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Kang HM, Subramaniam M, Targ S, Nguyen M, Maliskova L, McCarthy E, Wan E, Wong S, Byrnes L, Lanata CM, Gate RE, Mostafavi S, Marson A, Zaitlen N, Criswell LA, Ye CJ. Author Correction: Multiplexed droplet single-cell RNA-sequencing using natural genetic variation. Nat Biotechnol 2020; 38:1356. [PMID: 33057163 DOI: 10.1038/s41587-020-0715-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Hyun Min Kang
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, Michigan, USA.
| | - Meena Subramaniam
- Biological and Medical Informatics Graduate Program, University of California, San Francisco, San Francisco, California, USA.,Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA.,Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, California, USA.,Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Sasha Targ
- Biological and Medical Informatics Graduate Program, University of California, San Francisco, San Francisco, California, USA.,Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA.,Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, California, USA.,Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA.,Medical Scientist Training Program (MSTP), University of California, San Francisco, San Francisco, California, USA
| | - Michelle Nguyen
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA.,Diabetes Center, University of California, San Francisco, San Francisco, California, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, USA
| | - Lenka Maliskova
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA.,Department of Neurology, University of California, San Francisco, San Francisco, California, USA
| | - Elizabeth McCarthy
- Medical Scientist Training Program (MSTP), University of California, San Francisco, San Francisco, California, USA
| | - Eunice Wan
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA
| | - Simon Wong
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA
| | - Lauren Byrnes
- Developmental and Stem Cell Biology Graduate Program, University of California, San Francisco, San Francisco, California, USA
| | - Cristina M Lanata
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA.,Rosalind Russell/Ephraim P Engleman Rheumatology Research Center, University of California, San Francisco, San Francisco, California, USA
| | - Rachel E Gate
- Biological and Medical Informatics Graduate Program, University of California, San Francisco, San Francisco, California, USA.,Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA.,Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, California, USA.,Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Sara Mostafavi
- Department of Statistics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alexander Marson
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA.,Diabetes Center, University of California, San Francisco, San Francisco, California, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, USA.,Department of Medicine, University of California, San Francisco, San Francisco, California, USA.,UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, USA.,Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Noah Zaitlen
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA.,Department of Medicine, University of California, San Francisco, San Francisco, California, USA.,Lung Biology Center, University of California, San Francisco, San Francisco, California, USA
| | - Lindsey A Criswell
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA.,Department of Medicine, University of California, San Francisco, San Francisco, California, USA.,Rosalind Russell/Ephraim P Engleman Rheumatology Research Center, University of California, San Francisco, San Francisco, California, USA.,Department of Orofacial Sciences, University of California, San Francisco, San Francisco, USA
| | - Chun Jimmie Ye
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA. .,Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, California, USA. .,Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA. .,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA.
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Sörensen M, Kantorek J, Byrnes L, Boutin S, Mall MA, Lasitschka F, Zabeck H, Nguyen D, Dalpke AH. Corrigendum: Pseudomonas aeruginosa Modulates the Antiviral Response of Bronchial Epithelial Cells. Front Immunol 2020; 11:1453. [PMID: 32754158 PMCID: PMC7366873 DOI: 10.3389/fimmu.2020.01453] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 06/04/2020] [Indexed: 11/28/2022] Open
Affiliation(s)
- Michael Sörensen
- Department of Infectious Diseases, Medical Microbiology and Hygiene, University Hospital Heidelberg, Heidelberg, Germany.,Laboratory Enders and Partners, Stuttgart, Germany
| | - Julia Kantorek
- Department of Infectious Diseases, Medical Microbiology and Hygiene, University Hospital Heidelberg, Heidelberg, Germany
| | - Lauren Byrnes
- Department of Infectious Diseases, Medical Microbiology and Hygiene, University Hospital Heidelberg, Heidelberg, Germany
| | - Sébastien Boutin
- Department of Infectious Diseases, Medical Microbiology and Hygiene, University Hospital Heidelberg, Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), University Hospital Heidelberg, Heidelberg, Germany
| | - Marcus A Mall
- Department of Pediatric Pulmonology, Immunology and Intensive Care Medicine, Charité Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health (BIH), Berlin, Germany
| | - Felix Lasitschka
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,TI Biobanking, German Centre for Infection Research (DZIF), Heidelberg, Germany
| | - Heike Zabeck
- Thoraxklinik, University Hospital Heidelberg, Heidelberg, Germany
| | - Dao Nguyen
- Meakins-Christie Laboratories, Research Institute of the McGill University Health Centre, Montreal, QC, Canada.,Department of Medicine, McGill University, Montreal, QC, Canada
| | - Alexander H Dalpke
- Department of Infectious Diseases, Medical Microbiology and Hygiene, University Hospital Heidelberg, Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), University Hospital Heidelberg, Heidelberg, Germany.,Institute of Medical Microbiology and Hygiene, Medical Faculty, Technische Universität Dresden, Dresden, Germany
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Barruet E, Garcia SM, Striedinger K, Wu J, Lee S, Byrnes L, Wong A, Xuefeng S, Tamaki S, Brack AS, Pomerantz JH. Functionally heterogeneous human satellite cells identified by single cell RNA sequencing. eLife 2020; 9:51576. [PMID: 32234209 PMCID: PMC7164960 DOI: 10.7554/elife.51576] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [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: 09/04/2019] [Accepted: 03/27/2020] [Indexed: 12/19/2022] Open
Abstract
Although heterogeneity is recognized within the murine satellite cell pool, a comprehensive understanding of distinct subpopulations and their functional relevance in human satellite cells is lacking. We used a combination of single cell RNA sequencing and flow cytometry to identify, distinguish, and physically separate novel subpopulations of human PAX7+ satellite cells (Hu-MuSCs) from normal muscles. We found that, although relatively homogeneous compared to activated satellite cells and committed progenitors, the Hu-MuSC pool contains clusters of transcriptionally distinct cells with consistency across human individuals. New surface marker combinations were enriched in transcriptional subclusters, including a subpopulation of Hu-MuSCs marked by CXCR4/CD29/CD56/CAV1 (CAV1+). In vitro, CAV1+ Hu-MuSCs are morphologically distinct, and characterized by resistance to activation compared to CAV1- Hu-MuSCs. In vivo, CAV1+ Hu-MuSCs demonstrated increased engraftment after transplantation. Our findings provide a comprehensive transcriptional view of normal Hu-MuSCs and describe new heterogeneity, enabling separation of functionally distinct human satellite cell subpopulations.
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Affiliation(s)
- Emilie Barruet
- Departments of Surgery and Orofacial Sciences, Division of Plastic and Reconstructive Surgery, Program in Craniofacial Biology, Eli and Edythe Broad Center of Regeneration Medicine, University of California, San Francisco, San Francisco, United States
| | - Steven M Garcia
- Departments of Surgery and Orofacial Sciences, Division of Plastic and Reconstructive Surgery, Program in Craniofacial Biology, Eli and Edythe Broad Center of Regeneration Medicine, University of California, San Francisco, San Francisco, United States
| | - Katharine Striedinger
- Departments of Surgery and Orofacial Sciences, Division of Plastic and Reconstructive Surgery, Program in Craniofacial Biology, Eli and Edythe Broad Center of Regeneration Medicine, University of California, San Francisco, San Francisco, United States
| | - Jake Wu
- Departments of Surgery and Orofacial Sciences, Division of Plastic and Reconstructive Surgery, Program in Craniofacial Biology, Eli and Edythe Broad Center of Regeneration Medicine, University of California, San Francisco, San Francisco, United States
| | - Solomon Lee
- Departments of Surgery and Orofacial Sciences, Division of Plastic and Reconstructive Surgery, Program in Craniofacial Biology, Eli and Edythe Broad Center of Regeneration Medicine, University of California, San Francisco, San Francisco, United States
| | - Lauren Byrnes
- University of California San Francisco, San Francisco, United States
| | - Alvin Wong
- Departments of Surgery and Orofacial Sciences, Division of Plastic and Reconstructive Surgery, Program in Craniofacial Biology, Eli and Edythe Broad Center of Regeneration Medicine, University of California, San Francisco, San Francisco, United States
| | - Sun Xuefeng
- Department of Orthopedic Surgery, Eli and Edythe Broad Center of Regeneration Medicine, University of California, San Francisco, San Francisco, United States
| | - Stanley Tamaki
- Departments of Surgery and Orofacial Sciences, Division of Plastic and Reconstructive Surgery, Program in Craniofacial Biology, Eli and Edythe Broad Center of Regeneration Medicine, University of California, San Francisco, San Francisco, United States
| | - Andrew S Brack
- Department of Orthopedic Surgery, Eli and Edythe Broad Center of Regeneration Medicine, University of California, San Francisco, San Francisco, United States
| | - Jason H Pomerantz
- Departments of Surgery and Orofacial Sciences, Division of Plastic and Reconstructive Surgery, Program in Craniofacial Biology, Eli and Edythe Broad Center of Regeneration Medicine, University of California, San Francisco, San Francisco, United States
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4
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Sörensen M, Kantorek J, Byrnes L, Boutin S, Mall MA, Lasitschka F, Zabeck H, Nguyen D, Dalpke AH. Pseudomonas aeruginosa Modulates the Antiviral Response of Bronchial Epithelial Cells. Front Immunol 2020; 11:96. [PMID: 32117250 PMCID: PMC7025480 DOI: 10.3389/fimmu.2020.00096] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 08/27/2019] [Accepted: 01/14/2020] [Indexed: 01/22/2023] Open
Abstract
Cystic fibrosis (CF) patients frequently acquire Pseudomonas aeruginosa infections that have been associated with a bad prognosis and an increased rate of pulmonary exacerbations. Respiratory viruses can cause exacerbations in chronic pulmonary diseases including COPD or asthma and have been suggested to contribute to exacerbations also in CF. In this study we investigated a possible link between P. aeruginosa infection and susceptibility to respiratory viruses. We show that P. aeruginosa is able to block the antiviral response of airway epithelial cells thereby promoting virus infection and spread. Mechanistically, P. aeruginosa secretes the protease AprA in a LasR dependent manner, which is able of directly degrading epithelial-derived IFNλ resulting in inhibition of IFN signaling. In addition, we correlate the virus infection status of CF patients with the ability of patients' P. aeruginosa isolates to degrade IFNλ. In line with this, the infection status of CF patients correlated significantly with the amount of respiratory viruses in sputum. Our data suggest that the interplay between P. aeruginosa and respiratory virus infections might partially explain the association of increased rates of pulmonary exacerbations and P. aeruginosa infections in CF patients.
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Affiliation(s)
- Michael Sörensen
- Department of Infectious Diseases, Medical Microbiology and Hygiene, University Hospital Heidelberg, Heidelberg, Germany.,Laboratory Enders and Partners, Stuttgart, Germany
| | - Julia Kantorek
- Department of Infectious Diseases, Medical Microbiology and Hygiene, University Hospital Heidelberg, Heidelberg, Germany
| | - Lauren Byrnes
- Department of Infectious Diseases, Medical Microbiology and Hygiene, University Hospital Heidelberg, Heidelberg, Germany
| | - Sébastien Boutin
- Department of Infectious Diseases, Medical Microbiology and Hygiene, University Hospital Heidelberg, Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), University Hospital Heidelberg, Heidelberg, Germany
| | - Marcus A Mall
- Department of Pediatric Pulmonology, Immunology and Intensive Care Medicine, Charité Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health (BIH), Berlin, Germany
| | - Felix Lasitschka
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,TI Biobanking, German Centre for Infection Research (DZIF), Heidelberg, Germany
| | - Heike Zabeck
- Thoraxklinik, University Hospital Heidelberg, Heidelberg, Germany
| | - Dao Nguyen
- Meakins-Christie Laboratories, Research Institute of the McGill University Health Centre, Montreal, QC, Canada.,Department of Medicine, McGill University, Montreal, QC, Canada
| | - Alexander H Dalpke
- Department of Infectious Diseases, Medical Microbiology and Hygiene, University Hospital Heidelberg, Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), University Hospital Heidelberg, Heidelberg, Germany.,Institute of Medical Microbiology and Hygiene, Medical Faculty, Technische Universität Dresden, Dresden, Germany
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Kang HM, Subramaniam M, Targ S, Nguyen M, Maliskova L, McCarthy E, Wan E, Wong S, Byrnes L, Lanata CM, Gate RE, Mostafavi S, Marson A, Zaitlen N, Criswell LA, Ye CJ. Multiplexed droplet single-cell RNA-sequencing using natural genetic variation. Nat Biotechnol 2018; 36:89-94. [PMID: 29227470 PMCID: PMC5784859 DOI: 10.1038/nbt.4042] [Citation(s) in RCA: 483] [Impact Index Per Article: 80.5] [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: 03/20/2017] [Accepted: 11/16/2017] [Indexed: 12/25/2022]
Abstract
Droplet single-cell RNA-sequencing (dscRNA-seq) has enabled rapid, massively parallel profiling of transcriptomes. However, assessing differential expression across multiple individuals has been hampered by inefficient sample processing and technical batch effects. Here we describe a computational tool, demuxlet, that harnesses natural genetic variation to determine the sample identity of each droplet containing a single cell (singlet) and detect droplets containing two cells (doublets). These capabilities enable multiplexed dscRNA-seq experiments in which cells from unrelated individuals are pooled and captured at higher throughput than in standard workflows. Using simulated data, we show that 50 single-nucleotide polymorphisms (SNPs) per cell are sufficient to assign 97% of singlets and identify 92% of doublets in pools of up to 64 individuals. Given genotyping data for each of eight pooled samples, demuxlet correctly recovers the sample identity of >99% of singlets and identifies doublets at rates consistent with previous estimates. We apply demuxlet to assess cell-type-specific changes in gene expression in 8 pooled lupus patient samples treated with interferon (IFN)-β and perform eQTL analysis on 23 pooled samples.
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Affiliation(s)
- Hyun Min Kang
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Meena Subramaniam
- Biological and Medical Informatics Graduate Program, University of California, San Francisco, San Francisco, California, USA
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA
- Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, California, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Sasha Targ
- Biological and Medical Informatics Graduate Program, University of California, San Francisco, San Francisco, California, USA
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA
- Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, California, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
- Medical Scientist Training Program (MSTP), University of California, San Francisco, San Francisco, California, USA
| | - Michelle Nguyen
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA
- Diabetes Center, University of California, San Francisco, San Francisco, California, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, USA
| | - Lenka Maliskova
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA
- Department of Neurology, University of California, San Francisco, San Francisco, California, USA
| | - Elizabeth McCarthy
- Medical Scientist Training Program (MSTP), University of California, San Francisco, San Francisco, California, USA
| | - Eunice Wan
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA
| | - Simon Wong
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA
| | - Lauren Byrnes
- Developmental and Stem Cell Biology Graduate Program, University of California, San Francisco, San Francisco, California, USA
| | - Cristina M Lanata
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
- Rosalind Russell/Ephraim P Engleman Rheumatology Research Center, University of California, San Francisco, San Francisco, California, USA
| | - Rachel E Gate
- Biological and Medical Informatics Graduate Program, University of California, San Francisco, San Francisco, California, USA
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA
- Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, California, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Sara Mostafavi
- Department of Statistics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alexander Marson
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA
- Diabetes Center, University of California, San Francisco, San Francisco, California, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, USA
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Noah Zaitlen
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
- Lung Biology Center, University of California, San Francisco, San Francisco, California, USA
| | - Lindsey A Criswell
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
- Rosalind Russell/Ephraim P Engleman Rheumatology Research Center, University of California, San Francisco, San Francisco, California, USA
- Department of Orofacial Sciences, University of California, San Francisco, San Francisco, USA
| | - Chun Jimmie Ye
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA
- Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, California, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
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6
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Byrnes L, Mele S, Faber D. Fenceline Patrol. Am Sci 2011. [DOI: 10.1511/2011.88.76] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Diller L, Mauch P, Medeiros Nancarrow C, Byrnes L, Stevenson MA, Ng A, Garber J. A feasibility study of tamoxifen chemoprevention in Hodgkin's disease (HD) survivors. J Clin Oncol 2004. [DOI: 10.1200/jco.2004.22.90140.8551] [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: 11/20/2022] Open
Affiliation(s)
- L. Diller
- Dana-Farber Cancer Institute, Boston, MA; Brigham and Women's Hospital, Boston, MA; Beth Israel Deaconess Medical Center, Boston, MA
| | - P. Mauch
- Dana-Farber Cancer Institute, Boston, MA; Brigham and Women's Hospital, Boston, MA; Beth Israel Deaconess Medical Center, Boston, MA
| | - C. Medeiros Nancarrow
- Dana-Farber Cancer Institute, Boston, MA; Brigham and Women's Hospital, Boston, MA; Beth Israel Deaconess Medical Center, Boston, MA
| | - L. Byrnes
- Dana-Farber Cancer Institute, Boston, MA; Brigham and Women's Hospital, Boston, MA; Beth Israel Deaconess Medical Center, Boston, MA
| | - M. A. Stevenson
- Dana-Farber Cancer Institute, Boston, MA; Brigham and Women's Hospital, Boston, MA; Beth Israel Deaconess Medical Center, Boston, MA
| | - A. Ng
- Dana-Farber Cancer Institute, Boston, MA; Brigham and Women's Hospital, Boston, MA; Beth Israel Deaconess Medical Center, Boston, MA
| | - J. Garber
- Dana-Farber Cancer Institute, Boston, MA; Brigham and Women's Hospital, Boston, MA; Beth Israel Deaconess Medical Center, Boston, MA
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Abstract
The biological actions of the insulin-like growth factors (IGFs) are mediated primarily by the IGF-I receptor (IGF-IR), and the IGF family has been highly conserved throughout vertebrate evolution. In this study we report the isolation of a 3 kb cDNA clone for the zebrafish IGF-IR that includes the complete 3' untranslated region and polyA tail and mapping of the receptor gene to zebrafish linkage group 7. The open reading frame deduced from the cDNA sequence encompasses the juxtamembrane and protein tyrosine kinase portions of the receptor, and is 70 and 67% identical to the corresponding regions of the IGF-IRs of the turbot and Xenopus, respectively. By RT-PCR, zebrafish IGF-IR expression was detected from early blastula to early larval stages of development. Using whole mount in situ hybridization, IGF-IR expression was detected after gastrulation. Expression was evident in most tissues but was particularly evident in the tail, in eye and ear primordia and in the brain.
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Affiliation(s)
- E Ayaso
- Biochemistry Department, National University of Ireland, Galway, Ireland
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9
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Stenson C, McNair A, Byrnes L, Murphy M, Smith T, Gannon F. Atlantic salmon HNF-3/forkhead: cDNA sequence, evolution, expression, and functional analysis. DNA Cell Biol 2000; 19:59-68. [PMID: 10668792 DOI: 10.1089/104454900314717] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [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: 11/12/2022] Open
Abstract
We report the isolation and characterization of a cDNA encoding an HNF-3 family member (as HNF-3) from Atlantic salmon (Salmo salar L). The important functional domains of HNF-3 proteins that have been characterized previously are revealed by segments of high identity along the alignment of the asHNF-3 with winged helix/forkhead amino acid sequences isolated from other species. A comparison of asHNF-3 cDNA and genomic DNA indicated that there were no introns present in the asHNF-3 gene. Expression of asHNF-3 protein in adult salmon tissues was not exclusive to liver but was also present in the pancreas and intestine. An RT-PCR analysis performed on salmon development showed that asHNF3 expression is detectable before gastrulation at the mid blastula transition stage. Functional analysis of the asHNF-3 protein using a characterized HNF-3 consensus binding site demonstrated that the protein can recognize and bind to specific HNF-3 consensus sequences. We also report the identification of a novel HNF3 binding site in the promoter of the Atlantic salmon transferrin gene.
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Affiliation(s)
- C Stenson
- National Diagnostics Centre/BioResearch Ireland (NDC), Department of Microbiology, National University of Ireland, Galway
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10
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Abstract
Estrogens modulate the expression of many liver-specific genes in oviparous species. For instance, expression of the estrogen receptor and vitellogenin genes is strongly up-regulated by estradiol in rainbow trout liver. Using hepatocyte primary cultures, we demonstrate that trout albumin (Alb) gene is also regulated by this hormone. Indeed, treatment of hepatocytes with 1 microM estradiol led, after 24 h, to a dramatic decrease in Alb mRNA level. To investigate the mechanism of this down-regulation, run-off experiments were performed and mRNA half-lives were determined in the presence and absence of estradiol. The results show that the down-regulation of Alb mRNA expression by estrogens occurs only at the transcriptional level.
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Affiliation(s)
- G Flouriot
- Endocrinologie Moléculaire de la Reproduction, UPRES-A Biologie Cellulaire et Reproduction, INRA, Université de Rennes I, France
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11
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Stenson C, McNair A, Byrnes L, Gannon F. Cloning of an Atlantic salmon transcription factor. Biochem Soc Trans 1996; 24:106S. [PMID: 8674586 DOI: 10.1042/bst024106s] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- C Stenson
- Department of Microbiology, University College Galway
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12
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Deryckere F, Byrnes L, Wagner A, McMorrow T, Gannon F. Salmon HNF1: cDNA sequence, evolution, tissue specificity and binding to the salmon serum albumin promoter. J Mol Biol 1995; 247:1-10. [PMID: 7897653 DOI: 10.1006/jmbi.1994.0115] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [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: 01/27/2023]
Abstract
cDNA clones coding for the transcription factor HNF1 have been isolated from Atlantic salmon (Salmo salar L.). The 559 amino acid residue long encoded protein shows high conservation, with respect to other species, of the domains necessary for DNA-binding: the HNF1 atypical homeodomain, the POU related sequence and the dimerisation domain. Alignment with rat HNF1 protein reveals that the transcription activation domains ADI and ADIII are relatively conserved in the fish sequence whereas ADII is not. Phylogenetic analysis indicates that higher vertebrate HNF1s and the related variant HNF1s (vHNF1s) are more closely related to each other than any of them is to Salmon HNF1, suggesting that the duplication event from which HNF1 and vHNF1 genes arose occurred after the divergence of the tetrapod and teleost ancestors. Northern blot analysis show a single transcript, of about 2.6 kb, which is not exclusive to liver but is also present in intestine, kidney and spleen. Using polymerase chain reaction (PCR) we have isolated the salmon albumin gene promoter which contains, upstream of the TATA box, a potential binding site for HNF1. The salmon HNF1 protein synthesized by in vitro transcription-translation of the full-length cDNA is able to bind specifically with equivalent affinities to either the rat or salmon albumin promoter.
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Affiliation(s)
- F Deryckere
- National Diagnostics Centre/BioResearch Ireland, Department of Microbiology, University College Galway
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Hardiman G, Byrnes L, Peden J, Wolff J, Gannon F. Cloning and sequencing of the Atlantic salmon (Salmo salar) cytochrome c oxidase subunit III gene (coxIII) and analysis of coxIII expression during parr-smolt transformation. Mol Mar Biol Biotechnol 1994; 3:210-216. [PMID: 8000479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Smoltification is the process whereby salmon alter their metabolism in preparation for movement from freshwater to seawater. Differential screening of a cDNA library prepared from post-smolt salmon liver mRNA led to the selection of a smoltification-induced sequence. Analysis of this cDNA revealed that it partially encoded subunit III of the enzyme cytochrome c oxidase. The complete coxIII sequence was amplified from salmon genomic DNA using consensus oligonucleotides based on ATPase 6 and tRNA(GLY) sequences from Pacific salmonid species. Cytochrome c oxidase subunit III liver mRNA levels were found to be significantly increased in salmon smolts. Northern blot analysis revealed a coxIII transcript of approximately 750 bp in all salmon tissues tested except blood. The DNA sequence of coxIII employs the mammalian mitochondrial genetic code and is strongly conserved when compared with that of other species.
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Affiliation(s)
- G Hardiman
- Department of Microbiology, University College Galway, Ireland
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Abstract
Two similar, but distinct, cDNAs for Atlantic salmon serum albumin have been isolated from the same salmon liver. Comparison between the asSA-1 and asSA-2 sequences reveals 1% overall sequence difference.
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Affiliation(s)
- L Byrnes
- Department of Microbiology, University College, Galway, Ireland
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Powell R, Higgins DG, Wolff J, Byrnes L, Stack M, Sharp PM, Gannon F. The salmon gene encoding apolipoprotein A-I: cDNA sequence, tissue expression and evolution. Gene X 1991; 104:155-61. [PMID: 1916288 DOI: 10.1016/0378-1119(91)90245-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
A cDNA encoding an apolipoprotein (Apo) has been isolated from the Atlantic salmon (Salmo salar) and sequenced. It encodes a peptide of 258 amino acids (aa), including a signal peptide of 18 aa, with 5'- and 3'-untranslated regions of the mRNA of 12 and 329 nucleotides, respectively. The protein has structural features in common with other Apo's of human and avian origin, including conserved sequences in the signal peptide and a series of internal repeats of 22 aa. The sequence has been identified as salmon Apo A-I (sApoA-I), and has 23% aa identity with human ApoA-I. Northern-blot analysis using the sApoA-I cDNA probe against total RNA prepared from several salmon tissues detects the expression of this gene in liver, intestine and muscle. A phylogenetic analysis reveals that the mammalian ApoA-I, ApoA-IV and Apo-E aa sequences are more closely related to each other than any of them are to sApoA-I. This suggests that the duplication events, from which A-I, A-IV and E arose, occurred after the divergence of the tetrapod and teleost ancestors.
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Affiliation(s)
- R Powell
- Department of Microbiology, University College, Galway, Ireland
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Abstract
We report here the nucleotide sequence of a cDNA clone encoding a salmon (Salmo salar) ribosomal (r) protein. The encoded protein shows 62.3% and 62% similarity with the L14 and L18 r-proteins in Xenopus laevis and rat, respectively.
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Affiliation(s)
- R Powell
- Department of Microbiology, University College, Galway, Ireland
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Abstract
Atlantic salmon serum albumin is one of the most abundant proteins in salmon liver, representing 1.6% of all clones in a cDNA library made from salmon liver RNA. The DNA from a number of clones was sequenced to reveal an open reading frame of 1,827 bases encoding a 608-amino-acid protein. The sequenced 5' untranslated region is 69 bases long and the 3' untranslated region contains two putative polyadenylation signals and poly(A) tail. Sequence analysis of different clones indicates the presence of a second cDNA for salmon serum albumin. Multiple alignments of salmon serum albumin deduced amino acid sequence with Xenopus laevis, rat, bovine, and human serum albumins shows significant conservation of cysteine residues. The triple domain structure of serum albumin proteins is maintained. Unlike mammalian systems where serum albumin expression appears to be specific to liver only, salmon serum albumin is expressed in muscle also.
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Affiliation(s)
- L Byrnes
- Microbiology Department, University College, Galway, Ireland
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Abstract
Using an antibody against chicken apolipoprotein (apo) A-I, we identified multiple cDNA clones for the protein in two intestinal cDNA libraries in lambda gt11. The complete nucleotide sequence of chicken apoA-I cDNA was determined. The sequence predicts a mature protein of 240 amino acids, a 6-amino acid propeptide and an 18-amino acid signal peptide. Using a 32P-cDNA probe, we detected the presence of apoA-I mRNA in 21 day old chicken intestine, liver, kidney, spleen, breast muscle and brain. The primary sequence of apoA-I contains numerous tandem repeats of 11 and 22 residues in a manner similar to the mammalian proteins. Our analysis of apoA-I sequences from human, rabbit, dog, rat, and chicken indicates that the rate of amino acid substitution is considerably faster in the rat lineage than in other mammalian lineages.
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Affiliation(s)
- L Byrnes
- Department of Cell Biology, Baylor College of Medicine, Houston, TX 77030
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