zheng W, Tayebi N, Sidransky E. Macrophage models of Gaucher disease for evaluating disease pathogenesis and candidate drugs. Sci Transl Med 2015; 6:240ra73. [PMID: 24920659 DOI: 10.1126/scitranslmed.3008659] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Gaucher disease is caused by an inherited deficiency of glucocerebrosidase that manifests with storage of glycolipids in lysosomes, particularly in macrophages. Available cell lines modeling Gaucher disease do not demonstrate lysosomal storage of glycolipids; therefore, we set out to develop two macrophage models of Gaucher disease that exhibit appropriate substrate accumulation. We used these cellular models both to investigate altered macrophage biology in Gaucher disease and to evaluate candidate drugs for its treatment. We generated and characterized monocyte-derived macrophages from 20 patients carrying different Gaucher disease mutations. In addition, we created induced pluripotent stem cell (iPSC)-derived macrophages from five fibroblast lines taken from patients with type 1 or type 2 Gaucher disease. Macrophages derived from patient monocytes or iPSCs showed reduced glucocerebrosidase activity and increased storage of glucocerebroside and glucosylsphingosine in lysosomes. These macrophages showed efficient phagocytosis of bacteria but reduced production of intracellular reactive oxygen species and impaired chemotaxis. The disease phenotype was reversed with a noninhibitory small-molecule chaperone drug that enhanced glucocerebrosidase activity in the macrophages, reduced glycolipid storage, and normalized chemotaxis and production of reactive oxygen species. Macrophages differentiated from patient monocytes or patient-derived iPSCs provide cellular models that can be used to investigate disease pathogenesis and facilitate drug development.
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Affiliation(s)
- Elma Aflaki
- Section on Molecular Neurogenetics, Medical Genetics Branch, National Institutes of Health, Bethesda, MD 20892, USA
| | - Barbara K Stubblefield
- Section on Molecular Neurogenetics, Medical Genetics Branch, National Institutes of Health, Bethesda, MD 20892, USA
| | - Emerson Maniwang
- Section on Molecular Neurogenetics, Medical Genetics Branch, National Institutes of Health, Bethesda, MD 20892, USA
| | - Grisel Lopez
- Section on Molecular Neurogenetics, Medical Genetics Branch, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nima Moaven
- Section on Molecular Neurogenetics, Medical Genetics Branch, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ehud Goldin
- Section on Molecular Neurogenetics, Medical Genetics Branch, National Institutes of Health, Bethesda, MD 20892, USA
| | - Juan Marugan
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Samarjit Patnaik
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Amalia Dutra
- Cytogenetics and Microscopy Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Noel Southall
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Wei Zheng
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Nahid Tayebi
- Section on Molecular Neurogenetics, Medical Genetics Branch, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ellen Sidransky
- Section on Molecular Neurogenetics, Medical Genetics Branch, National Institutes of Health, Bethesda, MD 20892, USA.
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14
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Ito S, Barrett AJ, Dutra A, Pak E, Miner S, Keyvanfar K, Hensel NF, Rezvani K, Muranski P, Liu P, Larochelle A, Melenhorst JJ. Long term maintenance of myeloid leukemic stem cells cultured with unrelated human mesenchymal stromal cells. Stem Cell Res 2014; 14:95-104. [PMID: 25535865 DOI: 10.1016/j.scr.2014.11.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 11/20/2014] [Accepted: 11/29/2014] [Indexed: 02/02/2023] Open
Abstract
Mesenchymal stromal cells (MSCs) support the growth and differentiation of normal hematopoietic stem cells (HSCs). Here we studied the ability of MSCs to support the growth and survival of leukemic stem cells (LSCs) in vitro. Primary leukemic blasts isolated from the peripheral blood of 8 patients with acute myeloid leukemia (AML) were co-cultured with equal numbers of irradiated MSCs derived from unrelated donor bone marrow, with or without cytokines for up to 6weeks. Four samples showed CD34(+)CD38(-) predominance, and four were predominantly CD34(+)CD38(+). CD34(+) CD38(-) predominant leukemia cells maintained the CD34(+) CD38(-) phenotype and were viable for 6weeks when co-cultured with MSCs compared to co-cultures with cytokines or medium only, which showed rapid differentiation and loss of the LSC phenotype. In contrast, CD34(+) CD38(+) predominant leukemic cells maintained the CD34(+)CD38(+) phenotype when co-cultured with MSCs alone, but no culture conditions supported survival beyond 4weeks. Cell cycle analysis showed that MSCs maintained a higher proportion of CD34(+) blasts in G0 than leukemic cells cultured with cytokines. AML blasts maintained in culture with MSCs for up to 6weeks engrafted NSG mice with the same efficiency as their non-cultured counterparts, and the original karyotype persisted after co-culture. Chemosensitivity and transwell assays suggest that MSCs provide pro-survival benefits to leukemic blasts through cell-cell contact. We conclude that MSCs support long-term maintenance of LSCs in vitro. This simple and inexpensive approach will facilitate basic investigation of LSCs and enable screening of novel therapeutic agents targeting LSCs.
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Affiliation(s)
- Sawa Ito
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - A John Barrett
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amalia Dutra
- Cytogenetics and Microscopy Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Evgenia Pak
- Cytogenetics and Microscopy Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Samantha Miner
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Keyvan Keyvanfar
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nancy F Hensel
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Katayoun Rezvani
- University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Pawel Muranski
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paul Liu
- Oncogenesis and Development Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Andre Larochelle
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - J Joseph Melenhorst
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
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15
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Sangaré M, Hendrickson B, Sango HA, Chen K, Nofziger J, Amara A, Dutra A, Schindler AB, Guindo A, Traoré M, Harmison G, Pak E, Yaro FN, Bricceno K, Grunseich C, Chen G, Boehm M, Zukosky K, Bocoum N, Meilleur KG, Daou F, Bagayogo K, Coulibaly YI, Diakité M, Fay MP, Lee HS, Saad A, Gribaa M, Singleton AB, Maiga Y, Auh S, Landouré G, Fairhurst RM, Burnett BG, Scholl T, Fischbeck KH. Genetics of low spinal muscular atrophy carrier frequency in sub-Saharan Africa. Ann Neurol 2014; 75:525-32. [PMID: 24515897 PMCID: PMC4112719 DOI: 10.1002/ana.24114] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 01/27/2014] [Accepted: 01/30/2014] [Indexed: 12/14/2022]
Abstract
Objective Spinal muscular atrophy (SMA) is one of the most common severe hereditary diseases of infancy and early childhood in North America, Europe, and Asia. SMA is usually caused by deletions of the survival motor neuron 1 (SMN1) gene. A closely related gene, SMN2, modifies the disease severity. SMA carriers have only 1 copy of SMN1 and are relatively common (1 in 30–50) in populations of European and Asian descent. SMN copy numbers and SMA carrier frequencies have not been reliably estimated in Malians and other sub‐Saharan Africans. Methods We used a quantitative polymerase chain reaction assay to determine SMN1 and SMN2 copy numbers in 628 Malians, 120 Nigerians, and 120 Kenyans. We also explored possible mechanisms for SMN1 and SMN2 copy number differences in Malians, and investigated their effects on SMN mRNA and protein levels. Results The SMA carrier frequency in Malians is 1 in 209, lower than in Eurasians. Malians and other sub‐Saharan Africans are more likely to have ≥3 copies of SMN1 than Eurasians, and more likely to lack SMN2 than Europeans. There was no evidence of gene conversion, gene locus duplication, or natural selection from malaria resistance to account for the higher SMN1 copy numbers in Malians. High SMN1 copy numbers were not associated with increased SMN mRNA or protein levels in human cell lines. Interpretation SMA carrier frequencies are much lower in sub‐Saharan Africans than in Eurasians. This finding is important to consider in SMA genetic counseling in individuals with black African ancestry. Ann Neurol 2014;75:525–532
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Affiliation(s)
- Modibo Sangaré
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD; Institute of Biomedical Sciences, George Washington University, Washington, DC
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16
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Auer DR, Sysa-Shah P, Bedja D, Simmers JL, Pak E, Dutra A, Cohn R, Gabrielson KL, Chakravarti A, Kapoor A. Generation of a cre recombinase-conditional Nos1ap over-expression transgenic mouse. Biotechnol Lett 2014; 36:1179-85. [PMID: 24563304 DOI: 10.1007/s10529-014-1473-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 01/09/2014] [Indexed: 10/25/2022]
Abstract
Polymorphic non-coding variants at the NOS1AP locus have been associated with the common cardiac, metabolic and neurological traits and diseases. Although, in vitro gene targeting-based cellular and biochemical studies have shed some light on NOS1AP function in cardiac and neuronal tissue, to enhance our understanding of NOS1AP function in mammalian physiology and disease, we report the generation of cre recombinase-conditional Nos1ap over-expression transgenic mice (Nos1ap (Tg)). Conditional transgenic mice were generated by the pronuclear injection method and three independent, single-site, multiple copies integration event-based founder lines were selected. For heart-restricted over-expression, Nos1ap (Tg) mice were crossed with Mlc2v-cre and Nos1ap transcript over-expression was observed in left ventricles from Nos1ap (Tg); Mlc2v-cre F1 mice. We believe that with the potential of conditional over-expression, Nos1ap (Tg) mice will be a useful resource in studying NOS1AP function in various tissues under physiological and disease states.
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Affiliation(s)
- Dallas R Auer
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD, 21205, USA,
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17
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Punwani D, Gonzalez-Espinosa D, Comeau AM, Dutra A, Pak E, Puck J. Cellular calibrators to quantitate T-cell receptor excision circles (TRECs) in clinical samples. Mol Genet Metab 2012; 107:586-91. [PMID: 23062576 PMCID: PMC3483425 DOI: 10.1016/j.ymgme.2012.09.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 09/15/2012] [Accepted: 09/15/2012] [Indexed: 11/17/2022]
Abstract
T-cell receptor excision circles (TRECs) are circular DNA molecules formed during rearrangement of the T-cell receptor (TCR) genes during lymphocyte development. Copy number of the junctional portion of the δRec-ψJα TREC, assessed by quantitative PCR (qPCR) using DNA from dried blood spots (DBS), is a biomarker for newly formed T cells and absent or low numbers of TRECs indicate SCID (severe combined immunodeficiency) or T lymphocytopenia. No quantitation standard for TRECs exists. To permit comparison of TREC qPCR results with a reliable method for counting TRECs across different laboratories, we sought to construct a stable cell line containing a normal human chromosomal constitution and a single copy of the TREC junction sequence. A human EBV (Epstein Barr virus)-transformed B-cell line was transduced with a lentivirus encoding mCherry fluorescence, puromycin resistance and the δRec-ψJα TREC sequence. A TREC-EBV cell line, with each cell carrying a single lentiviral insertion was established, expanded and shown to have one TREC copy per diploid genome. Graded numbers of TREC-EBV cells added to aliquots of T lymphocyte depleted blood showed TREC copy number proportional to TREC-EBV cell number. TREC-EBV cells, therefore, constitute a reproducible cellular calibrator for TREC assays, useful for both population-based screening for severe combined immunodeficiency and evaluation of naïve T-cell production in clinical settings.
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Affiliation(s)
- Divya Punwani
- Dept. of Pediatrics, University of California San Francisco, San Francisco, CA 91413; USA
| | | | - Anne Marie Comeau
- New England Newborn Screening Program, Dept. of Pediatrics, University of Massachusetts Medical School, Worcester, MA 01610; USA
| | - Amalia Dutra
- National Human Genome Research Institute, NIH, Bethesda, MD 20892; USA
| | - Evgenia Pak
- National Human Genome Research Institute, NIH, Bethesda, MD 20892; USA
| | - Jennifer Puck
- Dept. of Pediatrics, University of California San Francisco, San Francisco, CA 91413; USA
- Corresponding author: Jennifer M. Puck, MD, UCSF Department of Pediatrics, Box 0519, 513 Parnassus Avenue, HSE 301A, San Francisco, CA 94143-0519,
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18
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Punwani D, Simon K, Choi Y, Dutra A, Gonzalez-Espinosa D, Pak E, Naradikian M, Song CH, Zhang J, Bodine DM, Puck JM. Transcription factor zinc finger and BTB domain 1 is essential for lymphocyte development. J Immunol 2012; 189:1253-64. [PMID: 22753936 PMCID: PMC3401355 DOI: 10.4049/jimmunol.1200623] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Absent T lymphocytes were unexpectedly found in homozygotes of a transgenic mouse from an unrelated project. T cell development did not progress beyond double-negative stage 1 thymocytes, resulting in a hypocellular, vestigial thymus. B cells were present, but NK cell number and B cell isotype switching were reduced. Transplantation of wild-type hematopoietic cells corrected the defect, which was traced to a deletion involving five contiguous genes at the transgene insertion site on chromosome 12C3. Complementation using bacterial artificial chromosome transgenesis implicated zinc finger BTB-POZ domain protein 1 (Zbtb1) in the immunodeficiency, confirming its role in T cell development and suggesting involvement in B and NK cell differentiation. Targeted disruption of Zbtb1 recapitulated the T(-)B(+)NK(-) SCID phenotype of the original transgenic animal. Knockouts for Zbtb1 had expanded populations of bone marrow hematopoietic stem cells and also multipotent and early lymphoid lineages, suggesting a differentiation bottleneck for common lymphoid progenitors. Expression of mRNA encoding Zbtb1, a predicted transcription repressor, was greatest in hematopoietic stem cells, thymocytes, and pre-B cells, highlighting its essential role in lymphoid development.
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MESH Headings
- Animals
- Cell Differentiation/genetics
- Cell Differentiation/immunology
- Hematopoietic Stem Cells/cytology
- Hematopoietic Stem Cells/immunology
- Hematopoietic Stem Cells/metabolism
- Lymphocyte Subsets/cytology
- Lymphocyte Subsets/immunology
- Lymphocyte Subsets/metabolism
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Mice, SCID
- Mice, Transgenic
- NIH 3T3 Cells
- Precursor Cells, B-Lymphoid/cytology
- Precursor Cells, B-Lymphoid/immunology
- Precursor Cells, B-Lymphoid/metabolism
- Precursor Cells, T-Lymphoid/cytology
- Precursor Cells, T-Lymphoid/immunology
- Precursor Cells, T-Lymphoid/metabolism
- RNA, Messenger/biosynthesis
- Repressor Proteins/deficiency
- Repressor Proteins/genetics
- Repressor Proteins/physiology
- Zinc Fingers/immunology
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Affiliation(s)
- Divya Punwani
- Dept. of Pediatrics, University of California San Francisco, San Francisco, CA 91413; USA
| | - Karen Simon
- National Human Genome Research Institute, NIH, Bethesda, MD 20892; USA
| | - Youngnim Choi
- Dept. of Oromaxillofacial Infection & Immunity, School of Dentistry, Seoul National University, Seoul, Korea 28 Yungun-dong, Jongno-gu, Seoul 110-74928
| | - Amalia Dutra
- National Human Genome Research Institute, NIH, Bethesda, MD 20892; USA
| | | | - Evgenia Pak
- National Human Genome Research Institute, NIH, Bethesda, MD 20892; USA
| | - Martin Naradikian
- Dept. of Pediatrics, University of California San Francisco, San Francisco, CA 91413; USA
- University of Pennsylvania, Philadelphia, Pennsylvania, PA 19104; USA
| | - Chang-Hwa Song
- Dept. of Pediatrics, University of California San Francisco, San Francisco, CA 91413; USA
- Dept. of Microbiology, College of Medicine, Chungnam National University, South Korea
| | - Jenny Zhang
- Dept. of Pediatrics, University of California San Francisco, San Francisco, CA 91413; USA
| | - David M. Bodine
- National Human Genome Research Institute, NIH, Bethesda, MD 20892; USA
| | - Jennifer M. Puck
- Dept. of Pediatrics, University of California San Francisco, San Francisco, CA 91413; USA
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19
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Stewart DR, Pemov A, Van Loo P, Beert E, Brems H, Sciot R, Claes K, Pak E, Dutra A, Lee CCR, Legius E. Mitotic recombination of chromosome arm 17q as a cause of loss of heterozygosity of NF1 in neurofibromatosis type 1-associated glomus tumors. Genes Chromosomes Cancer 2012; 51:429-37. [PMID: 22250039 DOI: 10.1002/gcc.21928] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Accepted: 12/12/2011] [Indexed: 12/16/2022] Open
Abstract
Neurofibromatosis type 1 (NF1) is a common, autosomal dominant, tumor-predisposition syndrome that arises secondary to mutations in NF1. Glomus tumors are painful benign tumors that originate from the glomus body in the fingers and toes due to biallelic inactivation of NF1. We karyotyped cultures from four previously reported and one new glomus tumor and hybridized tumor (and matching germline) DNA on Illumina HumanOmni1-Quad SNP arrays (≈ 1 × 10(6) SNPs). Two tumors displayed evidence of copy-neutral loss of heterozygosity of chromosome arm 17q not observed in the germline sample, consistent with a mitotic recombination event. One of these two tumors, NF1-G12, featured extreme polyploidy (near-tetraploidy, near-hexaploidy, or near-septaploidy) across all chromosomes. In the remaining four tumors, there were few cytogenetic abnormalities observed, and copy-number analysis was consistent with diploidy in all chromosomes. This is the first study of glomus tumors cytogenetics, to our knowledge, and the first to report biallelic inactivation of NF1 secondary to mitotic recombination of chromosome arm 17q in multiple NF1-associated glomus tumors. We have observed mitotic recombination in 22% of molecularly characterized NF1-associated glomus tumors, suggesting that it is a not uncommon mechanism in the reduction to homozygosity of the NF1 germline mutation in these tumors. In tumor NF1-G12, we hypothesize that mitotic recombination also "unmasked" (reduced to homozygosity) a hypomorphic germline allele in a gene on chromosome arm 17q associated with chromosomal instability, resulting in the extreme polyploidy.
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Affiliation(s)
- Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD 20852, USA.
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20
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Calvo KR, Vinh DC, Maric I, Wang W, Noel P, Stetler-Stevenson M, Arthur DC, Raffeld M, Dutra A, Pak E, Myung K, Hsu AP, Hickstein DD, Pittaluga S, Holland SM. Myelodysplasia in autosomal dominant and sporadic monocytopenia immunodeficiency syndrome: diagnostic features and clinical implications. Haematologica 2011; 96:1221-5. [PMID: 21508125 DOI: 10.3324/haematol.2011.041152] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
A novel, genetic immunodeficiency syndrome has been recently described, herein termed "MonoMAC". It is characterized by severe circulating monocytopenia, NK- and B-lymphocytopenia, severe infections with M. avium complex (MAC), and risk of progression to myelodysplasia/acute myelogenous leukemia. Detailed bone marrow analyses performed on 18 patients further define this disorder. The majority of patients had hypocellular marrows with reticulin fibrosis and multilineage dysplasia affecting the myeloid (72%), erythroid (83%) and megakaryocytic (100%) lineages. Cytogenetic abnormalities were present in 10 of 17 (59%). Despite B-lymphocytopenia, plasma cells were present but were abnormal (e.g. CD56(+)) in nearly half of cases. Increased T-cell large granular lymphocyte populations were present in 28% of patients. Chromosomal breakage studies, cell cycle checkpoint functions, and sequencing of TERT and K-RAS genes revealed no abnormalities. MonoMAC appears to be a unique, inherited syndrome of bone marrow failure. We describe distinctive bone marrow features to help in its recognition and diagnosis. (Clinicaltrials.gov identifiers: NCT00018044, NCT00923364, NCT01212055).
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Affiliation(s)
- Katherine R Calvo
- Hematology Section, Department of Laboratory Medicine, NIH Clinical Center, 10 Center Dr., Bethesda, MD 20892-1508, USA.
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21
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Kauvar EF, Hu P, Pineda-Alvarez DE, Solomon BD, Dutra A, Pak E, Blessing B, Proud V, Shanske AL, Stevens CA, Rosenfeld JA, Shaffer LG, Roessler E, Muenke M. Minimal evidence for a direct involvement of twisted gastrulation homolog 1 (TWSG1) gene in human holoprosencephaly. Mol Genet Metab 2011; 102:470-80. [PMID: 21227728 PMCID: PMC3152819 DOI: 10.1016/j.ymgme.2010.12.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2010] [Revised: 12/14/2010] [Accepted: 12/14/2010] [Indexed: 10/18/2022]
Abstract
Holoprosencephaly (HPE) is the most common disorder of human forebrain and facial development. Presently understood etiologies include both genetic and environmental factors, acting either alone, or more likely, in combination. The majority of patients without overt chromosomal abnormalities or recognizable associated syndromes have unidentified etiologies. A potential candidate gene, Twisted Gastrulation Homolog 1 (TWSG1), was previously suggested as a contributor to the complex genetics of human HPE based on (1) cytogenetic studies of patients with 18p deletions, (2) animal studies of TWSG1 deficient mice, and (3) the relationship of TWSG1 to bone morphogenetic protein (BMP) signaling, which modulates the primary pathway implicated in HPE, Sonic Hedgehog (SHH) signaling. Here we present the first analysis of a large cohort of patients with HPE for coding sequence variations in TWSG1. We also performed fine mapping of 18p for a subset of patients with partial 18p deletions. Surprisingly, minimal evidence for alterations of TWSG1 was found, suggesting that sequence alterations of TWSG1 are neither a common direct cause nor a frequent modifying factor for human HPE pathologies.
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Affiliation(s)
- Emily F. Kauvar
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Howard Hughes Medical Institute – National Institutes of Health Research Scholars Program, Bethesda, MD, USA
| | - Ping Hu
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Daniel E. Pineda-Alvarez
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Benjamin D. Solomon
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Amalia Dutra
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Evgenia Pak
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Brooke Blessing
- Division of Medical Genetics, Children’s Hospital of The King’s Daughters, Norfolk, VA, USA
| | - Virginia Proud
- Division of Medical Genetics, Children’s Hospital of The King’s Daughters, Norfolk, VA, USA
| | - Alan L. Shanske
- Center for Craniofacial Disorders, Children’s Hospital at Montefiore Medical Center, Bronx, NY, USA
| | - Cathy A. Stevens
- Department of Pediatrics, University of Tennessee College of Medicine, Chattanooga, TN, USA
| | | | | | - Erich Roessler
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Maximilian Muenke
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Corresponding author: Address: 35 Convent Drive, MSC 3717, Bldg 35, Rm 1B-203, Bethesda, MD, 20892-3717, USA. Tel: (301) 402-8167. Fax: (301) 480-7876. (M. Muenke)
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22
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Dutra A, Pak E, Wincovitch S, John K, Poirier MC, Olivero OA. Nuclear bud formation: a novel manifestation of Zidovudine genotoxicity. Cytogenet Genome Res 2010; 128:105-10. [PMID: 20407220 DOI: 10.1159/000298794] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Normal diploid somatic mammalian cell division generates 2 daughter cells as a result of a strict and well-controlled mitotic process. However, some defects during the progression of that process could generate an unbalanced distribution of chromosomes, aneuploidy and eventually, a malignant phenotype. Previous observations using a transgenic mouse model with diminished DNA repair capacity revealed the presence of nuclear buds (NBs) induced in vitro by the nucleoside analog zidovudine (Retrovir(R), 3'-azido-3'-deoxythymidine, AZT). Here we used bone marrow mesenchymal cells, taken from mice with the Xpa(-/-)Trp53(+/-) genotype, that were cultured and exposed to 0 and 100 muM AZT for 24 hours. Fixed and denatured cells were processed by fluorescence in situ hybridization (FISH) with whole chromosome painting probes used to identify chromosomes in cells growing on glass chamber slides (2 probes/slide). A variety of sizes and shapes of NBs were observed. Some NBs had a large connection with the main nucleus (>(1/4) of the NB diameter), others hada smaller connection (<(1/4) of the NB diameter), some were circular and positioned close to the nucleus, while some resided in the cytoplasm separated from the nucleus or connected by a thin chromatin strand. We had hypothesized that NBs would progress in the process of budding until separation occurred, but this was not proven by time-lapse photography studies performed for 20 hours. From 1,126 cells scored in the unexposed cultures, 10.39 % of cells carried NBs, while from 1,108 cells scored in the AZT-exposed cultures 29.16% of cells carried NBs (p = 0.001). In AZT-exposed cells there were a total of 322 NBs scored; 46.6% or 150 NBs contained positive signals for one or both probes used, while 53% or 172 NBs had no probe signal. In addition, FISH analysis showed no preferential localization of any chromosome within the NBs. Among the NBs that carried no probe signal, the presence of positive signals with inversion of DAPI imaging demonstrated centromeric content. It has been hypothesized that NBs occur as a result of expulsion of amplified DNA from the main nucleus; however, this data demonstrates that NBs may contain any chromosome, suggesting that NBs do not consist of just amplified DNA.
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Affiliation(s)
- A Dutra
- Cytogenetics and Microscopy Core, National Human Genome Research Institute, National Cancer Institute, NIH, Bethesda, MD 20892-4255, USA
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23
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Kauvar EF, Solomon BD, Curry CJR, van Essen AJ, Janssen N, Dutra A, Roessler E, Muenke M. Holoprosencephaly and agnathia spectrum: Presentation of two new patients and review of the literature. Am J Med Genet C Semin Med Genet 2010; 154C:158-69. [PMID: 20104613 DOI: 10.1002/ajmg.c.30235] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Holoprosencephaly (HPE), the most common developmental disorder of the human forebrain, is occasionally associated with the spectrum of agnathia, or virtual absence of the mandible. This condition results in a constellation of structural cerebral and craniofacial abnormalities. Here we present two new patients and review 30 patients from the literature with HPE and variants of agnathia. The majority of these patients are female and have the most severe forms of HPE, with cyclopia present more frequently than is usually observed in cohorts of patients with HPE. Also, many patients have additional clinical findings not typical in patients with classic HPE, particularly situs abnormalities. Recent animal studies suggest that the association of HPE and agnathia may relate to alterations in signaling from forebrain and foregut endoderm organizing centers and subsequent first pharyngeal arch development, although present models are inadequate to explain all of the clinical findings of this enigmatic human syndrome. Further research is required to better elucidate the causal and pathogenic basis of this association.
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Affiliation(s)
- Emily F Kauvar
- Medical Genetics Branch of the National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892-3717, USA
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24
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Sikdar N, Banerjee S, Lee KY, Wincovitch S, Pak E, Nakanishi K, Jasin M, Dutra A, Myung K. DNA damage responses by human ELG1 in S phase are important to maintain genomic integrity. Cell Cycle 2009; 8:3199-207. [PMID: 19755857 DOI: 10.4161/cc.8.19.9752] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Genomic integrity depends on DNA replication, recombination and repair, particularly in S phase. We demonstrate that a human homologue of yeast Elg1 plays an important role in S phase to preserve genomic stability. The level of ELG1 is induced during recovery from a variety of DNA damage. In response to DNA damage, ELG1 forms distinct foci at stalled DNA replication forks that are different from DNA double strand break foci. Targeted gene knockdown of ELG1 resulted in spontaneous foci formation of gamma-H2AX, 53BP1 and phosphorylated-ATM that mark chromosomal breaks. Abnormal chromosomes including fusions, inversions and hypersensitivity to DNA damaging agents were also observed in cells expressing low level of ELG1 by targeted gene knockdown. Knockdown of ELG1 by siRNA reduced homologous recombination frequency in the I-SceI induced double strand break-dependent assay. In contrast, spontaneous homologous recombination frequency and sister chromatin exchange rate were upregulated when ELG1 was silenced by shRNA. Taken together, we propose that ELG1 would be a new member of proteins involved in maintenance of genomic integrity.
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Affiliation(s)
- Nilabja Sikdar
- Genome Instability Section, Genetics and Molecular Biology Branch, National Institutes of Health, Bethesda, MD, USA
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25
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Washington AV, Gibot S, Acevedo I, Gattis J, Quigley L, Feltz R, De La Mota A, Schubert RL, Gomez-Rodriguez J, Cheng J, Dutra A, Pak E, Chertov O, Rivera L, Morales J, Lubkowski J, Hunter R, Schwartzberg PL, McVicar DW. TREM-like transcript-1 protects against inflammation-associated hemorrhage by facilitating platelet aggregation in mice and humans. J Clin Invest 2009; 119:1489-501. [PMID: 19436112 DOI: 10.1172/jci36175] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2008] [Accepted: 03/11/2009] [Indexed: 01/07/2023] Open
Abstract
Triggering receptor expressed on myeloid cells-like (TREM-like) transcript-1 (TLT-1), a type 1 single Ig domain orphan receptor specific to platelet and megakaryocyte alpha-granules, relocates to the platelet surface upon platelet stimulation. We found here that patients diagnosed with sepsis, in contrast to healthy individuals, had substantial levels of soluble TLT-1 (sTLT-1) in their plasma that correlated with the presence of disseminated intravascular coagulation. sTLT-1 bound to fibrinogen and augmented platelet aggregation in vitro. Furthermore, the cytoplasmic domain of TLT-1 could also bind ezrin/radixin/moesin family proteins, suggesting its ability to link fibrinogen to the platelet cytoskeleton. Accordingly, platelets of Treml1-/- mice failed to aggregate efficiently, extending tail-bleeding times. Lipopolysaccharide-treated Treml1-/- mice developed higher plasma levels of TNF and D-dimers than wild-type mice and were more likely to succumb during challenge. Finally, Treml1-/- mice were predisposed to hemorrhage associated with localized inflammatory lesions. Taken together, our findings suggest that TLT-1 plays a protective role during inflammation by dampening the inflammatory response and facilitating platelet aggregation at sites of vascular injury. Therefore, therapeutic modulation of TLT-1-mediated effects may provide clinical benefit to patients with hypercoagulatory conditions, including those associated with inflammation.
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Affiliation(s)
- A Valance Washington
- Laboratory of Anatomy and Cell Biology, Universidad Central del Caribe, Bayamón, Puerto Rico
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26
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Myung K, Banerjee S, Yang K, Sikdar N, Lee K, Cohn M, Wincovitch S, Pak E, Nakanishi K, Jasin M, Dutra A, D'Andrea A. Human ELG1 regulates the level of monoubiquitinated PCNA through interactions with PCNA, USP1, and polymerase η. FASEB J 2009. [DOI: 10.1096/fasebj.23.1_supplement.836.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | - Kailin Yang
- Radiation OncobolyHovard Medical SchoolBostonMA
| | | | | | - Martin Cohn
- Radiation OncobolyHovard Medical SchoolBostonMA
| | | | - Evgenia Pak
- Genetics and Molecular BiologyNHGRI, NIHBethesdaMD
| | - Koji Nakanishi
- Developmental Biology ProgramMemorial Sloan‐Kettering Cancer CenterNew YorkNY
| | - Maria Jasin
- Developmental Biology ProgramMemorial Sloan‐Kettering Cancer CenterNew YorkNY
| | - Amalia Dutra
- Genetics and Molecular BiologyNHGRI, NIHBethesdaMD
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27
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Tsipouri V, Schueler MG, Hu S, Dutra A, Pak E, Riethman H, Green ED. Comparative sequence analyses reveal sites of ancestral chromosomal fusions in the Indian muntjac genome. Genome Biol 2008; 9:R155. [PMID: 18957082 PMCID: PMC2760882 DOI: 10.1186/gb-2008-9-10-r155] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2008] [Revised: 10/15/2008] [Accepted: 10/28/2008] [Indexed: 01/22/2023] Open
Abstract
Comparative mapping and sequencing was used to characterize the sites of ancestral chromosomal fusions in the Indian muntjac genome. Background Indian muntjac (Muntiacus muntjak vaginalis) has an extreme mammalian karyotype, with only six and seven chromosomes in the female and male, respectively. Chinese muntjac (Muntiacus reevesi) has a more typical mammalian karyotype, with 46 chromosomes in both sexes. Despite this disparity, the two muntjac species are morphologically similar and can even interbreed to produce viable (albeit sterile) offspring. Previous studies have suggested that a series of telocentric chromosome fusion events involving telomeric and/or satellite repeats led to the extant Indian muntjac karyotype. Results We used a comparative mapping and sequencing approach to characterize the sites of ancestral chromosomal fusions in the Indian muntjac genome. Specifically, we screened an Indian muntjac bacterial artificial-chromosome library with a telomere repeat-specific probe. Isolated clones found by fluorescence in situ hybridization to map to interstitial regions on Indian muntjac chromosomes were further characterized, with a subset then subjected to shotgun sequencing. Subsequently, we isolated and sequenced overlapping clones extending from the ends of some of these initial clones; we also generated orthologous sequence from isolated Chinese muntjac clones. The generated Indian muntjac sequence has been analyzed for the juxtaposition of telomeric and satellite repeats and for synteny relationships relative to other mammalian genomes, including the Chinese muntjac. Conclusions The generated sequence data and comparative analyses provide a detailed genomic context for seven ancestral chromosome fusion sites in the Indian muntjac genome, which further supports the telocentric fusion model for the events leading to the unusual karyotypic differences among muntjac species.
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Affiliation(s)
- Vicky Tsipouri
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Bethesda, Maryland 20892, USA
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28
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Eckstrand K, Addington AM, Stromberg T, Merriman B, Miller R, Gochman P, Long R, Dutra A, Chen Z, Meltzer P, Nelson SF, Rapoport JL. Sex chromosome anomalies in childhood onset schizophrenia: an update. Mol Psychiatry 2008; 13:910-1. [PMID: 18800051 PMCID: PMC4316819 DOI: 10.1038/mp.2008.67] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Kristen Eckstrand
- Child Psychiatry Branch, National Institute of Mental Health, NIH, Bethesda, MD, USA
| | - Anjené M. Addington
- Child Psychiatry Branch, National Institute of Mental Health, NIH, Bethesda, MD, USA,To whom correspondence should be addressed.
| | - Thomas Stromberg
- Child Psychiatry Branch, National Institute of Mental Health, NIH, Bethesda, MD, USA
| | - Barry Merriman
- Department of Human Genetics, University of California, Los Angeles, CA, USA
| | - Rachel Miller
- Child Psychiatry Branch, National Institute of Mental Health, NIH, Bethesda, MD, USA
| | - Peter Gochman
- Child Psychiatry Branch, National Institute of Mental Health, NIH, Bethesda, MD, USA
| | - Robert Long
- Child Psychiatry Branch, National Institute of Mental Health, NIH, Bethesda, MD, USA
| | - Amalia Dutra
- Genetic Disease Research Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Zugen Chen
- Department of Human Genetics, University of California, Los Angeles, CA, USA
| | - Paul Meltzer
- Cancer Genetics Branch, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Stanley F. Nelson
- Department of Human Genetics, University of California, Los Angeles, CA, USA
| | - Judith L. Rapoport
- Child Psychiatry Branch, National Institute of Mental Health, NIH, Bethesda, MD, USA
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29
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Li L, Dutra A, Pak E, Labrie JE, Gerstein RM, Pandolfi PP, Recht LD, Ross AH. EGFRvIII expression and PTEN loss synergistically induce chromosomal instability and glial tumors. Neuro Oncol 2008; 11:9-21. [PMID: 18812521 DOI: 10.1215/15228517-2008-081] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Glioblastomas often show activation of epidermal growth factor receptor (EGFR) and loss of PTEN (phosphatase and tensin homolog deleted on chromosome 10) tumor suppressor, but it is not known if these two genetic lesions act together to transform cells. To answer this question, we infected PTEN-/- neural precursor cells with a retrovirus encoding EGFRvIII, which is a constitutively activated receptor. EGFRvIII PTEN-/- cells formed highly mitotic tumors with nuclear pleomorphism, necrotic areas, and glioblastoma markers. The transformed cells showed increased cell proliferation, centrosome amplification, colony formation in soft agar, self-renewal, expression of the stem cell marker CD133, and resistance to oxidative stress and ionizing radiation. The RAS/mitogen-activated protein kinase (ERK) and phosphoinositide 3-kinase/protein kinase B (PI3K/Akt) pathways were activated, and checkpoint kinase 1 (Chk1), the DNA damage regulator, was phosphorylated at S280 by Akt, suppressing Chk1 phosphorylation at S345 in response to ionizing irradiation. The PTEN-/- cells showed low levels of DNA damage in the absence of irradiation, which was increased by EGFRvIII expression. Finally, secondary changes occurred during tumor growth in mice. Cells from these tumors showed decreased tumor latencies and additional chromosomal aberrations. Most of these tumor lines showed translocations of mouse chromosome 15. Intracranial injections of one of these lines led to invasive, glial fibrillary acidic protein-positive, nestin-positive tumors. These results provide a molecular basis for the occurrence of these two genetic lesions in brain tumors and point to a role in induction of genomic instability.
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Affiliation(s)
- Li Li
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
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30
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Gómez-Rodríguez J, Washington V, Cheng J, Dutra A, Pak E, Liu P, McVicar DW, Schwartzberg PL. Advantages of q-PCR as a method of screening for gene targeting in mammalian cells using conventional and whole BAC-based constructs. Nucleic Acids Res 2008; 36:e117. [PMID: 18710883 PMCID: PMC2566865 DOI: 10.1093/nar/gkn523] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [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] [Indexed: 12/02/2022] Open
Abstract
We evaluate here the use of real-time quantitative PCR (q-PCR) as a method for screening for homologous recombinants generated in mammalian cells from either conventional gene-targeting constructs or whole BAC-based constructs. Using gene-targeted events at different loci, we show that q-PCR is a highly sensitive and accurate method for screening for conventional gene targeting that can reduce the number of clones requiring follow-up screening by Southern blotting. We further compared q-PCR to fluorescent in situ hybridization (FISH) for the detection of gene-targeting events using full-length BAC-based constructs designed to introduce mutations either into one gene or simultaneously into two adjacent genes. We find that although BAC-based constructs appeared to have high rates of homologous recombination when evaluated by FISH, screening by FISH was prone to false positives that were detected by q-PCR. Our results demonstrate the utility of q-PCR as a screening tool for gene targeting and further highlight potential problems with the use of whole BAC-based constructs for homologous recombination.
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Affiliation(s)
- Julio Gómez-Rodríguez
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
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31
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Matyakhina L, Bei TA, McWhinney SR, Pasini B, Cameron S, Gunawan B, Stergiopoulos SG, Boikos S, Muchow M, Dutra A, Pak E, Campo E, Cid MC, Gomez F, Gaillard RC, Assie G, Füzesi L, Baysal BE, Eng C, Carney JA, Stratakis CA. Genetics of carney triad: recurrent losses at chromosome 1 but lack of germline mutations in genes associated with paragangliomas and gastrointestinal stromal tumors. J Clin Endocrinol Metab 2007; 92:2938-43. [PMID: 17535989 DOI: 10.1210/jc.2007-0797] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.0] [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] [Indexed: 02/07/2023]
Abstract
CONTEXT Carney triad (CT) describes the association of paragangliomas (PGLs) with gastrointestinal stromal tumors (GISTs) and pulmonary chondromas. Inactivating mutations of the mitochondrial complex II succinate dehydrogenase (SDH) enzyme subunits SDHB, SDHC, and SDHD are found in PGLs, gain-of-function mutations of c-kit (KIT), and platelet-derived growth factor receptor A (PDGFRA) in GISTs. OBJECTIVE Our objective was to investigate the possibility that patients with CT and/or their tumors may harbor mutations of the SDHB, SDHC, SDHD, KIT, and PDGFRA genes and identify any other genetic alterations in CT tumors. DESIGN Three males and 34 females with CT were studied retrospectively. We sequenced the stated genes and performed comparative genomic hybridization on a total of 41 tumors. RESULTS No patient had coding sequence mutations of the investigated genes. Comparative genomic hybridization revealed a number of DNA copy number changes: losses dominated among benign lesions, there were an equal number of gains and losses in malignant lesions, and the average number of alterations in malignant tumors was higher compared with benign lesions. The most frequent and greatest contiguous change was 1q12-q21 deletion, a region that harbors the SDHC gene. Another frequent change was loss of 1p. Allelic losses of 1p and 1q were confirmed by fluorescent in situ hybridization and loss-of-heterozygosity studies. CONCLUSIONS We conclude that CT is not due to SDH-inactivating or KIT- and PDGFRA-activating mutations. GISTs and PGLs in CT are associated with chromosome 1 and other changes that appear to participate in tumor progression and point to their common genetic cause.
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Affiliation(s)
- Ludmila Matyakhina
- Section on Endocrinology and Genetics, Developmental Endocrinology Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
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32
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Rodriguez V, Chen Y, Elkahloun A, Dutra A, Pak E, Chandrasekharappa S. Chromosome 8 BAC array comparative genomic hybridization and expression analysis identify amplification and overexpression of TRMT12 in breast cancer. Genes Chromosomes Cancer 2007; 46:694-707. [PMID: 17440925 DOI: 10.1002/gcc.20454] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Genomic changes in chromosome 8 are commonly observed in breast cancer cell lines and tumors. To fine map such genomic changes by comparative genomic hybridization (CGH), a high resolution (100 kb) chromosome 8 array that can detect single copy changes was developed using Phi29 DNA polymerase amplified BAC (bacterial artificial chromosome) DNA. The BAC array CGH resolved the two known amplified regions (8q21 and 8q24) of a breast cancer cell line (SKBR3) into nine separate regions including six amplicons and three deleted regions, all of which were verified by Fluorescence in situ hybridization. The extent of the gain/loss for each region was validated by qPCR. CGH was performed with a total of 8 breast cancer cell lines, and common regions of genomic amplification/deletion were identified by segmentation analysis. A 1.2-Mb region (125.3-126.5 Mb) and a 1.0-Mb region (128.1-129.1 Mb) in 8q24 were amplified in 7/8 cell lines. A global expression analysis was performed to evaluate expression changes associated with genomic amplification/deletion: a novel gene, TRMT12 (at 125.5 Mb), amplified in 7/8 cell lines, showed highest expression in these cell lines. Further analysis by RT-qPCR using RNA from 30 breast tumors showed that TRMT12 was overexpressed >2 fold in 87% (26/30) of the tumors. TRMT12 is a homologue of a yeast gene encoding a tRNA methyltransferase involved in the posttranscriptional modification of tRNA(Phe), and exploring the biological consequence of its altered expression, may reveal novel pathways in tumorigenesis. This article contains Supplementary Material available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat.
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Affiliation(s)
- Virginia Rodriguez
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
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33
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Khan A, Hyde RK, Dutra A, Mohide P, Liu P. Core binding factor beta (CBFB) haploinsufficiency due to an interstitial deletion at 16q21q22 resulting in delayed cranial ossification, cleft palate, congenital heart anomalies, and feeding difficulties but favorable outcome. Am J Med Genet A 2007; 140:2349-54. [PMID: 17022082 DOI: 10.1002/ajmg.a.31479] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The core binding factor beta gene (CBFB), essential to bone morphogenesis, is located at 16q22.1. Homozygous deficiency of CBFB leads to ossification defects in mice. CBFB forms a heterodimer with RUNX2 (CBFA1) during embryonic bone development. RUNX2 mutations lead to cleidocranial dysplasia in humans. We describe an infant boy with an interstitial deletion of 16q21q22, delayed skull ossification, cleft palate, and heart anomalies who had a difficult course in infancy but eventually improved and is healthy. He was found to have CBFB haploinsufficiency, but did not have mutations in RUNX2. We suggest that 16q21q22 deletion be considered when there are antenatal or postnatal findings of enlarged cranial sutures with or without cleft palate. The finding of CBFB haploinsufficiency in our case and the similarity of cranial ossification defects with a mouse model of CBFB deletion suggest a role for CBFB in cranial bone development in humans.
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Affiliation(s)
- Aneal Khan
- Department of Pediatrics, McMaster Children's Hospital, McMaster University, Hamilton, Ontario, Canada.
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34
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Krygier G, Sosa A, Blanco A, Lombardo K, Castillo C, Dutra A, Cabrera S, Savio E, Muse I, Sabini G. ABV (doxorubicin [Adriamycin], bleomicin and vincristine) polychemotherapy regimen in HIV Kaposi’s Sarcoma: Uruguaian 10-year experience. J Clin Oncol 2006. [DOI: 10.1200/jco.2006.24.18_suppl.9559] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
9559 Background: Kaposi’s sarcoma is the most common malignancy among HIV patients and is considered to be one of the AIDS defining conditions. This abstract illustrates our 10 year experience with the treatment of 32 Kaposi’s sarcoma HIV patients with the same therapeutic approach. Methods: Between 04/95 and 03/05 we recruited 32 previously untreated patients that were diagnosed with Kaposi’s sarcoma and treated at the Servicio de Oncologia Clinica (Universitary Clinicas Hospital) in Montevideo. All of them received the same iv polychemotherapy plan (Adriamycin 10mg/m2, Bleomycin 10 U/m2 and Vincristine 1.4 mg/m2, every two weeks until tumor progression or severe toxicity). Results: 21 of the patients were good risk ones and the remaining 11 were poor risk patients (AIDS Clinical Trials Group staging classification). CD4 levels varied from 6 to 780/ml and the viral load ranges were 240 to 89000 copies. The patients received an average of 10.2 (4–21) polychemotherapy cycles. Grade 3–4 myelotoxicity was reported in 5 patients delaying the onset of the subsequent cycles. Grade 2 neurotoxicity was seen in 7 patients after 4, 5, 6, 8, 10, 11 and 13 cycles of ABV, changing vincristine for vinblastine (4mg/m2 every two weeks) in these patients. All the patients achieved a partial response with improvements in CD4 levels and viral load. 13/32 patients experienced a relapse (3–29 months after last chemotherapy cycle). 3 patients were retreated with paclitaxel 135 mg/m2 with 2/3 new partial responses of shorter duration. 5 patients received 4 additional ABV cycles achieving a new partial response. 5 patients refused further treatment dying due to progressive disease. One relapsed patient developed a second malignancy (High grade Non Hodgkin lymphoma) dying three months later. Conclusions: These data suggest that ABV regimen is still an effective treatment option for HIV-Kaposi’s sarcoma, specially in the undeveloped countries in which the cost of other better internationally approved options (liposomal doxorubicin and daunorubicin) makes them unaccesible for the majority of the population. No significant financial relationships to disclose.
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Affiliation(s)
- G. Krygier
- Servicio de Oncologia Clinicia Clinicias Hospital, Montevideo, Uruguay; Universitary Hospital de Clinicas, Montevideo, Uruguay; Contagious Diseases Institute, Montevideo, Uruguay
| | - A. Sosa
- Servicio de Oncologia Clinicia Clinicias Hospital, Montevideo, Uruguay; Universitary Hospital de Clinicas, Montevideo, Uruguay; Contagious Diseases Institute, Montevideo, Uruguay
| | - A. Blanco
- Servicio de Oncologia Clinicia Clinicias Hospital, Montevideo, Uruguay; Universitary Hospital de Clinicas, Montevideo, Uruguay; Contagious Diseases Institute, Montevideo, Uruguay
| | - K. Lombardo
- Servicio de Oncologia Clinicia Clinicias Hospital, Montevideo, Uruguay; Universitary Hospital de Clinicas, Montevideo, Uruguay; Contagious Diseases Institute, Montevideo, Uruguay
| | - C. Castillo
- Servicio de Oncologia Clinicia Clinicias Hospital, Montevideo, Uruguay; Universitary Hospital de Clinicas, Montevideo, Uruguay; Contagious Diseases Institute, Montevideo, Uruguay
| | - A. Dutra
- Servicio de Oncologia Clinicia Clinicias Hospital, Montevideo, Uruguay; Universitary Hospital de Clinicas, Montevideo, Uruguay; Contagious Diseases Institute, Montevideo, Uruguay
| | - S. Cabrera
- Servicio de Oncologia Clinicia Clinicias Hospital, Montevideo, Uruguay; Universitary Hospital de Clinicas, Montevideo, Uruguay; Contagious Diseases Institute, Montevideo, Uruguay
| | - E. Savio
- Servicio de Oncologia Clinicia Clinicias Hospital, Montevideo, Uruguay; Universitary Hospital de Clinicas, Montevideo, Uruguay; Contagious Diseases Institute, Montevideo, Uruguay
| | - I. Muse
- Servicio de Oncologia Clinicia Clinicias Hospital, Montevideo, Uruguay; Universitary Hospital de Clinicas, Montevideo, Uruguay; Contagious Diseases Institute, Montevideo, Uruguay
| | - G. Sabini
- Servicio de Oncologia Clinicia Clinicias Hospital, Montevideo, Uruguay; Universitary Hospital de Clinicas, Montevideo, Uruguay; Contagious Diseases Institute, Montevideo, Uruguay
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35
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Huang KM, Wu J, Duncan MK, Moy C, Dutra A, Favor J, Da T, Stambolian D. Xcat, a novel mouse model for Nance-Horan syndrome inhibits expression of the cytoplasmic-targeted Nhs1 isoform. Hum Mol Genet 2005; 15:319-27. [PMID: 16357105 DOI: 10.1093/hmg/ddi449] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [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: 11/12/2022] Open
Abstract
Nance-Horan syndrome (NHS) is an X-linked disorder characterized by congenital cataracts, dental anomalies, dysmorphic features and mental retardation. A recent report suggests that the novel gene NHS1 is involved in this disorder due to the presence of point mutations in NHS patients. A possible mouse model for NHS, Xcat, was mapped to a 2.11 Mb interval on the X-chromosome. Sequence and FISH analysis of the X-chromosome region containing the Xcat mutation reveal a large insertion between exons 1 and 2 of the mouse Nhs1 gene. The insertion inhibits the expression of the Nhs1 isoform containing exon 1 and results in exclusive expression of the alternative isoform containing exon 1A. Quantitative RT-PCR of Xcat cDNA shows reduced levels of Nhs1 transcripts. The Nhs1 protein is strongly expressed within the cytoplasm of elongating lens fiber cells from wild-type neonate lens, but is significantly reduced within the Xcat lens. Transient transfection studies of CHO cells with Nhs1-GFP fusion proteins were done to determine whether the amino acids encoded by exon 1 were critical for protein localization. We found the presence of Nhs1 exon 1 critical for localization of the fusion protein to the cytoplasm, whereas fusion proteins lacking Nhs1 exon 1 are predominantly nuclear. These results indicate that the first exon of Nhs1 contains crucial information required for the proper expression and localization of Nhs1 protein. Inhibition of expression of the exon 1 containing isoform results in the abnormal phenotype of Xcat.
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Affiliation(s)
- Kristen M Huang
- F.M. Kirby Center for Molecular Ophthalmology, Scheie Eye Institute, University of Pennsylvania School of Medicine, Philadelphia, USA
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36
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Tran SD, Wang J, Bandyopadhyay BC, Redman RS, Dutra A, Pak E, Swaim WD, Gerstenhaber JA, Bryant JM, Zheng C, Goldsmith CM, Kok MR, Wellner RB, Baum BJ. Primary culture of polarized human salivary epithelial cells for use in developing an artificial salivary gland. ACTA ACUST UNITED AC 2005; 11:172-81. [PMID: 15738672 DOI: 10.1089/ten.2005.11.172] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Therapeutic irradiation for head and neck cancer, and the autoimmune disease Sjogren's syndrome, lead to loss of salivary parenchyma. They are the two main causes of irreversible salivary gland hypofunction. Such patients cannot produce adequate levels of saliva, leading to considerable morbidity. We are working to develop an artificial salivary gland for such patients. A major problem in this endeavor has been the difficulty in obtaining a suitable autologous cellular component. This article describes a method of culturing and expanding primary salivary cells obtained from human submandibular glands (huSMGs) that is serum free and yields cells that are epithelial in nature. These include morphological (light and transmission electron microscopy [TEM]), protein expression (immunologically positive for ZO-1, claudin-1, and E-cadherin), and functional evidence. Under confocal microscopy, huSMG cells show polarization and appropriately localize tight junction proteins. TEM micrographs show an absence of dense core granules, but confirm the presence of tight and intermediate junctions and desmosomes between the cells. Functional assays showed that huSMG cells have high transepithelial electrical resistance and low rates of paracellular fluid movement. Additionally, huSMG cells show a normal karyotype without any morphological or numerical abnormalities, and most closely resemble striated and excretory duct cells in appearance. We conclude that this culture method for obtaining autologous human salivary cells should be useful in developing an artificial salivary gland.
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Affiliation(s)
- S D Tran
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland 20892, USA
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37
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Cheng J, Dutra A, Takesono A, Garrett-Beal L, Schwartzberg PL. Improved generation of C57BL/6J mouse embryonic stem cells in a defined serum-free media. Genesis 2005; 39:100-4. [PMID: 15170695 DOI: 10.1002/gene.20031] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
C57BL/6 is a well-characterized mouse strain that is used extensively for immunological and neurological research. The establishment of C57BL/6 ES cell lines has facilitated the study of gene-altered mice in a pure genetic background-however, relatively few such lines exist. Using a defined media supplement, knockout serum replacement (KSR) with knockout DMEM (KSR-KDMEM), we find that we can readily establish ES cell lines from blastocysts of C57BL/6J mice. Six lines were established, all of which were karyotypically normal and could be maintained in the undifferentiated state on mouse embryonic fibroblast (MEF) feeders. One line was further tested and found to be karyotypically stable and germline competent, both prior to manipulation and after gene targeting. For this cell line, efficiencies of cell cloning and chimera generation were greater when maintained in KSR-KDMEM. Our work suggests that the use of defined serum-free media may facilitate the generation of ES cells from inbred mouse strains.
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Affiliation(s)
- Jun Cheng
- Genetic Diseases Research Branch, National Human Genome Research Institute, Bethesda, Maryland, USA
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38
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Huang KM, Geunes-Boyer S, Wu S, Dutra A, Favor J, Stambolian D. Organization and annotation of the Xcat critical region: elimination of seven positional candidate genes. Genomics 2004; 83:893-901. [PMID: 15081118 DOI: 10.1016/j.ygeno.2003.10.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [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: 09/12/2003] [Revised: 10/23/2003] [Accepted: 10/29/2003] [Indexed: 11/18/2022]
Abstract
Xcat mice display X-linked congenital cataracts and are a mouse model for the human X-linked cataract disease Nance Horan syndrome (NHS). The genetic defect in Xcat mice and NHS patients is not known. We isolated and sequenced a BAC contig representing a portion of the Xcat critical region. We combined our sequencing data with the most recent mouse sequence assemblies from both Celera and public databases. The sequence of the 2.2-Mb Xcat critical region was then analyzed for potential Xcat candidate genes. The coding regions of the seven known genes within this area (Rai2, Rbbp7, Ctps2, Calb3, Grpr, Reps2, and Syap1) were sequenced in Xcat mice and no mutations were detected. The expression of Rai2 was quantitatively identical in wild-type and Xcat mutant eyes. These results indicate that the Xcat mutation is within a novel, undiscovered gene.
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Affiliation(s)
- Kristen M Huang
- F.M. Kirby Center for Molecular Ophthalmology, University of Pennsylvania School of Medicine, 422 Curie Boulevard, Philadelphia, PA 19104, USA
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39
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Castilla LH, Perrat P, Martinez NJ, Landrette SF, Keys R, Oikemus S, Flanegan J, Heilman S, Garrett L, Dutra A, Anderson S, Pihan GA, Wolff L, Liu PP. Identification of genes that synergize with Cbfb-MYH11 in the pathogenesis of acute myeloid leukemia. Proc Natl Acad Sci U S A 2004; 101:4924-9. [PMID: 15044690 PMCID: PMC387350 DOI: 10.1073/pnas.0400930101] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Acute myeloid leukemia subtype M4 with eosinophilia is associated with a chromosome 16 inversion that creates a fusion gene CBFB-MYH11. We have previously shown that CBFB-MYH11 is necessary but not sufficient for leukemogenesis. Here, we report the identification of genes that specifically cooperate with CBFB-MYH11 in leukemogenesis. Neonatal injection of Cbfb-MYH11 knock-in chimeric mice with retrovirus 4070A led to the development of acute myeloid leukemia in 2-5 months. Each leukemia sample contained one or a few viral insertions, suggesting that alteration of one gene could be sufficient to synergize with Cbfb-MYH11. The chromosomal position of 67 independent retroviral insertion sites (RISs) was determined, and 90% of the RISs mapped within 10 kb of a flanking gene. In total, 54 candidate genes were identified; six of them were common insertion sites (CISs). CIS genes included members of a zinc finger transcription factors family, Plag1 and Plagl2, with eight and two independent insertions, respectively. CIS genes also included Runx2, Myb, H2T24, and D6Mm5e. Comparison of the remaining 48 genes with single insertion sites with known leukemia-associated RISs indicated that 18 coincide with known RISs. To our knowledge, this retroviral genetic screen is the first to identify genes that cooperate with a fusion gene important for human myeloid leukemia.
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Affiliation(s)
- L H Castilla
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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40
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Slavotinek AM, Dutra A, Kpodzo D, Pak E, Nakane T, Turner J, Whiteford M, Biesecker LG, Stratton P. A female with complete lack of Müllerian fusion, postaxial polydactyly, and tetralogy of fallot: Genetic heterogeneity of McKusick-Kaufman syndrome or a unique syndrome? Am J Med Genet A 2004; 129A:69-72. [PMID: 15266619 DOI: 10.1002/ajmg.a.30071] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We report a 19-year-old, non-Amish Caucasian female patient with primary amenorrhea caused by complete lack of Müllerian fusion with vaginal agenesis or Müllerian aplasia (MA), postaxial polydactyly (PAP), and tetralogy of Fallot. The genital tract anomaly of MA with and without renal or skeletal anomalies comprises Mayer-Rokitansky-Kuster-Hauser syndrome, which has not been reported with tetralogy of Fallot. The phenotypic triad of anomalies most closely resembled McKusick-Kaufman syndrome (MKS; OMIM 236700), a rare multiple congenital anomaly syndrome comprised of hydrometrocolpos (HMC), PAP, and congenital heart malformation that is inherited in an autosomal recessive pattern. While upper reproductive tract anomalies have not been reported with MKS, they have been reported with Bardet-Biedl syndrome (BBS), a syndrome that significantly overlaps with MKS. Both MKS and BBS can be caused by mutations in the MKKS or BBS6 gene on chromosome 20p12 and BBS is also associated with mutations in other genes (BBS1, BBS2, BBS4, and BBS7). To address this heterogenity, we sequenced the causative genes in MKS and BBS but no mutations in these five genes were identified. Fluorescence in situ hybridization (FISH) excluded large deletions of chromosome 20p12 and microsatellite marker studies confirmed biparental inheritance for all of the known BBS loci. The dual midline fusion defects of tetralogy of Fallot and MA suggests that either this patient has a unique syndrome with a distinct genetic etiology or that she has a genetically heterogeneous or variant form of MKS.
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Affiliation(s)
- Anne M Slavotinek
- Genetic Diseases Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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41
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Singleton AB, Farrer M, Johnson J, Singleton A, Hague S, Kachergus J, Hulihan M, Peuralinna T, Dutra A, Nussbaum R, Lincoln S, Crawley A, Hanson M, Maraganore D, Adler C, Cookson MR, Muenter M, Baptista M, Miller D, Blancato J, Hardy J, Gwinn-Hardy K. alpha-Synuclein locus triplication causes Parkinson's disease. Science 2003; 302:841. [PMID: 14593171 DOI: 10.1126/science.1090278] [Citation(s) in RCA: 3185] [Impact Index Per Article: 151.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- A B Singleton
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD 20892, USA.
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42
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Eriksson M, Brown WT, Gordon LB, Glynn MW, Singer J, Scott L, Erdos MR, Robbins CM, Moses TY, Berglund P, Dutra A, Pak E, Durkin S, Csoka AB, Boehnke M, Glover TW, Collins FS. Recurrent de novo point mutations in lamin A cause Hutchinson-Gilford progeria syndrome. Nature 2003; 423:293-8. [PMID: 12714972 PMCID: PMC10540076 DOI: 10.1038/nature01629] [Citation(s) in RCA: 1484] [Impact Index Per Article: 70.7] [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: 01/24/2003] [Accepted: 04/01/2003] [Indexed: 02/06/2023]
Abstract
Hutchinson-Gilford progeria syndrome (HGPS) is a rare genetic disorder characterized by features reminiscent of marked premature ageing. Here, we present evidence of mutations in lamin A (LMNA) as the cause of this disorder. The HGPS gene was initially localized to chromosome 1q by observing two cases of uniparental isodisomy of 1q-the inheritance of both copies of this material from one parent-and one case with a 6-megabase paternal interstitial deletion. Sequencing of LMNA, located in this interval and previously implicated in several other heritable disorders, revealed that 18 out of 20 classical cases of HGPS harboured an identical de novo (that is, newly arisen and not inherited) single-base substitution, G608G(GGC > GGT), within exon 11. One additional case was identified with a different substitution within the same codon. Both of these mutations result in activation of a cryptic splice site within exon 11, resulting in production of a protein product that deletes 50 amino acids near the carboxy terminus. Immunofluorescence of HGPS fibroblasts with antibodies directed against lamin A revealed that many cells show visible abnormalities of the nuclear membrane. The discovery of the molecular basis of this disease may shed light on the general phenomenon of human ageing.
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Affiliation(s)
- Maria Eriksson
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York 10314, USA
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43
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Abstract
We report a Nigerian family with a late-onset autosomal dominant neuropathy consistent with Charcot-Marie-Tooth disease. Electrophysiological examination of the index patient confirmed a severe demyelinating neuropathy with secondary axonal features. Sequence analysis of the myelin protein zero (MPZ) gene identified a C-to-G transversion at nucleotide position 234, resulting in a serine-to-tryptophan mutation in codon 78 (S78W) of the translated protein. The presence of this novel missense mutation suggests a diagnosis of Charcot-Marie-Tooth disease type 1B. Our study confirms the worldwide distribution of this disorder and extends the genetic spectrum of mutations in the MPZ gene.
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Affiliation(s)
- R Kakar
- Laboratory of Neurogenetics, New Jersey Neuroscience Institute, Seton Hall University, 65 James Street, Edison, New Jersey 08818, USA
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44
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Kouprina N, Leem SH, Solomon G, Ly A, Koriabine M, Otstot J, Pak E, Dutra A, Zhao S, Barrett JC, Larionov V. Segments missing from the draft human genome sequence can be isolated by transformation-associated recombination cloning in yeast. EMBO Rep 2003; 4:257-62. [PMID: 12634842 PMCID: PMC1315894 DOI: 10.1038/sj.embor.embor766] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2002] [Revised: 12/05/2002] [Accepted: 12/18/2002] [Indexed: 11/09/2022] Open
Abstract
The reported draft human genome sequence includes many contigs that are separated by gaps of unknown sequence. These gaps may be due to chromosomal regions that are not present in the Escherichia coli libraries used for DNA sequencing because they cannot be cloned efficiently, if at all, in bacteria. Using a yeast artificial chromosome (YAC)/ bacterial artificial chromosome (BAC) library generated in yeast, we found that approximately 6% of human DNA sequences tested transformed E. coli cells less efficiently than yeast cells, and were less stable in E. coli than in yeast. When the ends of several YAC/BAC isolates cloned in yeast were sequenced and compared with the reported draft sequence, major inconsistencies were found with the sequences of those YAC/BAC isolates that transformed E. coli cells inefficiently. Two human genomic fragments were re-isolated from human DNA by transformation-associated recombination (TAR) cloning. Re-sequencing of these regions showed that the errors in the draft are the results of both missassembly and loss of specific DNA sequences during cloning in E. coli. These results show that TAR cloning might be a valuable method that could be widely used during the final stages of the Human Genome Project.
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Affiliation(s)
- Natalay Kouprina
- Laboratory of Biosystems and Cancer, National Cancer Institute, Building 37, Room 5031, Bethesda, Maryland 20892, USA.
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Karkera JD, Izraeli S, Roessler E, Dutra A, Kirsch I, Muenke M. The genomic structure, chromosomal localization, and analysis of SIL as a candidate gene for holoprosencephaly. Cytogenet Genome Res 2003; 97:62-7. [PMID: 12438740 DOI: 10.1159/000064057] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Holoprosencephaly (HPE) is the most common congenital malformation of the brain and face in humans. In this study we report the analysis of SIL (Sumacr;CL iumacr;nterrupting lumacr;ocus) as a candidate gene for HPE. Fluorescent in situ hybridization (FISH) analysis using a BAC 246e16 confirmed the assignment of SIL to 1p32. Computational analysis of SIL at the protein level revealed a 73% overall identity between the human and murine proteins. Denaturing high performance liquid chromatography (dHPLC) techniques were used to screen for mutations and these studies identified several common polymorphisms but no disease-associated mutations, suggesting that SIL is not a common factor in HPE pathogenesis in humans.
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Affiliation(s)
- J D Karkera
- Medical Genetics Branch, National Human Genome Research Institute, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
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46
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Lozier JN, Dutra A, Pak E, Zhou N, Zheng Z, Nichols TC, Bellinger DA, Read M, Morgan RA. The Chapel Hill hemophilia A dog colony exhibits a factor VIII gene inversion. Proc Natl Acad Sci U S A 2002; 99:12991-6. [PMID: 12242334 PMCID: PMC130574 DOI: 10.1073/pnas.192219599] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.6] [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: 04/11/2002] [Indexed: 11/18/2022] Open
Abstract
In the Chapel Hill colony of factor VIII-deficient dogs, abnormal sequence (ch8, for canine hemophilia 8, GenBank no. ) follows exons 1-22 in the factor VIII transcript in place of exons 23-26. The canine hemophilia 8 locus (ch8) sequence was found in a 140-kb normal dog genomic DNA bacterial artificial chromosome (BAC) clone that was completely outside the factor VIII gene, but not in BAC clones containing the factor VIII gene. The BAC clone that contained ch8 also contained a homologue of F8A (factor 8 associated) sequence, which participates in a common inversion that causes severe hemophilia A in humans. Fluorescence in situ hybridization analysis indicated that exons 1-26 normally proceed sequentially from telomere to centromere at Xq28, and ch8 is telomeric to the factor VIII gene. The appearance of an "upstream" genomic sequence element (ch8) at the end of the aberrant factor VIII transcript suggested that an inversion of genomic DNA replaced factor VIII exons 22-26 with ch8. The F8A sequence appeared also in overlapping normal BAC clones containing factor VIII sequence. We hypothesized that homologous recombination between copies of canine F8A inside and outside the factor VIII gene had occurred, as in human hemophilia A. High-resolution fluorescent in situ hybridization on hemophilia A dog DNA revealed a pattern consistent with this inversion mechanism. We also identified a HindIII restriction fragment length polymorphism of F8A fragments that distinguished hemophilia A, carrier, and normal dogs' DNA. The Chapel Hill hemophilia A dog colony therefore replicates the factor VIII gene inversion commonly seen in humans with severe hemophilia A.
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Affiliation(s)
- Jay N Lozier
- Food and Drug Administration, Center for Biologics Evaluation and Research, Rockville, MD 20852, USA.
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Xu ZP, Dutra A, Stellrecht CM, Wu C, Piatigorsky J, Saunders GF. Functional and structural characterization of the human gene BHLHB5, encoding a basic helix-loop-helix transcription factor. Genomics 2002; 80:311-8. [PMID: 12213201 DOI: 10.1006/geno.2002.6833] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.6] [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] [Indexed: 11/22/2022]
Abstract
The genes encoding basic helix-loop-helix (bHLH) transcription factors have been implicated in many aspects of neural development, including cell growth, differentiation, and cell migration. Using both genomic and cDNA mouse and human clones encoding a neural-specific bHLH protein, human BHLHB5 was cloned and mapped to a region on chromosome 8q13 that segregates with Duane syndrome. Genomic sequence analysis of human BHLHB5 and mouse Bhlhb5 revealed that they contain a single exon encoding 381- and 355-amino-acid bHLH proteins, respectively. Multiple amino acid sequence alignments of the Bhlhb5 family members revealed several conserved motifs and an identical 147-amino-acid carboxy-terminal region that contains a 60-amino-acid bHLH domain. A 27-bp trinucleotide repeat (CAG)(9) encoding polyserine was found in human BHLHB5, but only one CAG was found at the corresponding position in the mouse Bhlhb5 and hamster BETA3 genes. Northern blot analysis of human BHLHB5 revealed brain-specific expression with the highest abundance in the cerebellum. Mouse Bhlhb5 can strongly repress a human PAX6 promoter.
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Affiliation(s)
- Zheng-Ping Xu
- Laboratory of Molecular and Developmental Biology, National Eye Institute, Bethesda, Maryland 20890, USA
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Aldosari N, Wiltshire RN, Dutra A, Schrock E, McLendon RE, Friedman HS, Bigner DD, Bigner SH. Comprehensive molecular cytogenetic investigation of chromosomal abnormalities in human medulloblastoma cell lines and xenograft. Neuro Oncol 2002; 4:75-85. [PMID: 11916498 PMCID: PMC1920654 DOI: 10.1093/neuonc/4.2.75] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [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: 07/13/2001] [Accepted: 10/08/2001] [Indexed: 11/12/2022] Open
Abstract
Cell lines and xenografts derived from medulloblastomas are useful tools to investigate the chromosomal changes in these tumors. Here we used G-banding, fluorescence in situ hybridization (FISH), spectral karyotyping (SKY), and comparative genomic hybridization to study 4 medulloblastoma cell lines and 1 xenograft. Cell line D-425 Med had a relatively simple karyotype, with a terminal deletion of 10q and amplification of MYC in double-minutes (dmins). FISH demonstrated that an apparent isochromosome (17q) by routine karyotyping was actually an unbalanced translocation between 2 copies of chromosome 17. Cell line D-556 Med also had a simple near-diploid stemline with an unbalanced 1;13 translocation resulting in a gain of 1q, an isochromosome (17q), and dmins. These findings were initially described using routine G-banded preparations, and FISH showed that the dmins were an amplification of MYC and the i(17q) was an isodicentric 17q chromosome. The other finding was confirmed by FISH, SKY, and comparative genomic hybridization. Cell lines D-721 Med and D-581 Med had complex karyotypic patterns that could be completely characterized only when FISH and SKY were used. Xenograft D-690 Med also had a complex pattern that FISH and SKY were helpful in completely elucidating. Interestingly, balanced reciprocal translocations were seen as well as complicated unbalanced translocations and marker chromosomes. Comparative genomic hybridization demonstrated only a deletion of 10q22-10q24, supporting the idea that despite the complexity of the chromosomal rearrangements, minimal alterations in the overall chromosomal content had occurred. This study demonstrates that routine cytogenetic preparations are adequate to describe chromosomal abnormalities in occasional medulloblastoma samples, but a broader spectrum of molecular cytogenetic methods is required to completely analyze most of these tumor samples.
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Affiliation(s)
- Naji Aldosari
- Department of Pathology, Duke University Medical Center, Durham, NC 27710, USA
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Rozenblum E, Vahteristo P, Sandberg T, Bergthorsson JT, Syrjakoski K, Weaver D, Haraldsson K, Johannsdottir HK, Vehmanen P, Nigam S, Golberger N, Robbins C, Pak E, Dutra A, Gillander E, Stephan DA, Bailey-Wilson J, Juo SHH, Kainu T, Arason A, Barkardottir RB, Nevanlinna H, Borg A, Kallioniemi OP. A genomic map of a 6-Mb region at 13q21-q22 implicated in cancer development: identification and characterization of candidate genes. Hum Genet 2002; 110:111-21. [PMID: 11935316 DOI: 10.1007/s00439-001-0646-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.7] [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: 08/03/2001] [Accepted: 10/09/2001] [Indexed: 12/01/2022]
Abstract
Chromosomal region 13q21-q22 harbors a putative breast cancer susceptibility gene and has been implicated as a common site for somatic deletions in a variety of malignant tumors. We have built a complete physical clone contig for a region between D13S1308 and AFM220YE9 based on 18 yeast artificial chromosome and 81 bacterial artificial chromosome (BAC) clones linked together by 22 genetic markers and 61 other sequence tagged sites. Combining data from 47 sequenced BACs (as of June 2001), we have assembled in silico an integrated 5.7-Mb genomic map with 90% sequence coverage. This area contains eight known genes, two hypothetical proteins, 24 additional Unigene clusters, and approximately 100 predicted genes and exons. We have determined the cDNA and genomic sequence, and tissue expression profiles for the KIAA1008 protein (homologous to the yeast mitotic control protein dis3+), KLF12 (AP-2 repressor), progesterone induced blocking factor 1, zinc finger transcription factor KLF5, and LIM domain only-7, and for the hypothetical proteins FLJ22624 and FLJ21869. Mutation screening of the five known genes in 19 breast cancer families has revealed numerous polymorphisms, but no deleterious mutations. These data provide a basis and resources for further analyses of this chromosomal region in the development of cancer.
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Affiliation(s)
- Ester Rozenblum
- Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Clark RM, Marker PC, Roessler E, Dutra A, Schimenti JC, Muenke M, Kingsley DM. Reciprocal mouse and human limb phenotypes caused by gain- and loss-of-function mutations affecting Lmbr1. Genetics 2001; 159:715-26. [PMID: 11606546 PMCID: PMC1461845 DOI: 10.1093/genetics/159.2.715] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The major locus for dominant preaxial polydactyly in humans has been mapped to 7q36. In mice the dominant Hemimelic extra toes (Hx) and Hammertoe (Hm) mutations map to a homologous chromosomal region and cause similar limb defects. The Lmbr1 gene is entirely within the small critical intervals recently defined for both the mouse and human mutations and is misexpressed at the exact time that the mouse Hx phenotype becomes apparent during limb development. This result suggests that Lmbr1 may underlie preaxial polydactyly in both mice and humans. We have used deletion chromosomes to demonstrate that the dominant mouse and human limb defects arise from gain-of-function mutations and not from haploinsufficiency. Furthermore, we created a loss-of-function mutation in the mouse Lmbr1 gene that causes digit number reduction (oligodactyly) on its own and in trans to a deletion chromosome. The loss of digits that we observed in mice with reduced Lmbr1 activity is in contrast to the gain of digits observed in Hx mice and human polydactyly patients. Our results suggest that the Lmbr1 gene is required for limb formation and that reciprocal changes in levels of Lmbr1 activity can lead to either increases or decreases in the number of digits in the vertebrate limb.
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Affiliation(s)
- R M Clark
- Department of Developmental Biology, Stanford University, Stanford, California 94305-5327, USA
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