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Hong JS, Tindall JM, Tindall SR, Sorscher EJ. Mutation accumulation in H. sapiens F508del CFTR countermands dN/dS type genomic analysis. PLoS One 2024; 19:e0305832. [PMID: 39024311 PMCID: PMC11257350 DOI: 10.1371/journal.pone.0305832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 06/05/2024] [Indexed: 07/20/2024] Open
Abstract
Understanding the mechanisms that underlie de novo mutations (DNMs) can be essential for interpreting human evolution, including aspects such as rapidly diverging genes, conservation of non-coding regulatory elements, and somatic DNA adaptation, among others. DNM accumulation in Homo sapiens is often limited to evaluation of human trios or quads across a single generation. Moreover, human SNPs in exons, pseudogenes, or other non-coding elements can be ancient and difficult to date, including polymorphisms attributable to founder effects and identity by descent. In this report, we describe multigenerational evolution of a human coding locus devoid of natural selection, and delineate patterns and principles by which DNMs have accumulated over the past few thousand years. We apply a data set comprising cystic fibrosis transmembrane conductance regulator (CFTR) alleles from 2,393 individuals homozygous for the F508del defect. Additional polymorphism on the F508del background diversified subsequent to a single mutational event during recent human history. Because F508del CFTR is without function, SNPs observed on this haplotype are effectively attributable to factors that govern accumulating de novo mutations. We show profound enhancement of transition, synonymous, and positionally repetitive polymorphisms, indicating appearance of DNMs in a manner evolutionarily designed to protect protein coding DNA against mutational attrition while promoting diversity.
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Affiliation(s)
- Jeong S. Hong
- Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Janice M. Tindall
- Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Samuel R. Tindall
- Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Eric J. Sorscher
- Emory University School of Medicine, Atlanta, Georgia, United States of America
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2
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Tedbury PR, Manfredi C, Degenhardt F, Conway J, Horwath MC, McCracken C, Sorscher AJ, Moreau S, Wright C, Edwards C, Brewer J, Guarner J, de Wit E, Williamson BN, Suthar MS, Ong YT, Roback JD, Alter DN, Holter JC, Karlsen TH, Sacchi N, Romero-Gómez M, Invernizzi P, Fernández J, Buti M, Albillos A, Julià A, Valenti L, Asselta R, Banales JM, Bujanda L, de Cid R, Sarafianos SG, Hong JS, Sorscher EJ, Ehrhardt A. Mechanisms by which the cystic fibrosis transmembrane conductance regulator may influence SARS-CoV-2 infection and COVID-19 disease severity. FASEB J 2023; 37:e23220. [PMID: 37801035 PMCID: PMC10760435 DOI: 10.1096/fj.202300077r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 08/31/2023] [Accepted: 09/12/2023] [Indexed: 10/07/2023]
Abstract
Patients with cystic fibrosis (CF) exhibit pronounced respiratory damage and were initially considered among those at highest risk for serious harm from SARS-CoV-2 infection. Numerous clinical studies have subsequently reported that individuals with CF in North America and Europe-while susceptible to severe COVID-19-are often spared from the highest levels of virus-associated mortality. To understand features that might influence COVID-19 among patients with cystic fibrosis, we studied relationships between SARS-CoV-2 and the gene responsible for CF (i.e., the cystic fibrosis transmembrane conductance regulator, CFTR). In contrast to previous reports, we found no association between CFTR carrier status (mutation heterozygosity) and more severe COVID-19 clinical outcomes. We did observe an unexpected trend toward higher mortality among control individuals compared with silent carriers of the common F508del CFTR variant-a finding that will require further study. We next performed experiments to test the influence of homozygous CFTR deficiency on viral propagation and showed that SARS-CoV-2 production in primary airway cells was not altered by the absence of functional CFTR using two independent protocols. On the contrary, experiments performed in vitro strongly indicated that virus proliferation depended on features of the mucosal fluid layer known to be disrupted by absent CFTR in patients with CF, including both low pH and increased viscosity. These results point to the acidic, viscous, and mucus-obstructed airways in patients with cystic fibrosis as unfavorable for the establishment of coronaviral infection. Our findings provide new and important information concerning relationships between the CF clinical phenotype and severity of COVID-19.
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Affiliation(s)
- Philip R. Tedbury
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, United States
- Children’s Healthcare of Atlanta, Atlanta, Georgia, United States
| | - Candela Manfredi
- Children’s Healthcare of Atlanta, Atlanta, Georgia, United States
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, United States
| | - Frauke Degenhardt
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Joseph Conway
- Northeast Georgia Medical Center, Gainesville, Georgia, United States
| | - Michael C. Horwath
- Department of Pathology, Emory University School of Medicine, Atlanta, Georgia, United States
| | - Courtney McCracken
- Children’s Healthcare of Atlanta, Atlanta, Georgia, United States
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, United States
| | - Adam J. Sorscher
- Dartmouth University School of Medicine, Hanover, New Hampshire, United States
| | - Sandy Moreau
- Elliot Hospital, Manchester, New Hampshire, United States
| | | | - Carolina Edwards
- Northeast Georgia Medical Center, Gainesville, Georgia, United States
| | - Jo Brewer
- Northeast Georgia Medical Center, Gainesville, Georgia, United States
| | | | - Emmie de Wit
- Laboratory of Virology, Division of Intramural Research, NIAID, National Institutes of Health, Hamilton, Montana, United States
| | - Brandi N. Williamson
- Laboratory of Virology, Division of Intramural Research, NIAID, National Institutes of Health, Hamilton, Montana, United States
| | - Mehul S. Suthar
- Children’s Healthcare of Atlanta, Atlanta, Georgia, United States
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, United States
| | - Yee T. Ong
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, United States
- Children’s Healthcare of Atlanta, Atlanta, Georgia, United States
| | - John D. Roback
- Department of Pathology, Emory University School of Medicine, Atlanta, Georgia, United States
| | - David N. Alter
- Department of Pathology, Emory University School of Medicine, Atlanta, Georgia, United States
| | - Jan C. Holter
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Tom H. Karlsen
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Research Institute for Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet and University of Oslo, Oslo, Norway
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Section for Gastroenterology, Department of Transplantation Medicine, Division for Cancer Medicine, Surgery and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | | | - Manuel Romero-Gómez
- Hospital Universitario Virgen del Rocío de Sevilla, Sevilla, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Instituto de Biomedicina de Sevilla (IBIS), Sevilla, Spain
- University of Sevilla, Sevilla, Spain
- Digestive Diseases Unit, Virgen del Rocio University Hospital, Institute of Biomedicine of Seville, University of Seville, Seville, Spain
| | - Pietro Invernizzi
- European Reference Network on Hepatological Diseases (ERN RARE-LIVER), Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
- Division of Gastroenterology, Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Javier Fernández
- Hospital Clinic, University of Barcelona, and IDIBAPS, Barcelona, Spain
- European Foundation for the Study of Chronic Liver Failure (EF-CLIF), Barcelona, Spain
| | - Maria Buti
- Liver Unit. Hospital Universitario Valle Hebron and CIBEREHD del Instituto Carlos III. Barcelona, Spain
| | - Agustin Albillos
- Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Department of Gastroenterology, Hospital Universitario Ramón y Cajal, University of Alcalá, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Antonio Julià
- Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Barcelona, Spain
| | - Luca Valenti
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
- Biological Resorce Center, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico Milano, Milan Italy
| | - Rosanna Asselta
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
- IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Jesus M. Banales
- Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute – Donostia University Hospital, University of the Basque Country (UPV/EHU), CIBERehd, Ikerbasque, San Sebastian, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Luis Bujanda
- Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute – Donostia University Hospital, University of the Basque Country (UPV/EHU), CIBERehd, Ikerbasque, San Sebastian, Spain
| | - Rafael de Cid
- Genomes for Life-GCAT lab. German Trias I Pujol Research Institute (IGTP), Badalona, Spain
| | | | - Stefan G. Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, United States
- Children’s Healthcare of Atlanta, Atlanta, Georgia, United States
| | - Jeong S. Hong
- Children’s Healthcare of Atlanta, Atlanta, Georgia, United States
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, United States
| | - Eric J. Sorscher
- Children’s Healthcare of Atlanta, Atlanta, Georgia, United States
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, United States
| | - Annette Ehrhardt
- Children’s Healthcare of Atlanta, Atlanta, Georgia, United States
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, United States
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3
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Chatterjee R, Chowdhury AR, Mukherjee D, Chakravortty D. From Eberthella typhi to Salmonella Typhi: The Fascinating Journey of the Virulence and Pathogenicity of Salmonella Typhi. ACS OMEGA 2023; 8:25674-25697. [PMID: 37521659 PMCID: PMC10373206 DOI: 10.1021/acsomega.3c02386] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 06/30/2023] [Indexed: 08/01/2023]
Abstract
Salmonella Typhi (S. Typhi), the invasive typhoidal serovar of Salmonella enterica that causes typhoid fever in humans, is a severe threat to global health. It is one of the major causes of high morbidity and mortality in developing countries. According to recent WHO estimates, approximately 11-21 million typhoid fever illnesses occur annually worldwide, accounting for 0.12-0.16 million deaths. Salmonella infection can spread to healthy individuals by the consumption of contaminated food and water. Typhoid fever in humans sometimes is accompanied by several other critical extraintestinal complications related to the central nervous system, cardiovascular system, pulmonary system, and hepatobiliary system. Salmonella Pathogenicity Island-1 and Salmonella Pathogenicity Island-2 are the two genomic segments containing genes encoding virulent factors that regulate its invasion and systemic pathogenesis. This Review aims to shed light on a comparative analysis of the virulence and pathogenesis of the typhoidal and nontyphoidal serovars of S. enterica.
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Affiliation(s)
- Ritika Chatterjee
- Department
of Microbiology and Cell Biology, Division of Biological Sciences, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Atish Roy Chowdhury
- Department
of Microbiology and Cell Biology, Division of Biological Sciences, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Debapriya Mukherjee
- Department
of Microbiology and Cell Biology, Division of Biological Sciences, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Dipshikha Chakravortty
- Department
of Microbiology and Cell Biology, Division of Biological Sciences, Indian Institute of Science, Bangalore, Karnataka 560012, India
- Centre
for Biosystems Science and Engineering, Indian Institute of Science, Bangalore, Karnataka 560012, India
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4
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Gao H, Hamp T, Ede J, Schraiber JG, McRae J, Singer-Berk M, Yang Y, Dietrich ASD, Fiziev PP, Kuderna LFK, Sundaram L, Wu Y, Adhikari A, Field Y, Chen C, Batzoglou S, Aguet F, Lemire G, Reimers R, Balick D, Janiak MC, Kuhlwilm M, Orkin JD, Manu S, Valenzuela A, Bergman J, Rousselle M, Silva FE, Agueda L, Blanc J, Gut M, de Vries D, Goodhead I, Harris RA, Raveendran M, Jensen A, Chuma IS, Horvath JE, Hvilsom C, Juan D, Frandsen P, de Melo FR, Bertuol F, Byrne H, Sampaio I, Farias I, do Amaral JV, Messias M, da Silva MNF, Trivedi M, Rossi R, Hrbek T, Andriaholinirina N, Rabarivola CJ, Zaramody A, Jolly CJ, Phillips-Conroy J, Wilkerson G, Abee C, Simmons JH, Fernandez-Duque E, Kanthaswamy S, Shiferaw F, Wu D, Zhou L, Shao Y, Zhang G, Keyyu JD, Knauf S, Le MD, Lizano E, Merker S, Navarro A, Bataillon T, Nadler T, Khor CC, Lee J, Tan P, Lim WK, Kitchener AC, Zinner D, Gut I, Melin A, Guschanski K, Schierup MH, Beck RMD, Umapathy G, Roos C, Boubli JP, Lek M, Sunyaev S, O'Donnell-Luria A, Rehm HL, Xu J, Rogers J, Marques-Bonet T, Farh KKH. The landscape of tolerated genetic variation in humans and primates. Science 2023; 380:eabn8153. [PMID: 37262156 DOI: 10.1126/science.abn8197] [Citation(s) in RCA: 40] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 03/22/2023] [Indexed: 06/03/2023]
Abstract
Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole-genome sequencing data for 809 individuals from 233 primate species and identified 4.3 million common protein-altering variants with orthologs in humans. We show that these variants can be inferred to have nondeleterious effects in humans based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases.
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Affiliation(s)
- Hong Gao
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Tobias Hamp
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Jeffrey Ede
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Joshua G Schraiber
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Jeremy McRae
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Moriel Singer-Berk
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Boston, MA, 02142, USA
| | - Yanshen Yang
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | | | - Petko P Fiziev
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Lukas F K Kuderna
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Laksshman Sundaram
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Yibing Wu
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Aashish Adhikari
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Yair Field
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Chen Chen
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Serafim Batzoglou
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Francois Aguet
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Gabrielle Lemire
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Boston, MA, 02142, USA
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Rebecca Reimers
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Daniel Balick
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Mareike C Janiak
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Martin Kuhlwilm
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, 1030 Vienna, Austria
| | - Joseph D Orkin
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Département d'anthropologie, Université de Montréal, 3150 Jean-Brillant, Montréal, QC H3T 1N8, Canada
| | - Shivakumara Manu
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Alejandro Valenzuela
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Juraj Bergman
- Bioinformatics Research Centre, Aarhus University, Aarhus 8000, Denmark
- Section for Ecoinformatics & Biodiversity, Department of Biology, Aarhus University, 8000 Aarhus, Denmark
| | | | - Felipe Ennes Silva
- Research Group on Primate Biology and Conservation, Mamirauá Institute for Sustainable Development, Estrada da Bexiga 2584, Tefé, Amazonas, CEP 69553-225, Brazil
- Evolutionary Biology and Ecology (EBE), Département de Biologie des Organismes, Université libre de Bruxelles (ULB), Av. Franklin D. Roosevelt 50, CP 160/12, B-1050 Brussels, Belgium
| | - Lidia Agueda
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - Julie Blanc
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - Dorien de Vries
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Ian Goodhead
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - R Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Axel Jensen
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, SE-75236 Uppsala, Sweden
| | | | - Julie E Horvath
- North Carolina Museum of Natural Sciences, Raleigh, NC 27601, USA
- Department of Biological and Biomedical Sciences, North Carolina Central University, Durham, NC 27707, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - David Juan
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | | | | | - Fabrício Bertuol
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas, 69080-900, Brazil
| | - Hazel Byrne
- Department of Anthropology, University of Utah, Salt Lake City, UT 84102, USA
| | - Iracilda Sampaio
- Universidade Federal do Para, Guamá, Belém - PA, 66075-110, Brazil
| | - Izeni Farias
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas, 69080-900, Brazil
| | - João Valsecchi do Amaral
- Research Group on Terrestrial Vertebrate Ecology, Mamirauá Institute for Sustainable Development, Tefé, Amazonas, 69553-225, Brazil
- Rede de Pesquisa para Estudos sobre Diversidade, Conservação e Uso da Fauna na Amazônia - RedeFauna, Manaus, Amazonas, 69080-900, Brazil
- Comunidad de Manejo de Fauna Silvestre en la Amazonía y en Latinoamérica - ComFauna, Iquitos, Loreto, 16001, Peru
| | - Mariluce Messias
- Universidade Federal de Rondonia, Porto Velho, Rondônia, 78900-000, Brazil
- PPGREN - Programa de Pós-Graduação "Conservação e Uso dos Recursos Naturais and BIONORTE - Programa de Pós-Graduação em Biodiversidade e Biotecnologia da Rede BIONORTE, Universidade Federal de Rondonia, Porto Velho, Rondônia, 78900-000, Brazil
| | - Maria N F da Silva
- Instituto Nacional de Pesquisas da Amazonia, Petrópolis, Manaus - AM, 69067-375, Brazil
| | - Mihir Trivedi
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Rogerio Rossi
- Universidade Federal do Mato Grosso, Boa Esperança, Cuiabá - MT, 78060-900, Brazil
| | - Tomas Hrbek
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas, 69080-900, Brazil
- Department of Biology, Trinity University, San Antonio, TX 78212, USA
| | - Nicole Andriaholinirina
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, 401, Madagascar
| | - Clément J Rabarivola
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, 401, Madagascar
| | - Alphonse Zaramody
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, 401, Madagascar
| | | | | | - Gregory Wilkerson
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Christian Abee
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Joe H Simmons
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Eduardo Fernandez-Duque
- Yale University, New Haven, CT 06520, USA
- Universidad Nacional de Formosa, Argentina Fundacion ECO, Formosa, Argentina
| | | | - Fekadu Shiferaw
- Guinea Worm Eradication Program, The Carter Center Ethiopia, PoB 16316, Addis Ababa 1000, Ethiopia
| | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Long Zhou
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Guojie Zhang
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, China
- Women's Hospital, School of Medicine, Zhejiang University, 1 Xueshi Road, Shangcheng District, Hangzhou 310006, China
| | - Julius D Keyyu
- Tanzania Wildlife Research Institute (TAWIRI), Head Office, P.O. Box 661, Arusha, Tanzania
| | - Sascha Knauf
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald - Insei Riems, Germany
| | - Minh D Le
- Department of Environmental Ecology, Faculty of Environmental Sciences, University of Science and Central Institute for Natural Resources and Environmental Studies, Vietnam National University, Hanoi 100000, Vietnam
| | - Esther Lizano
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010 Barcelona, Spain
| | - Stefan Merker
- Department of Zoology, State Museum of Natural History Stuttgart, 70191 Stuttgart, Germany
| | - Arcadi Navarro
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Av. Doctor Aiguader, N88, 08003 Barcelona, Spain
- BarcelonaBeta Brain Research Center, Pasqual Maragall Foundation, C. Wellington 30, 08005 Barcelona, Spain
| | - Thomas Bataillon
- Bioinformatics Research Centre, Aarhus University, Aarhus 8000, Denmark
| | - Tilo Nadler
- Cuc Phuong Commune, Nho Quan District, Ninh Binh Province 430000, Vietnam
| | - Chiea Chuen Khor
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore
| | - Jessica Lee
- Mandai Nature, 80 Mandai Lake Road, Singapore 729826, Republic of Singapore
| | - Patrick Tan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore 168582, Republic of Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore 168582, Republic of Singapore
| | - Weng Khong Lim
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore 168582, Republic of Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore 168582, Republic of Singapore
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore 168582, Republic of Singapore
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, Chambers Street, Edinburgh EH1 1JF, UK
- School of Geosciences, University of Edinburgh, Drummond Street, Edinburgh EH8 9XP, UK
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, Germany Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Department of Primate Cognition, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
- Leibniz Science Campus Primate Cognition, 37077 Göttingen, Germany
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
- Universitat Pompeu Fabra, Pg. Luís Companys 23, 08010 Barcelona, Spain
| | - Amanda Melin
- Department of Anthropology & Archaeology, University of Calgary, 2500 University Dr NW, Calgary, AB T2N 1N4, Canada
- Department of Medical Genetics, 3330 Hospital Drive NW, HMRB 202, Calgary, AB T2N 4N1, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, 2500 University Dr NW, Calgary, AB T2N 1N4, Canada
| | - Katerina Guschanski
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, SE-75236 Uppsala, Sweden
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH8 9XP, UK
| | | | - Robin M D Beck
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Govindhaswamy Umapathy
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany
| | - Jean P Boubli
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Monkol Lek
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Shamil Sunyaev
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Anne O'Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Boston, MA, 02142, USA
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Heidi L Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Boston, MA, 02142, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jinbo Xu
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
- Toyota Technological Institute at Chicago, Chicago, IL 60637, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Kyle Kai-How Farh
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
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5
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Gao H, Hamp T, Ede J, Schraiber JG, McRae J, Singer-Berk M, Yang Y, Dietrich A, Fiziev P, Kuderna L, Sundaram L, Wu Y, Adhikari A, Field Y, Chen C, Batzoglou S, Aguet F, Lemire G, Reimers R, Balick D, Janiak MC, Kuhlwilm M, Orkin JD, Manu S, Valenzuela A, Bergman J, Rouselle M, Silva FE, Agueda L, Blanc J, Gut M, de Vries D, Goodhead I, Harris RA, Raveendran M, Jensen A, Chuma IS, Horvath J, Hvilsom C, Juan D, Frandsen P, de Melo FR, Bertuol F, Byrne H, Sampaio I, Farias I, do Amaral JV, Messias M, da Silva MNF, Trivedi M, Rossi R, Hrbek T, Andriaholinirina N, Rabarivola CJ, Zaramody A, Jolly CJ, Phillips-Conroy J, Wilkerson G, Abee C, Simmons JH, Fernandez-Duque E, Kanthaswamy S, Shiferaw F, Wu D, Zhou L, Shao Y, Zhang G, Keyyu JD, Knauf S, Le MD, Lizano E, Merker S, Navarro A, Batallion T, Nadler T, Khor CC, Lee J, Tan P, Lim WK, Kitchener AC, Zinner D, Gut I, Melin A, Guschanski K, Schierup MH, Beck RMD, Umapathy G, Roos C, Boubli JP, Lek M, Sunyaev S, O’Donnell A, Rehm H, Xu J, Rogers J, Marques-Bonet T, Kai-How Farh K. The landscape of tolerated genetic variation in humans and primates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.01.538953. [PMID: 37205491 PMCID: PMC10187174 DOI: 10.1101/2023.05.01.538953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole genome sequencing data for 809 individuals from 233 primate species, and identified 4.3 million common protein-altering variants with orthologs in human. We show that these variants can be inferred to have non-deleterious effects in human based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases. One Sentence Summary Deep learning classifier trained on 4.3 million common primate missense variants predicts variant pathogenicity in humans.
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Affiliation(s)
- Hong Gao
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Tobias Hamp
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Jeffrey Ede
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Joshua G. Schraiber
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Jeremy McRae
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Moriel Singer-Berk
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard; Boston, Massachusetts, 02142, USA
| | - Yanshen Yang
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Anastasia Dietrich
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Petko Fiziev
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Lukas Kuderna
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Laksshman Sundaram
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Yibing Wu
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Aashish Adhikari
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Yair Field
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Chen Chen
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Serafim Batzoglou
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Francois Aguet
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Gabrielle Lemire
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard; Boston, Massachusetts, 02142, USA
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
| | - Rebecca Reimers
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
| | - Daniel Balick
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
| | - Mareike C. Janiak
- School of Science, Engineering & Environment, University of Salford; Salford, M5 4WT, United Kingdom
| | - Martin Kuhlwilm
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Department of Evolutionary Anthropology, University of Vienna; Djerassiplatz 1, 1030, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna; 1030, Vienna, Austria
| | - Joseph D. Orkin
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Département d’anthropologie, Université de Montréal; 3150 Jean-Brillant, Montréal, QC, H3T 1N8, Canada
| | - Shivakumara Manu
- Academy of Scientific and Innovative Research (AcSIR); Ghaziabad, 201002, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology; Hyderabad, 500007, India
| | - Alejandro Valenzuela
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Juraj Bergman
- Bioinformatics Research Centre, Aarhus University; Aarhus, 8000, Denmark
- Section for Ecoinformatics & Biodiversity, Department of Biology, Aarhus University; Aarhus, 8000, Denmark
| | | | - Felipe Ennes Silva
- Research Group on Primate Biology and Conservation, Mamirauá Institute for Sustainable Development; Estrada da Bexiga 2584, Tefé, Amazonas, CEP 69553-225, Brazil
- Faculty of Sciences, Department of Organismal Biology, Unit of Evolutionary Biology and Ecology, Université Libre de Bruxelles (ULB); Avenue Franklin D. Roosevelt 50, 1050, Brussels, Belgium
| | - Lidia Agueda
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST); Baldiri i Reixac 4, 08028, Barcelona, Spain
| | - Julie Blanc
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST); Baldiri i Reixac 4, 08028, Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST); Baldiri i Reixac 4, 08028, Barcelona, Spain
| | - Dorien de Vries
- School of Science, Engineering & Environment, University of Salford; Salford, M5 4WT, United Kingdom
| | - Ian Goodhead
- School of Science, Engineering & Environment, University of Salford; Salford, M5 4WT, United Kingdom
| | - R. Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine; Houston, Texas, 77030, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine; Houston, Texas, 77030, USA
| | - Axel Jensen
- Department of Ecology and Genetics, Animal Ecology, Uppsala University; SE-75236, Uppsala, Sweden
| | | | - Julie Horvath
- North Carolina Museum of Natural Sciences; Raleigh, North Carolina, 27601, USA
- Department of Biological and Biomedical Sciences, North Carolina Central University; Durham, North Carolina , 27707, USA
- Department of Biological Sciences, North Carolina State University; Raleigh, North Carolina , 27695, USA
- Department of Evolutionary Anthropology, Duke University; Durham, North Carolina , 27708, USA
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - David Juan
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | | | | | - Fabricio Bertuol
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL); Manaus, Amazonas, 69080-900, Brazil
| | - Hazel Byrne
- Department of Anthropology, University of Utah; Salt Lake City, Utah, 84102, USA
| | - Iracilda Sampaio
- Universidade Federal do Para; Guamá, Belém - PA, 66075-110, Brazil
| | - Izeni Farias
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL); Manaus, Amazonas, 69080-900, Brazil
| | - João Valsecchi do Amaral
- Research Group on Terrestrial Vertebrate Ecology, Mamirauá Institute for Sustainable Development; Tefé, Amazonas, 69553-225, Brazil
- Rede de Pesquisa para Estudos sobre Diversidade, Conservação e Uso da Fauna na Amazônia – RedeFauna; Manaus, Amazonas, 69080-900, Brazil
- Comunidad de Manejo de Fauna Silvestre en la Amazonía y en Latinoamérica – ComFauna; Iquitos, Loreto, 16001, Peru
| | - Mariluce Messias
- Universidade Federal de Rondonia; Porto Velho, Rondônia, 78900-000, Brazil
- PPGREN - Programa de Pós-Graduação “Conservação e Uso dos Recursos Naturais and BIONORTE - Programa de Pós-Graduação em Biodiversidade e Biotecnologia da Rede BIONORTE, Universidade Federal de Rondonia; Porto Velho, Rondônia, 78900-000, Brazil
| | - Maria N. F. da Silva
- Instituto Nacional de Pesquisas da Amazonia; Petrópolis, Manaus - AM, 69067-375, Brazil
| | - Mihir Trivedi
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology; Hyderabad, 500007, India
| | - Rogerio Rossi
- Universidade Federal do Mato Grosso; Boa Esperança, Cuiabá - MT, 78060-900, Brazil
| | - Tomas Hrbek
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL); Manaus, Amazonas, 69080-900, Brazil
- Department of Biology, Trinity University; San Antonio, Texas, 78212, USA
| | - Nicole Andriaholinirina
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga; Mahajanga, 401, Madagascar
| | - Clément J. Rabarivola
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga; Mahajanga, 401, Madagascar
| | - Alphonse Zaramody
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga; Mahajanga, 401, Madagascar
| | | | | | - Gregory Wilkerson
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center; Houston, Texas, 77030, USA
| | | | - Joe H. Simmons
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center; Houston, Texas, 77030, USA
| | - Eduardo Fernandez-Duque
- Yale University; New Haven, Connecticut, 06520, USA
- Universidad Nacional de Formosa, Argentina Fundacion ECO, Formosa, Argentina
| | | | | | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences; Kunming, Yunnan, 650223, China
| | - Long Zhou
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences; Kunming, Yunnan, 650223, China
| | - Guojie Zhang
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen; Copenhagen, DK-2100, Denmark
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- Liangzhu Laboratory, Zhejiang University Medical Center; 1369 West Wenyi Road, Hangzhou, 311121, China
- Women’s Hospital, School of Medicine, Zhejiang University; 1 Xueshi Road, Shangcheng District, Hangzhou, 310006, China
| | - Julius D. Keyyu
- Tanzania Wildlife Research Institute (TAWIRI), Head Office; P.O.Box 661, Arusha, Tanzania
| | - Sascha Knauf
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health; 17493 Greifswald - Isle of Riems, Germany
| | - Minh D. Le
- Department of Environmental Ecology, Faculty of Environmental Sciences, University of Science and Central Institute for Natural Resources and Environmental Studies, Vietnam National University; Hanoi, 100000, Vietnam
| | - Esther Lizano
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain; Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Stefan Merker
- Department of Zoology, State Museum of Natural History Stuttgart; 70191 Stuttgart, Germany
| | - Arcadi Navarro
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) and Universitat Pompeu Fabra, Pg. Luís Companys 23, Barcelona, 08010, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology; Av. Doctor Aiguader, N88, Barcelona, 08003, Spain
- BarcelonaBeta Brain Research Center, Pasqual Maragall Foundation; C. Wellington 30, Barcelona, 08005, Spain
| | - Thomas Batallion
- Bioinformatics Research Centre, Aarhus University; Aarhus, 8000, Denmark
| | - Tilo Nadler
- Cuc Phuong Commune; Nho Quan District, Ninh Binh Province, 430000, Vietnam
| | - Chiea Chuen Khor
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore
| | - Jessica Lee
- Mandai Nature; 80 Mandai Lake Road, Singapore 729826, Republic of Singapore
| | - Patrick Tan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM); Singapore 168582, Republic of Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School; Singapore 168582, Republic of Singapore
| | - Weng Khong Lim
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM); Singapore 168582, Republic of Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School; Singapore 168582, Republic of Singapore
- SingHealth Duke-NUS Genomic Medicine Centre; Singapore 168582, Republic of Singapore
| | - Andrew C. Kitchener
- Department of Natural Sciences, National Museums Scotland; Chambers Street, Edinburgh, EH1 1JF, UK
- School of Geosciences, University of Edinburgh; Drummond Street, Edinburgh, EH8 9XP, UK
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, Germany Primate Center, Leibniz Institute for Primate Research; 37077 Göttingen, Germany
- Department of Primate Cognition, Georg-August-Universität Göttingen; 37077 Göttingen, Germany
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST); Baldiri i Reixac 4, 08028, Barcelona, Spain
- Universitat Pompeu Fabra, Pg. Luís Companys 23, Barcelona, 08010, Spain
| | - Amanda Melin
- Leibniz Science Campus Primate Cognition; 37077 Göttingen, Germany
- Department of Anthropology & Archaeology and Department of Medical Genetics
| | - Katerina Guschanski
- Department of Ecology and Genetics, Animal Ecology, Uppsala University; SE-75236, Uppsala, Sweden
- Alberta Children’s Hospital Research Institute; University of Calgary; 2500 University Dr NW T2N 1N4, Calgary, Alberta, Canada
| | | | - Robin M. D. Beck
- School of Science, Engineering & Environment, University of Salford; Salford, M5 4WT, United Kingdom
| | - Govindhaswamy Umapathy
- Academy of Scientific and Innovative Research (AcSIR); Ghaziabad, 201002, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology; Hyderabad, 500007, India
| | - Christian Roos
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh; Edinburgh, EH8 9XP, UK
| | - Jean P. Boubli
- School of Science, Engineering & Environment, University of Salford; Salford, M5 4WT, United Kingdom
| | - Monkol Lek
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research; Kellnerweg 4, 37077 Göttingen, Germany
| | - Shamil Sunyaev
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
- Department of Genetics, Yale School of Medicine; New Haven, Connecticut, 06520, USA
| | - Anne O’Donnell
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard; Boston, Massachusetts, 02142, USA
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Heidi Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard; Boston, Massachusetts, 02142, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School; Boston, Massachusetts, 02115, USA
| | - Jinbo Xu
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
- Toyota Technological Institute at Chicago; Chicago, Illinois, 60637, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine; Houston, Texas, 77030, USA
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST); Baldiri i Reixac 4, 08028, Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain; Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) and Universitat Pompeu Fabra, Pg. Luís Companys 23, Barcelona, 08010, Spain
| | - Kyle Kai-How Farh
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
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6
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Yu C, Kotsimbos T. Respiratory Infection and Inflammation in Cystic Fibrosis: A Dynamic Interplay among the Host, Microbes, and Environment for the Ages. Int J Mol Sci 2023; 24:ijms24044052. [PMID: 36835487 PMCID: PMC9966804 DOI: 10.3390/ijms24044052] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
The interplay between airway inflammation and infection is now recognized as a major factor in the pathobiology in cystic fibrosis (CF). A proinflammatory environment is seen throughout the CF airway resulting in classic marked and enduring neutrophilic infiltrations, irreversibly damaging the lung. Although this is seen to occur early, independent of infection, respiratory microbes arising at different timepoints in life and the world environment perpetuate this hyperinflammatory state. Several selective pressures have allowed for the CF gene to persist until today despite an early mortality. Comprehensive care systems, which have been a cornerstone of therapy for the past few decades, are now revolutionized by CF transmembrane conductance regulator (CTFR) modulators. The effects of these small-molecule agents cannot be overstated and can be seen as early as in utero. For an understanding of the future, this review looks into CF studies spanning the historical and present period.
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Affiliation(s)
- Christiaan Yu
- Department of Respiratory Medicine, Alfred Health, Melbourne, VIC 3004, Australia
- Correspondence: ; Tel.: +61-3-9076-20000
| | - Tom Kotsimbos
- Department of Respiratory Medicine, Alfred Health, Melbourne, VIC 3004, Australia
- Department of Medicine, Monash University, Alfred Campus, Melbourne, VIC 3004, Australia
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7
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Heyne HO, Karjalainen J, Karczewski KJ, Lemmelä SM, Zhou W, Havulinna AS, Kurki M, Rehm HL, Palotie A, Daly MJ. Mono- and biallelic variant effects on disease at biobank scale. Nature 2023; 613:519-525. [PMID: 36653560 PMCID: PMC9849130 DOI: 10.1038/s41586-022-05420-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 10/06/2022] [Indexed: 01/20/2023]
Abstract
Identifying causal factors for Mendelian and common diseases is an ongoing challenge in medical genetics1. Population bottleneck events, such as those that occurred in the history of the Finnish population, enrich some homozygous variants to higher frequencies, which facilitates the identification of variants that cause diseases with recessive inheritance2,3. Here we examine the homozygous and heterozygous effects of 44,370 coding variants on 2,444 disease phenotypes using data from the nationwide electronic health records of 176,899 Finnish individuals. We find associations for homozygous genotypes across a broad spectrum of phenotypes, including known associations with retinal dystrophy and novel associations with adult-onset cataract and female infertility. Of the recessive disease associations that we identify, 13 out of 20 would have been missed by the additive model that is typically used in genome-wide association studies. We use these results to find many known Mendelian variants whose inheritance cannot be adequately described by a conventional definition of dominant or recessive. In particular, we find variants that are known to cause diseases with recessive inheritance with significant heterozygous phenotypic effects. Similarly, we find presumed benign variants with disease effects. Our results show how biobanks, particularly in founder populations, can broaden our understanding of complex dosage effects of Mendelian variants on disease.
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Affiliation(s)
- H O Heyne
- Finnish Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki, Finland. .,Digital Health Center, Hasso Plattner Institute for Digital Engineering, University of Potsdam, Potsdam, Germany. .,Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Program for Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - J Karjalainen
- Finnish Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki, Finland.,Program for Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - K J Karczewski
- Finnish Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki, Finland.,Program for Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - S M Lemmelä
- Finnish Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki, Finland.,Finnish Institute for Health and Welfare, Helsinki, Finland
| | - W Zhou
- Finnish Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki, Finland.,Program for Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - A S Havulinna
- Finnish Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki, Finland.,Finnish Institute for Health and Welfare, Helsinki, Finland
| | - M Kurki
- Finnish Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki, Finland.,Program for Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - H L Rehm
- Program for Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - A Palotie
- Finnish Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki, Finland.,Program for Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.,Psychiatric and Neurodevelopmental Genetics Unit, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - M J Daly
- Finnish Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki, Finland. .,Program for Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA. .,Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
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8
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Lidsky PV, Yuan J, Rulison JM, Andino-Pavlovsky R. Is Aging an Inevitable Characteristic of Organic Life or an Evolutionary Adaptation? BIOCHEMISTRY. BIOKHIMIIA 2022; 87:1413-1445. [PMID: 36717438 PMCID: PMC9839256 DOI: 10.1134/s0006297922120021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 09/27/2022] [Accepted: 11/04/2022] [Indexed: 01/15/2023]
Abstract
Aging is an evolutionary paradox. Several hypotheses have been proposed to explain it, but none fully explains all the biochemical and ecologic data accumulated over decades of research. We suggest that senescence is a primitive immune strategy which acts to protect an individual's kin from chronic infections. Older organisms are exposed to pathogens for a longer period of time and have a higher likelihood of acquiring infectious diseases. Accordingly, the parasitic load in aged individuals is higher than in younger ones. Given that the probability of pathogen transmission is higher within the kin, the inclusive fitness cost of infection might exceed the benefit of living longer. In this case, programmed lifespan termination might be an evolutionarily stable strategy. Here, we discuss the classical evolutionary hypotheses of aging and compare them with the pathogen control hypothesis, discuss the consistency of these hypotheses with existing empirical data, and present a revised conceptual framework to understand the evolution of aging.
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Affiliation(s)
- Peter V Lidsky
- Department of Microbiology and Immunology, University of California San Francisco, CA, USA.
| | - Jing Yuan
- Department of Microbiology and Immunology, University of California San Francisco, CA, USA
| | - Jacob M Rulison
- Department of Microbiology and Immunology, University of California San Francisco, CA, USA
- University of California Berkeley, CA, USA
| | - Raul Andino-Pavlovsky
- Department of Microbiology and Immunology, University of California San Francisco, CA, USA.
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9
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Grotz S, Schäfer J, Wunderlich KA, Ellederova Z, Auch H, Bähr A, Runa-Vochozkova P, Fadl J, Arnold V, Ardan T, Veith M, Santamaria G, Dhom G, Hitzl W, Kessler B, Eckardt C, Klein J, Brymova A, Linnert J, Kurome M, Zakharchenko V, Fischer A, Blutke A, Döring A, Suchankova S, Popelar J, Rodríguez-Bocanegra E, Dlugaiczyk J, Straka H, May-Simera H, Wang W, Laugwitz KL, Vandenberghe LH, Wolf E, Nagel-Wolfrum K, Peters T, Motlik J, Fischer MD, Wolfrum U, Klymiuk N. Early disruption of photoreceptor cell architecture and loss of vision in a humanized pig model of usher syndromes. EMBO Mol Med 2022; 14:e14817. [PMID: 35254721 PMCID: PMC8988205 DOI: 10.15252/emmm.202114817] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 02/04/2022] [Accepted: 02/09/2022] [Indexed: 01/17/2023] Open
Abstract
Usher syndrome (USH) is the most common form of monogenic deaf-blindness. Loss of vision is untreatable and there are no suitable animal models for testing therapeutic strategies of the ocular constituent of USH, so far. By introducing a human mutation into the harmonin-encoding USH1C gene in pigs, we generated the first translational animal model for USH type 1 with characteristic hearing defect, vestibular dysfunction, and visual impairment. Changes in photoreceptor architecture, quantitative motion analysis, and electroretinography were characteristics of the reduced retinal virtue in USH1C pigs. Fibroblasts from USH1C pigs or USH1C patients showed significantly elongated primary cilia, confirming USH as a true and general ciliopathy. Primary cells also proved their capacity for assessing the therapeutic potential of CRISPR/Cas-mediated gene repair or gene therapy in vitro. AAV-based delivery of harmonin into the eye of USH1C pigs indicated therapeutic efficacy in vivo.
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Affiliation(s)
- Sophia Grotz
- Chair of Molecular Animal Breeding and Biotechnology, LMU Munich, Munich, Germany.,Center for Innovative Medical Models, LMU Munich, Munich, Germany
| | - Jessica Schäfer
- Institute of Molecular Physiology, Molecular Cell Biology, Johannes Gutenberg University (JGU), Mainz, Germany
| | - Kirsten A Wunderlich
- Institute of Molecular Physiology, Molecular Cell Biology, Johannes Gutenberg University (JGU), Mainz, Germany
| | - Zdenka Ellederova
- Institute of Animal Physiology and Genetics, Czech Academy of Science, Libechov, Czech Republic
| | - Hannah Auch
- Chair of Molecular Animal Breeding and Biotechnology, LMU Munich, Munich, Germany.,Center for Innovative Medical Models, LMU Munich, Munich, Germany
| | - Andrea Bähr
- Center for Innovative Medical Models, LMU Munich, Munich, Germany.,Large Animal Models in Cardiovascular Research, Internal Medical Department I, TU Munich, Munich, Germany
| | - Petra Runa-Vochozkova
- Large Animal Models in Cardiovascular Research, Internal Medical Department I, TU Munich, Munich, Germany
| | - Janet Fadl
- Chair of Molecular Animal Breeding and Biotechnology, LMU Munich, Munich, Germany.,Institute of Molecular Physiology, Molecular Cell Biology, Johannes Gutenberg University (JGU), Mainz, Germany
| | - Vanessa Arnold
- Institute of Molecular Physiology, Molecular Cell Biology, Johannes Gutenberg University (JGU), Mainz, Germany
| | - Taras Ardan
- Institute of Animal Physiology and Genetics, Czech Academy of Science, Libechov, Czech Republic
| | - Miroslav Veith
- Ophthalmology Clinic, University Hospital Kralovske Vinohrady, Praha, Czech Republic
| | - Gianluca Santamaria
- Large Animal Models in Cardiovascular Research, Internal Medical Department I, TU Munich, Munich, Germany
| | - Georg Dhom
- Chair of Molecular Animal Breeding and Biotechnology, LMU Munich, Munich, Germany.,Center for Innovative Medical Models, LMU Munich, Munich, Germany
| | - Wolfgang Hitzl
- Biostatistics and Data Science, Paracelsus Medical University, Salzburg, Austria
| | - Barbara Kessler
- Chair of Molecular Animal Breeding and Biotechnology, LMU Munich, Munich, Germany.,Center for Innovative Medical Models, LMU Munich, Munich, Germany
| | - Christian Eckardt
- Center for Innovative Medical Models, LMU Munich, Munich, Germany.,Large Animal Models in Cardiovascular Research, Internal Medical Department I, TU Munich, Munich, Germany
| | - Joshua Klein
- Institute of Molecular Physiology, Molecular Cell Biology, Johannes Gutenberg University (JGU), Mainz, Germany
| | - Anna Brymova
- Institute of Animal Physiology and Genetics, Czech Academy of Science, Libechov, Czech Republic
| | - Joshua Linnert
- Institute of Molecular Physiology, Molecular Cell Biology, Johannes Gutenberg University (JGU), Mainz, Germany
| | - Mayuko Kurome
- Chair of Molecular Animal Breeding and Biotechnology, LMU Munich, Munich, Germany.,Center for Innovative Medical Models, LMU Munich, Munich, Germany
| | - Valeri Zakharchenko
- Chair of Molecular Animal Breeding and Biotechnology, LMU Munich, Munich, Germany.,Center for Innovative Medical Models, LMU Munich, Munich, Germany
| | - Andrea Fischer
- Veterinary Faculty, Small Animal Clinics, LMU Munich, Munich, Germany
| | - Andreas Blutke
- Institute of Experimental Genetics, Helmholtz Center Munich, Neuherberg, Germany
| | - Anna Döring
- Veterinary Faculty, Small Animal Clinics, LMU Munich, Munich, Germany
| | - Stepanka Suchankova
- Institute of Experimental Medicine, Czech Academy of Science, Prague, Czech Republic
| | - Jiri Popelar
- Institute of Experimental Medicine, Czech Academy of Science, Prague, Czech Republic
| | - Eduardo Rodríguez-Bocanegra
- Centre for Ophthalmology, University Eye Hospital, University Hospital Tübingen, Tübingen, Germany.,Institute for Ophthalmic Research, Centre for Ophthalmology, University Hospital Tübingen, Tübingen, Germany
| | - Julia Dlugaiczyk
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital Zurich (USZ), University of Zurich, Zurich, Switzerland
| | - Hans Straka
- Faculty of Biology, LMU Munich, Planegg, Germany
| | - Helen May-Simera
- Institute of Molecular Physiology, Cilia Biology, JGU Mainz, Mainz, Germany
| | - Weiwei Wang
- Grousbeck Gene Therapy Center, Mass Eye and Ear and Harvard Medical School, Boston, MA, USA
| | - Karl-Ludwig Laugwitz
- Large Animal Models in Cardiovascular Research, Internal Medical Department I, TU Munich, Munich, Germany
| | - Luk H Vandenberghe
- Grousbeck Gene Therapy Center, Mass Eye and Ear and Harvard Medical School, Boston, MA, USA
| | - Eckhard Wolf
- Chair of Molecular Animal Breeding and Biotechnology, LMU Munich, Munich, Germany.,Center for Innovative Medical Models, LMU Munich, Munich, Germany
| | - Kerstin Nagel-Wolfrum
- Institute of Molecular Physiology, Molecular Cell Biology, Johannes Gutenberg University (JGU), Mainz, Germany.,Institute of Developmental Biology and Neurobiology, Johannes Gutenberg University (JGU), Mainz, Germany
| | - Tobias Peters
- Centre for Ophthalmology, University Eye Hospital, University Hospital Tübingen, Tübingen, Germany.,Institute for Ophthalmic Research, Centre for Ophthalmology, University Hospital Tübingen, Tübingen, Germany
| | - Jan Motlik
- Institute of Animal Physiology and Genetics, Czech Academy of Science, Libechov, Czech Republic
| | - M Dominik Fischer
- Oxford Eye Hospital, Oxford University NHS Foundation Trust, Oxford, UK.,Nuffield Laboratory of Ophthalmology, NDCN, University of Oxford, Oxford, UK
| | - Uwe Wolfrum
- Institute of Molecular Physiology, Molecular Cell Biology, Johannes Gutenberg University (JGU), Mainz, Germany
| | - Nikolai Klymiuk
- Center for Innovative Medical Models, LMU Munich, Munich, Germany.,Large Animal Models in Cardiovascular Research, Internal Medical Department I, TU Munich, Munich, Germany
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10
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Zheng BH, Hao WM, Lin HC, Shang GG, Liu H, Ni XJ. Samonella typhi infection-related appendicitis: A case report. World J Clin Cases 2021; 9:8782-8788. [PMID: 34734056 PMCID: PMC8546835 DOI: 10.12998/wjcc.v9.i29.8782] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/05/2021] [Accepted: 08/02/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Acute appendicitis is one of the most common acute abdominal emergencies around the world, which is always associated with infection. Infection with Salmonella typhi, an enteric pathogen, is a rare cause of acute appendicitis. We here report a patient with acute appendicitis associated with Samonella typhi infection, accompanied with spleen and kidney infarction, providing a rare example for a common surgical emergency. CASE SUMMARY A 25-year-old Pakistani man presented to the hospital with a 3-d history of fevers, vomiting, and abdominal pain. Computed tomography (CT) revealed a thickened intestinal wall of the ileocecal junction with multiple enlarged lymph nodes nearby. He was diagnosed with acute appendicitis and received laparoscopic appendectomy, which showed mild inflammation of the appendix. After the surgery, the patient presented again with a high fever (> 39 °C) and diarrhea. A CT angiography scan indicated spleen and kidney infarction. According to the blood culture, the diagnosis was finally clear to be Samonella typhi infection. The pyrexia and enteric symptoms were relieved after the application of intravenous levofloxacin. CONCLUSION This case, characterized by the combination of Salmonella typhi infection, acute appendicitis, and renal and splenic infraction, serves as a rare example for a common surgical emergency.
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Affiliation(s)
- Bo-Hao Zheng
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Wei-Ming Hao
- Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Hung-Chen Lin
- Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Guo-Guo Shang
- Department of Pathology, Zhongshan Hospital, Shanghai 200032, China
| | - Han Liu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Xiao-Jian Ni
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, China
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11
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Malagutti N, Fancello V, Cariani A, Battistini F, Fabbri C, Di Laora A, Valpiani G, Morotti C, Iannini V, Borin M, Ravani A, Bianchini C, Ciorba A, Stomeo F, Pelucchi S. Ion concentrations in nasal airway surface liquid: a prediction model for the identification of cystic fibrosis carriers. Rhinology 2021; 59:470-474. [PMID: 34398939 DOI: 10.4193/rhin21.064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND Cystic fibrosis (CF) carriers seem to have a higher risk to develop chronic rhino-sinusitis (CRS), although the full underlying mechanisms are unknown. Ion concentrations in nasal airway surface liquid (ASL) may be influenced by the heterozygosity for CF gene mutation, with possible impacts on the development of CRS. METHODS A cheap and feasible standardized technique was designed to measure the ion levels in nasal ASL. With this purpose we collected, under basal conditions, samples from the nasal cavity of 165 adults: 14 homozygous for CF, 83 carriers and 68 healthy controls. Sodium (Na) and Chlorine (Cl) concentrations were then evaluated among different groups. RESULTS Statistical analysis revealed a significant difference of Na and Cl values between controls and carriers and between controls and homozygotes. Receiver operating characteristic (ROC) curves and derived indicators (Youden's index and Area Under the Curve, AUC) were used to further evaluate the diagnostic capability of Na and Cl concentrations to differentiate heterozygotes from controls. ROC curves demonstrated that the optimal diagnostic cut-off value of Na is at 124, and the optimal cut-off value of Cl is at 103,2. CONCLUSION ASL sampling can be considered a new diagnostic tool for providing quantitative information on nasal ion composition. According to our findings, Na and Cl concentrations of nasal ASL could represent a useful tool to assess heterozygotes and healthy controls.
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Affiliation(s)
- N Malagutti
- ENT and Audiology Unit, Department of Neuroscience and Rehabilitation, University Hospital of Ferrara, Ferrara, Italy
| | - V Fancello
- ENT and Audiology Unit, Department of Neuroscience and Rehabilitation, University Hospital of Ferrara, Ferrara, Italy
| | - A Cariani
- Department of Biochemistry and Molecular Biology, University of Ferrara, Ferrara, Italy
| | - F Battistini
- Cystic Fibrosis Regional Center, Bufalini Hospital, Cesena, Italy
| | - C Fabbri
- ENT and Audiology Unit, Department of Neuroscience and Rehabilitation, University Hospital of Ferrara, Ferrara, Italy
| | - A Di Laora
- ENT and Audiology Unit, Department of Neuroscience and Rehabilitation, University Hospital of Ferrara, Ferrara, Italy
| | - G Valpiani
- Research Innovation Office, S. Anna University Hospital of Ferrara, Ferrara, Italy
| | - C Morotti
- Research Innovation Office, S. Anna University Hospital of Ferrara, Ferrara, Italy
| | - V Iannini
- ENT and Audiology Unit, Department of Neuroscience and Rehabilitation, University Hospital of Ferrara, Ferrara, Italy
| | - M Borin
- ENT and Audiology Unit, Department of Neuroscience and Rehabilitation, University Hospital of Ferrara, Ferrara, Italy
| | - A Ravani
- Unit of Medical Genetics Unit, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - C Bianchini
- ENT and Audiology Unit, Department of Neuroscience and Rehabilitation, University Hospital of Ferrara, Ferrara, Italy
| | - A Ciorba
- ENT and Audiology Unit, Department of Neuroscience and Rehabilitation, University Hospital of Ferrara, Ferrara, Italy
| | - F Stomeo
- ENT and Audiology Unit, Department of Neuroscience and Rehabilitation, University Hospital of Ferrara, Ferrara, Italy
| | - S Pelucchi
- ENT and Audiology Unit, Department of Neuroscience and Rehabilitation, University Hospital of Ferrara, Ferrara, Italy
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12
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Enteric Fever Diagnosis: Current Challenges and Future Directions. Pathogens 2021; 10:pathogens10040410. [PMID: 33915749 PMCID: PMC8065732 DOI: 10.3390/pathogens10040410] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 03/23/2021] [Accepted: 03/27/2021] [Indexed: 12/21/2022] Open
Abstract
Enteric fever is a life-threatening systemic febrile disease caused by Salmonella enterica serovars Typhi and Paratyphi (S. Typhi and S. Paratyphi). Unfortunately, the burden of the disease remains high primarily due to the global spread of various drug-resistant Salmonella strains despite continuous advancement in the field. An accurate diagnosis is critical for effective control of the disease. However, enteric fever diagnosis based on clinical presentations is challenging due to overlapping symptoms with other febrile illnesses that are also prevalent in endemic areas. Current laboratory tests display suboptimal sensitivity and specificity, and no diagnostic methods are available for identifying asymptomatic carriers. Several research programs have employed systemic approaches to identify more specific biomarkers for early detection and asymptomatic carrier detection. This review discusses the pros and cons of currently available diagnostic tests for enteric fever, the advancement of research toward improved diagnostic tests, and the challenges of discovering new ideal biomarkers and tests.
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13
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Palagiano A, Cozzolino M, Ubaldi FM, Palagiano C, Coccia ME. Effects of Hydrosalpinx on Endometrial Implantation Failures: Evaluating Salpingectomy in Women Undergoing in vitro fertilization. REVISTA BRASILEIRA DE GINECOLOGIA E OBSTETRÍCIA 2021; 43:304-310. [PMID: 33601465 PMCID: PMC10183881 DOI: 10.1055/s-0040-1722155] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Hydrosalpinx is a disease characterized by the obstruction of the salpinx, with progressive accumulation in the shape of a fluid-filled sac at the distal part of the tuba uterina, and closed to the ovary. Women with hydrosalpinges have lower implantation and pregnancy rates due to a combination of mechanical and chemical factors thought to disrupt the endometrial environment. Evidence suggests that the presence of hydrosalpinx reduces the rate of pregnancy with assisted reproductive technology. The main aim of the present is review to make an overview of the possible effects of hydrosalpinx on in vitro fertilization (IVF). We conducted a literature search on the PubMed, Ovid MEDLINE, and Google Scholar data bases regarding hydrosalpinx and IVF outcomes. Hydrosalpinx probably has a direct toxic effect on sperm motility and on the embryos. In addition, the increasing liquid inside the salpinges could alter the mechanisms of endometrial receptivity. The window of endometrial receptivity is essential in the implantation of blastocysts, and it triggers multiple reactions arising from the endometrium as well as the blastocysts. Hydrosalpinx could influence the expression of homeobox A10 (HOXA10) gene, which plays an essential role in directing embryonic development and implantation. Salpingectomy restores the endometrial expression of HOXA10; therefore, it may be one mechanism by which tubal removal could result in improved implantation rates in IVF. In addition, salpingectomy does not affect the ovarian response, nor reduces the antral follicle count. Further studies are needed to establish the therapeutic value of fluid aspiration under ultrasonographic guidance, during or after oocyte retrieval, in terms of pregnancy rate and ongoing pregnancy.
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Affiliation(s)
- Antonio Palagiano
- Department of General and Specialized Surgery for Women and Children, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Italy
| | - Mauro Cozzolino
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale School of Medicine, New Haven, Connecticut, United States.,Universidad Rey Juan Carlos, Madrid, Spain.,IVIRMA, IVI Foundation, Valencia, Spain
| | | | | | - Maria Elisabetta Coccia
- Department of Biomedical, Experimental and Clinical Sciences, Division of Obstetrics and Gynecology, Università degli Studi di Firenze, Azienda Ospedaliero Universitaria Careggi, Firenze, Italy
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14
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Ma PY, Tan JE, Hee EW, Yong DWX, Heng YS, Low WX, Wu XH, Cletus C, Kumar Chellappan D, Aung K, Yong CY, Liew YK. Human Genetic Variation Influences Enteric Fever Progression. Cells 2021; 10:cells10020345. [PMID: 33562108 PMCID: PMC7915608 DOI: 10.3390/cells10020345] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 02/02/2021] [Accepted: 02/04/2021] [Indexed: 01/06/2023] Open
Abstract
In the 21st century, enteric fever is still causing a significant number of mortalities, especially in high-risk regions of the world. Genetic studies involving the genome and transcriptome have revealed a broad set of candidate genetic polymorphisms associated with susceptibility to and the severity of enteric fever. This review attempted to explain and discuss the past and the most recent findings on human genetic variants affecting the progression of Salmonella typhoidal species infection, particularly toll-like receptor (TLR) 4, TLR5, interleukin (IL-) 4, natural resistance-associated macrophage protein 1 (NRAMP1), VAC14, PARK2/PACRG, cystic fibrosis transmembrane conductance regulator (CFTR), major-histocompatibility-complex (MHC) class II and class III. These polymorphisms on disease susceptibility or progression in patients could be related to multiple mechanisms in eliminating both intracellular and extracellular Salmonella typhoidal species. Here, we also highlighted the limitations in the studies reported, which led to inconclusive results in association studies. Nevertheless, the knowledge obtained through this review may shed some light on the development of risk prediction tools, novel therapies as well as strategies towards developing a personalised typhoid vaccine.
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Affiliation(s)
- Pei Yee Ma
- School of Postgraduate Studies, International Medical University, Bukit Jalil, Kuala Lumpur 57000, Malaysia;
| | - Jing En Tan
- School of Pharmacy, International Medical University, Kuala Lumpur 57000, Malaysia; (J.E.T.); (E.W.H.); (D.W.X.Y.); (Y.S.H.); (W.X.L.); (X.H.W.); (C.C.)
| | - Edd Wyn Hee
- School of Pharmacy, International Medical University, Kuala Lumpur 57000, Malaysia; (J.E.T.); (E.W.H.); (D.W.X.Y.); (Y.S.H.); (W.X.L.); (X.H.W.); (C.C.)
| | - Dylan Wang Xi Yong
- School of Pharmacy, International Medical University, Kuala Lumpur 57000, Malaysia; (J.E.T.); (E.W.H.); (D.W.X.Y.); (Y.S.H.); (W.X.L.); (X.H.W.); (C.C.)
| | - Yi Shuan Heng
- School of Pharmacy, International Medical University, Kuala Lumpur 57000, Malaysia; (J.E.T.); (E.W.H.); (D.W.X.Y.); (Y.S.H.); (W.X.L.); (X.H.W.); (C.C.)
| | - Wei Xiang Low
- School of Pharmacy, International Medical University, Kuala Lumpur 57000, Malaysia; (J.E.T.); (E.W.H.); (D.W.X.Y.); (Y.S.H.); (W.X.L.); (X.H.W.); (C.C.)
| | - Xun Hui Wu
- School of Pharmacy, International Medical University, Kuala Lumpur 57000, Malaysia; (J.E.T.); (E.W.H.); (D.W.X.Y.); (Y.S.H.); (W.X.L.); (X.H.W.); (C.C.)
| | - Christy Cletus
- School of Pharmacy, International Medical University, Kuala Lumpur 57000, Malaysia; (J.E.T.); (E.W.H.); (D.W.X.Y.); (Y.S.H.); (W.X.L.); (X.H.W.); (C.C.)
| | - Dinesh Kumar Chellappan
- Department of Life Sciences, International Medical University, Kuala Lumpur 57000, Malaysia;
| | - Kyan Aung
- Department of Pathology, International Medical University, Kuala Lumpur 57000, Malaysia;
| | - Chean Yeah Yong
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Selangor 43400, Malaysia;
| | - Yun Khoon Liew
- Department of Life Sciences, International Medical University, Kuala Lumpur 57000, Malaysia;
- Correspondence:
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15
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Gibani MM, Jin C, Shrestha S, Moore M, Norman L, Voysey M, Jones E, Blackwell L, Thomaides-Brears H, Hill J, Blohmke CJ, Dobinson HC, Baker P, Jones C, Campbell D, Mujadidi YF, Plested E, Preciado-Llanes L, Napolitani G, Simmons A, Gordon MA, Angus B, Darton TC, Cerundulo V, Pollard AJ. Homologous and heterologous re-challenge with Salmonella Typhi and Salmonella Paratyphi A in a randomised controlled human infection model. PLoS Negl Trop Dis 2020; 14:e0008783. [PMID: 33079959 PMCID: PMC7598925 DOI: 10.1371/journal.pntd.0008783] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 10/30/2020] [Accepted: 09/08/2020] [Indexed: 11/19/2022] Open
Abstract
Enteric fever is a systemic infection caused by Salmonella Typhi or Paratyphi A. In many endemic areas, these serovars co-circulate and can cause multiple infection-episodes in childhood. Prior exposure is thought to confer partial, but incomplete, protection against subsequent attacks of enteric fever. Empirical data to support this hypothesis are limited, and there are few studies describing the occurrence of heterologous-protection between these closely related serovars. We performed a challenge-re-challenge study using a controlled human infection model (CHIM) to investigate the extent of infection-derived immunity to Salmonella Typhi or Paratyphi A infection. We recruited healthy volunteers into two groups: naïve volunteers with no prior exposure to Salmonella Typhi/Paratyphi A and volunteers previously-exposed to Salmonella Typhi or Paratyphi A in earlier CHIM studies. Within each group, participants were randomised 1:1 to oral challenge with either Salmonella Typhi (104 CFU) or Paratyphi A (103 CFU). The primary objective was to compare the attack rate between naïve and previously challenged individuals, defined as the proportion of participants per group meeting the diagnostic criteria of temperature of ≥38°C persisting for ≥12 hours and/or S. Typhi/Paratyphi bacteraemia up to day 14 post challenge. The attack-rate in participants who underwent homologous re-challenge with Salmonella Typhi was reduced compared with challenged naïve controls, although this reduction was not statistically significant (12/27[44%] vs. 12/19[63%]; Relative risk 0.70; 95% CI 0.41-1.21; p = 0.24). Homologous re-challenge with Salmonella Paratyphi A also resulted in a lower attack-rate than was seen in challenged naïve controls (3/12[25%] vs. 10/18[56%]; RR0.45; 95% CI 0.16-1.30; p = 0.14). Evidence of protection was supported by a post hoc analysis in which previous exposure was associated with an approximately 36% and 57% reduced risk of typhoid or paratyphoid disease respectively on re-challenge. Individuals who did not develop enteric fever on primary exposure were significantly more likely to be protected on re-challenge, compared with individuals who developed disease on primary exposure. Heterologous re-challenge with Salmonella Typhi or Salmonella Paratyphi A was not associated with a reduced attack rate following challenge. Within the context of the model, prior exposure was not associated with reduced disease severity, altered microbiological profile or boosting of humoral immune responses. We conclude that prior Salmonella Typhi and Paratyphi A exposure may confer partial but incomplete protection against subsequent infection, but with a comparable clinical and microbiological phenotype. There is no demonstrable cross-protection between these serovars, consistent with the co-circulation of Salmonella Typhi and Paratyphi A. Collectively, these data are consistent with surveillance and modelling studies that indicate multiple infections can occur in high transmission settings, supporting the need for vaccines to reduce the burden of disease in childhood and achieve disease control. Trial registration NCT02192008; clinicaltrials.gov.
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Affiliation(s)
- Malick M. Gibani
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, United Kingdom
- Department of Infectious Diseases, Imperial College London, United Kingdom
| | - Celina Jin
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, United Kingdom
| | - Sonu Shrestha
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, United Kingdom
| | - Maria Moore
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, United Kingdom
| | - Lily Norman
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, United Kingdom
| | - Merryn Voysey
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, United Kingdom
| | - Elizabeth Jones
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, United Kingdom
| | - Luke Blackwell
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, United Kingdom
| | - Helena Thomaides-Brears
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, United Kingdom
| | - Jennifer Hill
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, United Kingdom
| | - Christoph J. Blohmke
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, United Kingdom
| | - Hazel C. Dobinson
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, United Kingdom
| | - Philip Baker
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, United Kingdom
| | - Claire Jones
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, United Kingdom
| | - Danielle Campbell
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, United Kingdom
| | - Yama F. Mujadidi
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, United Kingdom
| | - Emma Plested
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, United Kingdom
| | - Lorena Preciado-Llanes
- Institute for Infection and Global Health, University of Liverpool, United Kingdom
- Medical Research Council Human Immunology Unit, Radcliffe Department of Medicine, University of Oxford, United Kingdom
| | - Giorgio Napolitani
- Medical Research Council Human Immunology Unit, Radcliffe Department of Medicine, University of Oxford, United Kingdom
| | - Alison Simmons
- Medical Research Council Human Immunology Unit, Radcliffe Department of Medicine, University of Oxford, United Kingdom
| | - Melita A. Gordon
- Institute for Infection and Global Health, University of Liverpool, United Kingdom
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Brian Angus
- Nuffield Department of Medicine, University of Oxford, United Kingdom
| | - Thomas C. Darton
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, United Kingdom
| | - Vincenzo Cerundulo
- Medical Research Council Human Immunology Unit, Radcliffe Department of Medicine, University of Oxford, United Kingdom
| | - Andrew J. Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, United Kingdom
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16
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Lattanzi R, Maftei D, Fullone MR, Miele R. Trypanosoma cruzi trans-sialidase induces STAT3 and ERK activation by prokineticin receptor 2 binding. Cell Biochem Funct 2020; 39:326-334. [PMID: 32892338 DOI: 10.1002/cbf.3586] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 07/15/2020] [Accepted: 08/01/2020] [Indexed: 01/22/2023]
Abstract
Tc85, as other members of trans-sialidase family, is involved in Trypanosoma cruzi parasite adhesion to mammalian cells. Particularly, Tc85 acts through specific interactions with prokineticin receptor 2, a G-protein coupled receptor involved in diverse physiological and pathological processes. In this manuscript, through biochemical analyses, we demonstrated that LamG, a Tc85 domain, physically interacts with the prokineticin receptor 2. Moreover, expressing prokineticin receptor 1 and 2 we demonstrated that LamG specifically activates prokineticin receptor 2 through a strong coupling with Gαi or Gαq proteins in yeast strains and inducing ERK and NFAT phosphorylation in CHO mammalian cells. To demonstrate a Tc85 physiological role in T. cruzi infection of the nervous system, we evidenced a strong STAT3 and ERK activation by LamG in mice Dorsal Root Ganglia. L173R is the most common prokineticin receptor 2 mutation reported in Kallmann syndrome and it is a founder mutation. Our results demonstrated that in cells co-expressing prokineticin receptor 2 mutant (L173R) and wild-type, LamG is unable to induce signal transduction. The L173R mutation in heterozygosity may allow for a selective advantage due to increased protection from T. cruzi infection. SIGNIFICANCE OF THE STUDY: The Chagas' disease affecting millions of people worldwide is caused by an eukaryotic microorganism called T. cruzi. Pharmacological treatment for patients with Chagas' disease is still limited. Indeed, the small number of drugs available shows important side effects that can be debilitating for patient health. In order to replicate and produce new parasites T. cruzi uses a complex of different proteins produced by both the parasite and the human host cells. So, understanding the molecular details used by T. cruzi to be internalised by different types of human cells is an important step towards the development of new drugs for this disease. Prokineticin receptors are relevant for host-parasite interaction. To characterise the signal transduction cascade induced by their activation may help to understand the molecular details of cell infection, leading to novel therapeutic alternative for this debilitating disease.
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Affiliation(s)
- Roberta Lattanzi
- Department of Physiology and Pharmacology "Vittorio Erspamer", Sapienza University of Rome, Rome, Italy
| | - Daniela Maftei
- Department of Physiology and Pharmacology "Vittorio Erspamer", Sapienza University of Rome, Rome, Italy
| | - Maria Rosaria Fullone
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy
| | - Rossella Miele
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy
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17
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Bernut A, Dupont C, Ogryzko NV, Neyret A, Herrmann JL, Floto RA, Renshaw SA, Kremer L. CFTR Protects against Mycobacterium abscessus Infection by Fine-Tuning Host Oxidative Defenses. Cell Rep 2020; 26:1828-1840.e4. [PMID: 30759393 DOI: 10.1016/j.celrep.2019.01.071] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 12/17/2018] [Accepted: 01/17/2019] [Indexed: 01/03/2023] Open
Abstract
Infection by rapidly growing Mycobacterium abscessus is increasingly prevalent in cystic fibrosis (CF), a genetic disease caused by a defective CF transmembrane conductance regulator (CFTR). However, the potential link between a dysfunctional CFTR and vulnerability to M. abscessus infection remains unknown. Herein, we exploit a CFTR-depleted zebrafish model, recapitulating CF immuno-pathogenesis, to study the contribution of CFTR in innate immunity against M. abscessus infection. Loss of CFTR increases susceptibility to infection through impaired NADPH oxidase-dependent restriction of intracellular growth and reduced neutrophil chemotaxis, which together compromise granuloma formation and integrity. As a consequence, extracellular multiplication of M. abscessus expands rapidly, inducing abscess formation and causing lethal infections. Because these phenotypes are not observed with other mycobacteria, our findings highlight the crucial and specific role of CFTR in the immune control of M. abscessus by mounting effective oxidative responses.
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Affiliation(s)
- Audrey Bernut
- CNRS, UMR9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, Montpellier, France; Bateson Centre, University of Sheffield, Sheffield, UK; Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK.
| | - Christian Dupont
- CNRS, UMR9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, Montpellier, France
| | - Nikolay V Ogryzko
- Bateson Centre, University of Sheffield, Sheffield, UK; Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK
| | - Aymeric Neyret
- CNRS, UMR9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, Montpellier, France
| | | | - R Andres Floto
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Stephen A Renshaw
- Bateson Centre, University of Sheffield, Sheffield, UK; Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK
| | - Laurent Kremer
- CNRS, UMR9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, Montpellier, France; INSERM, IRIM, Montpellier, France.
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18
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Côté K, Simons AM. Genotype-environment interaction and the maintenance of genetic variation: an empirical study of Lobelia inflata (Campanulaceae). ROYAL SOCIETY OPEN SCIENCE 2020; 7:191720. [PMID: 32269800 PMCID: PMC7137973 DOI: 10.1098/rsos.191720] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 02/19/2020] [Indexed: 05/13/2023]
Abstract
High levels of genetic variation are often observed in natural populations, suggesting the action of processes such as frequency-dependent selection, heterozygote advantage and variable selection. However, the maintenance of genetic variation in fitness-related traits remains incompletely explained. The extent of genetic variation in obligately self-fertilizing populations of Lobelia inflata (Campanulaceae L.) strongly implies balancing selection. Lobelia inflata thus offers an exceptional opportunity for an empirical test of genotype-environment interaction (G × E) as a variance-maintaining mechanism under fluctuating selection: L. inflata is monocarpic and reproduces only by seed, facilitating assessment of lifetime fitness; genome-wide homozygosity precludes some mechanisms of balancing selection, and microsatellites are, in effect, genotypic lineage markers. Here, we find support for the temporal G × E hypothesis using a manipulated space-for-time approach across four environments: a field environment, an outdoor experimental plot and two differing growth-chamber environments. High genetic variance was confirmed: 83 field-collected individuals consisted of 45 distinct microsatellite lineages with, on average, 4.5 alleles per locus. Rank-order fitness, measured as lifetime fruit production in 16 replicated multilocus genotypes, changed significantly across environments. Phenotypic differences among microsatellite lineages were detected. Results thus support the G × E hypothesis in principle. However, the evaluation of the effect size of this mechanism and fitness effects of life-history traits will require a long-term study of fluctuating selection on labelled genotypes in the field.
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Affiliation(s)
| | - Andrew M. Simons
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, CanadaK1S 5B6
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19
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Rehman T, Yin L, Latif MB, Chen J, Wang K, Geng Y, Huang X, Abaidullah M, Guo H, Ouyang P. Adhesive mechanism of different Salmonella fimbrial adhesins. Microb Pathog 2019; 137:103748. [PMID: 31521802 DOI: 10.1016/j.micpath.2019.103748] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 09/10/2019] [Accepted: 09/11/2019] [Indexed: 02/01/2023]
Abstract
Salmonellosis is a serious threat to human and animal health. Salmonella adhesion to the host cell is an initial and most crucial step in the pathogenesis of salmonellosis. Many factors are involved in the adhesion process of Salmonella infection. Fimbriae are one of the most important factors in the adhesion of Salmonella. The Salmonella fimbriae are assembled in three types of assembly pathways: chaperon-usher, nucleation-precipitation, and type IV fimbriae. These assembly pathways lead to multiple types of fimbriae. Salmonella fimbriae bind to host cell receptors to initiate adhesion. So far, many receptors have been identified, such as Toll-like receptors. However, several receptors that may be involved in the adhesive mechanism of Salmonella fimbriae are still un-identified. This review aimed to summarize the types of Salmonella fimbriae produced by different assembly pathways and their role in adhesion. It also enlisted previously discovered receptors involved in adhesion. This review might help readers to develop a comprehensive understanding of Salmonella fimbriae, their role in adhesion, and recently developed strategies to counter Salmonella infection.
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Affiliation(s)
- Tayyab Rehman
- Department of Basic Veterinary, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
| | - Lizi Yin
- Department of Basic Veterinary, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
| | - Muhammad Bilal Latif
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, 44195, Ohio, USA.
| | - Jiehao Chen
- Department of Basic Veterinary, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
| | - Kaiyu Wang
- Department of Basic Veterinary, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
| | - Yi Geng
- Department of Basic Veterinary, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
| | - Xiaoli Huang
- Department of Aquaculture, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
| | - Muhammad Abaidullah
- Department of Basic Veterinary, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
| | - Hongrui Guo
- Department of Basic Veterinary, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
| | - Ping Ouyang
- Department of Basic Veterinary, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
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20
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Viljoen JW, de Villiers JP, van Zyl AJ, Mezzavilla M, Pepper MS. Establishment and equilibrium levels of deleterious mutations in large populations. Sci Rep 2019; 9:10384. [PMID: 31316137 PMCID: PMC6637196 DOI: 10.1038/s41598-019-46803-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 07/04/2019] [Indexed: 11/09/2022] Open
Abstract
Analytical and statistical stochastic approaches are used to model the dispersion of monogenic variants through large populations. These approaches are used to quantify the magnitude of the selective advantage of a monogenic heterozygous variant in the presence of a homozygous disadvantage. Dunbar's results regarding the cognitive upper limit of the number of stable social relationships that humans can maintain are used to determine a realistic effective community size from which an individual can select mates. By envisaging human community structure as a network where social proximity rather than physical geography predominates, a significant simplification is achieved, implicitly accounting for the effects of migration and consanguinity, and with population structure and genetic drift becoming emergent features of the model. Effective community size has a dramatic effect on the probability of establishing beneficial alleles. It also affects the eventual equilibrium values that are reached in the case of variants conferring a heterozygous selective advantage, but a homozygous disadvantage, as in the case of cystic fibrosis and sickle cell disease. The magnitude of this selective advantage can then be estimated based on observed occurrence levels of a specific allele in a population, without requiring prior information regarding its phenotypic manifestation.
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Affiliation(s)
- Johan W Viljoen
- Department of Electrical, Electronic and Computer Engineering, EBIT, University of Pretoria, Pretoria, 0028, South Africa. .,Development, Research and Technology Department, Hensoldt Optronics, Centurion, 0157, South Africa.
| | - J Pieter de Villiers
- Department of Electrical, Electronic and Computer Engineering, EBIT, University of Pretoria, Pretoria, 0028, South Africa.,Radar and Electronic Warfare Research and Applications Group, Council for Scientific and Industrial Research, Pretoria, 0001, South Africa
| | - Augustinus J van Zyl
- Department of Mathematics and Applied Mathematics, University of Pretoria, Pretoria, 0028, South Africa
| | - Massimo Mezzavilla
- Institute for Maternal and Child Health, IRCCS 'Burlo Garofolo', Trieste, Italy.,The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Michael S Pepper
- Institute for Cellular and Molecular Medicine, Department of Immunology, University of Pretoria, Pretoria, 0084, South Africa.,SAMRC Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, 0084, South Africa
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21
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Rao MC. Physiology of Electrolyte Transport in the Gut: Implications for Disease. Compr Physiol 2019; 9:947-1023. [PMID: 31187895 DOI: 10.1002/cphy.c180011] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We now have an increased understanding of the genetics, cell biology, and physiology of electrolyte transport processes in the mammalian intestine, due to the availability of sophisticated methodologies ranging from genome wide association studies to CRISPR-CAS technology, stem cell-derived organoids, 3D microscopy, electron cryomicroscopy, single cell RNA sequencing, transgenic methodologies, and tools to manipulate cellular processes at a molecular level. This knowledge has simultaneously underscored the complexity of biological systems and the interdependence of multiple regulatory systems. In addition to the plethora of mammalian neurohumoral factors and their cross talk, advances in pyrosequencing and metagenomic analyses have highlighted the relevance of the microbiome to intestinal regulation. This article provides an overview of our current understanding of electrolyte transport processes in the small and large intestine, their regulation in health and how dysregulation at multiple levels can result in disease. Intestinal electrolyte transport is a balance of ion secretory and ion absorptive processes, all exquisitely dependent on the basolateral Na+ /K+ ATPase; when this balance goes awry, it can result in diarrhea or in constipation. The key transporters involved in secretion are the apical membrane Cl- channels and the basolateral Na+ -K+ -2Cl- cotransporter, NKCC1 and K+ channels. Absorption chiefly involves apical membrane Na+ /H+ exchangers and Cl- /HCO3 - exchangers in the small intestine and proximal colon and Na+ channels in the distal colon. Key examples of our current understanding of infectious, inflammatory, and genetic diarrheal diseases and of constipation are provided. © 2019 American Physiological Society. Compr Physiol 9:947-1023, 2019.
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Affiliation(s)
- Mrinalini C Rao
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, Illinois, USA
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22
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Ghieh F, Mitchell V, Mandon-Pepin B, Vialard F. Genetic defects in human azoospermia. Basic Clin Androl 2019; 29:4. [PMID: 31024732 PMCID: PMC6477738 DOI: 10.1186/s12610-019-0086-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 03/07/2019] [Indexed: 02/07/2023] Open
Abstract
As with many other diseases, genetic testing in human azoospermia was initially restricted to karyotype analyses (leading to diagnostic chromosome rearrangement tests for Klinefelter and other syndromes). With the advent of molecular biology in the 1980s, genetic screening was broadened to analyses of Y chromosome microdeletions and the gene coding for the cystic fibrosis transmembrane conductance regulator (CFTR). Decades later, the emergence of whole-genome techniques has led to the identification of other genetic defects associated with human azoospermia. Although TEX11 and ADGRG2 defects are frequently described in men with azoospermia, most of the causal gene defects found to date are private (i.e. identified in a small number of consanguineous families). Here, we provide an up-to-date overview of all the types of genetic defects known to be linked to human azoospermia and try to give clinical practice guidelines according to azoospermia phenotype. Along with homozygous mutations, polymorphisms and epigenetic defects are also briefly discussed. However, as these variations predispose to azoospermia, a specific review will be needed to compile data on all the particular genetic variations reported in the literature.
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Affiliation(s)
- Farah Ghieh
- 1EA7404-GIG, UFR des Sciences de la Santé Simone Veil, UVSQ, Montigny le Bretonneux, France
| | - Valérie Mitchell
- 2CHU Lille, Reproductive Biology Institute-Spermiologie-CECOS, Jeanne de Flandre Hospital, Lille, France.,3EA4308 "Gametogenesis and Gamete Quality", University of Lille, Lille, France
| | | | - François Vialard
- 1EA7404-GIG, UFR des Sciences de la Santé Simone Veil, UVSQ, Montigny le Bretonneux, France.,Genetics Division, CHI de Poissy St Germain en Laye, Poissy, France
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23
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Was the Last Ice Age dusty climate instrumental in spreading of the three "Celtic" diseases (hemochromatosis, cystic fibrosis and palmar fibromatosis)? Med Hypotheses 2018; 122:134-138. [PMID: 30593397 DOI: 10.1016/j.mehy.2018.11.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 11/03/2018] [Accepted: 11/15/2018] [Indexed: 11/21/2022]
Abstract
Cystic fibrosis, hereditary hemochromatosis and palmar fibromatosis are often described as "Celtic", based on their contemporary prevalence. The former two are among genetically defined disorders that seem to provide survival advantages to heterozygote individuals, while severe health problems happen in homozygote mutation carriers. Although palmar fibromatosis has no defined mutations, its prevalence has been linked to the prevalence of Y-Chromosome Haplogroup I that expanded after the Last Ice Age, thus making th distribution of all three "Celtic" diseases dependent on the global climate from 40 to 8 Kya. During the Last Ice Age, the global climate was dry and dark due to dust-laden atmosphere (20-25 times more than today). It has been postulated that skin pigmentation was related to insolation, UV protection and skin synthesis of vitamin D, so when our ancestors moved to Eurasia, individuals with pale skin became advantageous. Deficiency of vitamin D has several health consequences and some of them have been proposed by other authors as important for the spreading of cystic fibrosis mutations: rickets/osteomalacia; susceptibility to diarrheal diseases and tuberculosis and salt induced arterial hypertension. The here proposed link is between vitamin D deficiency and the anaemia of chronic disease that might have facilitated spreading of the hemochromatosis mutation. It seems plausible that the risk of health problems in the offspring of close relatives might have resulted in social taboos of consanguinity in Eurasian protosocieties. Ancient steam bath rituals seem linked to lower incidences of cystic fibrosis in several European populations, thus suggesting health protection in an arid, dusty climate of the last glaciation, that made CFTR mutations in heterozygote carriers less advantageous.
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Chowdhury R, Das S, Ta A, Das S. Epithelial invasion by Salmonella Typhi using STIV-Met interaction. Cell Microbiol 2018; 21:e12982. [PMID: 30426648 DOI: 10.1111/cmi.12982] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 11/01/2018] [Accepted: 11/09/2018] [Indexed: 12/20/2022]
Abstract
Typhoid is a life-threatening febrile illness that affects ~24.2 million people worldwide and is caused by the intracellular bacteria Salmonella Typhi (S. Typhi). Intestinal epithelial invasion by S. Typhi is essential for the establishment of successful infection and is traditionally believed to depend on Salmonella pathogenicity island 1-encoded type 3 secretion system 1 (T3SS-1). We had previously reported that bacterial outer membrane protein T2942/STIV functions as a standalone invasin and contributes to the pathogenesis of S. Typhi by promoting epithelial invasion independent of T3SS-1 (Cell Microbiol, 2015). Here, we show that STIV, by using its 20-amino-acid extracellular loop, interacts with receptor tyrosine kinase, Met, of host intestinal epithelial cells. This interaction leads to Met phosphorylation and activation of a downstream signalling cascade, involving Src, phosphatidylinositol 3-kinase/Akt, and Rac1, which culminates into localized actin polymerisation and bacterial engulfment by the cell. Inhibition of Met tyrosine kinase activity severely limited intestinal invasion and systemic infection by S. Typhi in vivo, highlighting the importance of this invasion pathway in disease progression. This is the first report elucidating the mechanism of T3SS-1-independent epithelial invasion of S. Typhi, and this crucial host-pathogen interaction may be targeted therapeutically to restrict pathogenesis.
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Affiliation(s)
- Rimi Chowdhury
- Division of Clinical Medicine, National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Sayan Das
- Division of Clinical Medicine, National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Atri Ta
- Division of Clinical Medicine, National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Santasabuj Das
- Division of Clinical Medicine, National Institute of Cholera and Enteric Diseases, Kolkata, India
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Polgreen PM, Brown GD, Hornick DB, Ahmad F, London B, Stoltz DA, Comellas AP. CFTR Heterozygotes Are at Increased Risk of Respiratory Infections: A Population-Based Study. Open Forum Infect Dis 2018; 5:ofy219. [PMID: 30397620 PMCID: PMC6210382 DOI: 10.1093/ofid/ofy219] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 09/13/2018] [Indexed: 01/15/2023] Open
Abstract
Background Patients heterozygous for mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene may be more susceptible to respiratory infections than the general population. Methods We conducted a retrospective case-control study using health insurance claims. We identified patients as either highly likely to be CFTR heterozygotes (CF carriers diagnosed during genetic counseling, parents of children with a diagnosis of CF, and children of mothers diagnosed with CF) or likely CFTR heterozygotes (children of CF carriers diagnosed during genetic counseling and parents of CF carriers diagnosed during genetic counseling). Next, we examined the rates of respiratory infections and antimicrobial prescriptions between both groups of CFTR patients and only the highly likely subcohort, compared with age/sex-matched controls. We examined the presence of any claim using McNemar's test and the number of claims using the sign test. Results CFTR heterozygotes (the pooled highly likely and likely heterozygotes) were more prone to have at least 1 claim for a respiratory infection (odds ratio [OR], 1.28; P = .020) and to have a greater number of claims for respiratory infections (53.5%; P = .043) than controls. Patients in the highly likely cohort were also more prone to have at least 1 claim for a respiratory infection (OR, 1.30; P = .028) and more claims (54.3%; P = .039) than controls. In addition, the highly likely CFTR heterozygotes were more prone to be prescribed an antibiotic used to treat respiratory infections (OR, 1.34; P = .018) and to have more of these prescriptions (54.3%; P = .035) than controls. Conclusions Patients heterozygous for CFTR mutations are at higher risk for respiratory infections. Future work to describe clinical outcomes for CFTR heterozygotes is needed.
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Affiliation(s)
- Philip M Polgreen
- Department of Epidemiology, University of Iowa, Iowa City, Iowa.,Department of Internal Medicine, University of Iowa, Iowa City, Iowa
| | - Grant D Brown
- Department of Biostatistics, University of Iowa, Iowa City, Iowa
| | - Douglas B Hornick
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa
| | - Ferhaan Ahmad
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa
| | - Barry London
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa
| | - David A Stoltz
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa
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26
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Do GWAS and studies of heterozygotes for NPC1 and/or NPC2 explain why NPC disease cases are so rare? J Appl Genet 2018; 59:441-447. [PMID: 30209687 DOI: 10.1007/s13353-018-0465-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 08/31/2018] [Accepted: 09/04/2018] [Indexed: 12/15/2022]
Abstract
Early onset Niemann-Pick C diseases are extremely rare, especially Niemann-Pick C2. Perhaps unusually for autosomal recessive diseases, heterozygotes for mutations in NPC1 manifest many biological variations. NPC2 deficiency has large effects on fertility. These features of NPC1 and NPC2 are reviewed in regard to possible negative selection for heterozygotes carrying null and hypomorphic alleles.
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Dey I, Bradbury NA. Physiology of the Gut: Experimental Models for Investigating Intestinal Fluid and Electrolyte Transport. CURRENT TOPICS IN MEMBRANES 2018; 81:337-381. [PMID: 30243437 DOI: 10.1016/bs.ctm.2018.08.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Once thought to be exclusively an absorptive tissue, the intestine is now recognized as an important secretory tissue, playing a key role in body ion and fluid homeostasis. Given the intestine's role in fluid homeostasis, it is not surprising that important clinical pathologies arise from imbalances in fluid absorption and secretion. Perhaps the most important examples of this can be seen in enterotoxigenic secretory diarrheas with extreme fluid secretion, and Cystic Fibrosis with little or no fluid secretion. A mechanistic understanding of the cellular pathways regulating ion and fluid transport has been obtained from a variety of approaches and model systems. These have ranged from the intact intestine to a single intestinal epithelial cell type. Although for many years a reductionist approach has held sway for investigating intestinal transport, the growing realization that physiologic processes should really be examined within a physiological context has seen a marked increase in studies using models that are essentially mini-intestines in a dish. The aim of this chapter is to provide a historical context for our understanding of intestinal ion and fluid transport, and to highlight the model systems that have been used to acquire this knowledge.
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Affiliation(s)
- Isha Dey
- Department of Physiology and Biophysics, Chicago Medical School, North Chicago, IL, United States
| | - Neil A Bradbury
- Department of Physiology and Biophysics, Chicago Medical School, North Chicago, IL, United States
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28
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Identification of Parameters of Host Cell Vulnerability during Salmonella Infection by Quantitative Image Analysis and Modeling. Infect Immun 2017; 86:IAI.00644-17. [PMID: 29084895 DOI: 10.1128/iai.00644-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 10/23/2017] [Indexed: 02/07/2023] Open
Abstract
Salmonella targets and enters epithelial cells at permissive entry sites: some cells are more likely to be infected than others. However, the parameters that lead to host cell heterogeneity are not known. Here, we quantitatively characterized host cell vulnerability to Salmonella infection based on imaged parameters. We performed successive infections of the same host cell population followed by automated high-throughput microscopy and observed that infected cells have a higher probability of being reinfected. Establishing a predictive model, we identified two combined origins of host cell vulnerability: pathogen-induced cellular vulnerability emerging from Salmonella uptake and persisting at later stages of the infection and host cell-inherent vulnerability. We linked the host cell-inherent vulnerability with its morphological attributes, such as local cell crowding, and with host cell cholesterol content. This showed that the probability of Salmonella infection success can be forecast from morphological or molecular host cell parameters.
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Grzymajlo K, Ugorski M, Suchanski J, Kedzierska AE, Kolenda R, Jarzab A, Biernatowska A, Schierack P. The Novel Type 1 Fimbriae FimH Receptor Calreticulin Plays a Role in Salmonella Host Specificity. Front Cell Infect Microbiol 2017; 7:326. [PMID: 28770174 PMCID: PMC5516122 DOI: 10.3389/fcimb.2017.00326] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 07/03/2017] [Indexed: 01/25/2023] Open
Abstract
It was suggested that minor differences in the structure of FimH are most likely associated with differences in its adhesion specificities and may determine the tropism of various Salmonella serovars to different species and tissues. We have recently shown that FimH adhesins from host-adapted serovars, e.g., Salmonella Choleraesuis (SCh), bind to other glycoprotein receptors compared to FimH from host-unrestricted Salmonella Enteritidis (SE). Here we identify porcine calreticulin expressed by swine intestinal cells as a host-specific receptor for SCh FimH adhesin, suggesting that such an interaction may contribute to SCh host specificity. Calreticulin was identified by 2D electrophoresis and mass spectrometry as a glycoprotein that was bound specifically by recombinant SCh FimH protein, but not by FimH from SE. The functionality of calreticulin as a specific receptor of SCh FimH adhesin was further confirmed by adhesion and invasion of mutated strains of SCh carrying different variants of FimH proteins to IPEC-J2 cells with overexpression and silenced expression of calreticulin. It was found that SCh carrying the active variant of FimH adhered and invaded IPEC-J2 cells with calreticulin overexpression at significantly higher numbers than those of SCh expressing the non-active variant or SE variant of FimH. Moreover, binding of SCh carrying the active variant of FimH to IPEC-J2 with silenced calreticulin expression was significantly weaker. Furthermore, we observed that SCh infection induces translocation of calreticulin to cell membrane. All of the aforementioned results lead to the general conclusion that Salmonella host specificity requires not only special mechanisms and proteins expressed by the pathogen but also specifically recognized receptors expressed by a specific host.
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Affiliation(s)
- Krzysztof Grzymajlo
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Sciences, Wrocław University of Environmental and Life SciencesWrocław, Poland
| | - Maciej Ugorski
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Sciences, Wrocław University of Environmental and Life SciencesWrocław, Poland
| | - Jaroslaw Suchanski
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Sciences, Wrocław University of Environmental and Life SciencesWrocław, Poland
| | - Anna E Kedzierska
- Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of SciencesWrocław, Poland
| | - Rafal Kolenda
- Faculty of Environment and Natural Sciences, Institute of Biotechnology, Brandenburg University of Technology Cottbus-SenftenbergSenftenberg, Germany
| | - Anna Jarzab
- Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of SciencesWrocław, Poland
| | - Agnieszka Biernatowska
- Laboratory of Cytobiochemistry, Faculty of Biotechnology, University of WrocławWrocław, Poland
| | - Peter Schierack
- Faculty of Environment and Natural Sciences, Institute of Biotechnology, Brandenburg University of Technology Cottbus-SenftenbergSenftenberg, Germany
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Bosch L, Bosch B, De Boeck K, Nawrot T, Meyts I, Vanneste D, Le Bourlegat CA, Croda J, da Silva Filho LVRF. Cystic fibrosis carriership and tuberculosis: hints toward an evolutionary selective advantage based on data from the Brazilian territory. BMC Infect Dis 2017; 17:340. [PMID: 28499359 PMCID: PMC5429554 DOI: 10.1186/s12879-017-2448-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 05/07/2017] [Indexed: 12/21/2022] Open
Abstract
Background The reason why Cystic Fibrosis (CF) is the most common fatal genetic disease among Caucasians has been incompletely studied. We aimed at deepening the hypothesis that CF carriers have a relative protection against Mycobacterium tuberculosis (Mtb) infection. Methods Applying spatial epidemiology, we studied the link between CF carriership rate and tuberculosis (TB) incidence in Brazil. We corrected for 5 potential environmental and 2 immunological confounders in this relation: monthly income, sanitary provisions, literacy rates, racial composition and population density along with AIDS incidence rates and diabetes mellitus type 2. Smoking data were incomplete and not available for analysis. Results A significant, negative correlation between CF carriership rate and TB incidence, independent of any of the seven confounders was found. Conclusion We provide exploratory support for the hypothesis that carrying a single CFTR mutation arms against Mtb infections.
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Affiliation(s)
- Lander Bosch
- Department of Geography, University of Cambridge, Downing Place, Cambridge, CB2 3EN, UK.,Fundação Oswaldo Cruz Mato Grosso do Sul, Rua Gabriel Abrão s/n, Jardim das Nações, Campo Grande, MS, 79081-746, Brazil
| | - Barbara Bosch
- St Giles Laboratory of Human Genetics of Infectious Disease, Rockefeller branch, Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA. .,Department of Pediatrics, University Hospitals Leuven, Herestraat 49, 3000, Leuven, Belgium.
| | - Kris De Boeck
- Department of Pediatrics, University Hospitals Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Tim Nawrot
- Centre for Environmental Sciences, Hasselt University, Martelarenlaan 42, 3500, Hasselt, Belgium.,Department of Public Health & Primary Care, Occupational & Environmental Medicine, KULeuven, Herestraat 49, 3000, Leuven, Belgium
| | - Isabelle Meyts
- Department of Pediatrics, University Hospitals Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Dominique Vanneste
- Division of Geography, KULeuven, Celestijnenlaan 200E, 3001, Leuven, Belgium
| | - Cleonice Alexandre Le Bourlegat
- Mestrado e Doutorado em Desenvolvimento Local, Universidade Católica Dom Bosco, Av. Tamandaré 6000, Jardim Seminário, Campo Grande, MS, 70117-900, Brazil
| | - Julio Croda
- Fundação Oswaldo Cruz Mato Grosso do Sul, Rua Gabriel Abrão s/n, Jardim das Nações, Campo Grande, MS, 79081-746, Brazil.,Faculdade de Ciências da Saúde, Universidade Federal de Grande Dourados, Rodovia Dourados, Itahum km 12, Cidade Universitaria, Cx. Postal 533, Dourados, MS, 79804-970, Brazil
| | - Luiz Vicente Ribeiro Ferreira da Silva Filho
- Instituto da Criança, Hospital das Clínicas, University of São Paulo Medical School, Av. Dr. Enéas Carvalho de Aguiar 647, São Paulo, SP, 05403-000, Brazil.,Instituto de Ensino e Pesquisa, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, Morumbi, São Paulo, SP, 05652-000, Brazil
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Savisaar R, Hurst LD. Estimating the prevalence of functional exonic splice regulatory information. Hum Genet 2017; 136:1059-1078. [PMID: 28405812 PMCID: PMC5602102 DOI: 10.1007/s00439-017-1798-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 04/04/2017] [Indexed: 12/14/2022]
Abstract
In addition to coding information, human exons contain sequences necessary for correct splicing. These elements are known to be under purifying selection and their disruption can cause disease. However, the density of functional exonic splicing information remains profoundly uncertain. Several groups have experimentally investigated how mutations at different exonic positions affect splicing. They have found splice information to be distributed widely in exons, with one estimate putting the proportion of splicing-relevant nucleotides at >90%. These results suggest that splicing could place a major pressure on exon evolution. However, analyses of sequence conservation have concluded that the need to preserve splice regulatory signals only slightly constrains exon evolution, with a resulting decrease in the average human rate of synonymous evolution of only 1–4%. Why do these two lines of research come to such different conclusions? Among other reasons, we suggest that the methods are measuring different things: one assays the density of sites that affect splicing, the other the density of sites whose effects on splicing are visible to selection. In addition, the experimental methods typically consider short exons, thereby enriching for nucleotides close to the splice junction, such sites being enriched for splice-control elements. By contrast, in part owing to correction for nucleotide composition biases and to the assumption that constraint only operates on exon ends, the conservation-based methods can be overly conservative.
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Affiliation(s)
- Rosina Savisaar
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK.
| | - Laurence D Hurst
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
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32
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Barrila J, Yang J, Crabbé A, Sarker SF, Liu Y, Ott CM, Nelman-Gonzalez MA, Clemett SJ, Nydam SD, Forsyth RJ, Davis RR, Crucian BE, Quiriarte H, Roland KL, Brenneman K, Sams C, Loscher C, Nickerson CA. Three-dimensional organotypic co-culture model of intestinal epithelial cells and macrophages to study Salmonella enterica colonization patterns. NPJ Microgravity 2017; 3:10. [PMID: 28649632 PMCID: PMC5460263 DOI: 10.1038/s41526-017-0011-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/23/2016] [Accepted: 12/12/2016] [Indexed: 12/21/2022] Open
Abstract
Three-dimensional models of human intestinal epithelium mimic the differentiated form and function of parental tissues often not exhibited by two-dimensional monolayers and respond to Salmonella in key ways that reflect in vivo infections. To further enhance the physiological relevance of three-dimensional models to more closely approximate in vivo intestinal microenvironments encountered by Salmonella, we developed and validated a novel three-dimensional co-culture infection model of colonic epithelial cells and macrophages using the NASA Rotating Wall Vessel bioreactor. First, U937 cells were activated upon collagen-coated scaffolds. HT-29 epithelial cells were then added and the three-dimensional model was cultured in the bioreactor until optimal differentiation was reached, as assessed by immunohistochemical profiling and bead uptake assays. The new co-culture model exhibited in vivo-like structural and phenotypic characteristics, including three-dimensional architecture, apical-basolateral polarity, well-formed tight/adherens junctions, mucin, multiple epithelial cell types, and functional macrophages. Phagocytic activity of macrophages was confirmed by uptake of inert, bacteria-sized beads. Contribution of macrophages to infection was assessed by colonization studies of Salmonella pathovars with different host adaptations and disease phenotypes (Typhimurium ST19 strain SL1344 and ST313 strain D23580; Typhi Ty2). In addition, Salmonella were cultured aerobically or microaerobically, recapitulating environments encountered prior to and during intestinal infection, respectively. All Salmonella strains exhibited decreased colonization in co-culture (HT-29-U937) relative to epithelial (HT-29) models, indicating antimicrobial function of macrophages. Interestingly, D23580 exhibited enhanced replication/survival in both models following invasion. Pathovar-specific differences in colonization and intracellular co-localization patterns were observed. These findings emphasize the power of incorporating a series of related three-dimensional models within a study to identify microenvironmental factors important for regulating infection.
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Affiliation(s)
- Jennifer Barrila
- Center for Infectious Diseases and Vaccinology, The Biodesign Institute, Arizona State University, Tempe, AZ USA
| | - Jiseon Yang
- Center for Infectious Diseases and Vaccinology, The Biodesign Institute, Arizona State University, Tempe, AZ USA
| | - Aurélie Crabbé
- Center for Infectious Diseases and Vaccinology, The Biodesign Institute, Arizona State University, Tempe, AZ USA
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Shameema F. Sarker
- Center for Infectious Diseases and Vaccinology, The Biodesign Institute, Arizona State University, Tempe, AZ USA
| | - Yulong Liu
- Center for Infectious Diseases and Vaccinology, The Biodesign Institute, Arizona State University, Tempe, AZ USA
| | - C. Mark Ott
- Biomedical Research and Environmental Sciences Division, NASA Johnson Space Center, Houston, TX USA
| | | | | | - Seth D. Nydam
- Center for Infectious Diseases and Vaccinology, The Biodesign Institute, Arizona State University, Tempe, AZ USA
| | - Rebecca J. Forsyth
- Center for Infectious Diseases and Vaccinology, The Biodesign Institute, Arizona State University, Tempe, AZ USA
| | - Richard R. Davis
- Center for Infectious Diseases and Vaccinology, The Biodesign Institute, Arizona State University, Tempe, AZ USA
| | - Brian E. Crucian
- Biomedical Research and Environmental Sciences Division, NASA Johnson Space Center, Houston, TX USA
| | | | - Kenneth L. Roland
- Center for Infectious Diseases and Vaccinology, The Biodesign Institute, Arizona State University, Tempe, AZ USA
| | - Karen Brenneman
- Center for Infectious Diseases and Vaccinology, The Biodesign Institute, Arizona State University, Tempe, AZ USA
| | - Clarence Sams
- Biomedical Research and Environmental Sciences Division, NASA Johnson Space Center, Houston, TX USA
| | - Christine Loscher
- Immunomodulation Research Group, School of Biotechnology, Dublin City University, Glasnevin, Ireland
| | - Cheryl A. Nickerson
- Center for Infectious Diseases and Vaccinology, The Biodesign Institute, Arizona State University, Tempe, AZ USA
- School of Life Sciences, Arizona State University, Tempe, AZ USA
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Bayless AM, Smith JM, Song J, McMinn PH, Teillet A, August BK, Bent AF. Disease resistance through impairment of α-SNAP-NSF interaction and vesicular trafficking by soybean Rhg1. Proc Natl Acad Sci U S A 2016; 113:E7375-E7382. [PMID: 27821740 PMCID: PMC5127302 DOI: 10.1073/pnas.1610150113] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
α-SNAP [soluble NSF (N-ethylmaleimide-sensitive factor) attachment protein] and NSF proteins are conserved across eukaryotes and sustain cellular vesicle trafficking by mediating disassembly and reuse of SNARE protein complexes, which facilitate fusion of vesicles to target membranes. However, certain haplotypes of the Rhg1 (resistance to Heterodera glycines 1) locus of soybean possess multiple repeat copies of an α-SNAP gene (Glyma.18G022500) that encodes atypical amino acids at a highly conserved functional site. These Rhg1 loci mediate resistance to soybean cyst nematode (SCN; H. glycines), the most economically damaging pathogen of soybeans worldwide. Rhg1 is widely used in agriculture, but the mechanisms of Rhg1 disease resistance have remained unclear. In the present study, we found that the resistance-type Rhg1 α-SNAP is defective in interaction with NSF. Elevated in planta expression of resistance-type Rhg1 α-SNAPs depleted the abundance of SNARE-recycling 20S complexes, disrupted vesicle trafficking, induced elevated abundance of NSF, and caused cytotoxicity. Soybean, due to ancient genome duplication events, carries other loci that encode canonical (wild-type) α-SNAPs. Expression of these α-SNAPs counteracted the cytotoxicity of resistance-type Rhg1 α-SNAPs. For successful growth and reproduction, SCN dramatically reprograms a set of plant root cells and must sustain this sedentary feeding site for 2-4 weeks. Immunoblots and electron microscopy immunolocalization revealed that resistance-type α-SNAPs specifically hyperaccumulate relative to wild-type α-SNAPs at the nematode feeding site, promoting the demise of this biotrophic interface. The paradigm of disease resistance through a dysfunctional variant of an essential gene may be applicable to other plant-pathogen interactions.
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Affiliation(s)
- Adam M Bayless
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706
| | - John M Smith
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706
| | - Junqi Song
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706
| | - Patrick H McMinn
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706
| | - Alice Teillet
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706
| | - Benjamin K August
- University of Wisconsin School of Medicine and Public Health Electron Microscopy Facility, University of Wisconsin-Madison, Madison, WI 53706
| | - Andrew F Bent
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706;
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Fox AA, Shernan SK, Body SC. Predictive Genomics of Adverse Events After Cardiac Surgery. Semin Cardiothorac Vasc Anesth 2016; 8:297-315. [PMID: 15583791 DOI: 10.1177/108925320400800404] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Significant, yet highly individual, thrombotic and inflammatory responses to surgery provide an excellent opportunity for insight into the genomic impact upon a patient's postoperative course. Cardiac surgery elicits the most profound perioperative disturbance and is associated with the highest incidence of adverse outcomes of any elective surgical procedure. Thus, cardiac surgical patients are an ideal population in which to evaluate the influence of complex traits on perioperative morbidity and mortality. This review describes the application of fundamental genetics upon the occurrence of adverse outcomes after cardiac surgery and cardiac transplantation. Specific emphases include a brief primer of the principles of genetics concentrating on the effects of variation within the human genome upon clinical outcomes and the differences between so-called Mendelian traits and complex traits. Four important clinical diseases dealt with in this review as examples of the impact of genetic factors on clinical outcomes are the genetics of heparin-induced thrombocytopenia, heart transplantation rejection and vasculopathy, atrial fibrillation, and infection.
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Affiliation(s)
- Amanda A Fox
- Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
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35
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Ralhan A, Laval J, Lelis F, Ballbach M, Grund C, Hector A, Hartl D. Current Concepts and Controversies in Innate Immunity of Cystic Fibrosis Lung Disease. J Innate Immun 2016; 8:531-540. [PMID: 27362371 PMCID: PMC6738757 DOI: 10.1159/000446840] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 05/17/2016] [Accepted: 05/17/2016] [Indexed: 12/11/2022] Open
Abstract
Cystic fibrosis (CF) lung disease is characterized by chronic infection and inflammation. The inflammatory response in CF is dominated by the activation of the innate immune system. Bacteria and fungi represent the key pathogens chronically colonizing the CF airways. In response, innate immune pattern recognition receptors, expressed by airway epithelial and myeloid cells, sense the microbial threat and release chemoattractants to recruit large numbers of neutrophils into CF airways. However, neutrophils fail to efficiently clear the invading pathogens, but instead release harmful proteases and oxidants and finally cause tissue injury. Here, we summarize and discuss current concepts and controversies in the field of innate immunity in CF lung disease, facing the ongoing questions of whether inflammation is good or bad in CF and how innate immune mechanisms could be harnessed therapeutically.
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Affiliation(s)
- Anjali Ralhan
- Department of Pediatrics I, University of Tübingen, Tübingen, Germany
| | - Julie Laval
- Department of Pediatrics I, University of Tübingen, Tübingen, Germany
| | - Felipe Lelis
- Department of Pediatrics I, University of Tübingen, Tübingen, Germany
| | - Marlene Ballbach
- Department of Pediatrics I, University of Tübingen, Tübingen, Germany
| | - Charlotte Grund
- Department of Pediatrics I, University of Tübingen, Tübingen, Germany
| | - Andreas Hector
- Department of Pediatrics I, University of Tübingen, Tübingen, Germany
| | - Dominik Hartl
- Department of Pediatrics I, University of Tübingen, Tübingen, Germany
- Immunology, Inflammation and Infectious Diseases (I3) Discovery and Translational Area, Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, Basel, Switzerland
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36
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Crump JA, Sjölund-Karlsson M, Gordon MA, Parry CM. Epidemiology, Clinical Presentation, Laboratory Diagnosis, Antimicrobial Resistance, and Antimicrobial Management of Invasive Salmonella Infections. Clin Microbiol Rev 2015; 28:901-37. [PMID: 26180063 PMCID: PMC4503790 DOI: 10.1128/cmr.00002-15] [Citation(s) in RCA: 640] [Impact Index Per Article: 71.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Salmonella enterica infections are common causes of bloodstream infection in low-resource areas, where they may be difficult to distinguish from other febrile illnesses and may be associated with a high case fatality ratio. Microbiologic culture of blood or bone marrow remains the mainstay of laboratory diagnosis. Antimicrobial resistance has emerged in Salmonella enterica, initially to the traditional first-line drugs chloramphenicol, ampicillin, and trimethoprim-sulfamethoxazole. Decreased fluoroquinolone susceptibility and then fluoroquinolone resistance have developed in association with chromosomal mutations in the quinolone resistance-determining region of genes encoding DNA gyrase and topoisomerase IV and also by plasmid-mediated resistance mechanisms. Resistance to extended-spectrum cephalosporins has occurred more often in nontyphoidal than in typhoidal Salmonella strains. Azithromycin is effective for the management of uncomplicated typhoid fever and may serve as an alternative oral drug in areas where fluoroquinolone resistance is common. In 2013, CLSI lowered the ciprofloxacin susceptibility breakpoints to account for accumulating clinical, microbiologic, and pharmacokinetic-pharmacodynamic data suggesting that revision was needed for contemporary invasive Salmonella infections. Newly established CLSI guidelines for azithromycin and Salmonella enterica serovar Typhi were published in CLSI document M100 in 2015.
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Affiliation(s)
- John A Crump
- Centre for International Health, University of Otago, Dunedin, Otago, New Zealand Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Maria Sjölund-Karlsson
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Melita A Gordon
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Christopher M Parry
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, United Kingdom Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
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Gilchrist JJ, MacLennan CA, Hill AVS. Genetic susceptibility to invasive Salmonella disease. Nat Rev Immunol 2015; 15:452-63. [PMID: 26109132 DOI: 10.1038/nri3858] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Invasive Salmonella disease, in the form of enteric fever and invasive non-typhoidal Salmonella (iNTS) disease, causes substantial morbidity and mortality in children and adults in the developing world. The study of genetic variations in humans and mice that influence susceptibility of the host to Salmonella infection provides important insights into immunity to Salmonella. In this Review, we discuss data that have helped to elucidate the host genetic determinants of human enteric fever and iNTS disease, alongside data from the mouse model of Salmonella infection. Considered together, these studies provide a detailed picture of the immunobiology of human invasive Salmonella disease.
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Affiliation(s)
- James J Gilchrist
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford OX3 7BN, UK
| | - Calman A MacLennan
- 1] Jenner Institute, Nuffield Department of Medicine, Old Road Campus Research Building, Roosevelt Drive, University of Oxford, Oxford, OX3 7DQ, UK. [2] Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Adrian V S Hill
- 1] Wellcome Trust Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford OX3 7BN, UK. [2] Jenner Institute, Nuffield Department of Medicine, Old Road Campus Research Building, Roosevelt Drive, University of Oxford, Oxford, OX3 7DQ, UK
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38
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Banerji J. Asparaginase treatment side-effects may be due to genes with homopolymeric Asn codons (Review-Hypothesis). Int J Mol Med 2015; 36:607-26. [PMID: 26178806 PMCID: PMC4533780 DOI: 10.3892/ijmm.2015.2285] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 07/15/2015] [Indexed: 12/14/2022] Open
Abstract
The present treatment of childhood T-cell leukemias involves the systemic administration of prokary-otic L-asparaginase (ASNase), which depletes plasma Asparagine (Asn) and inhibits protein synthesis. The mechanism of therapeutic action of ASNase is poorly understood, as are the etiologies of the side-effects incurred by treatment. Protein expression from genes bearing Asn homopolymeric coding regions (N-hCR) may be particularly susceptible to Asn level fluctuation. In mammals, N-hCR are rare, short and conserved. In humans, misfunctions of genes encoding N-hCR are associated with a cluster of disorders that mimic ASNase therapy side-effects which include impaired glycemic control, dislipidemia, pancreatitis, compromised vascular integrity, and neurological dysfunction. This paper proposes that dysregulation of Asn homeostasis, potentially even by ASNase produced by the microbiome, may contribute to several clinically important syndromes by altering expression of N-hCR bearing genes. By altering amino acid abundance and modulating ribosome translocation rates at codon repeats, the microbiomic environment may contribute to genome decoding and to shaping the proteome. We suggest that impaired translation at poly Asn codons elevates diabetes risk and severity.
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Affiliation(s)
- Julian Banerji
- Center for Computational and Integrative Biology, MGH, Simches Research Center, Boston, MA 02114, USA
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Li K, Tang H, Xu W, Chen A, Shi Q, Sun Z, Wang L, Ni Y. Antisera preparation and epitope mapping of a recombinant protein comprising three peptide fragments of the cystic fibrosis transmembrane conductance regulator. Protein Expr Purif 2015; 114:23-9. [PMID: 26087025 DOI: 10.1016/j.pep.2015.06.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 05/28/2015] [Accepted: 06/09/2015] [Indexed: 10/23/2022]
Abstract
Antibodies targeting a single epitope of the cystic fibrosis transmembrane conductance regulator (CFTR) have been reported to influence the validity of immunological analyses; however, autoimmune mechanisms associated with CFTR epitopes are not well understood. In this study, antiserum raised against a multi-epitope recombinant protein composed of three peptide fragments of CFTR (r-CFTR-3P) was prepared and B cell epitope mapping of the protein was carried out using biosynthetic peptides. The r-CFTR-3P gene was cloned into the pSY621 expression plasmid and the protein was expressed in the BL21 strain of Escherichia coli. The rabbit r-CFTR-3P antiserum recognized the native CFTR antigen extracted from human sperm and the GST188 fusion peptides CFTR(25-36), CFTR(103-117), and CFTR(1387-1480) spanning different regions of CFTR. Four novel r-CFTR-3P B cell epitopes were identified: (29)RQRLEL(34), (104)RIIASY(109), (111)PDN(113), and (1447)VKLF(1450) of CFTR. Other proteins from various species shared sequence homology with the identified epitopes based on NCBI BLAST alignment. This study provides new tools for detecting CFTR protein and insight into the characteristics of minimal B cell epitopes of CFTR and associated immunological mechanisms.
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Affiliation(s)
- Kun Li
- Unit of Reproductive Physiology, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang 310013, China
| | - Haiping Tang
- National Population and Family Planning Key Laboratory of Contraceptive Drugs & Devices, Shanghai Institute of Planned Parenthood Research, Shanghai 200032, China
| | - Wanxiang Xu
- National Population and Family Planning Key Laboratory of Contraceptive Drugs & Devices, Shanghai Institute of Planned Parenthood Research, Shanghai 200032, China
| | - Aijun Chen
- Unit of Reproductive Physiology, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang 310013, China
| | - Qixian Shi
- Unit of Reproductive Physiology, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang 310013, China
| | - Zhida Sun
- National Population and Family Planning Key Laboratory of Contraceptive Drugs & Devices, Shanghai Institute of Planned Parenthood Research, Shanghai 200032, China
| | - Liyan Wang
- National Population and Family Planning Key Laboratory of Contraceptive Drugs & Devices, Shanghai Institute of Planned Parenthood Research, Shanghai 200032, China
| | - Ya Ni
- Unit of Reproductive Physiology, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang 310013, China.
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40
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Chowdhury R, Mandal RS, Ta A, Das S. An AIL family protein promotes type three secretion system-1-independent invasion and pathogenesis of Salmonella enterica serovar Typhi. Cell Microbiol 2014; 17:486-503. [PMID: 25308535 DOI: 10.1111/cmi.12379] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 09/25/2014] [Accepted: 10/04/2014] [Indexed: 02/05/2023]
Abstract
Adhesion and invasion of Intestinal Epithelial Cells (IECs) are critical for the pathogenesis of Salmonella Typhi, the aetiological agent of human typhoid fever. While type three secretion system-1 (T3SS-1) is a major invasion apparatus of Salmonella, independent invasion mechanisms were described for non-typhoidal Salmonellae. Here, we show that T2942, an AIL-like protein of S. Typhi Ty2 strain, is required for adhesion and invasion of cultured IECs. That invasion was T3SS-1 independent was proved by ectopic expression of T2942 in the non-invasive E. coli BL21 and double-mutant Ty2 (Ty2Δt2942ΔinvG) strains. Laminin and fibronectin were identified as the host-binding partners of T2942 with higher affinity for laminin. Standalone function of T2942 was confirmed by cell adhesion of the recombinant protein, while the protein or anti-T2942 antiserum blocked adhesion/invasion of S. Typhi, indicating specificity. A 20-amino acid extracellular loop was required for invasion, while several loop regions of T2942 contributed to adhesion. Further, T2942 cooperates with laminin-binding T2544 for adhesion and T3SS-1 for invasion. Finally, T2942 was required and synergistically worked with T3SS-1 for pathogenesis of S. Typhi in mice. Considering wide distribution of T2942 among clinical strains, the protein or the 20-mer peptide may be suitable for vaccine development.
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Affiliation(s)
- Rimi Chowdhury
- Division of Clinical Medicine, National Institute of Cholera and Enteric Diseases, P-33 Scheme XM C.I.T. Road, Beliaghata Kolkata, 700010, India
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41
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Dougan G, Baker S. Salmonella entericaSerovar Typhi and the Pathogenesis of Typhoid Fever. Annu Rev Microbiol 2014; 68:317-36. [DOI: 10.1146/annurev-micro-091313-103739] [Citation(s) in RCA: 191] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Gordon Dougan
- The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom;
| | - Stephen Baker
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Program, Oxford University, Clinical Research Unit, Ho Chi Minh City, Vietnam;
- Centre for Tropical Medicine, Oxford University, Oxford OX3 7FZ, United Kingdom
- The London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom
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42
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Solomon O, Bazak L, Levanon EY, Amariglio N, Unger R, Rechavi G, Eyal E. Characterizing of functional human coding RNA editing from evolutionary, structural, and dynamic perspectives. Proteins 2014; 82:3117-31. [DOI: 10.1002/prot.24672] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 07/28/2014] [Accepted: 08/11/2014] [Indexed: 12/29/2022]
Affiliation(s)
- Oz Solomon
- Cancer Research Center; Chaim Sheba Medical Center; Tel Hashomer 52621 Ramat Gan Israel
- The Everard & Mina Goodman Faculty of Life Sciences; Bar-Ilan University; Ramat Gan 52900 Israel
| | - Lily Bazak
- The Everard & Mina Goodman Faculty of Life Sciences; Bar-Ilan University; Ramat Gan 52900 Israel
| | - Erez Y. Levanon
- The Everard & Mina Goodman Faculty of Life Sciences; Bar-Ilan University; Ramat Gan 52900 Israel
| | - Ninette Amariglio
- Cancer Research Center; Chaim Sheba Medical Center; Tel Hashomer 52621 Ramat Gan Israel
| | - Ron Unger
- The Everard & Mina Goodman Faculty of Life Sciences; Bar-Ilan University; Ramat Gan 52900 Israel
| | - Gideon Rechavi
- Cancer Research Center; Chaim Sheba Medical Center; Tel Hashomer 52621 Ramat Gan Israel
- Sackler School of Medicine; Tel Aviv University; Tel Aviv 69978 Israel
| | - Eran Eyal
- Cancer Research Center; Chaim Sheba Medical Center; Tel Hashomer 52621 Ramat Gan Israel
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Borzan V, Tomašević B, Kurbel S. Hypothesis: Possible respiratory advantages for heterozygote carriers of cystic fibrosis linked mutations during dusty climate of last glaciation. J Theor Biol 2014; 363:164-8. [PMID: 25150458 DOI: 10.1016/j.jtbi.2014.08.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Revised: 08/04/2014] [Accepted: 08/09/2014] [Indexed: 11/29/2022]
Abstract
This paper puts forward a new hypothesis to interpret the high carrier frequency of CFTR mutations in individuals of European descent. The proposed heterozygote advantage factor is related to the specific climate conditions in Europe during the last 50 ky that might have heavily compromised the respiratory function of our ancestors in Eurasia. A large part of the last 50 ky was cold, and the coldest period was the Last Glacial Maximum (LGM) (26.5 to 19 kya). The global climate was dry with a dust-laden atmosphere (20 to 25 times more dust than the present level). High levels of atmospheric dust started more than 40 kya and ended less than 10 kya. Secretion of airway fluid is usually related to the submucosal tissue hydration, while salt reabsorption relies on activation of CFTRs that allow ENaCs to absorb salt and water. The water loss by evaporation depends on the air humidity and flow rate. Salt accumulation in the mucus is normally prevented by reabsorption of Na(+) and Cl(-) by epithelial cells if the presence of functional CFTRs is normal. If one gene for CFTR is mutated, the number of functional CFTRs is reduced and this limits the capacity of salt reabsorption by epithelial cells. This means that evaporation makes the airway fluid more hypertonic, and osmotic forces bring more water from the interstitial space, thus leading to a new balance in mucosal fluid traffic. Increased osmolarity and volume of airway fluid can be more moveable in cases when evaporation and dust exposure is increased. If both CFTR genes are mutated, low number of functional CFTRs diminishes salt resorption of epithelial cells. Salt accumulated in the mucous fluid within respiratory ducts, as previously described. The hypertonic ductal content forces more water and some electrolytes to enter the airway fluid from the interstitial fluid, and evaporation leads to further concentration of thick immobile mucus. The proposed interpretation is that CFTR mutations have spread among our ancestors that roamed the central Eurasia after the LGM. The heterozygote individuals might have benefitted from the limited water resorption in their respiratory mucosa that allowed improved airway cleansing.
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Affiliation(s)
- Vladimir Borzan
- Osijek University Hospital, Dept. of Internal Medicine, Osijek, Croatia
| | - Boris Tomašević
- Zagreb University Hospital, Dept. of Anesthesiology, Zagreb, Croatia
| | - Sven Kurbel
- Osijek Medical Faculty, Dept. of Physiology, Osijek, Croatia.
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44
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Sallenave JM. Phagocytic and signaling innate immune receptors: are they dysregulated in cystic fibrosis in the fight against Pseudomonas aeruginosa? Int J Biochem Cell Biol 2014; 52:103-7. [PMID: 24508137 DOI: 10.1016/j.biocel.2014.01.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 01/12/2014] [Accepted: 01/17/2014] [Indexed: 12/17/2022]
Abstract
Cystic fibrosis (CF) is a genetic disease that affects mainly the lung and the digestive system, causing progressive disability and organ failure. The most prevalent CFTR mutation dF508 (which constitutes 70% of all mutations) results in an incorrect targeting of the CFTR molecule to the membrane. It is now a well-accepted concept that mucosal innate immune responses are dysregulated in cystic fibrosis through a cycle of infectious and inflammatory episodes. However, although much work has focused on the late consequences of chronic lung inflammation in CF, very little is known on the early events leading to infection and colonization, such as that of Pseudomonas aeruginosa (P.a). We review here the involvement of a range of innate phagocytic/signaling receptors in the control of this pathogen (mannose receptor, complement receptor-3, Toll-like receptors, etc.) and evaluate the possibility that the activity of some of these receptors may be dysregulated in cystic fibrosis, potentially explaining the florid infections encountered in this disease.
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Affiliation(s)
- Jean-Michel Sallenave
- Institut Pasteur, Unité de Défense Innée et Inflammation, Paris, France; INSERM UMR1152 'Physiopathologie et épidémiologie des maladies respiratoires', France; University Paris Diderot, Sorbonne Paris Cité, Paris, France.
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45
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Abstract
Most pathogens are able to infect multiple hosts but some are highly adapted to a single-host species. A detailed understanding of the basis of host specificity can provide important insights into molecular pathogenesis, the evolution of pathogenic microbes, and the potential for pathogens to cross the species barrier to infect new hosts. Comparative genomics and the development of humanized mouse models have provided important new tools with which to explore the basis of generalism and specialism. This review will examine host specificity of bacterial pathogens with a focus on generalist and specialist serovars of Salmonella enterica.
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Affiliation(s)
- Andreas Bäumler
- Department of Medical Microbiology and Immunology, University of California, Davis School of Medicine, Davis, California 95616
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46
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Cystic Fibrosis: Alternative Approaches to the Treatment of a Genetic Disease. Mol Pharmacol 2012. [DOI: 10.1002/9781118451908.ch6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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47
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Roux N, Spagnolo J, de Bentzmann S. Neglected but amazingly diverse type IVb pili. Res Microbiol 2012; 163:659-73. [PMID: 23103334 DOI: 10.1016/j.resmic.2012.10.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Accepted: 10/19/2012] [Indexed: 01/12/2023]
Abstract
This review provides an overview of current knowledge concerning type IVb pili in Gram-negative bacteria. The number of these pili identified is steadily increasing with genome sequencing and mining studies, but studies of these pili are somewhat uneven, because their expression is tightly regulated and the signals or regulators controlling expression need to be identified. However, as illustrated here, they have a number of interesting functional, assembly-related and regulatory features.
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Affiliation(s)
- Nicolas Roux
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, CNRS UMR7255 - Aix Marseille University, Institut de Microbiologie de la Méditerranée, 31 Chemin Joseph Aiguier, 13402, cédex 20, Marseille, France
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48
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Avbelj Stefanija M, Jeanpierre M, Sykiotis GP, Young J, Quinton R, Abreu AP, Plummer L, Au MG, Balasubramanian R, Dwyer AA, Florez JC, Cheetham T, Pearce SH, Purushothaman R, Schinzel A, Pugeat M, Jacobson-Dickman EE, Ten S, Latronico AC, Gusella JF, Dode C, Crowley WF, Pitteloud N. An ancient founder mutation in PROKR2 impairs human reproduction. Hum Mol Genet 2012; 21:4314-24. [PMID: 22773735 DOI: 10.1093/hmg/dds264] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Congenital gonadotropin-releasing hormone (GnRH) deficiency manifests as absent or incomplete sexual maturation and infertility. Although the disease exhibits marked locus and allelic heterogeneity, with the causal mutations being both rare and private, one causal mutation in the prokineticin receptor, PROKR2 L173R, appears unusually prevalent among GnRH-deficient patients of diverse geographic and ethnic origins. To track the genetic ancestry of PROKR2 L173R, haplotype mapping was performed in 22 unrelated patients with GnRH deficiency carrying L173R and their 30 first-degree relatives. The mutation's age was estimated using a haplotype-decay model. Thirteen subjects were informative and in all of them the mutation was present on the same ~123 kb haplotype whose population frequency is ≤10%. Thus, PROKR2 L173R represents a founder mutation whose age is estimated at approximately 9000 years. Inheritance of PROKR2 L173R-associated GnRH deficiency was complex with highly variable penetrance among carriers, influenced by additional mutations in the other PROKR2 allele (recessive inheritance) or another gene (digenicity). The paradoxical identification of an ancient founder mutation that impairs reproduction has intriguing implications for the inheritance mechanisms of PROKR2 L173R-associated GnRH deficiency and for the relevant processes of evolutionary selection, including potential selective advantages of mutation carriers in genes affecting reproduction.
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Affiliation(s)
- Magdalena Avbelj Stefanija
- Harvard Reproductive Endocrine Sciences Center and the Reproductive Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston 02114, MA, USA
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Velge P, Wiedemann A, Rosselin M, Abed N, Boumart Z, Chaussé AM, Grépinet O, Namdari F, Roche SM, Rossignol A, Virlogeux-Payant I. Multiplicity of Salmonella entry mechanisms, a new paradigm for Salmonella pathogenesis. Microbiologyopen 2012; 1:243-58. [PMID: 23170225 PMCID: PMC3496970 DOI: 10.1002/mbo3.28] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Revised: 05/04/2012] [Accepted: 05/07/2012] [Indexed: 01/27/2023] Open
Abstract
The Salmonella enterica species includes about 2600 diverse serotypes, most of which cause a wide range of food- and water-borne diseases ranging from self-limiting gastroenteritis to typhoid fever in both humans and animals. Moreover, some serotypes are restricted to a few animal species, whereas other serotypes are able to infect plants as well as cold- and warm-blooded animals. An essential feature of the pathogenicity of Salmonella is its capacity to cross a number of barriers requiring invasion of a large variety of phagocytic and nonphagocytic cells. The aim of this review is to describe the different entry pathways used by Salmonella serotypes to enter different nonphagocytic cell types. Until recently, it was accepted that Salmonella invasion of eukaryotic cells required only the type III secretion system (T3SS) encoded by the Salmonella pathogenicity island-1. However, recent evidence shows that Salmonella can cause infection in a T3SS-1-independent manner. Currently, two outer membrane proteins Rck and PagN have been clearly identified as Salmonella invasins. As Rck mediates a Zipper-like entry mechanism, Salmonella is therefore the first bacterium shown to be able to induce both Zipper and Trigger mechanisms to invade host cells. In addition to these known entry pathways, recent data have shown that unknown entry routes could be used according to the serotype, the host and the cell type considered, inducing either Zipper-like or Trigger-like entry processes. The new paradigm presented here should change our classic view of Salmonella pathogenicity. It could also modify our understanding of the mechanisms leading to the different Salmonella-induced diseases and to Salmonella-host specificity.
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Affiliation(s)
- P Velge
- INRA, UMR1282 Infectiologie et Santé Publique F-37380, Nouzilly, France ; Université François Rabelais de Tours, UMR1282 Infectiologie et Santé Publique F-37000, Tours, France
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Abstract
Evolution has long provided a foundation for population genetics, but some major advances in evolutionary biology from the twentieth century that provide foundations for evolutionary medicine are only now being applied in molecular medicine. They include the need for both proximate and evolutionary explanations, kin selection, evolutionary models for cooperation, competition between alleles, co-evolution, and new strategies for tracing phylogenies and identifying signals of selection. Recent advances in genomics are transforming evolutionary biology in ways that create even more opportunities for progress at its interfaces with genetics, medicine, and public health. This article reviews 15 evolutionary principles and their applications in molecular medicine in hopes that readers will use them and related principles to speed the development of evolutionary molecular medicine.
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