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Joglekar P, Conlan S, Lee-Lin SQ, Deming C, Kashaf SS, Kong HH, Segre JA. Integrated genomic and functional analyses of human skin-associated Staphylococcus reveal extensive inter- and intra-species diversity. Proc Natl Acad Sci U S A 2023; 120:e2310585120. [PMID: 37956283 PMCID: PMC10666031 DOI: 10.1073/pnas.2310585120] [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: 07/04/2023] [Accepted: 10/11/2023] [Indexed: 11/15/2023] Open
Abstract
Human skin is stably colonized by a distinct microbiota that functions together with epidermal cells to maintain a protective physical barrier. Staphylococcus, a prominent genus of the skin microbiota, participates in colonization resistance, tissue repair, and host immune regulation in strain-specific manners. To unlock the potential of engineering skin microbial communities, we aim to characterize the diversity of this genus within the context of the skin environment. We reanalyzed an extant 16S rRNA amplicon dataset obtained from distinct body sites of healthy volunteers, providing a detailed biogeographic depiction of staphylococcal species that colonize our skin. S. epidermidis, S. capitis, and S. hominis were the most abundant staphylococcal species present in all volunteers and were detected at all body sites. Pan-genome analysis of isolates from these three species revealed that the genus-core was dominated by central metabolism genes. Species-restricted-core genes encoded known host colonization functions. The majority (~68%) of genes were detected only in a fraction of isolate genomes, underscoring the immense strain-specific gene diversity. Conspecific genomes grouped into phylogenetic clades, exhibiting body site preference. Each clade was enriched for distinct gene sets that are potentially involved in site tropism. Finally, we conducted gene expression studies of select isolates showing variable growth phenotypes in skin-like medium. In vitro expression revealed extensive intra- and inter-species gene expression variation, substantially expanding the functional diversification within each species. Our study provides an important resource for future ecological and translational studies to examine the role of shared and strain-specific staphylococcal genes within the skin environment.
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Affiliation(s)
- Payal Joglekar
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD20892
| | - Sean Conlan
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD20892
| | - Shih-Queen Lee-Lin
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD20892
| | - Clay Deming
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD20892
| | - Sara Saheb Kashaf
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD20892
| | | | - Heidi H. Kong
- Cutaneous Microbiome and Inflammation Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD20892
| | - Julia A. Segre
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD20892
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2
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Blaustein RA, Shen Z, Kashaf SS, Lee-Lin S, Conlan S, Bosticardo M, Delmonte OM, Holmes CJ, Taylor ME, Banania G, Nagao K, Dimitrova D, Kanakry JA, Su H, Holland SM, Bergerson JRE, Freeman AF, Notarangelo LD, Kong HH, Segre JA. Expanded microbiome niches of RAG-deficient patients. Cell Rep Med 2023; 4:101205. [PMID: 37757827 PMCID: PMC10591041 DOI: 10.1016/j.xcrm.2023.101205] [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: 09/13/2022] [Revised: 11/28/2022] [Accepted: 08/31/2023] [Indexed: 09/29/2023]
Abstract
The complex interplay between microbiota and immunity is important to human health. To explore how altered adaptive immunity influences the microbiome, we characterize skin, nares, and gut microbiota of patients with recombination-activating gene (RAG) deficiency-a rare genetically defined inborn error of immunity (IEI) that results in a broad spectrum of clinical phenotypes. Integrating de novo assembly of metagenomes from RAG-deficient patients with reference genome catalogs provides an expansive multi-kingdom view of microbial diversity. RAG-deficient patient microbiomes exhibit inter-individual variation, including expansion of opportunistic pathogens (e.g., Corynebacterium bovis, Haemophilus influenzae), and a relative loss of body site specificity. We identify 35 and 27 bacterial species derived from skin/nares and gut microbiomes, respectively, which are distinct to RAG-deficient patients compared to healthy individuals. Underscoring IEI patients as potential reservoirs for viral persistence and evolution, we further characterize the colonization of eukaryotic RNA viruses (e.g., Coronavirus 229E, Norovirus GII) in this patient population.
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Affiliation(s)
- Ryan A Blaustein
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Zeyang Shen
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Sara Saheb Kashaf
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - ShihQueen Lee-Lin
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Sean Conlan
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Marita Bosticardo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Ottavia M Delmonte
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Cassandra J Holmes
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD 20892, USA
| | - Monica E Taylor
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD 20892, USA
| | - Glenna Banania
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD 20892, USA
| | - Keisuke Nagao
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD 20892, USA
| | - Dimana Dimitrova
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Jennifer A Kanakry
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Helen Su
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Steven M Holland
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Jenna R E Bergerson
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Alexandra F Freeman
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Heidi H Kong
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD 20892, USA
| | - Julia A Segre
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA.
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3
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Joglekar P, Conlan S, Lee-Lin SQ, Deming C, Kashaf SS, Kong HH, Segre JA. Integrated genomic and functional analyses of human skin-associated Staphylococcus reveals extensive inter- and intra-species diversity. bioRxiv 2023:2023.06.22.546190. [PMID: 37503282 PMCID: PMC10370188 DOI: 10.1101/2023.06.22.546190] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Human skin is stably colonized by a distinct microbiota that functions together with epidermal cells to maintain a protective physical barrier. Staphylococcus, a prominent genus of the skin microbiota, participates in colonization resistance, tissue repair, and host immune regulation in strain specific manners. To unlock the potential of engineering skin microbial communities, we aim to fully characterize the functional diversity of this genus within the context of the skin environment. We conducted metagenome and pan-genome analyses of isolates obtained from distinct body sites of healthy volunteers, providing a detailed biogeographic depiction of staphylococcal species that colonize our skin. S. epidermidis, S. capitis, and S. hominis were the most abundant species present in all volunteers and were detected at all body sites. Pan-genome analysis of these three species revealed that the genus-core was dominated by central metabolism genes. Species-specific core genes were enriched in host colonization functions. The majority (~68%) of genes were detected only in a fraction of isolate genomes, underscoring the immense strain-specific gene diversity. Conspecific genomes grouped into phylogenetic clades, exhibiting body site preference. Each clade was enriched for distinct gene-sets that are potentially involved in site tropism. Finally, we conducted gene expression studies of select isolates showing variable growth phenotypes in skin-like medium. In vitro expression revealed extensive intra- and inter-species gene expression variation, substantially expanding the functional diversification within each species. Our study provides an important resource for future ecological and translational studies to examine the role of shared and strain-specific staphylococcal genes within the skin environment.
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Affiliation(s)
- Payal Joglekar
- Microbial Genomics Section, Translational and Functional Genomics Branch, NHGRI, NIH, Bethesda, Maryland, USA
| | - Sean Conlan
- Microbial Genomics Section, Translational and Functional Genomics Branch, NHGRI, NIH, Bethesda, Maryland, USA
| | - Shih-Queen Lee-Lin
- Microbial Genomics Section, Translational and Functional Genomics Branch, NHGRI, NIH, Bethesda, Maryland, USA
| | - Clay Deming
- Microbial Genomics Section, Translational and Functional Genomics Branch, NHGRI, NIH, Bethesda, Maryland, USA
| | - Sara Saheb Kashaf
- Microbial Genomics Section, Translational and Functional Genomics Branch, NHGRI, NIH, Bethesda, Maryland, USA
| | | | - Heidi H. Kong
- Cutaneous Microbiome and Inflammation Section, NIAMS, NIH, Bethesda, Maryland, USA
| | - Julia A. Segre
- Microbial Genomics Section, Translational and Functional Genomics Branch, NHGRI, NIH, Bethesda, Maryland, USA
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4
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Conlan S, Lau AF, Deming C, Spalding CD, Lee-Lin S, Thomas PJ, Park M, Dekker JP, Frank KM, Palmore TN, Segre JA. Plasmid Dissemination and Selection of a Multidrug-Resistant Klebsiella pneumoniae Strain during Transplant-Associated Antibiotic Therapy. mBio 2019; 10:e00652-19. [PMID: 31594809 PMCID: PMC6786864 DOI: 10.1128/mbio.00652-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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: 03/13/2019] [Accepted: 09/03/2019] [Indexed: 12/14/2022] Open
Abstract
Antibiotics, which are used both to prevent and to treat infections, are a mainstay therapy for lifesaving procedures such as transplantation. For this reason, and many others, increased antibiotic resistance among human-associated pathogens, such as the carbapenem-resistant Enterobacteriaceae species, is of grave concern. In this study, we report on a hematopoietic stem cell transplant recipient in whom cultures detected the emergence of carbapenem resistance and spread across five strains of bacteria that persisted for over a year. Carbapenem resistance in Citrobacter freundii, Enterobacter cloacae, Klebsiella aerogenes, and Klebsiella pneumoniae was linked to a pair of plasmids, each carrying the Klebsiella pneumoniae carbapenemase gene (blaKPC). Surveillance cultures identified a carbapenem-susceptible strain of Citrobacter freundii that may have become resistant through horizontal gene transfer of these plasmids. Selection of a multidrug-resistant Klebsiella pneumoniae strain was also detected following combination antibiotic therapy. Here we report a plasmid carrying the blaKPC gene with broad host range that poses the additional threat of spreading to endogenous members of the human gut microbiome.IMPORTANCE Antibiotic-resistant bacteria are a serious threat to medically fragile patient populations. The spread of antibiotic resistance through plasmid-mediated mechanisms is of grave concern as it can lead to the conversion of endogenous patient-associated strains to difficult-to-treat pathogens.
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Affiliation(s)
- Sean Conlan
- National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Anna F Lau
- National Institutes of Health Clinical Center, Bethesda, Maryland, USA
| | - Clay Deming
- National Human Genome Research Institute, Bethesda, Maryland, USA
| | | | | | - Pamela J Thomas
- National Institutes of Health Intramural Sequencing Center (NISC), Rockville, Maryland, USA
| | - Morgan Park
- National Institutes of Health Intramural Sequencing Center (NISC), Rockville, Maryland, USA
| | - John P Dekker
- National Institutes of Health Clinical Center, Bethesda, Maryland, USA
- National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Karen M Frank
- National Institutes of Health Clinical Center, Bethesda, Maryland, USA
| | - Tara N Palmore
- National Institutes of Health Clinical Center, Bethesda, Maryland, USA
| | - Julia A Segre
- National Human Genome Research Institute, Bethesda, Maryland, USA
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5
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Johnson RC, Deming C, Conlan S, Zellmer CJ, Michelin AV, Lee-Lin S, Thomas PJ, Park M, Weingarten RA, Less J, Dekker JP, Frank KM, Musser KA, McQuiston JR, Henderson DK, Lau AF, Palmore TN, Segre JA. Investigation of a Cluster of Sphingomonas koreensis Infections. N Engl J Med 2018; 379:2529-2539. [PMID: 30586509 PMCID: PMC6322212 DOI: 10.1056/nejmoa1803238] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [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: 12/13/2022]
Abstract
BACKGROUND Plumbing systems are an infrequent but known reservoir for opportunistic microbial pathogens that can infect hospitalized patients. In 2016, a cluster of clinical sphingomonas infections prompted an investigation. METHODS We performed whole-genome DNA sequencing on clinical isolates of multidrug-resistant Sphingomonas koreensis identified from 2006 through 2016 at the National Institutes of Health (NIH) Clinical Center. We cultured S. koreensis from the sinks in patient rooms and performed both whole-genome and shotgun metagenomic sequencing to identify a reservoir within the infrastructure of the hospital. These isolates were compared with clinical and environmental S. koreensis isolates obtained from other institutions. RESULTS The investigation showed that two isolates of S. koreensis obtained from the six patients identified in the 2016 cluster were unrelated, but four isolates shared more than 99.92% genetic similarity and were resistant to multiple antibiotic agents. Retrospective analysis of banked clinical isolates of sphingomonas from the NIH Clinical Center revealed the intermittent recovery of a clonal strain over the past decade. Unique single-nucleotide variants identified in strains of S. koreensis elucidated the existence of a reservoir in the hospital plumbing. Clinical S. koreensis isolates from other facilities were genetically distinct from the NIH isolates. Hospital remediation strategies were guided by results of microbiologic culturing and fine-scale genomic analyses. CONCLUSIONS This genomic and epidemiologic investigation suggests that S. koreensis is an opportunistic human pathogen that both persisted in the NIH Clinical Center infrastructure across time and space and caused health care-associated infections. (Funded by the NIH Intramural Research Programs.).
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Affiliation(s)
- Ryan C Johnson
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
| | - Clay Deming
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
| | - Sean Conlan
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
| | - Caroline J Zellmer
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
| | - Angela V Michelin
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
| | - ShihQueen Lee-Lin
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
| | - Pamela J Thomas
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
| | - Morgan Park
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
| | - Rebecca A Weingarten
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
| | - John Less
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
| | - John P Dekker
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
| | - Karen M Frank
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
| | - Kimberlee A Musser
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
| | - John R McQuiston
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
| | - David K Henderson
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
| | - Anna F Lau
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
| | - Tara N Palmore
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
| | - Julia A Segre
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
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6
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Tirosh O, Conlan S, Deming C, Lee-Lin SQ, Huang X, Su HC, Freeman AF, Segre JA, Kong HH. Expanded skin virome in DOCK8-deficient patients. Nat Med 2018; 24:1815-1821. [PMID: 30397357 PMCID: PMC6286253 DOI: 10.1038/s41591-018-0211-7] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [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: 06/06/2018] [Accepted: 09/05/2018] [Indexed: 12/25/2022]
Abstract
Human microbiome studies have revealed the intricate interplay of host immunity and bacterial communities to achieve homeostatic balance. Healthy skin microbial communities are dominated by bacteria with low viral representation1-3, mainly bacteriophage. Specific eukaryotic viruses have been implicated in both common and rare skin diseases, but cataloging skin viral communities has been limited. Alterations in host immunity provide an opportunity to expand our understanding of microbial-host interactions. Primary immunodeficient patients manifest with various viral, bacterial, fungal, and parasitic infections, including skin infections4. Dedicator of cytokinesis 8 (DOCK8) deficiency is a rare primary human immunodeficiency characterized by recurrent cutaneous and systemic infections, as well as atopy and cancer susceptibility5. DOCK8, encoding a guanine nucleotide exchange factor highly expressed in lymphocytes, regulates actin cytoskeleton, which is critical for migration through collagen-dense tissues such as skin6. Analyzing deep metagenomic sequencing data from DOCK8-deficient skin samples demonstrated a notable increase in eukaryotic viral representation and diversity compared with healthy volunteers. De novo assembly approaches identified hundreds of novel human papillomavirus genomes, illuminating microbial dark matter. Expansion of the skin virome in DOCK8-deficient patients underscores the importance of immune surveillance in controlling eukaryotic viral colonization and infection.
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Affiliation(s)
- Osnat Tirosh
- Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Sean Conlan
- Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Clay Deming
- Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Shih-Queen Lee-Lin
- Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Xin Huang
- Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Helen C Su
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Alexandra F Freeman
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Julia A Segre
- Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA.
| | - Heidi H Kong
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA.
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD, USA.
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7
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Unni AM, Lockwood WW, Zejnullahu K, Lee-Lin SQ, Varmus H. Evidence that synthetic lethality underlies the mutual exclusivity of oncogenic KRAS and EGFR mutations in lung adenocarcinoma. eLife 2015; 4:e06907. [PMID: 26047463 PMCID: PMC4478584 DOI: 10.7554/elife.06907] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Accepted: 06/04/2015] [Indexed: 01/07/2023] Open
Abstract
Human lung adenocarcinomas (LUAD) contain mutations in EGFR in ∼15% of cases and in KRAS in ∼30%, yet no individual adenocarcinoma appears to carry activating mutations in both genes, a finding we have confirmed by re-analysis of data from over 600 LUAD. Here we provide evidence that co-occurrence of mutations in these two genes is deleterious. In transgenic mice programmed to express both mutant oncogenes in the lung epithelium, the resulting tumors express only one oncogene. We also show that forced expression of a second oncogene in human cancer cell lines with an endogenous mutated oncogene is deleterious. The most prominent features accompanying loss of cell viability were vacuolization, other changes in cell morphology, and increased macropinocytosis. Activation of ERK, p38 and JNK in the dying cells suggests that an overly active MAPK signaling pathway may mediate the phenotype. Together, our findings indicate that mutual exclusivity of oncogenic mutations may reveal unexpected vulnerabilities and therapeutic possibilities. DOI:http://dx.doi.org/10.7554/eLife.06907.001 A person develops cancer when changes in a cell's DNA (called mutations) allow the cell to grow rapidly and spread around the body. The mutated genes are often involved in controlling the growth of cells, such as two genes called EGFR and KRAS, which are associated with forms of lung cancer. In a type of lung cancer called adenocarcinoma, the KRAS gene is mutated in about one-third of tumors and the EGFR gene is mutated in about 15%. However, the two mutations rarely or never occur in the same tumor. This could be because the effects of the mutations overlap, so that cells with both mutations have no advantages over cells with just one. Alternatively, it is possible that having both mutations may be harmful to tumor cells. Here, Unni, Lockwood et al. analyzed genetic data from over 600 lung tumors and confirmed that none of them have cancer-causing mutations in both KRAS and EGFR. Then, Unni, Lockwood et al. carried out experiments using genetically engineered mice with mutated forms of both KRAS and EGFR that are activated by a drug called doxycycline. As expected, the mice developed lung tumors when exposed to the drug, but these tumors didn't grow any faster than mouse tumors that had mutations in only one of the genes. In the mice with both mutant genes, only one of the two genes was actually active in most of the tumor cells. Unni, Lockwood et al. manipulated human lung tumor cells in the laboratory so that the cells had mutated versions of both genes. These cells developed serious abnormalities and died, which may be due to the over-activation of a communication pathway within the cells called MAPK signaling. The next challenges are to understand why the combination of these two mutant genes kills these cancer cells and to look for other combinations of mutations that can be toxic to cancer cells. In the future, it might be possible to develop drugs that can mimic the effects of these gene mutations to treat cancers. DOI:http://dx.doi.org/10.7554/eLife.06907.002
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Affiliation(s)
- Arun M Unni
- Cancer Biology Section, Cancer Genetics Branch, National Human Genome Research Institute, Bethesda, United States
| | - William W Lockwood
- Cancer Biology Section, Cancer Genetics Branch, National Human Genome Research Institute, Bethesda, United States
| | - Kreshnik Zejnullahu
- Cancer Biology Section, Cancer Genetics Branch, National Human Genome Research Institute, Bethesda, United States
| | - Shih-Queen Lee-Lin
- Cancer Biology Section, Cancer Genetics Branch, National Human Genome Research Institute, Bethesda, United States
| | - Harold Varmus
- Cancer Biology Section, Cancer Genetics Branch, National Human Genome Research Institute, Bethesda, United States
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8
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Sen SK, Barb JJ, Cherukuri PF, Accame DS, Elkahloun AG, Singh LN, Lee-Lin SQ, Kolodgie FD, Cheng Q, Zhao X, Chen MY, Arai AE, Green ED, Mullikin JC, Munson PJ, Biesecker LG. Identification of candidate genes involved in coronary artery calcification by transcriptome sequencing of cell lines. BMC Genomics 2014; 15:198. [PMID: 24628908 PMCID: PMC4003819 DOI: 10.1186/1471-2164-15-198] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Accepted: 03/04/2014] [Indexed: 01/08/2023] Open
Abstract
Background Massively-parallel cDNA sequencing (RNA-Seq) is a new technique that holds great promise for cardiovascular genomics. Here, we used RNA-Seq to study the transcriptomes of matched coronary artery disease cases and controls in the ClinSeq® study, using cell lines as tissue surrogates. Results Lymphoblastoid cell lines (LCLs) from 16 cases and controls representing phenotypic extremes for coronary calcification were cultured and analyzed using RNA-Seq. All cell lines were then independently re-cultured and along with another set of 16 independent cases and controls, were profiled with Affymetrix microarrays to perform a technical validation of the RNA-Seq results. Statistically significant changes (p < 0.05) were detected in 186 transcripts, many of which are expressed at extremely low levels (5–10 copies/cell), which we confirmed through a separate spike-in control RNA-Seq experiment. Next, by fitting a linear model to exon-level RNA-Seq read counts, we detected signals of alternative splicing in 18 transcripts. Finally, we used the RNA-Seq data to identify differential expression (p < 0.0001) in eight previously unannotated regions that may represent novel transcripts. Overall, differentially expressed genes showed strong enrichment (p = 0.0002) for prior association with cardiovascular disease. At the network level, we found evidence for perturbation in pathways involving both cardiovascular system development and function as well as lipid metabolism. Conclusions We present a pilot study for transcriptome involvement in coronary artery calcification and demonstrate how RNA-Seq analyses using LCLs as a tissue surrogate may yield fruitful results in a clinical sequencing project. In addition to canonical gene expression, we present candidate variants from alternative splicing and novel transcript detection, which have been unexplored in the context of this disease.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Leslie G Biesecker
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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9
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Andrés AM, Dennis MY, Kretzschmar WW, Cannons JL, Lee-Lin SQ, Hurle B, Schwartzberg PL, Williamson SH, Bustamante CD, Nielsen R, Clark AG, Green ED. Balancing selection maintains a form of ERAP2 that undergoes nonsense-mediated decay and affects antigen presentation. PLoS Genet 2010; 6:e1001157. [PMID: 20976248 PMCID: PMC2954825 DOI: 10.1371/journal.pgen.1001157] [Citation(s) in RCA: 179] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Accepted: 09/13/2010] [Indexed: 11/18/2022] Open
Abstract
A remarkable characteristic of the human major histocompatibility complex (MHC) is its extreme genetic diversity, which is maintained by balancing selection. In fact, the MHC complex remains one of the best-known examples of natural selection in humans, with well-established genetic signatures and biological mechanisms for the action of selection. Here, we present genetic and functional evidence that another gene with a fundamental role in MHC class I presentation, endoplasmic reticulum aminopeptidase 2 (ERAP2), has also evolved under balancing selection and contains a variant that affects antigen presentation. Specifically, genetic analyses of six human populations revealed strong and consistent signatures of balancing selection affecting ERAP2. This selection maintains two highly differentiated haplotypes (Haplotype A and Haplotype B), with frequencies 0.44 and 0.56, respectively. We found that ERAP2 expressed from Haplotype B undergoes differential splicing and encodes a truncated protein, leading to nonsense-mediated decay of the mRNA. To investigate the consequences of ERAP2 deficiency on MHC presentation, we correlated surface MHC class I expression with ERAP2 genotypes in primary lymphocytes. Haplotype B homozygotes had lower levels of MHC class I expressed on the surface of B cells, suggesting that naturally occurring ERAP2 deficiency affects MHC presentation and immune response. Interestingly, an ERAP2 paralog, endoplasmic reticulum aminopeptidase 1 (ERAP1), also shows genetic signatures of balancing selection. Together, our findings link the genetic signatures of selection with an effect on splicing and a cellular phenotype. Although the precise selective pressure that maintains polymorphism is unknown, the demonstrated differences between the ERAP2 splice forms provide important insights into the potential mechanism for the action of selection. It has long been known that the extremely high levels of genetic diversity present in the major histocompatibility locus (MHC) are due to balancing selection, a type of natural selection that maintains advantageous genetic diversity in populations. The MHC encodes for molecules required for a type of antigen presentation that mediates detection of infected and cancerous cells by the immune system; the genetic diversity of the MHC thus ensures an adequate response to the wide variety of pathogens that humans encounter. Here, we show that other genes involved in the same antigen-presentation pathway are also subject to balancing selection in humans. Specifically, we show that balancing selection acts to maintain two forms of the endoplasmic reticulum aminopeptidase 2 gene (ERAP2), which encodes a protein also involved in antigen presentation. Although the two ERAP2 forms are present in a similar frequency (close to 0.5), they are associated with differences with respect to the levels of MHC molecules on the cell surface of immune cells. In summary, our findings show that natural selection maintains variants of ERAP2 that affect immune surveillance; they also establish ERAP2 as one of the few examples of balancing selection in humans where the selected variant, its functional consequences, and its influence in interpersonal diversity are known.
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Affiliation(s)
- Aida M Andrés
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA.
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10
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Antonellis A, Huynh JL, Lee-Lin SQ, Vinton RM, Renaud G, Loftus SK, Elliot G, Wolfsberg TG, Green ED, McCallion AS, Pavan WJ. Identification of neural crest and glial enhancers at the mouse Sox10 locus through transgenesis in zebrafish. PLoS Genet 2008; 4:e1000174. [PMID: 18773071 PMCID: PMC2518861 DOI: 10.1371/journal.pgen.1000174] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2008] [Accepted: 07/17/2008] [Indexed: 11/18/2022] Open
Abstract
Sox10 is a dynamically regulated transcription factor gene that is essential for the development of neural crest-derived and oligodendroglial populations. Developmental genes often require multiple regulatory sequences that integrate discrete and overlapping functions to coordinate their expression. To identify Sox10 cis-regulatory elements, we integrated multiple model systems, including cell-based screens and transposon-mediated transgensis in zebrafish, to scrutinize mammalian conserved, noncoding genomic segments at the mouse Sox10 locus. We demonstrate that eight of 11 Sox10 genomic elements direct reporter gene expression in transgenic zebrafish similar to patterns observed in transgenic mice, despite an absence of observable sequence conservation between mice and zebrafish. Multiple segments direct expression in overlapping populations of neural crest derivatives and glial cells, ranging from pan-Sox10 and pan-neural crest regulatory control to the modulation of expression in subpopulations of Sox10-expressing cells, including developing melanocytes and Schwann cells. Several sequences demonstrate overlapping spatial control, yet direct expression in incompletely overlapping developmental intervals. We were able to partially explain neural crest expression patterns by the presence of head to head SoxE family binding sites within two of the elements. Moreover, we were able to use this transcription factor binding site signature to identify the corresponding zebrafish enhancers in the absence of overall sequence homology. We demonstrate the utility of zebrafish transgenesis as a high-fidelity surrogate in the dissection of mammalian gene regulation, especially those with dynamically controlled developmental expression.
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Affiliation(s)
- Anthony Antonellis
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jimmy L. Huynh
- McKusick–Nathans Institute of Genetic Medicine, Department of Molecular and Comparative Pathobiology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Shih-Queen Lee-Lin
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Ryan M. Vinton
- McKusick–Nathans Institute of Genetic Medicine, Department of Molecular and Comparative Pathobiology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Gabriel Renaud
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Stacie K. Loftus
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Gene Elliot
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Tyra G. Wolfsberg
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Eric D. Green
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Andrew S. McCallion
- McKusick–Nathans Institute of Genetic Medicine, Department of Molecular and Comparative Pathobiology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- * E-mail:
| | - William J. Pavan
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
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11
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Antonellis A, Lee-Lin SQ, Wasterlain A, Leo P, Quezado M, Goldfarb LG, Myung K, Burgess S, Fischbeck KH, Green ED. Functional analyses of glycyl-tRNA synthetase mutations suggest a key role for tRNA-charging enzymes in peripheral axons. J Neurosci 2006; 26:10397-406. [PMID: 17035524 PMCID: PMC6674701 DOI: 10.1523/jneurosci.1671-06.2006] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.7] [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] [Indexed: 12/11/2022] Open
Abstract
Charcot-Marie-Tooth disease type 2D (CMT2D) and distal spinal muscular atrophy type V (dSMA-V) are axonal neuropathies characterized by a phenotype that is more severe in the upper extremities. We previously implicated mutations in the gene encoding glycyl-tRNA synthetase (GARS) as the cause of CMT2D and dSMA-V. GARS is a member of the family of aminoacyl-tRNA synthetases responsible for charging tRNA with cognate amino acids; GARS ligates glycine to tRNA(Gly). Here, we present functional analyses of disease-associated GARS mutations and show that there are not any significant mutation-associated changes in GARS expression levels; that the majority of identified GARS mutations modeled in yeast severely impair viability; and that, in most cases, mutant GARS protein mislocalizes in neuronal cells. Indeed, four of the five mutations studied show loss-of-function features in at least one assay, suggesting that tRNA-charging deficits play a role in disease pathogenesis. Finally, we detected endogenous GARS-associated granules in the neurite projections of cultured neurons and in the peripheral nerve axons of normal human tissue. These data are particularly important in light of the recent identification of CMT-associated mutations in another tRNA synthetase gene [YARS (tyrosyl-tRNA synthetase gene)]. Together, these findings suggest that tRNA-charging enzymes play a key role in maintaining peripheral axons.
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Affiliation(s)
| | | | | | - Paul Leo
- Genetic Disease Research Branch, and
| | | | | | - Kyungjae Myung
- Genetics and Molecular Biology Branch, National Human Genome Research Institute
| | | | - Kenneth H. Fischbeck
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892
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12
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Antonellis A, Bennett WR, Menheniott TR, Prasad AB, Lee-Lin SQ, Green ED, Paisley D, Kelsh RN, Pavan WJ, Ward A. Deletion of long-range sequences at Sox10 compromises developmental expression in a mouse model of Waardenburg-Shah (WS4) syndrome. Hum Mol Genet 2005; 15:259-71. [PMID: 16330480 DOI: 10.1093/hmg/ddi442] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [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: 11/13/2022] Open
Abstract
The transcription factor SOX10 is mutated in the human neurocristopathy Waardenburg-Shah syndrome (WS4), which is characterized by enteric aganglionosis and pigmentation defects. SOX10 directly regulates genes expressed in neural crest lineages, including the enteric ganglia and melanocytes. Although some SOX10 target genes have been reported, the mechanisms by which SOX10 expression is regulated remain elusive. Here, we describe a transgene-insertion mutant mouse line (Hry) that displays partial enteric aganglionosis, a loss of melanocytes, and decreased Sox10 expression in homozygous embryos. Mutation analysis of Sox10 coding sequences was negative, suggesting that non-coding regulatory sequences are disrupted. To isolate the Hry molecular defect, Sox10 genomic sequences were collected from multiple species, comparative sequence analysis was performed and software was designed (ExactPlus) to identify identical sequences shared among species. Mutation analysis of conserved sequences revealed a 15.9 kb deletion located 47.3 kb upstream of Sox10 in Hry mice. ExactPlus revealed three clusters of highly conserved sequences within the deletion, one of which shows strong enhancer potential in cultured melanocytes. These studies: (i) present a novel hypomorphic Sox10 mutation that results in a WS4-like phenotype in mice; (ii) demonstrate that a 15.9 kb deletion underlies the observed phenotype and likely removes sequences essential for Sox10 expression; (iii) combine a novel in silico method for comparative sequence analysis with in vitro functional assays to identify candidate regulatory sequences deleted in this strain. These studies will direct further analyses of Sox10 regulation and provide candidate sequences for mutation detection in WS4 patients lacking a SOX10-coding mutation.
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Affiliation(s)
- Anthony Antonellis
- Geome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
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13
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Antonellis A, Ellsworth RE, Sambuughin N, Puls I, Abel A, Lee-Lin SQ, Jordanova A, Kremensky I, Christodoulou K, Middleton LT, Sivakumar K, Ionasescu V, Funalot B, Vance JM, Goldfarb LG, Fischbeck KH, Green ED. Glycyl tRNA synthetase mutations in Charcot-Marie-Tooth disease type 2D and distal spinal muscular atrophy type V. Am J Hum Genet 2003; 72:1293-9. [PMID: 12690580 PMCID: PMC1180282 DOI: 10.1086/375039] [Citation(s) in RCA: 408] [Impact Index Per Article: 19.4] [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: 01/28/2003] [Accepted: 02/20/2003] [Indexed: 11/03/2022] Open
Abstract
Charcot-Marie-Tooth disease type 2D (CMT2D) and distal spinal muscular atrophy type V (dSMA-V) are axonal peripheral neuropathies inherited in an autosomal dominant fashion. Our previous genetic and physical mapping efforts localized the responsible gene(s) to a well-defined region on human chromosome 7p. Here, we report the identification of four disease-associated missense mutations in the glycyl tRNA synthetase gene in families with CMT2D and dSMA-V. This is the first example of an aminoacyl tRNA synthetase being implicated in a human genetic disease, which makes genes that encode these enzymes relevant candidates for other inherited neuropathies and motor neuron diseases.
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Affiliation(s)
- Anthony Antonellis
- Genome Technology Branch, National Human Genome Research Institute, Neurogenetics Branch and Clinical Neurogenetics Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda; Barrow Neurological Institute, Phoenix; Graduate Genetics Program, The George Washington University, Washington, DC; Laboratory of Molecular Pathology, Sofia Medical University, Sofia; Molecular Genetics Department D, The Cyprus Institute of Neurology and Genetics, Nicosia; Division of Medical Genetics, Department of Pediatrics, University of Iowa, Iowa City; Department of Neurology and INSERM U573, Hôpital Sainte-Anne, Paris; and Center for Human Genetics, Institute for Genomic Sciences and Policy, Duke University, Durham, NC
| | - Rachel E. Ellsworth
- Genome Technology Branch, National Human Genome Research Institute, Neurogenetics Branch and Clinical Neurogenetics Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda; Barrow Neurological Institute, Phoenix; Graduate Genetics Program, The George Washington University, Washington, DC; Laboratory of Molecular Pathology, Sofia Medical University, Sofia; Molecular Genetics Department D, The Cyprus Institute of Neurology and Genetics, Nicosia; Division of Medical Genetics, Department of Pediatrics, University of Iowa, Iowa City; Department of Neurology and INSERM U573, Hôpital Sainte-Anne, Paris; and Center for Human Genetics, Institute for Genomic Sciences and Policy, Duke University, Durham, NC
| | - Nyamkhishig Sambuughin
- Genome Technology Branch, National Human Genome Research Institute, Neurogenetics Branch and Clinical Neurogenetics Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda; Barrow Neurological Institute, Phoenix; Graduate Genetics Program, The George Washington University, Washington, DC; Laboratory of Molecular Pathology, Sofia Medical University, Sofia; Molecular Genetics Department D, The Cyprus Institute of Neurology and Genetics, Nicosia; Division of Medical Genetics, Department of Pediatrics, University of Iowa, Iowa City; Department of Neurology and INSERM U573, Hôpital Sainte-Anne, Paris; and Center for Human Genetics, Institute for Genomic Sciences and Policy, Duke University, Durham, NC
| | - Imke Puls
- Genome Technology Branch, National Human Genome Research Institute, Neurogenetics Branch and Clinical Neurogenetics Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda; Barrow Neurological Institute, Phoenix; Graduate Genetics Program, The George Washington University, Washington, DC; Laboratory of Molecular Pathology, Sofia Medical University, Sofia; Molecular Genetics Department D, The Cyprus Institute of Neurology and Genetics, Nicosia; Division of Medical Genetics, Department of Pediatrics, University of Iowa, Iowa City; Department of Neurology and INSERM U573, Hôpital Sainte-Anne, Paris; and Center for Human Genetics, Institute for Genomic Sciences and Policy, Duke University, Durham, NC
| | - Annette Abel
- Genome Technology Branch, National Human Genome Research Institute, Neurogenetics Branch and Clinical Neurogenetics Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda; Barrow Neurological Institute, Phoenix; Graduate Genetics Program, The George Washington University, Washington, DC; Laboratory of Molecular Pathology, Sofia Medical University, Sofia; Molecular Genetics Department D, The Cyprus Institute of Neurology and Genetics, Nicosia; Division of Medical Genetics, Department of Pediatrics, University of Iowa, Iowa City; Department of Neurology and INSERM U573, Hôpital Sainte-Anne, Paris; and Center for Human Genetics, Institute for Genomic Sciences and Policy, Duke University, Durham, NC
| | - Shih-Queen Lee-Lin
- Genome Technology Branch, National Human Genome Research Institute, Neurogenetics Branch and Clinical Neurogenetics Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda; Barrow Neurological Institute, Phoenix; Graduate Genetics Program, The George Washington University, Washington, DC; Laboratory of Molecular Pathology, Sofia Medical University, Sofia; Molecular Genetics Department D, The Cyprus Institute of Neurology and Genetics, Nicosia; Division of Medical Genetics, Department of Pediatrics, University of Iowa, Iowa City; Department of Neurology and INSERM U573, Hôpital Sainte-Anne, Paris; and Center for Human Genetics, Institute for Genomic Sciences and Policy, Duke University, Durham, NC
| | - Albena Jordanova
- Genome Technology Branch, National Human Genome Research Institute, Neurogenetics Branch and Clinical Neurogenetics Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda; Barrow Neurological Institute, Phoenix; Graduate Genetics Program, The George Washington University, Washington, DC; Laboratory of Molecular Pathology, Sofia Medical University, Sofia; Molecular Genetics Department D, The Cyprus Institute of Neurology and Genetics, Nicosia; Division of Medical Genetics, Department of Pediatrics, University of Iowa, Iowa City; Department of Neurology and INSERM U573, Hôpital Sainte-Anne, Paris; and Center for Human Genetics, Institute for Genomic Sciences and Policy, Duke University, Durham, NC
| | - Ivo Kremensky
- Genome Technology Branch, National Human Genome Research Institute, Neurogenetics Branch and Clinical Neurogenetics Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda; Barrow Neurological Institute, Phoenix; Graduate Genetics Program, The George Washington University, Washington, DC; Laboratory of Molecular Pathology, Sofia Medical University, Sofia; Molecular Genetics Department D, The Cyprus Institute of Neurology and Genetics, Nicosia; Division of Medical Genetics, Department of Pediatrics, University of Iowa, Iowa City; Department of Neurology and INSERM U573, Hôpital Sainte-Anne, Paris; and Center for Human Genetics, Institute for Genomic Sciences and Policy, Duke University, Durham, NC
| | - Kyproula Christodoulou
- Genome Technology Branch, National Human Genome Research Institute, Neurogenetics Branch and Clinical Neurogenetics Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda; Barrow Neurological Institute, Phoenix; Graduate Genetics Program, The George Washington University, Washington, DC; Laboratory of Molecular Pathology, Sofia Medical University, Sofia; Molecular Genetics Department D, The Cyprus Institute of Neurology and Genetics, Nicosia; Division of Medical Genetics, Department of Pediatrics, University of Iowa, Iowa City; Department of Neurology and INSERM U573, Hôpital Sainte-Anne, Paris; and Center for Human Genetics, Institute for Genomic Sciences and Policy, Duke University, Durham, NC
| | - Lefkos T. Middleton
- Genome Technology Branch, National Human Genome Research Institute, Neurogenetics Branch and Clinical Neurogenetics Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda; Barrow Neurological Institute, Phoenix; Graduate Genetics Program, The George Washington University, Washington, DC; Laboratory of Molecular Pathology, Sofia Medical University, Sofia; Molecular Genetics Department D, The Cyprus Institute of Neurology and Genetics, Nicosia; Division of Medical Genetics, Department of Pediatrics, University of Iowa, Iowa City; Department of Neurology and INSERM U573, Hôpital Sainte-Anne, Paris; and Center for Human Genetics, Institute for Genomic Sciences and Policy, Duke University, Durham, NC
| | - Kumaraswamy Sivakumar
- Genome Technology Branch, National Human Genome Research Institute, Neurogenetics Branch and Clinical Neurogenetics Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda; Barrow Neurological Institute, Phoenix; Graduate Genetics Program, The George Washington University, Washington, DC; Laboratory of Molecular Pathology, Sofia Medical University, Sofia; Molecular Genetics Department D, The Cyprus Institute of Neurology and Genetics, Nicosia; Division of Medical Genetics, Department of Pediatrics, University of Iowa, Iowa City; Department of Neurology and INSERM U573, Hôpital Sainte-Anne, Paris; and Center for Human Genetics, Institute for Genomic Sciences and Policy, Duke University, Durham, NC
| | - Victor Ionasescu
- Genome Technology Branch, National Human Genome Research Institute, Neurogenetics Branch and Clinical Neurogenetics Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda; Barrow Neurological Institute, Phoenix; Graduate Genetics Program, The George Washington University, Washington, DC; Laboratory of Molecular Pathology, Sofia Medical University, Sofia; Molecular Genetics Department D, The Cyprus Institute of Neurology and Genetics, Nicosia; Division of Medical Genetics, Department of Pediatrics, University of Iowa, Iowa City; Department of Neurology and INSERM U573, Hôpital Sainte-Anne, Paris; and Center for Human Genetics, Institute for Genomic Sciences and Policy, Duke University, Durham, NC
| | - Benoit Funalot
- Genome Technology Branch, National Human Genome Research Institute, Neurogenetics Branch and Clinical Neurogenetics Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda; Barrow Neurological Institute, Phoenix; Graduate Genetics Program, The George Washington University, Washington, DC; Laboratory of Molecular Pathology, Sofia Medical University, Sofia; Molecular Genetics Department D, The Cyprus Institute of Neurology and Genetics, Nicosia; Division of Medical Genetics, Department of Pediatrics, University of Iowa, Iowa City; Department of Neurology and INSERM U573, Hôpital Sainte-Anne, Paris; and Center for Human Genetics, Institute for Genomic Sciences and Policy, Duke University, Durham, NC
| | - Jeffery M. Vance
- Genome Technology Branch, National Human Genome Research Institute, Neurogenetics Branch and Clinical Neurogenetics Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda; Barrow Neurological Institute, Phoenix; Graduate Genetics Program, The George Washington University, Washington, DC; Laboratory of Molecular Pathology, Sofia Medical University, Sofia; Molecular Genetics Department D, The Cyprus Institute of Neurology and Genetics, Nicosia; Division of Medical Genetics, Department of Pediatrics, University of Iowa, Iowa City; Department of Neurology and INSERM U573, Hôpital Sainte-Anne, Paris; and Center for Human Genetics, Institute for Genomic Sciences and Policy, Duke University, Durham, NC
| | - Lev G. Goldfarb
- Genome Technology Branch, National Human Genome Research Institute, Neurogenetics Branch and Clinical Neurogenetics Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda; Barrow Neurological Institute, Phoenix; Graduate Genetics Program, The George Washington University, Washington, DC; Laboratory of Molecular Pathology, Sofia Medical University, Sofia; Molecular Genetics Department D, The Cyprus Institute of Neurology and Genetics, Nicosia; Division of Medical Genetics, Department of Pediatrics, University of Iowa, Iowa City; Department of Neurology and INSERM U573, Hôpital Sainte-Anne, Paris; and Center for Human Genetics, Institute for Genomic Sciences and Policy, Duke University, Durham, NC
| | - Kenneth H. Fischbeck
- Genome Technology Branch, National Human Genome Research Institute, Neurogenetics Branch and Clinical Neurogenetics Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda; Barrow Neurological Institute, Phoenix; Graduate Genetics Program, The George Washington University, Washington, DC; Laboratory of Molecular Pathology, Sofia Medical University, Sofia; Molecular Genetics Department D, The Cyprus Institute of Neurology and Genetics, Nicosia; Division of Medical Genetics, Department of Pediatrics, University of Iowa, Iowa City; Department of Neurology and INSERM U573, Hôpital Sainte-Anne, Paris; and Center for Human Genetics, Institute for Genomic Sciences and Policy, Duke University, Durham, NC
| | - Eric D. Green
- Genome Technology Branch, National Human Genome Research Institute, Neurogenetics Branch and Clinical Neurogenetics Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda; Barrow Neurological Institute, Phoenix; Graduate Genetics Program, The George Washington University, Washington, DC; Laboratory of Molecular Pathology, Sofia Medical University, Sofia; Molecular Genetics Department D, The Cyprus Institute of Neurology and Genetics, Nicosia; Division of Medical Genetics, Department of Pediatrics, University of Iowa, Iowa City; Department of Neurology and INSERM U573, Hôpital Sainte-Anne, Paris; and Center for Human Genetics, Institute for Genomic Sciences and Policy, Duke University, Durham, NC
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14
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Antonellis A, Ellsworth RE, Sambuughin N, Puls I, Abel A, Lee-Lin SQ, Jordanova A, Kremensky I, Christodoulou K, Middleton LT, Sivakumar K, Ionasescu V, Funalot B, Vance JM, Goldfarb LG, Fischbeck KH, Green ED. Glycyl tRNA synthetase mutations in Charcot-Marie-Tooth disease type 2D and distal spinal muscular atrophy type V. Am J Hum Genet 2003. [PMID: 12690580 DOI: 10.1086/375039/s0002-9297(07)60657-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Charcot-Marie-Tooth disease type 2D (CMT2D) and distal spinal muscular atrophy type V (dSMA-V) are axonal peripheral neuropathies inherited in an autosomal dominant fashion. Our previous genetic and physical mapping efforts localized the responsible gene(s) to a well-defined region on human chromosome 7p. Here, we report the identification of four disease-associated missense mutations in the glycyl tRNA synthetase gene in families with CMT2D and dSMA-V. This is the first example of an aminoacyl tRNA synthetase being implicated in a human genetic disease, which makes genes that encode these enzymes relevant candidates for other inherited neuropathies and motor neuron diseases.
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Affiliation(s)
- Anthony Antonellis
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
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15
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Thomas JW, Schueler MG, Summers TJ, Blakesley RW, McDowell JC, Thomas PJ, Idol JR, Maduro VVB, Lee-Lin SQ, Touchman JW, Bouffard GG, Beckstrom-Sternberg SM, Green ED. Pericentromeric duplications in the laboratory mouse. Genome Res 2003; 13:55-63. [PMID: 12529306 PMCID: PMC430956 DOI: 10.1101/gr.791403] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [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: 11/24/2022]
Abstract
Duplications have long been postulated to be an important mechanism by which genomes evolve. Interspecies genomic comparisons are one method by which the origin and molecular mechanism of duplications can be inferred. By comparative mapping in human, mouse, and rat, we previously found evidence for a recent chromosome-fission event that occurred in the mouse lineage. Cytogenetic mapping revealed that the genomic segments flanking the fission site appeared to be duplicated, with copies residing near the centromere of multiple mouse chromosomes. Here we report the mapping and sequencing of the regions of mouse chromosomes 5 and 6 involved in this chromosome-fission event as well as the results of comparative sequence analysis with the orthologous human and rat genomic regions. Our data indicate that the duplications associated with mouse chromosomes 5 and 6 are recent and that the resulting duplicated segments share significant sequence similarity with a series of regions near the centromeres of the mouse chromosomes previously identified by cytogenetic mapping. We also identified pericentromeric duplicated segments shared between mouse chromosomes 5 and 1. Finally, novel mouse satellite sequences as well as putative chimeric transcripts were found to be associated with the duplicated segments. Together, these findings demonstrate that pericentromeric duplications are not restricted to primates and may be a common mechanism for genome evolution in mammals.
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Affiliation(s)
- James W Thomas
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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16
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Thomas JW, Prasad AB, Summers TJ, Lee-Lin SQ, Maduro VVB, Idol JR, Ryan JF, Thomas PJ, McDowell JC, Green ED. Parallel construction of orthologous sequence-ready clone contig maps in multiple species. Genome Res 2002; 12:1277-85. [PMID: 12176935 PMCID: PMC186643 DOI: 10.1101/gr.283202] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.6] [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: 01/24/2023]
Abstract
Comparison is a fundamental tool for analyzing DNA sequence. Interspecies sequence comparison is particularly powerful for inferring genome function and is based on the simple premise that conserved sequences are likely to be important. Thus, the comparison of a genomic sequence with its orthologous counterpart from another species is increasingly becoming an integral component of genome analysis. In ideal situations, such comparisons are performed with orthologous sequences from multiple species. To facilitate multispecies comparative sequence analysis, a robust and scalable strategy for simultaneously constructing sequence-ready bacterial artificial chromosome (BAC) contig maps from targeted genomic regions has been developed. Central to this approach is the generation and utilization of "universal" oligonucleotide-based hybridization probes ("overgo" probes), which are designed from sequences that are highly conserved between distantly related species. Large collections of these probes are used en masse to screen BAC libraries from multiple species in parallel, with the isolated clones assembled into physical contig maps. To validate the effectiveness of this strategy, efforts were focused on the construction of BAC-based physical maps from multiple mammalian species (chimpanzee, baboon, cat, dog, cow, and pig). Using available human and mouse genomic sequence and a newly developed computer program to design the requisite probes, sequence-ready maps were constructed in all species for a series of targeted regions totaling approximately 16 Mb in the human genome. The described approach can be used to facilitate the multispecies comparative sequencing of targeted genomic regions and can be adapted for constructing BAC contig maps in other vertebrates.
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Affiliation(s)
- James W Thomas
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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17
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Summers TJ, Thomas JW, Lee-Lin SQ, Maduro VV, Idol JR, Green ED. Comparative physical mapping of targeted regions of the rat genome. Mamm Genome 2001; 12:508-12. [PMID: 11420612 DOI: 10.1007/s003350020021] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [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: 12/05/2000] [Accepted: 02/27/2001] [Indexed: 12/01/2022]
Abstract
The comparative mapping and sequencing of vertebrate genomes is now a key priority for the Human Genome Project. In addition to finishing the human genome sequence and generating a 'working draft' of the mouse genome sequence, significant attention is rapidly turning to the analysis of other model organisms, such as the laboratory rat (Rattus norvegicus). As a complement to genome-wide mapping and sequencing efforts, it is often important to generate detailed maps and sequence data for specific regions of interest. Using an adaptation of our previously described approach for constructing mouse comparative and physical maps, we have established a general strategy for targeted mapping of the rat genome. Specifically, we constructed a framework comparative map of human Chromosome (Chr) 7 and the orthologous regions of the rat genome, as well as two large (>1-Mb) P1-derived artificial chromosome (PAC)-based physical maps. Generation of these physical maps involved the use of mouse-derived probes that cross-hybridized with rat PAC clones. The first PAC map encompasses the cystic fibrosis transmembrane conductance regulator gene (Cftr), while the second map allows a three-species comparison of a genomic region containing intra- and inter-chromosomal evolutionary rearrangements. The studies reported here further demonstrate that cross-species hybridization between related animals, such as rat and mouse, can be readily used for the targeted construction of clone-based physical maps, thereby accelerating the analysis of biologically interesting regions of vertebrate genomes.
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Affiliation(s)
- T J Summers
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, 49 Convent Dr., Bldg. 49, Rm. 2A08 Bethesda, Maryland 20892, USA
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18
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Thomas JW, Summers TJ, Lee-Lin SQ, Maduro VV, Idol JR, Mastrian SD, Ryan JF, Jamison DC, Green ED. Comparative genome mapping in the sequence-based era: early experience with human chromosome 7. Genome Res 2000; 10:624-33. [PMID: 10810084 PMCID: PMC310865 DOI: 10.1101/gr.10.5.624] [Citation(s) in RCA: 22] [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: 11/24/2022]
Abstract
The success of the ongoing Human Genome Project has resulted in accelerated plans for completing the human genome sequence and the earlier-than-anticipated initiation of efforts to sequence the mouse genome. As a complement to these efforts, we are utilizing the available human sequence to refine human-mouse comparative maps and to assemble sequence-ready mouse physical maps. Here we describe how the first glimpses of genomic sequence from human chromosome 7 are directly facilitating these activities. Specifically, we are actively enhancing the available human-mouse comparative map by analyzing human chromosome 7 sequence for the presence of orthologs of mapped mouse genes. Such orthologs can then be precisely positioned relative to mapped human STSs and other genes. The chromosome 7 sequence generated to date has allowed us to more than double the number of genes that can be placed on the comparative map. The latter effort reveals that human chromosome 7 is represented by at least 20 orthologous segments of DNA in the mouse genome. A second component of our program involves systematically analyzing the evolving human chromosome 7 sequence for the presence of matching mouse genes and expressed-sequence tags (ESTs). Mouse-specific hybridization probes are designed from such sequences and used to screen a mouse bacterial artificial chromosome (BAC) library, with the resulting data used to assemble BAC contigs based on probe-content data. Nascent contigs are then expanded using probes derived from newly generated BAC-end sequences. This approach produces BAC-based sequence-ready maps that are known to contain a gene(s) and are homologous to segments of the human genome for which sequence is already available. Our ongoing efforts have thus far resulted in the isolation and mapping of >3,800 mouse BACs, which have been assembled into >100 contigs. These contigs include >250 genes and represent approximately 40% of the mouse genome that is homologous to human chromosome 7. Together, these approaches illustrate how the availability of genomic sequence directly facilitates studies in comparative genomics and genome evolution.
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Affiliation(s)
- J W Thomas
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892 USA
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19
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Sahoo T, Johnson EW, Thomas JW, Kuehl PM, Jones TL, Dokken CG, Touchman JW, Gallione CJ, Lee-Lin SQ, Kosofsky B, Kurth JH, Louis DN, Mettler G, Morrison L, Gil-Nagel A, Rich SS, Zabramski JM, Boguski MS, Green ED, Marchuk DA. Mutations in the gene encoding KRIT1, a Krev-1/rap1a binding protein, cause cerebral cavernous malformations (CCM1). Hum Mol Genet 1999; 8:2325-33. [PMID: 10545614 DOI: 10.1093/hmg/8.12.2325] [Citation(s) in RCA: 268] [Impact Index Per Article: 10.7] [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: 11/13/2022] Open
Abstract
Cerebral cavernous malformations (CCM) are congenital vascular anomalies of the brain that can cause significant neurological disabilities, including intractable seizures and hemorrhagic stroke. One locus for autosomal dominant CCM ( CCM1 ) maps to chromosome 7q21-q22. Recombination events in linked family members define a critical region of approximately 2 Mb and a shared disease haplotype associated with a presumed founder effect in families of Mexican-American descent points to a potentially smaller region of interest. Using a genomic sequence-based positional cloning strategy, we have identified KRIT1, encoding a protein that interacts with the Krev-1/rap1a tumor suppressor, as the CCM1 gene. Seven different KRIT1 mutations have been identified in 23 distinct CCM1 families. The identical mutation is present in 16 of 21 Mexican-American families analyzed, substantiating a founder effect in this population. Other Mexican-American and non-Hispanic Caucasian CCM1 kindreds harbor other KRIT1 mutations. Identification of a common Mexican-American mutation has potential clinical significance for presymptomatic diagnosis of CCM in this population. In addition, these data point to a key role for the Krev-1/rap1a signaling pathway in angiogenesis and cerebrovascular disease.
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Affiliation(s)
- T Sahoo
- Department of Genetics, Duke University Medical Center, Durham, NC 27710, USA
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20
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Thomas JW, Lee-Lin SQ, Green ED. Human-mouse comparative mapping of the genomic region containing CDK6: localization of an evolutionary breakpoint. Mamm Genome 1999; 10:764-7. [PMID: 10384057 DOI: 10.1007/s003359901088] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- J W Thomas
- Genome Technology Branch, National Human Genome Research Institute, 49 Convent Drive, Bldg 49, Room 2A08, National Institutes of Health, Bethesda, Maryland 20892, USA
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21
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Bunnell BA, Kluge KA, Lee-Lin SQ, Byrne ER, Orlic D, Metzger ME, Agricola BA, Wersto RP, Bodine DM, Morgan RA, Donahue RE. Transplantation of transduced nonhuman primate CD34+ cells using a gibbon ape leukemia virus vector: restricted expression of the gibbon ape leukemia virus receptor to a subset of CD34+ cells. Gene Ther 1999; 6:48-56. [PMID: 10341875 DOI: 10.1038/sj.gt.3300808] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [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: 11/08/2022]
Abstract
The transduction efficiencies of immunoselected rhesus macaque (Macaca mulatta) CD34+ cells and colony-forming progenitor cells based on polymerase chain reaction (PCR) analysis were comparable for an amphotropic Moloney murine leukemia virus (MLV) retroviral vector and a retroviral vector derived from the gibbon ape leukemia virus (GaLV) packaging cell line, PG13. On performing autologous transplantation studies using immunoselected CD34+ cells transduced with the GaLV envelope (env) retroviral vector, less than 1% of peripheral blood (PB) contained provirus. This was true whether bone marrow (BM) or cytokine-mobilized PB immunoselected CD34+ cells were reinfused. This level of marking was evident in two animals whose platelet counts never fell below 50,000/microliter and whose leukocyte counts had recovered by days 8 and 10 after having received 1.7 x 10(7) or greater of cytokine-mobilized CD34+ PB cells/kg. Reverse transcriptase(RT)-PCR analysis of CD34+ subsets for both the GaLV and amphotropic receptor were performed. The expression of the GaLV receptor was determined to be restricted to CD34+ Thy-1+ cells, and both CD34+ CD38+ and CD34+ CD38dim cells, while the amphotropic receptor was present on all CD34+ cell subsets examined. Our findings suggest that, in rhesus macaques, PG13-derived retroviral vectors may only be able to transduce a subset of CD34+ cells as only CD34+ Thy-1+ cells express the GaLV receptor.
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Affiliation(s)
- B A Bunnell
- Clinical Gene Therapy Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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22
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Abstract
We wish to report the initial characterization of a recombinant clone containing the BamHI methylase gene. Genomic chromosomal DNA purified from Bacillus amyloliquefaciens was partially cleaved with HindIII, fractionated by size, and cloned into pSP64. Plasmid DNA from this library was challenged with BamHI endonuclease and transformed into Escherichia coli HB101. A recombinant plasmid pBamM6.5 and a subclone pBamM2.5 were shown to contain the BamHI methylase gene based on three independent observations. Both plasmids were found to be resistant to BamHI endonuclease cleavage, and chromosomal DNA isolated from E.coli HB101 cells harboring either of the plasmids pBamM6.5 or pBamM2.5 was resistant to cleavage by BamHI endonuclease. In addition, DNA isolated from lambda phage passaged through E.coli HB101 containing either plasmid was also resistant to BamHI cleavage. Expression of the BamHI methylase gene is dependent on orientation in pSP64. In these clones preliminary evidence indicates that methylase gene expression may be under the direction of the plasmid encoded LacZ promoter.
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Affiliation(s)
- J F Connaughton
- Department of Biochemistry, Georgetown University, School of Medicine, Washington, D. C. 20007
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