1
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Yoo S, Garg E, Elliott LT, Hung RJ, Halevy AR, Brooks JD, Bull SB, Gagnon F, Greenwood C, Lawless JF, Paterson AD, Sun L, Zawati MH, Lerner-Ellis J, Abraham R, Birol I, Bourque G, Garant JM, Gosselin C, Li J, Whitney J, Thiruvahindrapuram B, Herbrick JA, Lorenti M, Reuter MS, Adeoye OO, Liu S, Allen U, Bernier FP, Biggs CM, Cheung AM, Cowan J, Herridge M, Maslove DM, Modi BP, Mooser V, Morris SK, Ostrowski M, Parekh RS, Pfeffer G, Suchowersky O, Taher J, Upton J, Warren RL, Yeung R, Aziz N, Turvey SE, Knoppers BM, Lathrop M, Jones S, Scherer SW, Strug LJ. HostSeq: a Canadian whole genome sequencing and clinical data resource. BMC Genom Data 2023; 24:26. [PMID: 37131148 PMCID: PMC10152008 DOI: 10.1186/s12863-023-01128-3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 02/22/2023] [Indexed: 05/04/2023] Open
Abstract
HostSeq was launched in April 2020 as a national initiative to integrate whole genome sequencing data from 10,000 Canadians infected with SARS-CoV-2 with clinical information related to their disease experience. The mandate of HostSeq is to support the Canadian and international research communities in their efforts to understand the risk factors for disease and associated health outcomes and support the development of interventions such as vaccines and therapeutics. HostSeq is a collaboration among 13 independent epidemiological studies of SARS-CoV-2 across five provinces in Canada. Aggregated data collected by HostSeq are made available to the public through two data portals: a phenotype portal showing summaries of major variables and their distributions, and a variant search portal enabling queries in a genomic region. Individual-level data is available to the global research community for health research through a Data Access Agreement and Data Access Compliance Office approval. Here we provide an overview of the collective project design along with summary level information for HostSeq. We highlight several statistical considerations for researchers using the HostSeq platform regarding data aggregation, sampling mechanism, covariate adjustment, and X chromosome analysis. In addition to serving as a rich data source, the diversity of study designs, sample sizes, and research objectives among the participating studies provides unique opportunities for the research community.
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Affiliation(s)
- S Yoo
- The Hospital for Sick Children, Toronto, ON, Canada
- University of Ottawa, Ottawa, ON, Canada
| | - E Garg
- Simon Fraser University, Burnaby, BC, Canada
| | - L T Elliott
- Simon Fraser University, Burnaby, BC, Canada
| | - R J Hung
- University of Toronto, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | - A R Halevy
- The Hospital for Sick Children, Toronto, ON, Canada
| | - J D Brooks
- University of Toronto, Toronto, ON, Canada
| | - S B Bull
- University of Toronto, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | - F Gagnon
- University of Toronto, Toronto, ON, Canada
| | - Cmt Greenwood
- McGill University, Montreal, QC, Canada
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada
| | - J F Lawless
- University of Waterloo, Waterloo, ON, Canada
| | - A D Paterson
- The Hospital for Sick Children, Toronto, ON, Canada
- University of Toronto, Toronto, ON, Canada
| | - L Sun
- University of Toronto, Toronto, ON, Canada
| | | | - J Lerner-Ellis
- University of Toronto, Toronto, ON, Canada
- Sinai Health System, Toronto, ON, Canada
| | - Rjs Abraham
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - I Birol
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - G Bourque
- McGill University, Montreal, QC, Canada
| | - J-M Garant
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - C Gosselin
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - J Li
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - J Whitney
- The Hospital for Sick Children, Toronto, ON, Canada
| | | | - J-A Herbrick
- The Hospital for Sick Children, Toronto, ON, Canada
| | - M Lorenti
- The Hospital for Sick Children, Toronto, ON, Canada
| | - M S Reuter
- The Hospital for Sick Children, Toronto, ON, Canada
| | - O O Adeoye
- The Hospital for Sick Children, Toronto, ON, Canada
| | - S Liu
- The Hospital for Sick Children, Toronto, ON, Canada
| | - U Allen
- The Hospital for Sick Children, Toronto, ON, Canada
- University of Toronto, Toronto, ON, Canada
| | - F P Bernier
- University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital, Calgary, AB, Canada
| | - C M Biggs
- University of British Columbia, Vancouver, BC, Canada
- BC Children's Hospital, Vancouver, BC, Canada
- St. Paul's Hospital, Vancouver, BC, Canada
| | - A M Cheung
- University Health Network, Toronto, ON, Canada
| | - J Cowan
- University of Ottawa, Ottawa, ON, Canada
- The Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - M Herridge
- University Health Network, Toronto, ON, Canada
| | | | - B P Modi
- BC Children's Hospital, Vancouver, BC, Canada
| | - V Mooser
- McGill University, Montreal, QC, Canada
| | - S K Morris
- The Hospital for Sick Children, Toronto, ON, Canada
- University of Toronto, Toronto, ON, Canada
| | - M Ostrowski
- University of Toronto, Toronto, ON, Canada
- St. Michael's Hospital, Unity Health, Toronto, ON, Canada
| | - R S Parekh
- The Hospital for Sick Children, Toronto, ON, Canada
- University of Toronto, Toronto, ON, Canada
- Women's College Hospital, Toronto, ON, Canada
| | - G Pfeffer
- University of Calgary, Calgary, AB, Canada
| | | | - J Taher
- University of Toronto, Toronto, ON, Canada
- Sinai Health System, Toronto, ON, Canada
| | - J Upton
- The Hospital for Sick Children, Toronto, ON, Canada
- University of Toronto, Toronto, ON, Canada
| | - R L Warren
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Rsm Yeung
- The Hospital for Sick Children, Toronto, ON, Canada
- University of Toronto, Toronto, ON, Canada
| | - N Aziz
- The Hospital for Sick Children, Toronto, ON, Canada
| | - S E Turvey
- University of British Columbia, Vancouver, BC, Canada
- BC Children's Hospital, Vancouver, BC, Canada
| | | | - M Lathrop
- McGill University, Montreal, QC, Canada
| | - Sjm Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - S W Scherer
- The Hospital for Sick Children, Toronto, ON, Canada
- University of Toronto, Toronto, ON, Canada
| | - L J Strug
- The Hospital for Sick Children, Toronto, ON, Canada.
- University of Toronto, Toronto, ON, Canada.
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2
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Xu J, Liu Y, Li H, Tarashansky AJ, Kalicki CH, Hung RJ, Hu Y, Comjean A, Kolluru SS, Wang B, Quake SR, Luo L, McMahon AP, Dow JAT, Perrimon N. Transcriptional and functional motifs defining renal function revealed by single-nucleus RNA sequencing. Proc Natl Acad Sci U S A 2022; 119:e2203179119. [PMID: 35696569 PMCID: PMC9231607 DOI: 10.1073/pnas.2203179119] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 05/11/2022] [Indexed: 01/09/2023] Open
Abstract
Recent advances in single-cell sequencing provide a unique opportunity to gain novel insights into the diversity, lineage, and functions of cell types constituting a tissue/organ. Here, we performed a single-nucleus study of the adult Drosophila renal system, consisting of Malpighian tubules and nephrocytes, which shares similarities with the mammalian kidney. We identified 11 distinct clusters representing renal stem cells, stellate cells, regionally specific principal cells, garland nephrocyte cells, and pericardial nephrocytes. Characterization of the transcription factors specific to each cluster identified fruitless (fru) as playing a role in stem cell regeneration and Hepatocyte nuclear factor 4 (Hnf4) in regulating glycogen and triglyceride metabolism. In addition, we identified a number of genes, including Rho guanine nucleotide exchange factor at 64C (RhoGEF64c), Frequenin 2 (Frq2), Prip, and CG1093 that are involved in regulating the unusual star shape of stellate cells. Importantly, the single-nucleus dataset allows visualization of the expression at the organ level of genes involved in ion transport and junctional permeability, providing a systems-level view of the organization and physiological roles of the tubules. Finally, a cross-species analysis allowed us to match the fly kidney cell types to mouse kidney cell types and planarian protonephridia, knowledge that will help the generation of kidney disease models. Altogether, our study provides a comprehensive resource for studying the fly kidney.
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Affiliation(s)
- Jun Xu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University, Boston, MA 02115
| | - Yifang Liu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University, Boston, MA 02115
| | - Hongjie Li
- Department of Biology, Stanford University, Stanford, CA 94305
- HHMI, Stanford University, Stanford, CA 94305
| | - Alexander J. Tarashansky
- Department of Bioengineering, Stanford University, Stanford, CA 94305
- Chan Zuckerberg Biohub, San Francisco, CA 94158
| | - Colin H. Kalicki
- Department of Bioengineering, Stanford University, Stanford, CA 94305
| | - Ruei-Jiun Hung
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University, Boston, MA 02115
| | - Yanhui Hu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University, Boston, MA 02115
| | - Aram Comjean
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University, Boston, MA 02115
| | - Sai Saroja Kolluru
- Department of Bioengineering, Stanford University, Stanford, CA 94305
- Chan Zuckerberg Biohub, San Francisco, CA 94158
| | - Bo Wang
- Department of Bioengineering, Stanford University, Stanford, CA 94305
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Stephen R. Quake
- Department of Bioengineering, Stanford University, Stanford, CA 94305
- Chan Zuckerberg Biohub, San Francisco, CA 94158
| | - Liqun Luo
- Department of Biology, Stanford University, Stanford, CA 94305
- HHMI, Stanford University, Stanford, CA 94305
| | - Andrew P. McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089
| | - Julian A. T. Dow
- Institute of Molecular, Cell & Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University, Boston, MA 02115
- HHMI, Harvard University, Boston, MA 02115
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3
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Li H, Janssens J, De Waegeneer M, Kolluru SS, Davie K, Gardeux V, Saelens W, David F, Brbić M, Spanier K, Leskovec J, McLaughlin CN, Xie Q, Jones RC, Brueckner K, Shim J, Tattikota SG, Schnorrer F, Rust K, Nystul TG, Carvalho-Santos Z, Ribeiro C, Pal S, Mahadevaraju S, Przytycka TM, Allen AM, Goodwin SF, Berry CW, Fuller MT, White-Cooper H, Matunis EL, DiNardo S, Galenza A, O’Brien LE, Dow JAT, Jasper H, Oliver B, Perrimon N, Deplancke B, Quake SR, Luo L, Aerts S, Agarwal D, Ahmed-Braimah Y, Arbeitman M, Ariss MM, Augsburger J, Ayush K, Baker CC, Banisch T, Birker K, Bodmer R, Bolival B, Brantley SE, Brill JA, Brown NC, Buehner NA, Cai XT, Cardoso-Figueiredo R, Casares F, Chang A, Clandinin TR, Crasta S, Desplan C, Detweiler AM, Dhakan DB, Donà E, Engert S, Floc'hlay S, George N, González-Segarra AJ, Groves AK, Gumbin S, Guo Y, Harris DE, Heifetz Y, Holtz SL, Horns F, Hudry B, Hung RJ, Jan YN, Jaszczak JS, Jefferis GSXE, Karkanias J, Karr TL, Katheder NS, Kezos J, Kim AA, Kim SK, Kockel L, Konstantinides N, Kornberg TB, Krause HM, Labott AT, Laturney M, Lehmann R, Leinwand S, Li J, Li JSS, Li K, Li K, Li L, Li T, Litovchenko M, Liu HH, Liu Y, Lu TC, Manning J, Mase A, Matera-Vatnick M, Matias NR, McDonough-Goldstein CE, McGeever A, McLachlan AD, Moreno-Roman P, Neff N, Neville M, Ngo S, Nielsen T, O'Brien CE, Osumi-Sutherland D, Özel MN, Papatheodorou I, Petkovic M, Pilgrim C, Pisco AO, Reisenman C, Sanders EN, Dos Santos G, Scott K, Sherlekar A, Shiu P, Sims D, Sit RV, Slaidina M, Smith HE, Sterne G, Su YH, Sutton D, Tamayo M, Tan M, Tastekin I, Treiber C, Vacek D, Vogler G, Waddell S, Wang W, Wilson RI, Wolfner MF, Wong YCE, Xie A, Xu J, Yamamoto S, Yan J, Yao Z, Yoda K, Zhu R, Zinzen RP. Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly. Science 2022; 375:eabk2432. [PMID: 35239393 PMCID: PMC8944923 DOI: 10.1126/science.abk2432] [Citation(s) in RCA: 202] [Impact Index Per Article: 101.0] [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: 01/23/2023]
Abstract
For more than 100 years, the fruit fly Drosophila melanogaster has been one of the most studied model organisms. Here, we present a single-cell atlas of the adult fly, Tabula Drosophilae, that includes 580,000 nuclei from 15 individually dissected sexed tissues as well as the entire head and body, annotated to >250 distinct cell types. We provide an in-depth analysis of cell type-related gene signatures and transcription factor markers, as well as sexual dimorphism, across the whole animal. Analysis of common cell types between tissues, such as blood and muscle cells, reveals rare cell types and tissue-specific subtypes. This atlas provides a valuable resource for the Drosophila community and serves as a reference to study genetic perturbations and disease models at single-cell resolution.
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Affiliation(s)
- Hongjie Li
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA,Huffington Center on Aging and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jasper Janssens
- VIB-KU Leuven Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium,Laboratory of Computational Biology, Department of Human Genetics, KU Leuven, Leuven 3000, Belgium
| | - Maxime De Waegeneer
- VIB-KU Leuven Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium,Laboratory of Computational Biology, Department of Human Genetics, KU Leuven, Leuven 3000, Belgium
| | - Sai Saroja Kolluru
- Departments of Bioengineering and Applied Physics, Stanford University, Stanford CA USA, and Chan Zuckerberg Biohub, San Francisco CA, USA
| | - Kristofer Davie
- VIB-KU Leuven Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium
| | - Vincent Gardeux
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Wouter Saelens
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Fabrice David
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Maria Brbić
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA, and Chan Zuckerberg Biohub, San Francisco CA, USA
| | - Katina Spanier
- VIB-KU Leuven Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium,Laboratory of Computational Biology, Department of Human Genetics, KU Leuven, Leuven 3000, Belgium
| | - Jure Leskovec
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA, and Chan Zuckerberg Biohub, San Francisco CA, USA
| | - Colleen N. McLaughlin
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Qijing Xie
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Robert C. Jones
- Departments of Bioengineering and Applied Physics, Stanford University, Stanford CA USA, and Chan Zuckerberg Biohub, San Francisco CA, USA
| | - Katja Brueckner
- Department of Cell and Tissue Biology, University of California, San Francisco, CA 94143, USA
| | - Jiwon Shim
- Department of Life Science, College of Natural Science, Hanyang University, Seoul, Republic of Korea 04763
| | - Sudhir Gopal Tattikota
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University, Boston, MA 02115; Howard Hughes Medical Institute, Boston, MA, USA
| | - Frank Schnorrer
- Aix-Marseille University, CNRS, IBDM (UMR 7288), Turing Centre for Living systems, 13009 Marseille, France
| | - Katja Rust
- Institute of Physiology and Pathophysiology, Department of Molecular Cell Physiology, Philipps-University, Marburg, Germany,Department of Anatomy, University of California, San Francisco, CA 94143, USA
| | - Todd G. Nystul
- Department of Anatomy, University of California, San Francisco, CA 94143, USA
| | - Zita Carvalho-Santos
- Behavior and Metabolism Laboratory, Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Carlos Ribeiro
- Behavior and Metabolism Laboratory, Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Soumitra Pal
- National Center of Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD 20894, USA
| | - Sharvani Mahadevaraju
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Kidney and Digestive Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Teresa M. Przytycka
- National Center of Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD 20894, USA
| | - Aaron M. Allen
- Centre for Neural Circuits & Behaviour, University of Oxford, Tinsley Building, Mansfield road, Oxford, OX1 3SR, UK
| | - Stephen F. Goodwin
- Centre for Neural Circuits & Behaviour, University of Oxford, Tinsley Building, Mansfield road, Oxford, OX1 3SR, UK
| | - Cameron W. Berry
- Department of Developmental Biology and Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Margaret T. Fuller
- Department of Developmental Biology and Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Helen White-Cooper
- Molecular Biosciences Division, Cardiff University, Cardiff, CF10 3AX UK
| | - Erika L. Matunis
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Stephen DiNardo
- Perelman School of Medicine, The University of Pennsylvania, and The Penn Institute for Regenerative Medicine Philadelphia, PA 19104, USA
| | - Anthony Galenza
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford CA 94305, USA
| | - Lucy Erin O’Brien
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford CA 94305, USA
| | - Julian A. T. Dow
- Institute of Molecular, Cell & Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - FCA Consortium
- FCA Consortium: All authors listed before Acknowledgements, and all contributions and affiliations listed in the Supplementary Materials
| | - Heinrich Jasper
- Immunology Discovery, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Brian Oliver
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Kidney and Digestive Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University, Boston, MA 02115; Howard Hughes Medical Institute, Boston, MA, USA,corresponding authors: (N.P.), (B.D.), (S.R.Q.), (L.L.), (S.A.)
| | - Bart Deplancke
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland,corresponding authors: (N.P.), (B.D.), (S.R.Q.), (L.L.), (S.A.)
| | - Stephen R. Quake
- Departments of Bioengineering and Applied Physics, Stanford University, Stanford CA USA, and Chan Zuckerberg Biohub, San Francisco CA, USA,corresponding authors: (N.P.), (B.D.), (S.R.Q.), (L.L.), (S.A.)
| | - Liqun Luo
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA,corresponding authors: (N.P.), (B.D.), (S.R.Q.), (L.L.), (S.A.)
| | - Stein Aerts
- VIB-KU Leuven Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium,Laboratory of Computational Biology, Department of Human Genetics, KU Leuven, Leuven 3000, Belgium,corresponding authors: (N.P.), (B.D.), (S.R.Q.), (L.L.), (S.A.)
| | - Devika Agarwal
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK
| | | | - Michelle Arbeitman
- Biomedical Sciences Department, Florida State University, Tallahassee, FL, USA
| | - Majd M Ariss
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Jordan Augsburger
- Department of Cell and Tissue Biology, University of California, San Francisco, CA 94143, USA
| | - Kumar Ayush
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Catherine C Baker
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Torsten Banisch
- Skirball Institute and HHMI, New York University Langone Medical Center, New York City, NY 10016, USA
| | - Katja Birker
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Rolf Bodmer
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Benjamin Bolival
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Susanna E Brantley
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Julie A Brill
- Cell Biology Program, The Hospital for Sick Children (SickKids), Toronto, ON M5G 0A4, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Nora C Brown
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Norene A Buehner
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Xiaoyu Tracy Cai
- Immunology Discovery, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Rita Cardoso-Figueiredo
- Behavior and Metabolism Laboratory, Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Fernando Casares
- CABD (Andalusian Centre for Developmental Biology), CSIC-UPO-JA, Seville 41013, Spain
| | - Amy Chang
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Thomas R Clandinin
- Department of Neurobiology, Stanford University, Stanford, CA 94305, USA
| | - Sheela Crasta
- Department of Bioengineering, Stanford University, Stanford, CA, USA.,Department of Applied Physics, Stanford University, Stanford, CA, USA.,Chan Zuckerberg Biohub, San Francisco CA, USA
| | - Claude Desplan
- Department of Biology, New York University, New York, New York 10003, USA
| | | | - Darshan B Dhakan
- Behavior and Metabolism Laboratory, Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Erika Donà
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Stefanie Engert
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Swann Floc'hlay
- VIB-KU Leuven Center for Brain and Disease Research, KU Leuven, Leuven 3000, Belgium.,Laboratory of Computational Biology, Department of Human Genetics, KU Leuven, Leuven 3000, Belgium
| | - Nancy George
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
| | - Amanda J González-Segarra
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Andrew K Groves
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Samantha Gumbin
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yanmeng Guo
- Department of Physiology, Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, San Francisco, CA, USA
| | - Devon E Harris
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yael Heifetz
- The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Stephen L Holtz
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Felix Horns
- Department of Bioengineering and Biophysics Graduate Program, Stanford University, Stanford, CA 94305, USA
| | - Bruno Hudry
- Université Côte d'Azur, CNRS, INSERM, iBV, France
| | - Ruei-Jiun Hung
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Yuh Nung Jan
- Department of Physiology, Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, San Francisco, CA, USA
| | - Jacob S Jaszczak
- Department of Physiology, Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, San Francisco, CA, USA
| | | | | | - Timothy L Karr
- Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA
| | | | - James Kezos
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Anna A Kim
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA.,University of California, Santa Barbara, CA 93106, USA.,Uppsala University, Sweden
| | - Seung K Kim
- Department of Developmental Biology and Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.,Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lutz Kockel
- Department of Developmental Biology and Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nikolaos Konstantinides
- Institut Jacques Monod, Centre National de la Recherche Scientifique-UMR 7592, Université Paris Diderot, Paris, France
| | - Thomas B Kornberg
- Cardiovascular Research Institute, University of California, San Francisco, CA 94143, USA
| | - Henry M Krause
- Donnelly Centre for Cellular and Biomolecular Research, Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Andrew Thomas Labott
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Meghan Laturney
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ruth Lehmann
- Skirball Institute, Department of Cell Biology and HHMI, New York University Langone Medical Center, New York City, NY 10016
| | - Sarah Leinwand
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jiefu Li
- Howard Hughes Medical Institute, Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Joshua Shing Shun Li
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Kai Li
- Department of Physiology, Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, San Francisco, CA, USA
| | - Ke Li
- Department of Physiology, Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, San Francisco, CA, USA
| | - Liying Li
- Department of Physiology, Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, San Francisco, CA, USA
| | - Tun Li
- Department of Physiology, Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, San Francisco, CA, USA
| | - Maria Litovchenko
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Han-Hsuan Liu
- Department of Physiology, Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, San Francisco, CA, USA
| | - Yifang Liu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Tzu-Chiao Lu
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jonathan Manning
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
| | - Anjeli Mase
- Department of Cell and Tissue Biology, University of California, San Francisco, CA 94143, USA
| | | | - Neuza Reis Matias
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Caitlin E McDonough-Goldstein
- Department of Biology, Syracuse University, Syracuse, NY, USA.,Department of Evolutionary Biology, University of Vienna, Vienna, Austria
| | | | - Alex D McLachlan
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Paola Moreno-Roman
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Norma Neff
- Chan Zuckerberg Biohub, San Francisco CA, USA
| | - Megan Neville
- Centre for Neural Circuits and Behaviour, University of Oxford, Oxford OX1 3SR, UK
| | - Sang Ngo
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Tanja Nielsen
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Caitlin E O'Brien
- Department of Physiology, Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, San Francisco, CA, USA
| | - David Osumi-Sutherland
- European Bioinformatics Institute (EMBL/EBI), Wellcome Trust Genome Campus, Cambridge, UK
| | | | - Irene Papatheodorou
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
| | - Maja Petkovic
- Department of Physiology, Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, San Francisco, CA, USA
| | - Clare Pilgrim
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
| | | | - Carolina Reisenman
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Erin Nicole Sanders
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Gilberto Dos Santos
- The Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
| | - Kristin Scott
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Aparna Sherlekar
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Philip Shiu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - David Sims
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK
| | - Rene V Sit
- Chan Zuckerberg Biohub, San Francisco CA, USA
| | - Maija Slaidina
- Skirball Institute, Faculty of Medicine, New York University, New York, NY 10016
| | - Harold E Smith
- Genomics Core, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, MD, USA
| | - Gabriella Sterne
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Yu-Han Su
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Daniel Sutton
- Graduate Program in Genetics and Genomics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Marco Tamayo
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | | | - Ibrahim Tastekin
- Behavior and Metabolism Laboratory, Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Christoph Treiber
- Centre for Neural Circuits and Behaviour, University of Oxford, Tinsley Building, Mansfield Road, Oxford OX1 3TA, UK
| | - David Vacek
- Howard Hughes Medical Institute, Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Georg Vogler
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Scott Waddell
- Centre for Neural Circuits and Behaviour, University of Oxford, Tinsley Building, Mansfield Road, Oxford OX1 3TA, UK
| | - Wanpeng Wang
- Cardiovascular Research Institute, University of California, San Francisco, CA 94143, USA
| | - Rachel I Wilson
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Mariana F Wolfner
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Yiu-Cheung E Wong
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Anthony Xie
- Howard Hughes Medical Institute, Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Jun Xu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Jia Yan
- Chan Zuckerberg Biohub, San Francisco CA, USA
| | - Zepeng Yao
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Kazuki Yoda
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ruijun Zhu
- Department of Physiology, Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, San Francisco, CA, USA
| | - Robert P Zinzen
- Laboratory for Systems Biology of Neural Tissue Differentiation, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrueck Centre for Molecular Medicine (MDC) in the Helmholtz Association, Robert-Roessle-Strasse 12, 13125 Berlin, Germany
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4
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Hung RJ, Li JSS, Liu Y, Perrimon N. Defining cell types and lineage in the Drosophila midgut using single cell transcriptomics. Curr Opin Insect Sci 2021; 47:12-17. [PMID: 33609768 DOI: 10.1016/j.cois.2021.02.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/05/2021] [Accepted: 02/08/2021] [Indexed: 06/12/2023]
Abstract
The Drosophila midgut has emerged in recent years as a model system to study stem cell renewal and differentiation and tissue homeostasis. Histological, genetic and gene expression studies have provided a wealth of information on gut cell types, regionalization, genes and pathways involved in cell proliferation and differentiation, stem cell renewal, and responses to changes in environmental factors such as the microbiota and nutrients. Here, we review the contribution of single cell transcriptomic methods to our understanding of gut cell type diversity, lineage and behavior.
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Affiliation(s)
- Ruei-Jiun Hung
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, United States
| | - Joshua Shing Shun Li
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, United States
| | - Yifang Liu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, United States
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, United States; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, United States.
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5
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Yoon J, Wu H, Hung RJ, Terman JR. Enhanced Production of the Mical Redox Domain for Enzymology and F-actin Disassembly Assays. Int J Mol Sci 2021; 22:ijms22041991. [PMID: 33671465 PMCID: PMC7922515 DOI: 10.3390/ijms22041991] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/09/2021] [Accepted: 02/13/2021] [Indexed: 11/16/2022] Open
Abstract
To change their behaviors, cells require actin proteins to assemble together into long polymers/filaments—and so a critical goal is to understand the factors that control this actin filament (F-actin) assembly and stability. We have identified a family of unusual actin regulators, the MICALs, which are flavoprotein monooxygenase/hydroxylase enzymes that associate with flavin adenine dinucleotide (FAD) and use the co-enzyme nicotinamide adenine dinucleotide phosphate (NADPH) in Redox reactions. F-actin is a specific substrate for these MICAL Redox enzymes, which oxidize specific amino acids within actin to destabilize actin filaments. Furthermore, this MICAL-catalyzed reaction is reversed by another family of Redox enzymes (SelR/MsrB enzymes)—thereby revealing a reversible Redox signaling process and biochemical mechanism regulating actin dynamics. Interestingly, in addition to the MICALs’ Redox enzymatic portion through which MICALs covalently modify and affect actin, MICALs have multiple other domains. Less is known about the roles of these other MICAL domains. Here we provide approaches for obtaining high levels of recombinant protein for the Redox only portion of Mical and demonstrate its catalytic and F-actin disassembly activity. These results provide a ground state for future work aimed at defining the role of the other domains of Mical — including characterizing their effects on Mical’s Redox enzymatic and F-actin disassembly activity.
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Affiliation(s)
- Jimok Yoon
- Departments of Neuroscience and Pharmacology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; (J.Y.); (H.W.); (R.-J.H.)
- Neuroscience Graduate Program, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Heng Wu
- Departments of Neuroscience and Pharmacology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; (J.Y.); (H.W.); (R.-J.H.)
| | - Ruei-Jiun Hung
- Departments of Neuroscience and Pharmacology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; (J.Y.); (H.W.); (R.-J.H.)
- Neuroscience Graduate Program, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jonathan R. Terman
- Departments of Neuroscience and Pharmacology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; (J.Y.); (H.W.); (R.-J.H.)
- Neuroscience Graduate Program, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Correspondence: ; Tel.: +1-214-648-1464; Fax: +1-214-648-1801
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6
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Tattikota SG, Cho B, Liu Y, Hu Y, Barrera V, Steinbaugh MJ, Yoon SH, Comjean A, Li F, Dervis F, Hung RJ, Nam JW, Ho Sui S, Shim J, Perrimon N. A single-cell survey of Drosophila blood. eLife 2020; 9:e54818. [PMID: 32396065 PMCID: PMC7237219 DOI: 10.7554/elife.54818] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [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: 12/30/2019] [Accepted: 05/08/2020] [Indexed: 12/30/2022] Open
Abstract
Drosophila blood cells, called hemocytes, are classified into plasmatocytes, crystal cells, and lamellocytes based on the expression of a few marker genes and cell morphologies, which are inadequate to classify the complete hemocyte repertoire. Here, we used single-cell RNA sequencing (scRNA-seq) to map hemocytes across different inflammatory conditions in larvae. We resolved plasmatocytes into different states based on the expression of genes involved in cell cycle, antimicrobial response, and metabolism together with the identification of intermediate states. Further, we discovered rare subsets within crystal cells and lamellocytes that express fibroblast growth factor (FGF) ligand branchless and receptor breathless, respectively. We demonstrate that these FGF components are required for mediating effective immune responses against parasitoid wasp eggs, highlighting a novel role for FGF signaling in inter-hemocyte crosstalk. Our scRNA-seq analysis reveals the diversity of hemocytes and provides a rich resource of gene expression profiles for a systems-level understanding of their functions.
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Affiliation(s)
| | - Bumsik Cho
- Department of Life Science, Hanyang UniversitySeoulRepublic of Korea
| | - Yifang Liu
- Department of Genetics, Blavatnik Institute, Harvard Medical SchoolBostonUnited States
| | - Yanhui Hu
- Department of Genetics, Blavatnik Institute, Harvard Medical SchoolBostonUnited States
| | | | | | - Sang-Ho Yoon
- Department of Life Science, Hanyang UniversitySeoulRepublic of Korea
| | - Aram Comjean
- Department of Genetics, Blavatnik Institute, Harvard Medical SchoolBostonUnited States
| | - Fangge Li
- Department of Genetics, Blavatnik Institute, Harvard Medical SchoolBostonUnited States
| | - Franz Dervis
- Department of Genetics, Blavatnik Institute, Harvard Medical SchoolBostonUnited States
| | - Ruei-Jiun Hung
- Department of Genetics, Blavatnik Institute, Harvard Medical SchoolBostonUnited States
| | - Jin-Wu Nam
- Department of Life Science, Hanyang UniversitySeoulRepublic of Korea
| | | | - Jiwon Shim
- Department of Life Science, Hanyang UniversitySeoulRepublic of Korea
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical SchoolBostonUnited States
- Howard Hughes Medical InstituteBostonUnited States
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7
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Hung RJ, Hu Y, Kirchner R, Liu Y, Xu C, Comjean A, Tattikota SG, Li F, Song W, Ho Sui S, Perrimon N. A cell atlas of the adult Drosophila midgut. Proc Natl Acad Sci U S A 2020; 117:1514-1523. [PMID: 31915294 PMCID: PMC6983450 DOI: 10.1073/pnas.1916820117] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [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] [Indexed: 12/13/2022] Open
Abstract
Studies of the adult Drosophila midgut have led to many insights in our understanding of cell-type diversity, stem cell regeneration, tissue homeostasis, and cell fate decision. Advances in single-cell RNA sequencing provide opportunities to identify new cell types and molecular features. We used single-cell RNA sequencing to characterize the transcriptome of midgut epithelial cells and identified 22 distinct clusters representing intestinal stem cells, enteroblasts, enteroendocrine cells (EEs), and enterocytes. This unbiased approach recovered most of the known intestinal stem cells/enteroblast and EE markers, highlighting the high quality of the dataset, and led to insights on intestinal stem cell biology, cell type-specific organelle features, the roles of new transcription factors in progenitors and regional variation along the gut, 5 additional EE gut hormones, EE hormonal expression diversity, and paracrine function of EEs. To facilitate mining of this rich dataset, we provide a web-based resource for visualization of gene expression in single cells. Altogether, our study provides a comprehensive resource for addressing functions of genes in the midgut epithelium.
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Affiliation(s)
- Ruei-Jiun Hung
- Department of Genetics, Harvard Medical School, Boston, MA 02115;
| | - Yanhui Hu
- Drosophila RNAi Screening Center, Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Rory Kirchner
- Bioinformatics Core, Harvard T. H. Chan School of Public Health, Boston, MA 02115
| | - Yifang Liu
- Department of Genetics, Harvard Medical School, Boston, MA 02115
- Drosophila RNAi Screening Center, Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Chiwei Xu
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Aram Comjean
- Drosophila RNAi Screening Center, Department of Genetics, Harvard Medical School, Boston, MA 02115
| | | | - Fangge Li
- Drosophila RNAi Screening Center, Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Wei Song
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Shannan Ho Sui
- Bioinformatics Core, Harvard T. H. Chan School of Public Health, Boston, MA 02115
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, Boston, MA 02115;
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115
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8
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Xu C, Tang HW, Hung RJ, Hu Y, Ni X, Housden BE, Perrimon N. The Septate Junction Protein Tsp2A Restricts Intestinal Stem Cell Activity via Endocytic Regulation of aPKC and Hippo Signaling. Cell Rep 2019; 26:670-688.e6. [PMID: 30650359 PMCID: PMC6394833 DOI: 10.1016/j.celrep.2018.12.079] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [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: 02/06/2018] [Revised: 07/24/2018] [Accepted: 12/17/2018] [Indexed: 01/23/2023] Open
Abstract
Hippo signaling and the activity of its transcriptional coactivator, Yorkie (Yki), are conserved and crucial regulators of tissue homeostasis. In the Drosophila midgut, after tissue damage, Yki activity increases to stimulate stem cell proliferation, but how Yki activity is turned off once the tissue is repaired is unknown. From an RNAi screen, we identified the septate junction (SJ) protein tetraspanin 2A (Tsp2A) as a tumor suppressor. Tsp2A undergoes internalization to facilitate the endocytic degradation of atypical protein kinase C (aPKC), a negative regulator of Hippo signaling. In the Drosophila midgut epithelium, adherens junctions (AJs) and SJs are prominent in intestinal stem cells or enteroblasts (ISCs or EBs) and enterocytes (ECs), respectively. We show that when ISCs differentiate toward ECs, Tsp2A is produced, participates in SJ assembly, and turns off aPKC and Yki-JAK-Stat activity. Altogether, our study uncovers a mechanism allowing the midgut to restore Hippo signaling and restrict proliferation once tissue repair is accomplished.
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Affiliation(s)
- Chiwei Xu
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Hong-Wen Tang
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Ruei-Jiun Hung
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Yanhui Hu
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Xiaochun Ni
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Benjamin E Housden
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
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9
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Hancock DB, Guo Y, Reginsson GW, Gaddis NC, Lutz SM, Sherva R, Loukola A, Minica CC, Markunas CA, Han Y, Young KA, Gudbjartsson DF, Gu F, McNeil DW, Qaiser B, Glasheen C, Olson S, Landi MT, Madden PAF, Farrer LA, Vink J, Saccone NL, Neale MC, Kranzler HR, McKay J, Hung RJ, Amos CI, Marazita ML, Boomsma DI, Baker TB, Gelernter J, Kaprio J, Caporaso NE, Thorgeirsson TE, Hokanson JE, Bierut LJ, Stefansson K, Johnson EO. Genome-wide association study across European and African American ancestries identifies a SNP in DNMT3B contributing to nicotine dependence. Mol Psychiatry 2018; 23:1911-1919. [PMID: 28972577 PMCID: PMC5882602 DOI: 10.1038/mp.2017.193] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 07/14/2017] [Accepted: 07/17/2017] [Indexed: 11/09/2022]
Abstract
Cigarette smoking is a leading cause of preventable mortality worldwide. Nicotine dependence, which reduces the likelihood of quitting smoking, is a heritable trait with firmly established associations with sequence variants in nicotine acetylcholine receptor genes and at other loci. To search for additional loci, we conducted a genome-wide association study (GWAS) meta-analysis of nicotine dependence, totaling 38,602 smokers (28,677 Europeans/European Americans and 9925 African Americans) across 15 studies. In this largest-ever GWAS meta-analysis for nicotine dependence and the largest-ever cross-ancestry GWAS meta-analysis for any smoking phenotype, we reconfirmed the well-known CHRNA5-CHRNA3-CHRNB4 genes and further yielded a novel association in the DNA methyltransferase gene DNMT3B. The intronic DNMT3B rs910083-C allele (frequency=44-77%) was associated with increased risk of nicotine dependence at P=3.7 × 10-8 (odds ratio (OR)=1.06 and 95% confidence interval (CI)=1.04-1.07 for severe vs mild dependence). The association was independently confirmed in the UK Biobank (N=48,931) using heavy vs never smoking as a proxy phenotype (P=3.6 × 10-4, OR=1.05, and 95% CI=1.02-1.08). Rs910083-C is also associated with increased risk of squamous cell lung carcinoma in the International Lung Cancer Consortium (N=60,586, meta-analysis P=0.0095, OR=1.05, and 95% CI=1.01-1.09). Moreover, rs910083-C was implicated as a cis-methylation quantitative trait locus (QTL) variant associated with higher DNMT3B methylation in fetal brain (N=166, P=2.3 × 10-26) and a cis-expression QTL variant associated with higher DNMT3B expression in adult cerebellum from the Genotype-Tissue Expression project (N=103, P=3.0 × 10-6) and the independent Brain eQTL Almanac (N=134, P=0.028). This novel DNMT3B cis-acting QTL variant highlights the importance of genetically influenced regulation in brain on the risks of nicotine dependence, heavy smoking and consequent lung cancer.
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Affiliation(s)
- D B Hancock
- Behavioral and Urban Health Program, Behavioral Health and Criminal Justice Division, RTI International, Research Triangle Park, NC, USA.
| | - Y Guo
- Center for Genomics in Public Health and Medicine, RTI International, Research Triangle Park, NC, USA
| | | | - N C Gaddis
- Research Computing Division, RTI International, Research Triangle Park, NC, USA
| | - S M Lutz
- Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - R Sherva
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
| | - A Loukola
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - C C Minica
- Department of Biological Psychology, Vrije Universiteit, Amsterdam, The Netherlands
| | - C A Markunas
- Behavioral and Urban Health Program, Behavioral Health and Criminal Justice Division, RTI International, Research Triangle Park, NC, USA
| | - Y Han
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - K A Young
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - D F Gudbjartsson
- deCODE Genetics/Amgen, Reykjavik, Iceland
- Department of Engineering and Natural Sciences, University of Iceland, Reykjavík, Iceland
| | - F Gu
- Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, United States Department of Health and Human Services, Bethesda, MD, USA
| | - D W McNeil
- Department of Psychology, West Virginia University, Morgantown, WV, USA
- Department of Dental Practice and Rural Health, West Virginia University, Morgantown, WV, USA
| | - B Qaiser
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - C Glasheen
- Behavioral and Urban Health Program, Behavioral Health and Criminal Justice Division, RTI International, Research Triangle Park, NC, USA
| | - S Olson
- Public Health Informatics Program, eHealth, Quality and Analytics Division, RTI International, Research Triangle Park, NC, USA
| | - M T Landi
- Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, United States Department of Health and Human Services, Bethesda, MD, USA
| | - P A F Madden
- Department of Psychiatry, Washington University, St. Louis, MO, USA
| | - L A Farrer
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
- Department of Ophthalmology, Boston University School of Medicine, Boston, MA, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - J Vink
- Department of Biological Psychology, Vrije Universiteit, Amsterdam, The Netherlands
- Behavioural Science Institute, Radboud University, Nijmegen, The Netherlands
| | - N L Saccone
- Department of Genetics, Washington University, St. Louis, MO, USA
| | - M C Neale
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - H R Kranzler
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Crescenz VA Medical Center, Philadelphia, PA, USA
| | - J McKay
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - R J Hung
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, University of Toronto, Toronto, ON, Canada
| | - C I Amos
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - M L Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - D I Boomsma
- Department of Biological Psychology, Vrije Universiteit, Amsterdam, The Netherlands
| | - T B Baker
- Center for Tobacco Research and Intervention, Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - J Gelernter
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
- VA CT Healthcare Center, Department of Psychiatry, West Haven, CT, USA
| | - J Kaprio
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - N E Caporaso
- Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, United States Department of Health and Human Services, Bethesda, MD, USA
| | | | - J E Hokanson
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - L J Bierut
- Department of Psychiatry, Washington University, St. Louis, MO, USA
| | | | - E O Johnson
- Fellow Program and Behavioral Health and Criminal Justice Division, RTI International, Research Triangle Park, NC, USA
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10
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Abstract
The MICALs are a family of phylogenetically conserved cytoplasmic proteins that modulate numerous cellular behaviors and play critical roles in semaphorin-plexin signaling. Our recent results have revealed that the MICALs are an unusual family of actin regulatory proteins that use actin filaments (F-actin) as a direct substrate-controlling F-actin dynamics via stereospecific oxidation of conserved methionine (Met44 and Met47) residues within actin. In particular, the MICALs have a highly conserved flavoprotein monooxygenase (redox) enzymatic domain in their N-terminus that directly oxidizes and destabilizes F-actin. Here, we describe methods to characterize MICAL-mediated F-actin disassembly using in vitro assays with purified proteins.
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Affiliation(s)
- Jimok Yoon
- Departments of Neuroscience and Pharmacology and Neuroscience Graduate Program, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Ruei-Jiun Hung
- Departments of Neuroscience and Pharmacology and Neuroscience Graduate Program, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Jonathan R Terman
- Departments of Neuroscience and Pharmacology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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11
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Kim K, Hung RJ, Perrimon N. miR-263a Regulates ENaC to Maintain Osmotic and Intestinal Stem Cell Homeostasis in Drosophila. Dev Cell 2016; 40:23-36. [PMID: 28017617 DOI: 10.1016/j.devcel.2016.11.023] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 11/04/2016] [Accepted: 11/26/2016] [Indexed: 11/30/2022]
Abstract
Proper regulation of osmotic balance and response to tissue damage is crucial in maintaining intestinal stem cell (ISC) homeostasis. We found that Drosophila miR-263a downregulates the expression of epithelial sodium channel (ENaC) subunits in enterocytes (ECs) to maintain osmotic and ISC homeostasis. In the absence of miR-263a, the intraluminal surface of the intestine displays dehydration-like phenotypes, Na+ levels are increased in ECs, stress pathways are activated in ECs, and ISCs overproliferate. Furthermore, miR-263a mutants have increased bacterial load and expression of antimicrobial peptides. Strikingly, these phenotypes are reminiscent of the pathophysiology of cystic fibrosis (CF) in which loss-of-function mutations in the chloride channel CF transmembrane conductance regulator can elevate the activity of ENaC, suggesting that Drosophila could be used as a model for CF. Finally, we provide evidence that overexpression of miR-183, the human ortholog of miR-263a, can also directly target the expressions of all three subunits of human ENaC.
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Affiliation(s)
- Kevin Kim
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
| | - Ruei-Jiun Hung
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.
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12
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Grintsevich EE, Yesilyurt HG, Rich SK, Hung RJ, Terman JR, Reisler E. F-actin dismantling through a redox-driven synergy between Mical and cofilin. Nat Cell Biol 2016; 18:876-85. [PMID: 27454820 PMCID: PMC4966907 DOI: 10.1038/ncb3390] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 06/21/2016] [Indexed: 02/06/2023]
Abstract
Numerous cellular functions depend on actin filament (F-actin) disassembly. The
best-characterized disassembly proteins, the ADF/cofilins/twinstar, sever filaments and
recycle monomers to promote actin assembly. Cofilin is also a relatively weak actin
disassembler, posing questions about mechanisms of cellular F-actin destabilization. Here
we uncover a key link to targeted F-actin disassembly by finding that F-actin is
efficiently dismantled through a post-translational-mediated synergism between cofilin and
the actin-oxidizing enzyme Mical. We find that Mical-mediated oxidation of actin improves
cofilin binding to filaments, where their combined effect dramatically accelerates F-actin
disassembly compared to either effector alone. This synergism is also necessary and
sufficient for F-actin disassembly in vivo, magnifying the effects of
both Mical and cofilin on cellular remodeling, axon guidance, and Semaphorin/Plexin
repulsion. Mical and cofilin, therefore, form a Redox-dependent synergistic pair that
promotes F-actin instability by rapidly dismantling F-actin and generating
post-translationally modified actin that has altered assembly properties.
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Affiliation(s)
- Elena E Grintsevich
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California 90095, USA
| | - Hunkar Gizem Yesilyurt
- Departments of Neuroscience and Pharmacology and Neuroscience Graduate Program, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Shannon K Rich
- Departments of Neuroscience and Pharmacology and Neuroscience Graduate Program, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Ruei-Jiun Hung
- Departments of Neuroscience and Pharmacology and Neuroscience Graduate Program, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Jonathan R Terman
- Departments of Neuroscience and Pharmacology and Neuroscience Graduate Program, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Emil Reisler
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California 90095, USA.,Molecular Biology Institute, University of California-Los Angeles, Los Angeles, California 90095, USA
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13
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Wu H, Hung RJ, Terman JR. A simple and efficient method for generating high-quality recombinant Mical enzyme for in vitro assays. Protein Expr Purif 2016; 127:116-124. [PMID: 27223600 DOI: 10.1016/j.pep.2016.05.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 05/12/2016] [Accepted: 05/14/2016] [Indexed: 01/06/2023]
Abstract
We have recently identified a new family of multidomain oxidoreductase (redox) enzymes, the MICALs, that directly regulate the actin cytoskeletal elements necessary for the morphology, motility, and trajectory of cells. Our genetic assays reveal that Mical is both necessary and sufficient for actin organization and cellular effects in vivo and our biochemical assays with purified Mical protein reveal that Mical utilizes its redox activity to directly disassemble actin filaments. These results identify Mical proteins as novel actin disassembly factors and uncover a redox signaling mechanism that directly regulates the actin cytoskeleton. These results have also set the stage for in-depth characterization of the Mical enzyme. However, it has been difficult to obtain sufficient amounts of highly-pure Mical protein to conduct further biochemical, structural, imaging, catalytic, and other high-precision studies. Herein, we describe a means for expressing high levels of soluble recombinant Mical protein in bacteria. Likewise, we have designed a new purification strategy that enables the rapid and efficient purification of milligram quantities of highly-pure and >99% active Mical protein. This new strategy for generating large amounts of highly-pure and active Mical protein will aid research objectives designed to characterize the biochemical, enzymology, and structural biology of Mical and its effects on actin filament dynamics.
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Affiliation(s)
- Heng Wu
- Departments of Neuroscience and Pharmacology and Neuroscience Graduate Program, Harold C. Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Ruei-Jiun Hung
- Departments of Neuroscience and Pharmacology and Neuroscience Graduate Program, Harold C. Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Jonathan R Terman
- Departments of Neuroscience and Pharmacology and Neuroscience Graduate Program, Harold C. Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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14
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Grintsevich EE, Gizem Yesilyurt H, Rich SK, Hung RJ, Terman JR, Reisler E. Targeted Actin Disassembly by Mical and Cofilin. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.1910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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15
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Pesatori AC, Carugno M, Consonni D, Hung RJ, Papadoupolos A, Landi MT, Brenner H, Müller H, Harris CC, Duell EJ, Andrew AS, McLaughlin JR, Schwartz AG, Wenzlaff AS, Stucker I. Hormone use and risk for lung cancer: a pooled analysis from the International Lung Cancer Consortium (ILCCO). Br J Cancer 2013; 109:1954-64. [PMID: 24002594 PMCID: PMC3790162 DOI: 10.1038/bjc.2013.506] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [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: 04/17/2013] [Revised: 07/17/2013] [Accepted: 08/04/2013] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND The association between oral contraceptive (OC) use, hormone replacement therapy (HRT) and lung cancer risk in women is still debated. METHODS We performed a pooled analysis of six case-control studies (1961 cases and 2609 controls) contributing to the International Lung Cancer Consortium. Potential associations were investigated with multivariable unconditional logistic regression and meta-analytic models. Multinomial logistic regressions were performed to investigate lung cancer risk across histologic types. RESULTS A reduced lung cancer risk was found for OC (odds ratio (OR)=0.81; 95% confidence interval (CI): 0.68-0.97) and HRT ever users (OR=0.77; 95% CI: 0.66-0.90). Both oestrogen only and oestrogen+progestin HRT were associated with decreased risk (OR=0.76; 95% CI: 0.61-0.94, and OR=0.66; 95% CI: 0.49-0.88, respectively). No dose-response relationship was observed with years of OC/HRT use. The greatest risk reduction was seen for squamous cell carcinoma (OR=0.53; 95% CI: 0.37-0.76) in OC users and in both adenocarcinoma (OR=0.79; 95% CI: 0.66-0.95) and small cell carcinoma (OR=0.37; 95% CI: 0.19-0.71) in HRT users. No interaction with smoking status or BMI was observed. CONCLUSION Our findings suggest that exogenous hormones can play a protective role in lung cancer aetiology. However, given inconsistencies with epidemiological evidence from cohort studies, further and larger investigations are needed for a more comprehensive view of lung cancer development in women.
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Affiliation(s)
- A C Pesatori
- 1] EPOCA, Epidemiology Research Center, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, via San Barnaba 8, 20122 Milan, Italy [2] Epidemiology Unit, Fondazione IRCCS Ca' Granda-Ospedale Maggiore Policlinico, via San Barnaba 8, 20122 Milan, Italy
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16
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Abstract
Different types of cell behavior, including growth, motility, and navigation, require actin proteins to assemble into filaments. Here, we describe a biochemical process that was able to disassemble actin filaments and limit their reassembly. Actin was a specific substrate of the multidomain oxidation-reduction enzyme, Mical, a poorly understood actin disassembly factor that directly responds to Semaphorin/Plexin extracellular repulsive cues. Actin filament subunits were directly modified by Mical on their conserved pointed-end, which is critical for filament assembly. Mical posttranslationally oxidized the methionine 44 residue within the D-loop of actin, simultaneously severing filaments and decreasing polymerization. This mechanism underlying actin cytoskeletal collapse may have broad physiological and pathological ramifications.
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Affiliation(s)
- Ruei-Jiun Hung
- Departments of Neuroscience and Pharmacology and Neuroscience Graduate Program, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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17
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Hung RJ, Terman JR. Extracellular inhibitors, repellents, and semaphorin/plexin/MICAL-mediated actin filament disassembly. Cytoskeleton (Hoboken) 2011; 68:415-33. [PMID: 21800438 PMCID: PMC3612987 DOI: 10.1002/cm.20527] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [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: 06/18/2011] [Accepted: 07/21/2011] [Indexed: 01/29/2023]
Abstract
Multiple extracellular signals have been identified that regulate actin dynamics within motile cells, but how these instructive cues present on the cell surface exert their precise effects on the internal actin cytoskeleton is still poorly understood. One particularly interesting class of these cues is a group of extracellular proteins that negatively alter the movement of cells and their processes. Over the years, these types of events have been described using a variety of terms and herein we provide an overview of inhibitory/repulsive cellular phenomena and highlight the largest known protein family of repulsive extracellular cues, the Semaphorins. Specifically, the Semaphorins (Semas) utilize Plexin cell-surface receptors to dramatically collapse the actin cytoskeleton and we summarize what is known of the direct molecular and biochemical mechanisms of Sema-triggered actin filament (F-actin) disassembly. We also discuss new observations from our lab that reveal that the multidomain oxidoreductase (Redox) enzyme Molecule Interacting with CasL (MICAL), an important mediator of Sema/Plexin repulsion, is a novel F-actin disassembly factor. Our results indicate that MICAL triggers Sema/Plexin-mediated reorganization of the F-actin cytoskeleton and suggest a role for specific Redox signaling events in regulating actin dynamics.
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Affiliation(s)
- Ruei-Jiun Hung
- Departments of Neuroscience and Pharmacology, and Neuroscience Graduate Program, Harold C. Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jonathan R. Terman
- Departments of Neuroscience and Pharmacology, and Neuroscience Graduate Program, Harold C. Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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18
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Szymańska K, Hung RJ, Wünsch-Filho V, Eluf-Neto J, Curado MP, Koifman S, Matos E, Menezes A, Fernandez L, Daudt AW, Boffetta P, Brennan P. Alcohol and tobacco, and the risk of cancers of the upper aerodigestive tract in Latin America: a case-control study. Cancer Causes Control 2011; 22:1037-46. [PMID: 21607590 DOI: 10.1007/s10552-011-9779-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2010] [Accepted: 05/11/2011] [Indexed: 10/18/2022]
Abstract
BACKGROUND Cancers of the upper aerodigestive tract (UADT; including oral cavity, pharynx, larynx and oesophagus) have high incidence rates all over the world, and they are especially frequent in some parts of Latin America. However, the data on the role of the major risk factors in these areas are still limited. METHODS We have evaluated the role of alcohol and tobacco consumption, based on 2,252 upper aerodigestive squamous-cell carcinoma cases and 1,707 controls from seven centres in Brazil, Argentina, and Cuba. RESULTS We show that alcohol drinkers have a risk of UADT cancers that is up to five times higher than that of never-drinkers. A very strong effect of aperitifs and spirits as compared to other alcohol types was observed, with the ORs reaching 12.76 (CI 5.37-30.32) for oesophagus. Tobacco smokers were up to six times more likely to develop aerodigestive cancers than never-smokers, with the ORs reaching 11.14 (7.72-16.08) among current smokers for hypopharynx and larynx cancer. There was a trend for a decrease in risk after quitting alcohol drinking or tobacco smoking for all sites. The interactive effect of alcohol and tobacco was more than multiplicative. In this study, 65% of all UADT cases were attributable to a combined effect of alcohol and tobacco use. CONCLUSIONS In this largest study on UADT cancer in Latin America, we have shown for the first time that a prevailing majority of UADT cancer cases is due to a combined effect of alcohol and tobacco use and could be prevented by quitting the use of either of these two agents.
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Affiliation(s)
- K Szymańska
- International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008, Lyon Cedex, France
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19
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Lin RZ, Wang TP, Hung RJ, Chuang YJ, Chien CCM, Chang HY. Tumor-induced endothelial cell apoptosis: Roles of NAD(P)H oxidase-derived reactive oxygen species. J Cell Physiol 2011; 226:1750-62. [DOI: 10.1002/jcp.22504] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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20
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Hung RJ, Yazdani U, Yoon J, Wu H, Yang T, Gupta N, Huang Z, van Berkel WJH, Terman JR. Mical links semaphorins to F-actin disassembly. Nature 2010; 463:823-7. [PMID: 20148037 DOI: 10.1038/nature08724] [Citation(s) in RCA: 195] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2009] [Accepted: 11/26/2009] [Indexed: 12/22/2022]
Abstract
How instructive cues present on the cell surface have their precise effects on the actin cytoskeleton is poorly understood. Semaphorins are one of the largest families of these instructive cues and are widely studied for their effects on cell movement, navigation, angiogenesis, immunology and cancer. Semaphorins/collapsins were characterized in part on the basis of their ability to drastically alter actin cytoskeletal dynamics in neuronal processes, but despite considerable progress in the identification of semaphorin receptors and their signalling pathways, the molecules linking them to the precise control of cytoskeletal elements remain unknown. Recently, highly unusual proteins of the Mical family of enzymes have been found to associate with the cytoplasmic portion of plexins, which are large cell-surface semaphorin receptors, and to mediate axon guidance, synaptogenesis, dendritic pruning and other cell morphological changes. Mical enzymes perform reduction-oxidation (redox) enzymatic reactions and also contain domains found in proteins that regulate cell morphology. However, nothing is known of the role of Mical or its redox activity in mediating morphological changes. Here we report that Mical directly links semaphorins and their plexin receptors to the precise control of actin filament (F-actin) dynamics. We found that Mical is both necessary and sufficient for semaphorin-plexin-mediated F-actin reorganization in vivo. Likewise, we purified Mical protein and found that it directly binds F-actin and disassembles both individual and bundled actin filaments. We also found that Mical utilizes its redox activity to alter F-actin dynamics in vivo and in vitro, indicating a previously unknown role for specific redox signalling events in actin cytoskeletal regulation. Mical therefore is a novel F-actin-disassembly factor that provides a molecular conduit through which actin reorganization-a hallmark of cell morphological changes including axon navigation-can be precisely achieved spatiotemporally in response to semaphorins.
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Affiliation(s)
- Ruei-Jiun Hung
- Department of Neuroscience, Neuroscience Graduate Program, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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Karami S, Boffetta P, Rothman N, Hung RJ, Stewart T, Zaridze D, Navritalova M, Mates D, Janout V, Kollarova H, Bencko V, Szeszenia-Dabrowska N, Holcatova I, Mukeria A, Gromiec J, Chanock SJ, Brennan P, Chow WH, Moore LE. Renal cell carcinoma, occupational pesticide exposure and modification by glutathione S-transferase polymorphisms. Carcinogenesis 2008; 29:1567-71. [PMID: 18566013 DOI: 10.1093/carcin/bgn153] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
This study investigated associations between occupational pesticide exposure and renal cell carcinoma (RCC) risk. To follow-up on a previous report by Buzio et al., we also considered whether this association could be modified by glutathione S-transferase M1 and T1 (GSTM1 and GSTT1) genotypes. About 1097 RCC cases and 1476 controls from Central and Eastern Europe were interviewed to collect data on lifetime occupational histories. Occupational information for jobs held for at least 12 months duration was coded for pesticide exposures and assessed for frequency and intensity of exposure. GSTM1 and GSTT1 gene deletions were analyzed using TaqMan assays. A significant increase in RCC risk was observed among subjects ever exposed to pesticides [odds ratio (OR): 1.60; 95% confidence interval (CI): 1.00-2.55]. After stratification by genotypes, increased risk was observed among exposed subjects with at least one GSTM1 active allele (OR: 4.00; 95% CI: 1.55-10.33) but not among exposed subjects with two GSTM1 inactive alleles compared with unexposed subjects with two inactive alleles (P-interaction: 0.04). Risk was highest among exposed subjects with both GSTM1 and GSTT1 active genotypes (OR: 6.47; 95% CI: 1.82-23.00; P-interaction: 0.02) compared with unexposed subjects with at least one GSTM1 or T1 inactive genotype. In the largest RCC case-control study with genotype information conducted to date, we observed that risk associated with pesticide exposure was exclusive to individuals with active GSTM1/T1 genotypes. These findings further support the hypothesis that glutathione S-transferase polymorphisms can modify RCC risk associated with occupational pesticide exposure.
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Affiliation(s)
- S Karami
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20852, USA.
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22
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Karami S, Brennan P, Hung RJ, Boffetta P, Toro J, Wilson RT, Zaridze D, Navratilova M, Chatterjee N, Mates D, Janout V, Kollarova H, Bencko V, Szeszenia-Dabrowska N, Holcatova I, Moukeria A, Welch R, Chanock S, Rothman N, Chow WH, Moore LE. Vitamin D receptor polymorphisms and renal cancer risk in Central and Eastern Europe. J Toxicol Environ Health A 2008; 71:367-72. [PMID: 18246496 PMCID: PMC2799224 DOI: 10.1080/15287390701798685] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Previous studies investigated the role of vitamin D intake and cancer risk. The kidney is a major organ for vitamin D metabolism, activity, and calcium homeostasis; therefore, it was hypothesized that dietary vitamin D intake and polymorphisms in the vitamin D receptor (VDR) gene may modify renal cell carcinoma (RCC) risk. Three common VDR gene polymorphisms (BsmI, FokI, TaqI) were evaluated among 925 RCC cases and 1192 controls enrolled in a hospital-based case-control study conducted in Central and Eastern Europe. Overall associations with RCC risk were not observed; however, subgroup analyses revealed associations after stratification by median age of diagnosis and family history of cancer. Among subjects over 60 yr, reduced risks were observed among carriers of the f alleles in the FokI single-nucleotide polymorphism (SNP) (odds ratio [OR] = 0.61 for Ff and OR = 0.74 for ff genotypes) compared to subjects with the FF genotype (P trend = 0.04; P interaction = 0.004). Subjects with the BB BsmI genotype and a positive family history of cancer had lower risk compared to subjects with the bb allele (OR = 0.60; 95% CI: 0.33-1.1; P trend = 0.05). Genotype associations with these subgroups were not modified when dietary sources of vitamin D or calcium were considered. Additional studies of genetic variation in the VDR gene are warranted.
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Affiliation(s)
- S Karami
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA. karamis@ mail.nih.gov
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Moore LE, Brennan P, Karami S, Hung RJ, Hsu C, Boffetta P, Toro J, Zaridze D, Janout V, Bencko V, Navratilova M, Szeszenia-Dabrowska N, Mates D, Mukeria A, Holcatova I, Welch R, Chanock S, Rothman N, Chow WH. Glutathione S -transferase polymorphisms, cruciferous vegetable intake and cancer risk in the Central and Eastern European Kidney Cancer Study. Carcinogenesis 2007; 28:1960-4. [PMID: 17617661 DOI: 10.1093/carcin/bgm151] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [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
High consumption of cruciferous vegetables has been associated with reduced kidney cancer risk in many studies. Isothiocyanates, thought to be responsible for the chemopreventive properties of this food group, are conjugated to glutathione by glutathione S-transferases (GSTs) before urinary excretion. Modification of this relationship by host genetic factors is unknown. We investigated cruciferous vegetable intake in 1097 cases and 1555 controls enrolled in a multicentric case-control study from the Czech Republic, Poland, Romania and Russia. To assess possible gene-diet interactions, genotyped cases (N = 925) and controls (N = 1247) for selected functional or non-synonymous polymorphisms including the GSTM1 deletion, GSTM3 3 bp deletion (IVS6 + 22-AGG) and V224I G>A substitution, GSTT1 deletion and the GSTP1 I105V A>G substitution. The odds ratio (OR) for low (less than once per month) versus high (at least once per week) intake of cruciferous vegetables was 1.29 [95% confidence interval (CI): 1.02-1.62; P-trend = 0.03]. When low intake of cruciferous vegetables (less than once per month) was stratified by GST genotype, higher kidney cancer risks were observed among individuals with the GSTT1 null (OR = 1.86; 95% CI: 1.07-3.23; P-interaction = 0.05) or with both GSTM1/T1 null genotypes (OR = 2.49; 95% CI: 1.08-5.77; P-interaction = 0.05). These data provide additional evidence for the role of cruciferous vegetables in cancer prevention among individuals with common, functional genetic polymorphisms.
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Affiliation(s)
- L E Moore
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892, USA.
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Hung RJ, Chien HS, Lin RZ, Lin CT, Vatsyayan J, Peng HL, Chang HY. Comparative analysis of two UDP-glucose dehydrogenases in Pseudomonas aeruginosa PAO1. J Biol Chem 2007; 282:17738-48. [PMID: 17442666 DOI: 10.1074/jbc.m701824200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [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: 11/06/2022] Open
Abstract
UDP-glucose dehydrogenase (UGDH) catalyzes a two-step NAD(+)-dependent oxidation of UDP-glucose to produce UDP-glucuronic acid, which is a common substrate for the biosynthesis of exopolysaccharide. Searching the Pseudomonas aeruginosa PAO1 genome data base for a UGDH has helped identify two open reading frames, PA2022 and PA3559, which may encode a UGDH. To elucidate their enzymatic identity, the two genes were cloned and overexpressed in Escherichia coli, and the recombinant proteins were purified. Both the gene products are active as dimers and are capable of utilizing UDP-glucose as a substrate to generate UDP-glucuronic acid. The K(m) values of PA2022 and PA3559 for UDP-glucose are approximately 0.1 and 0.4 mM, whereas the K(m) values for NAD(+) are 0.5 and 2.0 mM, respectively. Compared with PA3559, PA2022 exhibits broader substrate specificity, utilizing TDP-glucose and UDP-N-acetylglucosamine with one-third the velocity of that with UDP-glucose. The PA2022 mutant and PA2022-PA3559 double mutant, but not the PA3559 mutant, are more susceptible to chloramphenicol, cefotaxime, and ampicillin. The PA3559 mutant, however, shows a reduced resistance to polymyxin B compared with wild type PAO1. Finally, real time PCR analysis indicates that PA3559 is expressed primarily in low concentrations of Mg(2+), which contrasts with the constitutive expression of PA2022. Although both the enzymes catalyze the same reaction, their enzymatic properties and gene expression profiles indicate that they play distinct physiological roles in P. aeruginosa, as reflected by different phenotypes displayed by the mutants.
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Affiliation(s)
- Ruei-Jiun Hung
- Institute of Molecular Medicine, National Tsing Hua University, Hsin Chu 300, Taiwan
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Abstract
A number of compounds reported in the literature as N-aminomaleimides (2) are, instead, isomeric N-aminoisomaleimides (3). The ubiquity of this mischaracterization and its propagation within the literature are discussed. In addition, the first general synthetic route to aliphatic and aromatic N-substituted aminomaleimides is described. As an illustration, the compound reported to be N-(4-bromophenylamino)maleimide (2b) was prepared and determined to be N-(4-bromophenylamino)isomaleimide (3b). The authentic compound was synthesized by the condensation of 4-bromophenylhydrazine (7b) and the exo-furan/maleic anhydride Diels-Alder adduct (8) in acetic acid to produce the furan-protected aminomaleimide 10b, followed by heating to remove furan through the retro Diels-Alder reaction. The structures of 2b, 3b, and 10b were established unequivocally by X-ray crystallography and other spectroscopic techniques.
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Affiliation(s)
- N R Conley
- The University of Texas at Austin, Department of Chemistry and Biochemistry, 1 University Station, A5300, Austin, TX 78712-0164, USA
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Hung RJ, Hsu IWJ, Dreiling JL, Lee MJ, Williams CA, Oberst MD, Dickson RB, Lin CY. Assembly of adherens junctions is required for sphingosine 1-phosphate-induced matriptase accumulation and activation at mammary epithelial cell-cell contacts. Am J Physiol Cell Physiol 2004; 286:C1159-69. [PMID: 15075215 DOI: 10.1152/ajpcell.00400.2003] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [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: 11/22/2022]
Abstract
Sphingosine 1-phosphate (S1P), a bioactive phospholipid, simultaneously induces actin cytoskeletal rearrangements and activation of matriptase, a membrane-associated serine protease in human mammary epithelial cells. In this study, we used a monoclonal antibody selective for activated, two-chain matriptase to examine the functional relationship between these two S1P-induced events. Ten minutes after exposure of 184 A1N4 mammary epithelial cells to S1P, matriptase was observed to accumulate at cell-cell contacts. Activated matriptase first began to appear as small spots at cell-cell contacts, and then its deposits elongated along cell-cell contacts. Concomitantly, S1P induced assembly of adherens junctions and subcortical actin belts. Matriptase localization was observed to be coincident with markers of adherens junctions at cell-cell contacts but likely not to be incorporated into the tightly bound adhesion plaque. Disruption of subcortical actin belt formation and prevention of adherens junction assembly led to prevention of accumulation and activation of the protease at cell-cell contacts. These data suggest that S1P-induced accumulation and activation of matriptase depend on the S1P-induced adherens junction assembly. Although MAb M32, directed against one of the low-density lipoprotein receptor class A domains of matriptase, blocked S1P-induced activation of the enzyme, the antibody had no effect on S1P-induced actin cytoskeletal rearrangement. Together, these data indicate that actin cytoskeletal rearrangement is necessary but not sufficient for S1P-induced activation of matriptase at cell-cell contacts. The coupling of matriptase activation to adherens junction assembly and actin cytoskeletal rearrangement may serve to ensure tight control of matriptase activity, restricted to cell-cell junctions of mammary epithelial cells.
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Affiliation(s)
- Ruei-Jiun Hung
- Lombardi Cancer Center, Georgetown Univ. Medical Center 3970 Reservoir Rd. NW, Washington, DC 20057-1412, USA
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Hung RJ, Tsao YD, Spauling GF. Gravity effect on lymphocyte deformation through cell shape change. Proc Natl Sci Counc Repub China B 1995; 19:19-42. [PMID: 7770549] [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: 01/27/2023]
Abstract
The effects on human cells (lymphocyte) immersed in a culture liquid under microgravity environment has been investigated. The study was based on the numerical simulation of the Morphology of human cells affected by the time dependent variation of gravity acceleration ranging from 10(-3) to 2 g(o) (g(o) = 9.81 m/s2) in 15 s. Both the free floating cells and the cells which came into contact with the upper and lower inclined walls imposed by the time-dependent reduced gravity acceleration were considered in this study. The results show that, when the gravity acceleration increased, the cell morphology changed from spherical to horizontally elongated ellipsoid for both the free floating cells and the stationary cells on the lower inclined wall while the cell morphology varied from spherical to vertically-elongated ellipsoid for the cells hanging on the upper inclined wall. A test of the deformation of human cells exposed to the variation of gravity levels, carried out in the KC-135 free fall aircraft, show that the results of experimental observations agree exactly with the theoretical model computation described in this paper. These results will be useful for study of the behavior and morphology of cells in space.
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Affiliation(s)
- R J Hung
- Department of Mechanical and Aerospace Engineering, University of Alabama in Huntsville 35899, USA
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