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Crandall JG, Zhou X, Rokas A, Hittinger CT. Specialization restricts the evolutionary paths available to yeast sugar transporters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.22.604696. [PMID: 39091816 PMCID: PMC11291069 DOI: 10.1101/2024.07.22.604696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Functional innovation at the protein level is a key source of evolutionary novelties. The constraints on functional innovations are likely to be highly specific in different proteins, which are shaped by their unique histories and the extent of global epistasis that arises from their structures and biochemistries. These contextual nuances in the sequence-function relationship have implications both for a basic understanding of the evolutionary process and for engineering proteins with desirable properties. Here, we have investigated the molecular basis of novel function in a model member of an ancient, conserved, and biotechnologically relevant protein family. These Major Facilitator Superfamily sugar porters are a functionally diverse group of proteins that are thought to be highly plastic and evolvable. By dissecting a recent evolutionary innovation in an α-glucoside transporter from the yeast Saccharomyces eubayanus, we show that the ability to transport a novel substrate requires high-order interactions between many protein regions and numerous specific residues proximal to the transport channel. To reconcile the functional diversity of this family with the constrained evolution of this model protein, we generated new, state-of-the-art genome annotations for 332 Saccharomycotina yeast species spanning approximately 400 million years of evolution. By integrating phylogenetic and phenotypic analyses across these species, we show that the model yeast α-glucoside transporters likely evolved from a multifunctional ancestor and became subfunctionalized. The accumulation of additive and epistatic substitutions likely entrenched this subfunction, which made the simultaneous acquisition of multiple interacting substitutions the only reasonably accessible path to novelty.
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Affiliation(s)
- Johnathan G. Crandall
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Xiaofan Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China
- Department of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Antonis Rokas
- Department of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Chris Todd Hittinger
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA
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2
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Ostridge HJ, Fontsere C, Lizano E, Soto DC, Schmidt JM, Saxena V, Alvarez-Estape M, Barratt CD, Gratton P, Bocksberger G, Lester JD, Dieguez P, Agbor A, Angedakin S, Assumang AK, Bailey E, Barubiyo D, Bessone M, Brazzola G, Chancellor R, Cohen H, Coupland C, Danquah E, Deschner T, Dotras L, Dupain J, Egbe VE, Granjon AC, Head J, Hedwig D, Hermans V, Hernandez-Aguilar RA, Jeffery KJ, Jones S, Junker J, Kadam P, Kaiser M, Kalan AK, Kambere M, Kienast I, Kujirakwinja D, Langergraber KE, Lapuente J, Larson B, Laudisoit A, Lee KC, Llana M, Maretti G, Martín R, Meier A, Morgan D, Neil E, Nicholl S, Nixon S, Normand E, Orbell C, Ormsby LJ, Orume R, Pacheco L, Preece J, Regnaut S, Robbins MM, Rundus A, Sanz C, Sciaky L, Sommer V, Stewart FA, Tagg N, Tédonzong LR, van Schijndel J, Vendras E, Wessling EG, Willie J, Wittig RM, Yuh YG, Yurkiw K, Vigilant L, Piel A, Boesch C, Kühl HS, Dennis MY, Marques-Bonet T, Arandjelovic M, Andrés AM. Local genetic adaptation to habitat in wild chimpanzees. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.09.601734. [PMID: 39026872 PMCID: PMC11257515 DOI: 10.1101/2024.07.09.601734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
How populations adapt to their environment is a fundamental question in biology. Yet we know surprisingly little about this process, especially for endangered species such as non-human great apes. Chimpanzees, our closest living relatives, are particularly interesting because they inhabit diverse habitats, from rainforest to woodland-savannah. Whether genetic adaptation facilitates such habitat diversity remains unknown, despite having wide implications for evolutionary biology and conservation. Using 828 newly generated exomes from wild chimpanzees, we find evidence of fine-scale genetic adaptation to habitat. Notably, adaptation to malaria in forest chimpanzees is mediated by the same genes underlying adaptation to malaria in humans. This work demonstrates the power of non-invasive samples to reveal genetic adaptations in endangered populations and highlights the importance of adaptive genetic diversity for chimpanzees.
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Affiliation(s)
- Harrison J Ostridge
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Claudia Fontsere
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Esther Lizano
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Daniela C Soto
- University of California, Davis, Genome Center, MIND Institute, Department of Biochemistry & Molecular Medicine, One Shields Drive, Davis, CA, 95616, USA
| | - Joshua M Schmidt
- Flinders Health and Medical Research Institute (FHMRI), Department of Ophthalmology, Flinders University Sturt Rd, Bedford Park South Australia 5042 Australia
| | - Vrishti Saxena
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Marina Alvarez-Estape
- University of California, Davis, Genome Center, MIND Institute, Department of Biochemistry & Molecular Medicine, One Shields Drive, Davis, CA, 95616, USA
| | - Christopher D Barratt
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, the Netherlands
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Leipzig-Jena, Puschstrasse 4, 04103 Leipzig, Germany
| | - Paolo Gratton
- University of Rome "Tor Vergata" Department of Biology Via Cracovia, 1, Roma, Italia
| | - Gaëlle Bocksberger
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage, 60325 Frankfurt am Main, Germany
| | - Jack D Lester
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Paula Dieguez
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Leipzig-Jena, Puschstrasse 4, 04103 Leipzig, Germany
| | - Anthony Agbor
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Samuel Angedakin
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Alfred Kwabena Assumang
- Department of Wildlife and Range Management, Faculty of Renewable Natural Resources, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Emma Bailey
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Donatienne Barubiyo
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Mattia Bessone
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
- University of Konstanz, Centre for the Advanced Study of Collective Behaviour, Universitätsstraße 10, 78464, Konstanz, Germany
| | - Gregory Brazzola
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Rebecca Chancellor
- West Chester University, Depts of Anthropology & Sociology and Psychology, West Chester, PA, 19382 USA
| | - Heather Cohen
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Leipzig-Jena, Puschstrasse 4, 04103 Leipzig, Germany
| | - Charlotte Coupland
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Emmanuel Danquah
- Department of Wildlife and Range Management, Faculty of Renewable Natural Resources, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Tobias Deschner
- Institute of Cognitive Science, University of Osnabrück, Artilleriestrasse 34, 49076 Osnabrück, Germany
| | - Laia Dotras
- Jane Goodall Institute Spain and Senegal, Dindefelo Biological Station, Dindefelo, Kedougou, Senegal
- Department of Social Psychology and Quantitative Psychology, Serra Hunter Programme, University of Barcelona, Barcelona, Spain
| | - Jef Dupain
- Antwerp Zoo Foundation, RZSA, Kon.Astridplein 26, 2018 Antwerp, Belgium
| | - Villard Ebot Egbe
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Anne-Céline Granjon
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Josephine Head
- The Biodiversity Consultancy, 3E Kings Parade, Cambridge, CB2 1SJ, UK
| | - Daniela Hedwig
- Elephant Listening Project, K. Lisa Yang Center for Conservation Bioacoustics, Cornell Lab of Ornithology, Cornell University, 159 Sapsucker Woods Road, Ithaca, NY 14850, USA
| | - Veerle Hermans
- KMDA, Centre for Research and Conservation, Royal Zoological Society of Antwerp, Koningin Astridplein 20-26, B-2018 Antwerp, Belgium
| | - R Adriana Hernandez-Aguilar
- Jane Goodall Institute Spain and Senegal, Dindefelo Biological Station, Dindefelo, Kedougou, Senegal
- Department of Social Psychology and Quantitative Psychology, Serra Hunter Programme, University of Barcelona, Barcelona, Spain
| | - Kathryn J Jeffery
- School of Natural Sciences, University of Stirling, UK
- Agence National des Parcs Nationaux (ANPN) Batterie 4, BP20379, Libreville, Gabon
| | - Sorrel Jones
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Jessica Junker
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Leipzig-Jena, Puschstrasse 4, 04103 Leipzig, Germany
| | - Parag Kadam
- Greater Mahale Ecosystem Research and Conservation Project
| | - Michael Kaiser
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Ammie K Kalan
- Department of Anthropology, University of Victoria, 3800 Finnerty Rd, Victoria, BC V8P 5C2, Canada
| | - Mbangi Kambere
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Ivonne Kienast
- Department of Natural Resources and the Environment, Cornell University, Ithaca, NY 14850, USA
- K. Lisa Yang Center for Conservation Bioacoustics, Cornell Lab of Ornithology, Cornell University, Ithaca, NY 14850, USA
| | - Deo Kujirakwinja
- Wildlife Conservation Society (WCS), 2300 Southern Boulevard. Bronx, New York 10460, USA
| | - Kevin E Langergraber
- School of Human Evolution and Social Change, Institute of Human Origins, Arizona State University, 777 East University Drive, Tempe, AZ 85287 Arizona State University, PO Box 872402, Tempe, AZ 85287-2402 USA
- Institute of Human Origins, Arizona State University, 900 Cady Mall, Tempe, AZ 85287 Arizona State University, PO Box 872402, Tempe, AZ 85287-2402 USA
| | - Juan Lapuente
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | | | | | - Kevin C Lee
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
- K. Lisa Yang Center for Conservation Bioacoustics, Cornell Lab of Ornithology, Cornell University, Ithaca, NY 14850, USA
| | - Manuel Llana
- Jane Goodall Institute Spain and Senegal, Dindefelo Biological Station, Dindefelo, Kedougou, Senegal
| | - Giovanna Maretti
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Rumen Martín
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Amelia Meier
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
- Hawai'i Insititute of Marine Biology, University of Hawai'i at Manoa, 46-007 Lilipuna Place, Kaneohe, HI, 96744, USA
| | - David Morgan
- Lester E. Fisher Center for the Study and Conservation of Apes, Lincoln Park Zoo, 2001 North Clark Street, Chicago, Illinois 60614 USA
| | - Emily Neil
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Sonia Nicholl
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Stuart Nixon
- North of England Zoological Society, Chester Zoo, Upton by Chester, CH2 1LH, United Kingdom
| | | | - Christopher Orbell
- Panthera, 8 W 40TH ST, New York, NY 10018, USA
- School of Natural Sciences, University of Stirling, UK
| | - Lucy Jayne Ormsby
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Robinson Orume
- Korup Rainforest Conservation Society, c/o Korup National Park, P.O. Box 36 Mundemba, South West Region, Cameroon
| | - Liliana Pacheco
- Save the Dogs and Other Animals, DJ 223 Km 3, 905200 Cernavoda CT, Romania
| | - Jodie Preece
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | | | - Martha M Robbins
- Max Planck Institute for Evolutionary Anthropology, Department of Primate Behavior and Evolution, Deutscher Platz 6, 04103 Leipzig
| | - Aaron Rundus
- West Chester University, Depts of Anthropology & Sociology and Psychology, West Chester, PA, 19382 USA
| | - Crickette Sanz
- Washington University in Saint Louis, Department of Anthropology, One Brookings Drive, St. Louis, MO 63130, USA
- Congo Program, Wildlife Conservation Society, 151 Avenue Charles de Gaulle, Brazzaville, Republic of Congo
| | - Lilah Sciaky
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Volker Sommer
- University College London, Department of Anthropology, 14 Taviton Street, London WC1H 0BW, UK
| | - Fiona A Stewart
- University College London, Department of Anthropology, 14 Taviton Street, London WC1H 0BW, UK
- Department of Human Origins, Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Nikki Tagg
- KMDA, Centre for Research and Conservation, Royal Zoological Society of Antwerp, Koningin Astridplein 20-26, B-2018 Antwerp, Belgium
- Born Free Foundation, Floor 2 Frazer House, 14 Carfax, Horsham, RH12 1ER, UK
| | - Luc Roscelin Tédonzong
- KMDA, Centre for Research and Conservation, Royal Zoological Society of Antwerp, Koningin Astridplein 20-26, B-2018 Antwerp, Belgium
| | - Joost van Schijndel
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Elleni Vendras
- Frankfurt Zoological Society, Bernhard-Grzimek-Allee 1, 60316 Frankfurt, Germany
| | - Erin G Wessling
- Johann-Friedrich-Blumenbach Institute for Zoology and Anthropology, Georg-August-University Göttingen,Göttingen, Germany
- German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Jacob Willie
- KMDA, Centre for Research and Conservation, Royal Zoological Society of Antwerp, Koningin Astridplein 20-26, B-2018 Antwerp, Belgium
- Terrestrial Ecology Unit (TEREC), Department of Biology, Ghent University (UGent), K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Roman M Wittig
- Ape Social Mind Lab, Institute for Cognitive Sciences Marc Jeannerod, CNRS UMR 5229 CNRS, 67 bd Pinel, 69675 Bron CEDEX, France
- Taï Chimpanzee Project, Centre Suisse de Recherches Scientifiques, BP 1301, Abidjan 01, CI
| | - Yisa Ginath Yuh
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Kyle Yurkiw
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Linda Vigilant
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Alex Piel
- University College London, Department of Anthropology, 14 Taviton Street, London WC1H 0BW, UK
| | | | - Hjalmar S Kühl
- Senckenberg Museum for Natural History Görlitz, Senckenberg - Member of the Leibniz Association Am Museum 1, 02826 Görlitz, Germany
- International Institute Zittau, Technische Universität Dresden, Markt 23, 02763 Zittau, Germany
| | - Megan Y Dennis
- University of California, Davis, Genome Center, MIND Institute, Department of Biochemistry & Molecular Medicine, One Shields Drive, Davis, CA, 95616, USA
| | - Tomas Marques-Bonet
- 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
- 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, Edifici ICTA-ICP, c/ Columnes s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Mimi Arandjelovic
- Max Planck Institute for Evolutionary Anthropology, Department of Primate Behavior and Evolution, Deutscher Platz 6, 04103 Leipzig
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103
| | - Aida M Andrés
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
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3
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Stucke EM, Lawton JG, Travassos MA. ApoE: A new piece to the severe malaria puzzle. Pediatr Res 2024; 96:12-14. [PMID: 38388820 DOI: 10.1038/s41390-024-03096-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 01/23/2024] [Indexed: 02/24/2024]
Affiliation(s)
- Emily M Stucke
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Jonathan G Lawton
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Mark A Travassos
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA.
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4
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Haffener PE, Al-Riyami AZ, Al-Zadjali S, Al-Rawahi M, Al Hosni S, Al Marhoobi A, Al Sheriyani A, Leffler EM. Characterization of Blood Group Variants in an Omani Population by Comparison of Whole Genome Sequencing and Serology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.17.599396. [PMID: 38948735 PMCID: PMC11212902 DOI: 10.1101/2024.06.17.599396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Although blood group variation was first described over a century ago, our understanding of the genetic variation affecting antigenic expression on the red blood cell surface in many populations is lacking. This deficit limits the ability to accurately type patients, especially as serological testing is not available for all described blood groups, and targeted genotyping panels may lack rare or population-specific variants. Here, we perform serological assays across 24 antigens and whole genome sequencing on 100 Omanis, a population underrepresented in genomic databases. We inferred blood group phenotypes using the most commonly typed genetic variants. The comparison of serological to inferred phenotypes resulted in an average concordance of 96.9%. Among the 22 discordances, we identify seven known variants in four blood groups that, to our knowledge, have not been previously reported in Omanis. Incorporating these variants for phenotype inference, concordance increases to 98.8%. Additionally, we describe five candidate variants in the Lewis, Lutheran, MNS, and P1 blood groups that may affect antigenic expression, although further functional confirmation is required. Notably, we identify several blood group alleles most common in African populations, likely introduced to Oman by gene flow over the last thousand years. These findings highlight the need to evaluate individual populations and their population history when considering variants to include in genotype panels for blood group typing. This research will inform future work in blood banks and transfusion services.
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Affiliation(s)
- Paige E. Haffener
- Department of Human Genetics, The University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Arwa Z. Al-Riyami
- Department of Hematology, Sultan Qaboos University Hospital, University Medical City, Muscat, Oman
| | - Shoaib Al-Zadjali
- Sultan Qaboos Comprehensive Cancer Center, University Medical City, Muscat, Oman
| | - Mohammed Al-Rawahi
- Department of Hematology, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Saif Al Hosni
- Department of Hematology, Sultan Qaboos University Hospital, University Medical City, Muscat, Oman
| | - Ali Al Marhoobi
- Department of Hematology, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | | | - Ellen M. Leffler
- Department of Human Genetics, The University of Utah School of Medicine, Salt Lake City, UT, USA
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5
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Nelder MP, Schats R, Poinar HN, Cooke A, Brickley MB. Pathogen prospecting of museums: Reconstructing malaria epidemiology. Proc Natl Acad Sci U S A 2024; 121:e2310859121. [PMID: 38527214 PMCID: PMC11009618 DOI: 10.1073/pnas.2310859121] [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] [Indexed: 03/27/2024] Open
Abstract
Malaria is a disease of global significance. Ongoing changes to the earth's climate, antimalarial resistance, insecticide resistance, and socioeconomic decline test the resilience of malaria prevention programs. Museum insect specimens present an untapped resource for studying vector-borne pathogens, spurring the question: Do historical mosquito collections contain Plasmodium DNA, and, if so, can museum specimens be used to reconstruct the historical epidemiology of malaria? In this Perspective, we explore molecular techniques practical to pathogen prospecting, which, more broadly, we define as the science of screening entomological museum specimens for human, animal, or plant pathogens. Historical DNA and pathogen prospecting provide a means of describing the coevolution of human, vector, and parasite, informing the development of insecticides, diagnostics, therapeutics, and vaccines.
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Affiliation(s)
- Mark P. Nelder
- Enteric, Zoonotic and Vector-Borne Diseases, Health Protection, Public Health Ontario, Toronto, ONM5G 1M1, Canada
| | - Rachel Schats
- Laboratory for Human Osteoarchaeology, Faculty of Archaeology, Leiden University, 2333 CCLeiden, The Netherlands
| | - Hendrik N. Poinar
- Department of Anthropology, McMaster University, Hamilton, ONL8S 4L9, Canada
- Department of Biochemistry, McMaster University, Hamilton, ONL8S 4L9, Canada
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ONL8S 4L9, Canada
| | - Amanda Cooke
- Department of Anthropology, McMaster University, Hamilton, ONL8S 4L9, Canada
| | - Megan B. Brickley
- Department of Anthropology, McMaster University, Hamilton, ONL8S 4L9, Canada
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Röltgen K, Boyd SD. Antibody and B Cell Responses to SARS-CoV-2 Infection and Vaccination: The End of the Beginning. ANNUAL REVIEW OF PATHOLOGY 2024; 19:69-97. [PMID: 37738512 DOI: 10.1146/annurev-pathmechdis-031521-042754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
As the COVID-19 pandemic has evolved during the past years, interactions between human immune systems, rapidly mutating and selected SARS-CoV-2 viral variants, and effective vaccines have complicated the landscape of individual immunological histories. Here, we review some key findings for antibody and B cell-mediated immunity, including responses to the highly mutated omicron variants; immunological imprinting and other impacts of successive viral antigenic variant exposures on antibody and B cell memory; responses in secondary lymphoid and mucosal tissues and non-neutralizing antibody-mediated immunity; responses in populations vulnerable to severe disease such as those with cancer, immunodeficiencies, and other comorbidities, as well as populations showing apparent resistance to severe disease such as many African populations; and evidence of antibody involvement in postacute sequelae of infection or long COVID. Despite the initial phase of the pandemic ending, human populations will continue to face challenges presented by this unpredictable virus.
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Affiliation(s)
- Katharina Röltgen
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Scott D Boyd
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA;
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, California, USA
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7
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Alimohamadi H, Rangamani P. Effective cell membrane tension protects red blood cells against malaria invasion. PLoS Comput Biol 2023; 19:e1011694. [PMID: 38048346 PMCID: PMC10721198 DOI: 10.1371/journal.pcbi.1011694] [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: 06/18/2023] [Revised: 12/14/2023] [Accepted: 11/16/2023] [Indexed: 12/06/2023] Open
Abstract
A critical step in how malaria parasites invade red blood cells (RBCs) is the wrapping of the membrane around the egg-shaped merozoites. Recent experiments have revealed that RBCs can be protected from malaria invasion by high membrane tension. While cellular and biochemical aspects of parasite actomyosin motor forces during the malaria invasion have been well studied, the important role of the biophysical forces induced by the RBC membrane-cytoskeleton composite has not yet been fully understood. In this study, we use a theoretical model for lipid bilayer mechanics, cytoskeleton deformation, and membrane-merozoite interactions to systematically investigate the influence of effective RBC membrane tension, which includes contributions from the lipid bilayer tension, spontaneous tension, interfacial tension, and the resistance of cytoskeleton against shear deformation on the progression of membrane wrapping during the process of malaria invasion. Our model reveals that this effective membrane tension creates a wrapping energy barrier for a complete merozoite entry. We calculate the tension threshold required to impede the malaria invasion. We find that the tension threshold is a nonmonotonic function of spontaneous tension and undergoes a sharp transition from large to small values as the magnitude of interfacial tension increases. We also predict that the physical properties of the RBC cytoskeleton layer-particularly the resting length of the cytoskeleton-play key roles in specifying the degree of the membrane wrapping. We also found that the shear energy of cytoskeleton deformation diverges at the full wrapping state, suggesting the local disassembly of the cytoskeleton is required to complete the merozoite entry. Additionally, using our theoretical framework, we predict the landscape of myosin-mediated forces and the physical properties of the RBC membrane in regulating successful malaria invasion. Our findings on the crucial role of RBC membrane tension in inhibiting malaria invasion can have implications for developing novel antimalarial therapeutic or vaccine-based strategies.
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Affiliation(s)
- Haleh Alimohamadi
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, California, United States of America
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, California, United States of America
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8
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Walker IS, Rogerson SJ. Pathogenicity and virulence of malaria: Sticky problems and tricky solutions. Virulence 2023; 14:2150456. [PMID: 36419237 PMCID: PMC9815252 DOI: 10.1080/21505594.2022.2150456] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 10/18/2022] [Accepted: 10/19/2022] [Indexed: 11/25/2022] Open
Abstract
Infections with Plasmodium falciparum and Plasmodium vivax cause over 600,000 deaths each year, concentrated in Africa and in young children, but much of the world's population remain at risk of infection. In this article, we review the latest developments in the immunogenicity and pathogenesis of malaria, with a particular focus on P. falciparum, the leading malaria killer. Pathogenic factors include parasite-derived toxins and variant surface antigens on infected erythrocytes that mediate sequestration in the deep vasculature. Host response to parasite toxins and to variant antigens is an important determinant of disease severity. Understanding how parasites sequester, and how antibody to variant antigens could prevent sequestration, may lead to new approaches to treat and prevent disease. Difficulties in malaria diagnosis, drug resistance, and specific challenges of treating P. vivax pose challenges to malaria elimination, but vaccines and other preventive strategies may offer improved disease control.
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Affiliation(s)
- Isobel S Walker
- Department of Infectious Diseases, The University of Melbourne, The Doherty Institute, Melbourne, Australia
| | - Stephen J Rogerson
- Department of Infectious Diseases, The University of Melbourne, The Doherty Institute, Melbourne, Australia
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9
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Liu Z, Huang YF. Deep multiple-instance learning accurately predicts gene haploinsufficiency and deletion pathogenicity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.29.555384. [PMID: 37693607 PMCID: PMC10491176 DOI: 10.1101/2023.08.29.555384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Copy number losses (deletions) are a major contributor to the etiology of severe genetic disorders. Although haploinsufficient genes play a critical role in deletion pathogenicity, current methods for deletion pathogenicity prediction fail to integrate multiple lines of evidence for haploinsufficiency at the gene level, limiting their power to pinpoint deleterious deletions associated with genetic disorders. Here we introduce DosaCNV, a deep multiple-instance learning framework that, for the first time, models deletion pathogenicity jointly with gene haploinsufficiency. By integrating over 30 gene-level features potentially predictive of haploinsufficiency, DosaCNV shows unmatched performance in prioritizing pathogenic deletions associated with a broad spectrum of genetic disorders. Furthermore, DosaCNV outperforms existing methods in predicting gene haploinsufficiency even though it is not trained on known haploinsufficient genes. Finally, DosaCNV leverages a state-of-the-art technique to quantify the contributions of individual gene-level features to haploinsufficiency, allowing for human-understandable explanations of model predictions. Altogether, DosaCNV is a powerful computational tool for both fundamental and translational research.
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Affiliation(s)
- Zhihan Liu
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
- Molecular, Cellular, and Integrative Biosciences Program, Pennsylvania State University, University Park, PA 16802, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Yi-Fei Huang
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
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10
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Soto DC, Uribe-Salazar JM, Shew CJ, Sekar A, McGinty S, Dennis MY. Genomic structural variation: A complex but important driver of human evolution. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 181 Suppl 76:118-144. [PMID: 36794631 PMCID: PMC10329998 DOI: 10.1002/ajpa.24713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 01/21/2023] [Accepted: 02/05/2023] [Indexed: 02/17/2023]
Abstract
Structural variants (SVs)-including duplications, deletions, and inversions of DNA-can have significant genomic and functional impacts but are technically difficult to identify and assay compared with single-nucleotide variants. With the aid of new genomic technologies, it has become clear that SVs account for significant differences across and within species. This phenomenon is particularly well-documented for humans and other primates due to the wealth of sequence data available. In great apes, SVs affect a larger number of nucleotides than single-nucleotide variants, with many identified SVs exhibiting population and species specificity. In this review, we highlight the importance of SVs in human evolution by (1) how they have shaped great ape genomes resulting in sensitized regions associated with traits and diseases, (2) their impact on gene functions and regulation, which subsequently has played a role in natural selection, and (3) the role of gene duplications in human brain evolution. We further discuss how to incorporate SVs in research, including the strengths and limitations of various genomic approaches. Finally, we propose future considerations in integrating existing data and biospecimens with the ever-expanding SV compendium propelled by biotechnology advancements.
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Affiliation(s)
- Daniela C. Soto
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, USA
- Integrative Genetics and Genomics Graduate Group, University of California, Davis, CA, USA
| | - José M. Uribe-Salazar
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, USA
- Integrative Genetics and Genomics Graduate Group, University of California, Davis, CA, USA
| | - Colin J. Shew
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, USA
- Integrative Genetics and Genomics Graduate Group, University of California, Davis, CA, USA
| | - Aarthi Sekar
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, USA
- Integrative Genetics and Genomics Graduate Group, University of California, Davis, CA, USA
| | - Sean McGinty
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, USA
- Integrative Genetics and Genomics Graduate Group, University of California, Davis, CA, USA
| | - Megan Y. Dennis
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, USA
- Integrative Genetics and Genomics Graduate Group, University of California, Davis, CA, USA
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11
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Langlois AWR, El-Boraie A, Pouget JG, Cox LS, Ahluwalia JS, Fukunaga K, Mushiroda T, Knight J, Chenoweth MJ, Tyndale RF. Genotyping, characterization, and imputation of known and novel CYP2A6 structural variants using SNP array data. J Hum Genet 2023:10.1038/s10038-023-01148-y. [PMID: 37059825 DOI: 10.1038/s10038-023-01148-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/23/2023] [Accepted: 03/30/2023] [Indexed: 04/16/2023]
Abstract
CYP2A6 metabolically inactivates nicotine. Faster CYP2A6 activity is associated with heavier smoking and higher lung cancer risk. The CYP2A6 gene is polymorphic, including functional structural variants (SV) such as gene deletions (CYP2A6*4), duplications (CYP2A6*1 × 2), and hybrids with the CYP2A7 pseudogene (CYP2A6*12, CYP2A6*34). SVs are challenging to genotype due to their complex genetic architecture. Our aims were to develop a reliable protocol for SV genotyping, functionally phenotype known and novel SVs, and investigate the feasibility of CYP2A6 SV imputation from SNP array data in two ancestry populations. European- (EUR; n = 935) and African- (AFR; n = 964) ancestry individuals from smoking cessation trials were genotyped for SNPs using an Illumina array and for CYP2A6 SVs using Taqman copy number (CN) assays. SV-specific PCR amplification and Sanger sequencing was used to characterize a novel SV. Individuals with SVs were phenotyped using the nicotine metabolite ratio, a biomarker of CYP2A6 activity. SV diplotype and SNP array data were integrated and phased to generate ancestry-specific SV reference panels. Leave-one-out cross-validation was used to investigate the feasibility of CYP2A6 SV imputation. A minimal protocol requiring three Taqman CN assays for CYP2A6 SV genotyping was developed and known SV associations with activity were replicated. The first domain swap CYP2A6-CYP2A7 hybrid SV, CYP2A6*53, was identified, sequenced, and associated with lower CYP2A6 activity. In both EURs and AFRs, most SV alleles were identified using imputation (>70% and >60%, respectively); importantly, false positive rates were <1%. These results confirm that CYP2A6 SV imputation can identify most SV alleles, including a novel SV.
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Affiliation(s)
- Alec W R Langlois
- Department of Pharmacology and Toxicology, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, 100 Stokes Street, Toronto, ON, M6J 1H4, Canada
| | - Ahmed El-Boraie
- Department of Pharmacology and Toxicology, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, 100 Stokes Street, Toronto, ON, M6J 1H4, Canada
| | - Jennie G Pouget
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, 100 Stokes Street, Toronto, ON, M6J 1H4, Canada
- Department of Psychiatry, University of Toronto, 250 College Street, Toronto, ON, M5T 1R8, Canada
| | - Lisa Sanderson Cox
- Department of Population Health, University of Kansas School of Medicine, Kansas City, KS, 66160, USA
| | - Jasjit S Ahluwalia
- Departments of Behavioral and Social Sciences and Medicine, Brown University School of Public Health, Providence, RI, 02912, USA
| | - Koya Fukunaga
- Center for Integrative Medical Sciences, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Taisei Mushiroda
- Center for Integrative Medical Sciences, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Jo Knight
- Data Science Institute and Medical School, Lancaster University, Lancaster, UK
| | - Meghan J Chenoweth
- Department of Pharmacology and Toxicology, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, 100 Stokes Street, Toronto, ON, M6J 1H4, Canada
- Department of Psychiatry, University of Toronto, 250 College Street, Toronto, ON, M5T 1R8, Canada
| | - Rachel F Tyndale
- Department of Pharmacology and Toxicology, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada.
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, 100 Stokes Street, Toronto, ON, M6J 1H4, Canada.
- Department of Psychiatry, University of Toronto, 250 College Street, Toronto, ON, M5T 1R8, Canada.
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12
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Dobkin J, Wu L, Mangalmurti NS. The ultimate tradeoff: how red cell adaptations to malaria alter the host response during critical illness. Am J Physiol Lung Cell Mol Physiol 2023; 324:L169-L178. [PMID: 36594846 PMCID: PMC9902222 DOI: 10.1152/ajplung.00127.2022] [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: 04/18/2022] [Revised: 12/09/2022] [Accepted: 12/22/2022] [Indexed: 01/04/2023] Open
Abstract
The human immune system evolved in response to pathogens. Among these pathogens, malaria has proven to be one of the deadliest and has exerted the most potent selective pressures on its target cell, the red blood cell. Red blood cells have recently gained recognition for their immunomodulatory properties, yet how red cell adaptations contribute to the host response during critical illness remains understudied. This review will discuss how adaptations that may have been advantageous for host survival might influence immune responses in modern critical illness. We will highlight the current evidence for divergent host resilience arising from the adaptations to malaria and summarize how understanding evolutionary red cell adaptations to malaria may provide insight into the heterogeneity of the host response to critical illness, perhaps driving future precision medicine approaches to syndromes affecting the critically ill such as sepsis and acute respiratory distress syndrome (ARDS).
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Affiliation(s)
- Jane Dobkin
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ling Wu
- Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Nilam S Mangalmurti
- Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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13
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Joof F, Hartmann E, Jarvis A, Colley A, Cross JH, Avril M, Prentice AM, Cerami C. Genetic variations in human ATP2B4 gene alter Plasmodium falciparum in vitro growth in RBCs from Gambian adults. Malar J 2023; 22:5. [PMID: 36604655 PMCID: PMC9817369 DOI: 10.1186/s12936-022-04359-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 11/03/2022] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Polymorphisms in ATP2B4 coding for PMCA4b, the primary regulator of erythrocyte calcium concentration, have been shown by GWAS and cross-sectional studies to protect against severe malaria but the mechanism remains unknown. METHODS Using a recall-by-genotype design, we investigated the impact of a common haplotype variant in ATP2B4 using in vitro assays that model erythrocyte stage malaria pathogenesis. Ninety-six donors representing homozygote (carriers of the minor allele, C/C), heterozygote (T/C) and wildtype (T/T) carriers of the tagging SNP rs1541252 were selected from a cohort of over 12,000 participants in the Keneba Biobank. RESULTS Red blood cells (RBCs) from homozygotes showed reduced PMCA4b protein expression (mean fluorescence intensities (MFI = 2428 ± 124, 3544 ± 159 and 4261 ± 283], for homozygotes, heterozygotes and wildtypes respectively, p < 0.0001) and slower rates of calcium expulsion (calcium t½ ± SD = 4.7 ± 0.5, 1.8 ± 0.3 and 1.9 ± 0.4 min, p < 0.0001). Growth of a Plasmodium falciparum laboratory strain (FCR3) and two Gambian field isolates was decreased in RBCs from homozygotes compared to heterozygotes and wildtypes (p < 0.01). Genotype group did not affect parasite adhesion in vitro or var-gene expression in malaria-infected RBCs. Parasite growth was inhibited by a known inhibitor of PMCA4b, aurintricarboxylic acid (IC50 = 122uM CI: 110-134) confirming its sensitivity to calcium channel blockade. CONCLUSION The data support the hypothesis that this ATP2B4 genotype, common in The Gambia and other malaria-endemic areas, protects against severe malaria through the suppression of parasitaemia during an infection. Reduction in parasite density plays a pivotal role in disease outcome by minimizing all aspects of malaria pathogenesis. Follow up studies are needed to further elucidate the mechanism of protection and to determine if this ATP2B4 genotype carries a fitness cost or increases susceptibility to other human disease.
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Affiliation(s)
- Fatou Joof
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | | | | | - Alhassan Colley
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - James H Cross
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | | | - Andrew M Prentice
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Carla Cerami
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia.
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14
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Weiland AS. Recent Advances in Imported Malaria Pathogenesis, Diagnosis, and Management. CURRENT EMERGENCY AND HOSPITAL MEDICINE REPORTS 2023; 11:49-57. [PMID: 37213266 PMCID: PMC10091340 DOI: 10.1007/s40138-023-00264-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/28/2023] [Indexed: 05/23/2023]
Abstract
Purpose of Review Malaria is an important human parasitic disease affecting the population of tropical, subtropical regions as well as travelers to these areas.The purpose of this article is to provide clinicians practicing in non-endemic areas with a comprehensive overview of the recent data on microbiologic and pathophysiologic features of five Plasmodium parasites, clinical presentation of uncomplicated and severe cases, modern diagnostic methods, and treatment of malaria. Recent Findings Employment of robust surveillance programs, rapid diagnostic tests, highly active artemisinin-based therapy, and the first malaria vaccine have led to decline in malaria incidence; however, emerging drug resistance, disruptions due to the COVID-19 pandemic, and other socio-economic factors have stalled the progress. Summary Clinicians practicing in non-endemic areas such as the United States should consider a diagnosis of malaria in returning travelers presenting with fever, utilize rapid diagnostic tests if available at their practice locations in addition to microscopy, and timely initiate guideline-directed management as delays in treatment can lead to poor clinical outcomes.
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Affiliation(s)
- Anastasia S. Weiland
- Department of Medicine, Case Western Reserve University/University Hospitals Cleveland Medical Center, Cleveland, OH USA
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15
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Nortey LN, Anning AS, Nakotey GK, Ussif AM, Opoku YK, Osei SA, Aboagye B, Ghartey-Kwansah G. Genetics of cerebral malaria: pathogenesis, biomarkers and emerging therapeutic interventions. Cell Biosci 2022; 12:91. [PMID: 35715862 PMCID: PMC9204375 DOI: 10.1186/s13578-022-00830-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 06/07/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Cerebral malaria (CM) is a preeminent cause of severe disease and premature deaths in Sub-Saharan Africa, where an estimated 90% of cases occur. The key features of CM are a deep, unarousable coma that persists for longer than 1 h in patients with peripheral Plasmodium falciparum and no other explanation for encephalopathy. Significant research efforts on CM in the last few decades have focused on unravelling the molecular underpinnings of the disease pathogenesis and the identification of potential targets for therapeutic or pharmacologic intervention. These efforts have been greatly aided by the generation and study of mouse models of CM, which have provided great insights into key events of CM pathogenesis, revealed an interesting interplay of host versus parasite factors that determine the progression of malaria to severe disease and exposed possible targets for therapeutic intervention in severe disease.
Main Body
This paper reviews our current understanding of the pathogenic and immunologic factors involved in CM. We present the current view of the roles of certain gene products e.g., the var gene, ABCA-1, ICAM-1, TNF-alpha, CD-36, PfEMP-1 and G6PD, in CM pathogenesis. We also present alterations in the blood–brain barrier as a consequence of disease proliferation as well as complicated host and parasite interactions, including the T-cell immune reaction, reduced deformation of erythrocytes and cytoadherence. We further looked at recent advances in cerebral malaria treatment interventions by emphasizing on biomarkers, new diagnostic tools and emerging therapeutic options.
Conclusion
Finally, we discuss how the current understanding of some of these pathogenic and immunologic factors could inform the development of novel therapeutic interventions to fight CM.
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16
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Erythrocyte-Plasmodium interactions: genetic manipulation of the erythroid lineage. Curr Opin Microbiol 2022; 70:102221. [PMID: 36242898 DOI: 10.1016/j.mib.2022.102221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 08/14/2022] [Accepted: 09/12/2022] [Indexed: 01/25/2023]
Abstract
Targeting critical host factors is an emerging concept in the treatment of infectious diseases. As obligate pathogens of erythrocytes, the Plasmodium spp. parasites that cause malaria must exploit erythroid host factors for their survival. However, our understanding of this important aspect of the malaria lifecycle is limited, in part because erythrocytes are enucleated cells that lack a nucleus and DNA, rendering them genetically intractable. Recent advances in genetic analysis of the erythroid lineage using small-hairpin RNAs and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated nuclease 9 (Cas9) in red-blood cells derived from stem cells have generated new insights into the functions of several candidate host factors for Plasmodium parasites. Along with efforts in other hematopoietic cells, these advances have also laid a strong foundation for genetic screens to identify novel erythrocyte host factors for malaria.
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17
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Wang Y, Ling Y, Gong J, Zhao X, Zhou H, Xie B, Lou H, Zhuang X, Jin L, Fan S, Zhang G, Xu S. PGG.SV: a whole-genome-sequencing-based structural variant resource and data analysis platform. Nucleic Acids Res 2022; 51:D1109-D1116. [PMID: 36243989 PMCID: PMC9825616 DOI: 10.1093/nar/gkac905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/21/2022] [Accepted: 10/04/2022] [Indexed: 01/30/2023] Open
Abstract
Structural variations (SVs) play important roles in human evolution and diseases, but there is a lack of data resources concerning representative samples, especially for East Asians. Taking advantage of both next-generation sequencing and third-generation sequencing data at the whole-genome level, we developed the database PGG.SV to provide a practical platform for both regionally and globally representative structural variants. In its current version, PGG.SV archives 584 277 SVs obtained from whole-genome sequencing data of 6048 samples, including 1030 long-read sequencing genomes representing 177 global populations. PGG.SV provides (i) high-quality SVs with fine-scale and precise genomic locations in both GRCh37 and GRCh38, covering underrepresented SVs in existing sequencing and microarray data; (ii) hierarchical estimation of SV prevalence in geographical populations; (iii) informative annotations of SV-related genes, potential functions and clinical effects; (iv) an analysis platform to facilitate SV-based case-control association studies and (v) various visualization tools for understanding the SV structures in the human genome. Taken together, PGG.SV provides a user-friendly online interface, easy-to-use analysis tools and a detailed presentation of results. PGG.SV is freely accessible via https://www.biosino.org/pggsv.
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Affiliation(s)
| | | | | | - Xiaohan Zhao
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China,Human Phenome Institute, Zhangjiang Fudan International Innovation Center, and Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai 201203, China
| | - Hanwen Zhou
- Key Laboratory of Computational Biology, National Genomics Data Center & Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Bo Xie
- Key Laboratory of Computational Biology, National Genomics Data Center & Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Haiyi Lou
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xinhao Zhuang
- Key Laboratory of Computational Biology, National Genomics Data Center & Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China,Human Phenome Institute, Zhangjiang Fudan International Innovation Center, and Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai 201203, China
| | | | - Shaohua Fan
- Correspondence may also be addressed to Shaohua Fan.
| | - Guoqing Zhang
- Correspondence may also be addressed to Guoqing Zhang.
| | - Shuhua Xu
- To whom correspondence should be addressed. Tel: +86 21 31246617; Fax: +86 21 31246617;
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18
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Henry B, Volle G, Akpovi H, Gineau L, Roussel C, Ndour PA, Tossou F, Suarez F, Palstra F, Fricot A, Chambrion C, Solinc J, Nguyen J, Garé M, Aussenac F, Cottart CH, Keyser C, Adamou R, Tichit M, Hardy D, Fievet N, Clain J, Garcia A, Courtin D, Hermine O, Sabbagh A, Buffet P. Splenic clearance of rigid erythrocytes as an inherited mechanism for splenomegaly and natural resistance to malaria. EBioMedicine 2022; 82:104167. [PMID: 35843175 PMCID: PMC9297103 DOI: 10.1016/j.ebiom.2022.104167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/25/2022] [Accepted: 06/30/2022] [Indexed: 11/18/2022] Open
Affiliation(s)
- Benoît Henry
- Université Paris Cité, Biologie Intégrée du Globule Rouge, UMR_S1134, BIGR, INSERM, Paris, France; Laboratoire d'Excellence Gr-Ex, Paris, France; Institut National de la Transfusion Sanguine, Paris, France; Service des maladies infectieuses et tropicales, APHP, Hôpital Necker Enfants Malades, Centre d'Infectiologie Necker-Pasteur, Institut Imagine, Paris, France; Service des maladies infectieuses et tropicales, APHP. Université Paris Saclay, Hôpital Bicêtre, Le Kremlin-Bicêtre, France
| | - Geoffroy Volle
- Université Paris Cité, Biologie Intégrée du Globule Rouge, UMR_S1134, BIGR, INSERM, Paris, France; Laboratoire d'Excellence Gr-Ex, Paris, France; Institut National de la Transfusion Sanguine, Paris, France
| | - Hilaire Akpovi
- CERPAGE (Centre d'Etude et de Recherche sur les Pathologies Associées à la Grossesse et à l'Enfance), Cotonou, Bénin
| | - Laure Gineau
- Laboratoire d'Excellence Gr-Ex, Paris, France; Université Paris Cité, IRD, MERIT, Paris, France
| | - Camille Roussel
- Université Paris Cité, Biologie Intégrée du Globule Rouge, UMR_S1134, BIGR, INSERM, Paris, France; Laboratoire d'Excellence Gr-Ex, Paris, France; Institut National de la Transfusion Sanguine, Paris, France
| | - Papa Alioune Ndour
- Université Paris Cité, Biologie Intégrée du Globule Rouge, UMR_S1134, BIGR, INSERM, Paris, France; Laboratoire d'Excellence Gr-Ex, Paris, France; Institut National de la Transfusion Sanguine, Paris, France
| | - Félicien Tossou
- Centre Interfacultaire de Formation et de Recherche en Environnement pour le Développement Durable (CIFRED), Université d'Abomey-Calavi, Cotonou, Bénin; Ministère de la Santé, Cotonou, Bénin
| | - Felipe Suarez
- Laboratoire d'Excellence Gr-Ex, Paris, France; Service d'hématologie adultes, APHP, Hôpital Necker Enfants Malades, Paris, France; Université Paris Cité, INSERM U1163, CNRS ERL 8654, Paris, France
| | - Friso Palstra
- Laboratoire d'Excellence Gr-Ex, Paris, France; Université Paris Cité, IRD, MERIT, Paris, France
| | - Aurélie Fricot
- Université Paris Cité, Biologie Intégrée du Globule Rouge, UMR_S1134, BIGR, INSERM, Paris, France; Laboratoire d'Excellence Gr-Ex, Paris, France; Institut National de la Transfusion Sanguine, Paris, France
| | - Charlotte Chambrion
- Université Paris Cité, Biologie Intégrée du Globule Rouge, UMR_S1134, BIGR, INSERM, Paris, France; Laboratoire d'Excellence Gr-Ex, Paris, France; Institut National de la Transfusion Sanguine, Paris, France
| | - Julien Solinc
- Université Paris Cité, Biologie Intégrée du Globule Rouge, UMR_S1134, BIGR, INSERM, Paris, France; Laboratoire d'Excellence Gr-Ex, Paris, France; Institut National de la Transfusion Sanguine, Paris, France
| | - Julie Nguyen
- Laboratoire d'Excellence Gr-Ex, Paris, France; Université Paris Cité, IRD, MERIT, Paris, France
| | - Mathilde Garé
- CERPAGE (Centre d'Etude et de Recherche sur les Pathologies Associées à la Grossesse et à l'Enfance), Cotonou, Bénin; Université Paris Cité, IRD, MERIT, Paris, France
| | - Florentin Aussenac
- CERPAGE (Centre d'Etude et de Recherche sur les Pathologies Associées à la Grossesse et à l'Enfance), Cotonou, Bénin; Université Paris Cité, IRD, MERIT, Paris, France
| | - Charles-Henry Cottart
- Service de biochimie générale, APHP, Hôpital Necker Enfants Malades, Faculté de pharmacie, Paris, France
| | | | - Rafiou Adamou
- CERPAGE (Centre d'Etude et de Recherche sur les Pathologies Associées à la Grossesse et à l'Enfance), Cotonou, Bénin
| | - Magali Tichit
- Institut Pasteur, Experimental Neuropathology Unit, Paris, France
| | - David Hardy
- Institut Pasteur, Experimental Neuropathology Unit, Paris, France
| | - Nadine Fievet
- Laboratoire d'Excellence Gr-Ex, Paris, France; CERPAGE (Centre d'Etude et de Recherche sur les Pathologies Associées à la Grossesse et à l'Enfance), Cotonou, Bénin; Université Paris Cité, IRD, MERIT, Paris, France
| | - Jérôme Clain
- Laboratoire d'Excellence Gr-Ex, Paris, France; Université Paris Cité, IRD, MERIT, Paris, France
| | - André Garcia
- Laboratoire d'Excellence Gr-Ex, Paris, France; CERPAGE (Centre d'Etude et de Recherche sur les Pathologies Associées à la Grossesse et à l'Enfance), Cotonou, Bénin; Université Paris Cité, IRD, MERIT, Paris, France
| | - David Courtin
- Laboratoire d'Excellence Gr-Ex, Paris, France; CERPAGE (Centre d'Etude et de Recherche sur les Pathologies Associées à la Grossesse et à l'Enfance), Cotonou, Bénin; Université Paris Cité, IRD, MERIT, Paris, France
| | - Olivier Hermine
- Laboratoire d'Excellence Gr-Ex, Paris, France; Service d'hématologie adultes, APHP, Hôpital Necker Enfants Malades, Paris, France; Université Paris Cité, INSERM U1163, CNRS ERL 8654, Paris, France
| | - Audrey Sabbagh
- Laboratoire d'Excellence Gr-Ex, Paris, France; Université Paris Cité, IRD, MERIT, Paris, France
| | - Pierre Buffet
- Université Paris Cité, Biologie Intégrée du Globule Rouge, UMR_S1134, BIGR, INSERM, Paris, France; Laboratoire d'Excellence Gr-Ex, Paris, France; Institut National de la Transfusion Sanguine, Paris, France; Institut Pasteur, Paris, France.
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19
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The impact of malaria-protective red blood cell polymorphisms on parasite biomass in children with severe Plasmodium falciparum malaria. Nat Commun 2022; 13:3307. [PMID: 35676275 PMCID: PMC9178016 DOI: 10.1038/s41467-022-30990-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/24/2022] [Indexed: 11/08/2022] Open
Abstract
Severe falciparum malaria is a major cause of preventable child mortality in sub-Saharan Africa. Plasma concentrations of P. falciparum Histidine-Rich Protein 2 (PfHRP2) have diagnostic and prognostic value in severe malaria. We investigate the potential use of plasma PfHRP2 and the sequestration index (the ratio of PfHRP2 to parasite density) as quantitative traits for case-only genetic association studies of severe malaria. Data from 2198 Kenyan children diagnosed with severe malaria, genotyped for 14 major candidate genes, show that polymorphisms in four major red cell genes that lead to hemoglobin S, O blood group, α-thalassemia, and the Dantu blood group, are associated with substantially lower admission plasma PfHRP2 concentrations, consistent with protective effects against extensive parasitized erythrocyte sequestration. In contrast the known protective ATP2B4 polymorphism is associated with higher plasma PfHRP2 concentrations, lower parasite densities and a higher sequestration index. We provide testable hypotheses for the mechanism of protection of ATP2B4.
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20
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Introini V, Govendir MA, Rayner JC, Cicuta P, Bernabeu M. Biophysical Tools and Concepts Enable Understanding of Asexual Blood Stage Malaria. Front Cell Infect Microbiol 2022; 12:908241. [PMID: 35711656 PMCID: PMC9192966 DOI: 10.3389/fcimb.2022.908241] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 04/27/2022] [Indexed: 12/02/2022] Open
Abstract
Forces and mechanical properties of cells and tissues set constraints on biological functions, and are key determinants of human physiology. Changes in cell mechanics may arise from disease, or directly contribute to pathogenesis. Malaria gives many striking examples. Plasmodium parasites, the causative agents of malaria, are single-celled organisms that cannot survive outside their hosts; thus, thost-pathogen interactions are fundamental for parasite’s biological success and to the host response to infection. These interactions are often combinations of biochemical and mechanical factors, but most research focuses on the molecular side. However, Plasmodium infection of human red blood cells leads to changes in their mechanical properties, which has a crucial impact on disease pathogenesis because of the interaction of infected red blood cells with other human tissues through various adhesion mechanisms, which can be probed and modelled with biophysical techniques. Recently, natural polymorphisms affecting red blood cell biomechanics have also been shown to protect human populations, highlighting the potential of understanding biomechanical factors to inform future vaccines and drug development. Here we review biophysical techniques that have revealed new aspects of Plasmodium falciparum invasion of red blood cells and cytoadhesion of infected cells to the host vasculature. These mechanisms occur differently across Plasmodium species and are linked to malaria pathogenesis. We highlight promising techniques from the fields of bioengineering, immunomechanics, and soft matter physics that could be beneficial for studying malaria. Some approaches might also be applied to other phases of the malaria lifecycle and to apicomplexan infections with complex host-pathogen interactions.
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Affiliation(s)
- Viola Introini
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
- Cavendish Laboratory, University of Cambridge, Cambridge, United Kingdom
- *Correspondence: Viola Introini,
| | - Matt A. Govendir
- European Molecular Biology Laboratory (EMBL) Barcelona, Barcelona, Spain
| | - Julian C. Rayner
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Pietro Cicuta
- Cavendish Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Maria Bernabeu
- European Molecular Biology Laboratory (EMBL) Barcelona, Barcelona, Spain
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21
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The erythrocyte membrane properties of beta thalassaemia heterozygotes and their consequences for Plasmodium falciparum invasion. Sci Rep 2022; 12:8934. [PMID: 35624125 PMCID: PMC9142571 DOI: 10.1038/s41598-022-12060-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 05/03/2022] [Indexed: 11/17/2022] Open
Abstract
Malaria parasites such as Plasmodium falciparum have exerted formidable selective pressures on the human genome. Of the human genetic variants associated with malaria protection, beta thalassaemia (a haemoglobinopathy) was the earliest to be associated with malaria prevalence. However, the malaria protective properties of beta thalassaemic erythrocytes remain unclear. Here we studied the mechanics and surface protein expression of beta thalassaemia heterozygous erythrocytes, measured their susceptibility to P. falciparum invasion, and calculated the energy required for merozoites to invade them. We found invasion-relevant differences in beta thalassaemic cells versus matched controls, specifically: elevated membrane tension, reduced bending modulus, and higher levels of expression of the major invasion receptor basigin. However, these differences acted in opposition to each other with respect to their likely impact on invasion, and overall we did not observe beta thalassaemic cells to have lower P. falciparum invasion efficiency for any of the strains tested.
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22
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Identification of ATP2B4 Regulatory Element Containing Functional Genetic Variants Associated with Severe Malaria. Int J Mol Sci 2022; 23:ijms23094849. [PMID: 35563239 PMCID: PMC9101746 DOI: 10.3390/ijms23094849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/15/2022] [Accepted: 04/22/2022] [Indexed: 12/04/2022] Open
Abstract
Genome-wide association studies for severe malaria (SM) have identified 30 genetic variants mostly located in non-coding regions. Here, we aimed to identify potential causal genetic variants located in these loci and demonstrate their functional activity. We systematically investigated the regulatory effect of the SNPs in linkage disequilibrium (LD) with the malaria-associated genetic variants. Annotating and prioritizing genetic variants led to the identification of a regulatory region containing five ATP2B4 SNPs in LD with rs10900585. We found significant associations between SM and rs10900585 and our candidate SNPs (rs11240734, rs1541252, rs1541253, rs1541254, and rs1541255) in a Senegalese population. Then, we demonstrated that both individual SNPs and the combination of SNPs had regulatory effects. Moreover, CRISPR/Cas9-mediated deletion of this region decreased ATP2B4 transcript and protein levels and increased Ca2+ intracellular concentration in the K562 cell line. Our data demonstrate that severe malaria-associated genetic variants alter the expression of ATP2B4 encoding a plasma membrane calcium-transporting ATPase 4 (PMCA4) expressed on red blood cells. Altering the activity of this regulatory element affects the risk of SM, likely through calcium concentration effect on parasitaemia.
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23
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Groomes PV, Kanjee U, Duraisingh MT. RBC membrane biomechanics and Plasmodium falciparum invasion: probing beyond ligand-receptor interactions. Trends Parasitol 2022; 38:302-315. [PMID: 34991983 PMCID: PMC8917059 DOI: 10.1016/j.pt.2021.12.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 10/19/2022]
Abstract
A critical step in malaria blood-stage infections is the invasion of red blood cells (RBCs) by merozoite forms of the Plasmodium parasite. Much progress has been made in defining the parasite ligands and host receptors that mediate this critical step. However, less well understood are the RBC biophysical determinants that influence parasite invasion. In this review we explore how Plasmodium falciparum merozoites interact with the RBC membrane during invasion to modulate RBC deformability and facilitate invasion. We further highlight RBC biomechanics-related polymorphisms that might have been selected for in human populations due to their ability to reduce parasite invasion. Such an understanding will reveal the translational potential of targeting host pathways affecting RBC biomechanical properties for the treatment of malaria.
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Affiliation(s)
- Patrice V Groomes
- Department of Immunology & Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Usheer Kanjee
- Department of Immunology & Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Manoj T Duraisingh
- Department of Immunology & Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.
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24
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Global diversity and balancing selection of 23 leading Plasmodium falciparum candidate vaccine antigens. PLoS Comput Biol 2022; 18:e1009801. [PMID: 35108259 PMCID: PMC8843232 DOI: 10.1371/journal.pcbi.1009801] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 02/14/2022] [Accepted: 01/03/2022] [Indexed: 12/30/2022] Open
Abstract
Investigation of the diversity of malaria parasite antigens can help prioritize and validate them as vaccine candidates and identify the most common variants for inclusion in vaccine formulations. Studies of vaccine candidates of the most virulent human malaria parasite, Plasmodium falciparum, have focused on a handful of well-known antigens, while several others have never been studied. Here we examine the global diversity and population structure of leading vaccine candidate antigens of P. falciparum using the MalariaGEN Pf3K (version 5.1) resource, comprising more than 2600 genomes from 15 malaria endemic countries. A stringent variant calling pipeline was used to extract high quality antigen gene 'haplotypes' from the global dataset and a new R-package named VaxPack was used to streamline population genetic analyses. In addition, a newly developed algorithm that enables spatial averaging of selection pressure on 3D protein structures was applied to the dataset. We analysed the genes encoding 23 leading and novel candidate malaria vaccine antigens including csp, trap, eba175, ama1, rh5, and CelTOS. Our analysis shows that current malaria vaccine formulations are based on rare haplotypes and thus may have limited efficacy against natural parasite populations. High levels of diversity with evidence of balancing selection was detected for most of the erythrocytic and pre-erythrocytic antigens. Measures of natural selection were then mapped to 3D protein structures to predict targets of functional antibodies. For some antigens, geographical variation in the intensity and distribution of these signals on the 3D structure suggests adaptation to different human host or mosquito vector populations. This study provides an essential framework for the diversity of P. falciparum antigens to be considered in the design of the next generation of malaria vaccines.
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25
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Luo P, Cheng S, Zhang F, Feng R, Xu K, Jing W, Xu P. A large-scale genetic correlation scan between rheumatoid arthritis and human plasma protein. Bone Joint Res 2022; 11:134-142. [PMID: 35200038 PMCID: PMC8882322 DOI: 10.1302/2046-3758.112.bjr-2021-0270.r1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Aims The aim of this study was to explore the genetic correlation and causal relationship between blood plasma proteins and rheumatoid arthritis (RA). Methods Based on the genome-wide association studies (GWAS) summary statistics of RA from European descent and the GWAS summary datasets of 3,622 plasma proteins, we explored the relationship between RA and plasma proteins from three aspects. First, linkage disequilibrium score regression (LD score regression) was applied to detect the genetic correlation between RA and plasma proteins. Mendelian randomization (MR) analysis was then used to evaluate the causal association between RA and plasma proteins. Finally, GEO2R was used to screen the differentially expressed genes (DEGs) between patients with RA and healthy controls. Results We found that seven kinds of plasma proteins had genetic correlations with RA, such as Soluble Receptor for Advanced Glycation End Products (sRAGE) (correlation coefficient = 0.2582, p = 0.049), vesicle transport protein USE1 (correlation coefficient = 0.1337, p = 0.018), and spermatogenesis-associated protein 20 (correlation coefficient = 0.3706, p = 0.018). There was a significant causal relationship between sRAGE and RA. By comparing the genes encoding seven plasma proteins, we found that only USE1 was a DEG associated with RA. Conclusion Our study identified a set of candidate plasma proteins that showed signals correlated with RA. Since the results of this study need further experimental verification, they should be interpreted with caution. However, we hope that this paper will provide new insights for the discovery of pathogenic genes and RA pathogenesis in the future. Cite this article: Bone Joint Res 2022;11(2):134–142.
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Affiliation(s)
- Pan Luo
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Shiqiang Cheng
- Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Feng Zhang
- Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Ruoyang Feng
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Ke Xu
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Wensen Jing
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Peng Xu
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, China
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26
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Voinson M, Nunn CL, Goldberg A. Primate malarias as a model for cross-species parasite transmission. eLife 2022; 11:e69628. [PMID: 35086643 PMCID: PMC8798051 DOI: 10.7554/elife.69628] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 01/14/2022] [Indexed: 12/16/2022] Open
Abstract
Parasites regularly switch into new host species, representing a disease burden and conservation risk to the hosts. The distribution of these parasites also gives insight into characteristics of ecological networks and genetic mechanisms of host-parasite interactions. Some parasites are shared across many species, whereas others tend to be restricted to hosts from a single species. Understanding the mechanisms producing this distribution of host specificity can enable more effective interventions and potentially identify genetic targets for vaccines or therapies. As ecological connections between human and local animal populations increase, the risk to human and wildlife health from novel parasites also increases. Which of these parasites will fizzle out and which have the potential to become widespread in humans? We consider the case of primate malarias, caused by Plasmodium parasites, to investigate the interacting ecological and evolutionary mechanisms that put human and nonhuman primates at risk for infection. Plasmodium host switching from nonhuman primates to humans led to ancient introductions of the most common malaria-causing agents in humans today, and new parasite switching is a growing threat, especially in Asia and South America. Based on a wild host-Plasmodium occurrence database, we highlight geographic areas of concern and potential areas to target further sampling. We also discuss methodological developments that will facilitate clinical and field-based interventions to improve human and wildlife health based on this eco-evolutionary perspective.
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Affiliation(s)
- Marina Voinson
- Department of Evolutionary Anthropology, Duke UniversityDurhamUnited States
| | - Charles L Nunn
- Department of Evolutionary Anthropology, Duke UniversityDurhamUnited States
- Duke Global Health, Duke UniversityDurhamUnited States
| | - Amy Goldberg
- Department of Evolutionary Anthropology, Duke UniversityDurhamUnited States
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27
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Ebel ER, Uricchio LH, Petrov DA, Egan ES. Revisiting the malaria hypothesis: accounting for polygenicity and pleiotropy. Trends Parasitol 2022; 38:290-301. [PMID: 35065882 PMCID: PMC8916997 DOI: 10.1016/j.pt.2021.12.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 10/19/2022]
Abstract
The malaria hypothesis predicts local, balancing selection of deleterious alleles that confer strong protection from malaria. Three protective variants, recently discovered in red cell genes, are indeed more common in African than European populations. Still, up to 89% of the heritability of severe malaria is attributed to many genome-wide loci with individually small effects. Recent analyses of hundreds of genome-wide association studies (GWAS) in humans suggest that most functional, polygenic variation is pleiotropic for multiple traits. Interestingly, GWAS alleles and red cell traits associated with small reductions in malaria risk are not enriched in African populations. We propose that other selective and neutral forces, in addition to malaria prevalence, explain the global distribution of most genetic variation impacting malaria risk.
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28
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Band G, Leffler EM, Jallow M, Sisay-Joof F, Ndila CM, Macharia AW, Hubbart C, Jeffreys AE, Rowlands K, Nguyen T, Gonçalves S, Ariani CV, Stalker J, Pearson RD, Amato R, Drury E, Sirugo G, d'Alessandro U, Bojang KA, Marsh K, Peshu N, Saelens JW, Diakité M, Taylor SM, Conway DJ, Williams TN, Rockett KA, Kwiatkowski DP. Malaria protection due to sickle haemoglobin depends on parasite genotype. Nature 2021; 602:106-111. [PMID: 34883497 PMCID: PMC8810385 DOI: 10.1038/s41586-021-04288-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 11/29/2021] [Indexed: 11/30/2022]
Abstract
Host genetic factors can confer resistance against malaria1, raising the question of whether this has led to evolutionary adaptation of parasite populations. Here we searched for association between candidate host and parasite genetic variants in 3,346 Gambian and Kenyan children with severe malaria caused by Plasmodium falciparum. We identified a strong association between sickle haemoglobin (HbS) in the host and three regions of the parasite genome, which is not explained by population structure or other covariates, and which is replicated in additional samples. The HbS-associated alleles include nonsynonymous variants in the gene for the acyl-CoA synthetase family member2–4PfACS8 on chromosome 2, in a second region of chromosome 2, and in a region containing structural variation on chromosome 11. The alleles are in strong linkage disequilibrium and have frequencies that covary with the frequency of HbS across populations, in particular being much more common in Africa than other parts of the world. The estimated protective effect of HbS against severe malaria, as determined by comparison of cases with population controls, varies greatly according to the parasite genotype at these three loci. These findings open up a new avenue of enquiry into the biological and epidemiological significance of the HbS-associated polymorphisms in the parasite genome and the evolutionary forces that have led to their high frequency and strong linkage disequilibrium in African P. falciparum populations. A strong association has been found between three regions of the Plasmodium falciparum genome and sickle haemoglobin in children with severe malaria, suggesting parasites have adapted to overcome natural host immunity.
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Affiliation(s)
- Gavin Band
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK. .,Wellcome Sanger Institute, Hinxton, Cambridge, UK. .,Big Data Institute, Li Ka Shing Centre for Health and Information Discovery, Old Road Campus, Oxford, USA.
| | - Ellen M Leffler
- Wellcome Sanger Institute, Hinxton, Cambridge, UK.,Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Muminatou Jallow
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, The Gambia.,Edward Francis Small Teaching Hospital (formerly Royal Victoria Teaching Hospital), Independence Drive, Banjul, The Gambia
| | - Fatoumatta Sisay-Joof
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, The Gambia
| | - Carolyne M Ndila
- KEMRI-Wellcome Trust Research Programme, PO Box 230, Kilifi, Kenya
| | | | - Christina Hubbart
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Anna E Jeffreys
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Kate Rowlands
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Thuy Nguyen
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | | | | | - Jim Stalker
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Richard D Pearson
- Wellcome Sanger Institute, Hinxton, Cambridge, UK.,Big Data Institute, Li Ka Shing Centre for Health and Information Discovery, Old Road Campus, Oxford, USA
| | | | | | - Giorgio Sirugo
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, The Gambia.,Division of Translational Medicine and Human Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Umberto d'Alessandro
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, The Gambia
| | - Kalifa A Bojang
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, The Gambia
| | - Kevin Marsh
- KEMRI-Wellcome Trust Research Programme, PO Box 230, Kilifi, Kenya.,Nuffield Department of Medicine, NDM Research Building, Roosevelt Drive, Headington, Oxford, UK
| | - Norbert Peshu
- KEMRI-Wellcome Trust Research Programme, PO Box 230, Kilifi, Kenya
| | - Joseph W Saelens
- Division of Infectious Diseases, Duke University School of Medicine, Durham, NC, USA
| | - Mahamadou Diakité
- Malaria Research and Training Center, University of Sciences, Techniques, and Technologies of Bamako, Bamako, Mali
| | - Steve M Taylor
- Division of Infectious Diseases, Duke University School of Medicine, Durham, NC, USA.,Duke Global Health Institute, Duke University, Durham, NC, USA
| | - David J Conway
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, The Gambia.,Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - Thomas N Williams
- KEMRI-Wellcome Trust Research Programme, PO Box 230, Kilifi, Kenya.,Institute for Global Health Innovation, Department of Surgery and Cancer, Imperial College, London, London, UK
| | - Kirk A Rockett
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK. .,Wellcome Sanger Institute, Hinxton, Cambridge, UK.
| | - Dominic P Kwiatkowski
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK. .,Wellcome Sanger Institute, Hinxton, Cambridge, UK. .,Big Data Institute, Li Ka Shing Centre for Health and Information Discovery, Old Road Campus, Oxford, USA.
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29
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Ren E, Liu C, Lv P, Wang J, Liu G. Genetically Engineered Cellular Membrane Vesicles as Tailorable Shells for Therapeutics. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2100460. [PMID: 34494387 PMCID: PMC8564451 DOI: 10.1002/advs.202100460] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 07/20/2021] [Indexed: 05/04/2023]
Abstract
Benefiting from the blooming interaction of nanotechnology and biotechnology, biosynthetic cellular membrane vesicles (Bio-MVs) have shown superior characteristics for therapeutic transportation because of their hydrophilic cavity and hydrophobic bilayer structure, as well as their inherent biocompatibility and negligible immunogenicity. These excellent cell-like features with specific functional protein expression on the surface can invoke their remarkable ability for Bio-MVs based recombinant protein therapy to facilitate the advanced synergy in poly-therapy. To date, various tactics have been developed for Bio-MVs surface modification with functional proteins through hydrophobic insertion or multivalent electrostatic interactions. While the Bio-MVs grow through genetically engineering strategies can maintain binding specificity, sort orders, and lead to strict information about artificial proteins in a facile and sustainable way. In this progress report, the most current technology of Bio-MVs is discussed, with an emphasis on their multi-functionalities as "tailorable shells" for delivering bio-functional moieties and therapeutic entities. The most notable success and challenges via genetically engineered tactics to achieve the new generation of Bio-MVs are highlighted. Besides, future perspectives of Bio-MVs in novel bio-nanotherapy are provided.
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Affiliation(s)
- En Ren
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics & Center for Molecular Imaging and Translational MedicineSchool of Public HealthXiamen UniversityXiamen361102China
| | - Chao Liu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics & Center for Molecular Imaging and Translational MedicineSchool of Public HealthXiamen UniversityXiamen361102China
| | - Peng Lv
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics & Center for Molecular Imaging and Translational MedicineSchool of Public HealthXiamen UniversityXiamen361102China
| | - Junqing Wang
- School of Pharmaceutical Sciences (Shenzhen)Sun Yat‐sen UniversityGuangzhou510275China
| | - Gang Liu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics & Center for Molecular Imaging and Translational MedicineSchool of Public HealthXiamen UniversityXiamen361102China
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30
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Abstract
[Figure: see text].
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Affiliation(s)
- Melissa Gymrek
- Department of Medicine, University of California San Diego, La Jolla, CA, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Alon Goren
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
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31
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Ebel ER, Kuypers FA, Lin C, Petrov DA, Egan ES. Common host variation drives malaria parasite fitness in healthy human red cells. eLife 2021; 10:e69808. [PMID: 34553687 PMCID: PMC8497061 DOI: 10.7554/elife.69808] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 09/22/2021] [Indexed: 12/11/2022] Open
Abstract
The replication of Plasmodium falciparum parasites within red blood cells (RBCs) causes severe disease in humans, especially in Africa. Deleterious alleles like hemoglobin S are well-known to confer strong resistance to malaria, but the effects of common RBC variation are largely undetermined. Here, we collected fresh blood samples from 121 healthy donors, most with African ancestry, and performed exome sequencing, detailed RBC phenotyping, and parasite fitness assays. Over one-third of healthy donors unknowingly carried alleles for G6PD deficiency or hemoglobinopathies, which were associated with characteristic RBC phenotypes. Among non-carriers alone, variation in RBC hydration, membrane deformability, and volume was strongly associated with P. falciparum growth rate. Common genetic variants in PIEZO1, SPTA1/SPTB, and several P. falciparum invasion receptors were also associated with parasite growth rate. Interestingly, we observed little or negative evidence for divergent selection on non-pathogenic RBC variation between Africans and Europeans. These findings suggest a model in which globally widespread variation in a moderate number of genes and phenotypes modulates P. falciparum fitness in RBCs.
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Affiliation(s)
- Emily R Ebel
- Department of Biology, Stanford UniversityStanfordUnited States
- Department of Pediatrics, Stanford University School of MedicineStanfordUnited States
| | - Frans A Kuypers
- Children's Hospital Oakland Research InstituteOaklandUnited States
| | - Carrie Lin
- Department of Pediatrics, Stanford University School of MedicineStanfordUnited States
| | - Dmitri A Petrov
- Department of Biology, Stanford UniversityStanfordUnited States
| | - Elizabeth S Egan
- Department of Pediatrics, Stanford University School of MedicineStanfordUnited States
- Department of Microbiology & Immunology, Stanford University School of MedicineStanfordUnited States
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32
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Hollox EJ, Zuccherato LW, Tucci S. Genome structural variation in human evolution. Trends Genet 2021; 38:45-58. [PMID: 34284881 DOI: 10.1016/j.tig.2021.06.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 01/01/2023]
Abstract
Structural variation (SV) is a large difference (typically >100 bp) in the genomic structure of two genomes and includes both copy number variation and variation that does not change copy number of a genomic region, such as an inversion. Improved reference genomes, combined with widespread genome sequencing using short-read sequencing technology, and increasingly using long-read sequencing, have reignited interest in SV. Recent large-scale studies and functional focused analyses have highlighted the role of SV in human evolution. In this review, we highlight human-specific SVs involved in changes in the brain, population-specific SVs that affect response to the environment, including adaptation to diet and infectious diseases, and summarise the contribution of archaic hominin admixture to present-day human SV.
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Affiliation(s)
- Edward J Hollox
- Department of Genetics and Genome Biology, University of Leicester, UK.
| | - Luciana W Zuccherato
- Núcleo de Ensino e Pesquisa, Instituto Mário Penna, Belo Horizonte, Brazil; Departmento de Bioquímica e Imunologia, Universidade de Minas Gerais, Belo Horizonte, Brazil
| | - Serena Tucci
- Department of Anthropology, Yale University, New Haven, CT, USA
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33
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Watson JA, Ndila CM, Uyoga S, Macharia A, Nyutu G, Mohammed S, Ngetsa C, Mturi N, Peshu N, Tsofa B, Rockett K, Leopold S, Kingston H, George EC, Maitland K, Day NPJ, Dondorp AM, Bejon P, Williams TN, Holmes CC, White NJ. Improving statistical power in severe malaria genetic association studies by augmenting phenotypic precision. eLife 2021; 10:e69698. [PMID: 34225842 PMCID: PMC8315799 DOI: 10.7554/elife.69698] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 06/22/2021] [Indexed: 12/14/2022] Open
Abstract
Severe falciparum malaria has substantially affected human evolution. Genetic association studies of patients with clinically defined severe malaria and matched population controls have helped characterise human genetic susceptibility to severe malaria, but phenotypic imprecision compromises discovered associations. In areas of high malaria transmission, the diagnosis of severe malaria in young children and, in particular, the distinction from bacterial sepsis are imprecise. We developed a probabilistic diagnostic model of severe malaria using platelet and white count data. Under this model, we re-analysed clinical and genetic data from 2220 Kenyan children with clinically defined severe malaria and 3940 population controls, adjusting for phenotype mis-labelling. Our model, validated by the distribution of sickle trait, estimated that approximately one-third of cases did not have severe malaria. We propose a data-tilting approach for case-control studies with phenotype mis-labelling and show that this reduces false discovery rates and improves statistical power in genome-wide association studies.
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Affiliation(s)
- James A Watson
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol UniversityBangkokThailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
| | - Carolyne M Ndila
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol UniversityBangkokThailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
| | - Sophie Uyoga
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-CoastKilifiKenya
| | - Alexander Macharia
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-CoastKilifiKenya
| | - Gideon Nyutu
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-CoastKilifiKenya
| | - Shebe Mohammed
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-CoastKilifiKenya
| | - Caroline Ngetsa
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-CoastKilifiKenya
| | - Neema Mturi
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-CoastKilifiKenya
| | - Norbert Peshu
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-CoastKilifiKenya
| | - Benjamin Tsofa
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-CoastKilifiKenya
| | - Kirk Rockett
- The Wellcome Sanger InstituteCambridgeUnited Kingdom
- Wellcome Trust Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
| | - Stije Leopold
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol UniversityBangkokThailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
| | - Hugh Kingston
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol UniversityBangkokThailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
| | - Elizabeth C George
- Medical Research Council Clinical Trials Unit, University College LondonLondonUnited Kingdom
| | - Kathryn Maitland
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-CoastKilifiKenya
- Institute of Global Health Innovation, Imperial College, LondonLondonUnited Kingdom
| | - Nicholas PJ Day
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol UniversityBangkokThailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
| | - Arjen M Dondorp
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol UniversityBangkokThailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
| | - Philip Bejon
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-CoastKilifiKenya
| | - Thomas N Williams
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-CoastKilifiKenya
- Institute of Global Health Innovation, Imperial College, LondonLondonUnited Kingdom
| | - Chris C Holmes
- Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
- Department of Statistics, University of OxfordOxfordUnited Kingdom
| | - Nicholas J White
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol UniversityBangkokThailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
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34
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Jongruamklang P, Rebetz J, Kapur R, Persson KEM, Olsson ML, Semple JW, Storry JR. Platelets inhibit erythrocyte invasion by Plasmodium falciparum at physiological platelet:erythrocyte ratios. Transfus Med 2021; 32:168-174. [PMID: 33987889 DOI: 10.1111/tme.12791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 10/05/2020] [Accepted: 12/27/2020] [Indexed: 11/27/2022]
Abstract
OBJECTIVE To evaluate the effect of platelet:erythrocyte (P:E) ratios on Plasmodium falciparum erythrocyte invasion. BACKGROUND Recent reports have shown that platelets are directly involved in the immune response towards P. falciparum during erythrocyte invasion. However, the literature both supports and conflicts with a role for platelets in limiting invasion. Also, the effect of platelet numbers on invasion (parasitemia) has not been thoroughly investigated. METHODS/MATERIALS The P. falciparum strains FCR3S1.2 and W2mef were cultured with group O erythrocytes. The cultures were synchronised and supplemented with pooled platelets at P:E ratios ranging from 1:100 to 1:2. Parasitemia was measured at 40 h by flow cytometry and by microscopy of blood smears. RESULTS A linear relationship was observed between reduced invasion and increased platelet numbers at P:E ratios ranging from 1:100 to 1:20. However, this effect was reversed at lower ratios (1:10-1:2). Microscopic evaluation revealed aggregation and attachment of platelets to erythrocytes, but not specifically to parasitised erythrocytes. CONCLUSION We have shown that under physiological P:E ratios (approx. 1:10-1:40), platelets inhibited P. falciparum invasion in a dose-dependent manner. At ratios of 1:10 and below, platelets did not further increase the inhibitory effect and, although the trend was reversed, inhibition was still maintained.
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Affiliation(s)
- Philaiphon Jongruamklang
- Department of Laboratory Medicine, Division of Hematology and Transfusion Medicine, Lund University, Lund, Sweden.,Department of Medical Technology, School of Allied Health Sciences, University of Phayao, Phayao, Thailand
| | - Johan Rebetz
- Department of Laboratory Medicine, Division of Hematology and Transfusion Medicine, Lund University, Lund, Sweden
| | - Rick Kapur
- Department of Experimental Immunohematology, Sanquin Research, Amsterdam, The Netherlands.,Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Kristina E M Persson
- Department of Laboratory Medicine, Division of Clinical Chemistry and Pharmacology, Lund University, Lund, Sweden.,Clinical Chemistry and Pharmacology, Laboratory Medicine, Office for Medical Services, Region Skåne, Lund, Sweden
| | - Martin L Olsson
- Department of Laboratory Medicine, Division of Hematology and Transfusion Medicine, Lund University, Lund, Sweden.,Clinical Immunology and Transfusion Medicine, Laboratory Medicine, Office for Medical Services, Region Skåne, Lund, Sweden
| | - John W Semple
- Department of Laboratory Medicine, Division of Hematology and Transfusion Medicine, Lund University, Lund, Sweden.,Clinical Immunology and Transfusion Medicine, Laboratory Medicine, Office for Medical Services, Region Skåne, Lund, Sweden
| | - Jill R Storry
- Department of Laboratory Medicine, Division of Hematology and Transfusion Medicine, Lund University, Lund, Sweden.,Clinical Immunology and Transfusion Medicine, Laboratory Medicine, Office for Medical Services, Region Skåne, Lund, Sweden
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35
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Thorball CW, Fellay J, Borghesi A. Immunological lessons from genome-wide association studies of infections. Curr Opin Immunol 2021; 72:87-93. [PMID: 33878603 DOI: 10.1016/j.coi.2021.03.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/24/2021] [Accepted: 03/27/2021] [Indexed: 02/06/2023]
Abstract
Over the past few years, genome-wide association studies (GWAS) have been increasingly applied to identify host genetic factors influencing clinical and laboratory traits related to immunity and infection, and to understand the interplay between the host and the microbial genomes. By screening large cohorts of individuals suffering from various infectious diseases, GWAS explored resistance against infection, natural history of the disease, development of life-threatening clinical signs, and innate and adaptive immune responses. These efforts provided fundamental insight on the role of major genes in the interindividual variability in the response to infection and on the mechanisms of the immune response against human pathogens both at the individual and population levels.
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Affiliation(s)
- Christian W Thorball
- Precision Medicine Unit, Lausanne University Hospital (CHUV), University of Lausanne, Lausanne, Switzerland
| | - Jacques Fellay
- Precision Medicine Unit, Lausanne University Hospital (CHUV), University of Lausanne, Lausanne, Switzerland; School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Alessandro Borghesi
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Neonatal Intensive Care Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.
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36
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Tennessen JA, Duraisingh MT. Three Signatures of Adaptive Polymorphism Exemplified by Malaria-Associated Genes. Mol Biol Evol 2021; 38:1356-1371. [PMID: 33185667 PMCID: PMC8042748 DOI: 10.1093/molbev/msaa294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Malaria has been one of the strongest selective pressures on our species. Many of the best-characterized cases of adaptive evolution in humans are in genes tied to malaria resistance. However, the complex evolutionary patterns at these genes are poorly captured by standard scans for nonneutral evolution. Here, we present three new statistical tests for selection based on population genetic patterns that are observed more than once among key malaria resistance loci. We assess these tests using forward-time evolutionary simulations and apply them to global whole-genome sequencing data from humans, and thus we show that they are effective at distinguishing selection from neutrality. Each test captures a distinct evolutionary pattern, here called Divergent Haplotypes, Repeated Shifts, and Arrested Sweeps, associated with a particular period of human prehistory. We clarify the selective signatures at known malaria-relevant genes and identify additional genes showing similar adaptive evolutionary patterns. Among our top outliers, we see a particular enrichment for genes involved in erythropoiesis and for genes previously associated with malaria resistance, consistent with a major role for malaria in shaping these patterns of genetic diversity. Polymorphisms at these genes are likely to impact resistance to malaria infection and contribute to ongoing host-parasite coevolutionary dynamics.
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37
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Seixas FA, Edelman NB, Mallet J. Synteny-Based Genome Assembly for 16 Species of Heliconius Butterflies, and an Assessment of Structural Variation across the Genus. Genome Biol Evol 2021; 13:6207971. [PMID: 33792688 PMCID: PMC8290116 DOI: 10.1093/gbe/evab069] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/29/2021] [Indexed: 12/11/2022] Open
Abstract
Heliconius butterflies (Lepidoptera: Nymphalidae) are a group of 48 neotropical species widely studied in evolutionary research. Despite the wealth of genomic data generated in past years, chromosomal level genome assemblies currently exist for only two species, Heliconius melpomene and Heliconius erato, each a representative of one of the two major clades of the genus. Here, we use these reference genomes to improve the contiguity of previously published draft genome assemblies of 16 Heliconius species. Using a reference-assisted scaffolding approach, we place and order the scaffolds of these genomes onto chromosomes, resulting in 95.7-99.9% of their genomes anchored to chromosomes. Genome sizes are somewhat variable among species (270-422 Mb) and in one small group of species (Heliconius hecale, Heliconius elevatus, and Heliconius pardalinus) expansions in genome size are driven mainly by repetitive sequences that map to four small regions in the H. melpomene reference genome. Genes from these repeat regions show an increase in exon copy number, an absence of internal stop codons, evidence of constraint on nonsynonymous changes, and increased expression, all of which suggest that at least some of the extra copies are functional. Finally, we conducted a systematic search for inversions and identified five moderately large inversions fixed between the two major Heliconius clades. We infer that one of these inversions was transferred by introgression between the lineages leading to the erato/sara and burneyi/doris clades. These reference-guided assemblies represent a major improvement in Heliconius genomic resources that enable further genetic and evolutionary discoveries in this genus.
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Affiliation(s)
- Fernando A Seixas
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Nathaniel B Edelman
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA.,Yale Institute for Biospheric Studies, Yale University, New Haven, Connecticut, USA
| | - James Mallet
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
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38
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Thiam LG, Nyarko PB, Kusi KA, Niang M, Aniweh Y, Awandare GA. Blood donor variability is a modulatory factor for P. falciparum invasion phenotyping assays. Sci Rep 2021; 11:7129. [PMID: 33782439 PMCID: PMC8007732 DOI: 10.1038/s41598-021-86438-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 03/12/2021] [Indexed: 11/26/2022] Open
Abstract
Human erythrocytes are indispensable for Plasmodium falciparum development. Unlike other eukaryotic cells, there is no existing erythroid cell line capable of supporting long-term P. falciparum in vitro experiments. Consequently, invasion phenotyping experiments rely on erythrocytes of different individuals. However, the contribution of the erythrocytes variation in influencing invasion rates remains unknown, which represents a challenge for conducting large-scale comparative studies. Here, we used erythrocytes of different blood groups harboring different hemoglobin genotypes to assess the relative contribution of blood donor variability in P. falciparum invasion phenotyping assays. For each donor, we investigated the relationship between parasite invasion phenotypes and erythrocyte phenotypic characteristics, including the expression levels of surface receptors (e.g. the human glycophorins A and C, the complement receptor 1 and decay accelerating factor), blood groups (e.g. ABO/Rh system), and hemoglobin genotypes (e.g. AA, AS and AC). Across all donors, there were significant differences in invasion efficiency following treatment with either neuraminidase, trypsin or chymotrypsin relative to the control erythrocytes. Primarily, we showed that the levels of key erythrocyte surface receptors and their sensitivity to enzyme treatment significantly differed across donors. However, invasion efficiency did not correlate with susceptibility to enzyme treatment or with the levels of the selected erythrocyte surface receptors. Furthermore, we found no relationship between P. falciparum invasion phenotype and blood group or hemoglobin genotype. Altogether, our findings demonstrate the need to consider erythrocyte donor uniformity and anticipate challenges associated with blood donor variability in early stages of large-scale study design.
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Affiliation(s)
- Laty G Thiam
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Ghana.,Department of Biochemistry Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Legon, Ghana.,G4 MEGA Vaccines, Institut Pasteur de Dakar, Dakar, Senegal
| | - Prince B Nyarko
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Ghana.,Department of Biochemistry Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Legon, Ghana.,Laboratory of Pathogen-Host Interaction, UMR5235, CNRS, University of Montpellier, Montpellier, France
| | - Kwadwo A Kusi
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Ghana.,Department of Immunology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Makhtar Niang
- Pôle Immunophysiopathologie et Maladies Infectieuses, Institut Pasteur de Dakar, Dakar, Senegal
| | - Yaw Aniweh
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Ghana. .,Department of Biochemistry Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Legon, Ghana.
| | - Gordon A Awandare
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Ghana. .,Department of Biochemistry Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Legon, Ghana.
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39
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Altable M, de la Serna JM. Protection against COVID-19 in African population: Immunology, genetics, and malaria clues for therapeutic targets. Virus Res 2021; 299:198347. [PMID: 33631219 PMCID: PMC7898966 DOI: 10.1016/j.virusres.2021.198347] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 02/14/2021] [Accepted: 02/15/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND There is a marked discrepancy between SARS-CoV-2 seroprevalence and COVID-19 cases and deaths in Africa. MAIN: SARS-CoV-2 stimulates humoral and cellular immunity systems, as well as mitogen-activated protein kinase (MAPK) and nuclear NF-kB signalling pathways, which regulate inflammatory gene expression and immune cell differentiation. The result is pro-inflammatory cytokines release, hyperinflammatory condition, and cytokine storm, which provoke severe lung alterations that can lead to multi-organ failure in COVID-19. Multiple genetic and immunologic factors may contribute to the severity of COVID-19 in African individuals when compared to the rest of the global population. In this article, the role of malaria, NF-kB and MAPK pathways, caspase-12 expression, high level of LAIR-1-containing antibodies, and differential glycophorins (GYPA/B) expression in COVID-19 are discussed. CONCLUSION Understanding pathophysiological mechanisms can help identify target points for drugs and vaccines development against COVID-19. To our knowledge, this is the first study that explores this link and proposes a biological and molecular answer to the epidemiologic discrepancy in COVID-19 in Africa.
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Affiliation(s)
- Marcos Altable
- Private Practice of Neurology, Neuroceuta. (Virgen de África Clinic), Ceuta, Spain.
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40
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Musa HH, Musa TH, Musa IH, Musa IH, Ranciaro A, Campbell MC. Addressing Africa's pandemic puzzle: Perspectives on COVID-19 transmission and mortality in sub-Saharan Africa. Int J Infect Dis 2021; 102:483-488. [PMID: 33010461 PMCID: PMC7526606 DOI: 10.1016/j.ijid.2020.09.1456] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 09/21/2020] [Indexed: 12/12/2022] Open
Abstract
To date, SARS-CoV-2 (the virus that causes COVID-19) has spread to almost every region of the world, infecting millions and resulting in the deaths of hundreds of thousands of people. Although it was predicted that Africa would suffer a massive loss of life due to this pandemic, the number of COVID-19 cases has been relatively low across the continent. Researchers have speculated that several factors may be responsible for this outcome in Africa, including the extensive experience that countries have with infectious diseases and the young median age of their populations. However, it is still important for African countries to adopt aggressive and bold approaches against COVID-19, in case the nature of the pandemic changes. This short review will summarize the status of the outbreak in Africa and propose possible reasons for current trends, as well as discuss interventions aimed at preventing a rapid increase in the number of COVID-19 cases in the future.
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Affiliation(s)
- Hassan H Musa
- Biomedical Research Institute, Darfur College, Nyala, Sudan; Faculty of Medical Laboratory Sciences, University of Khartoum, Sudan
| | - Taha H Musa
- Biomedical Research Institute, Darfur College, Nyala, Sudan; School of Medicine, Darfur College, Nyala, Sudan
| | | | - Ibrahim H Musa
- Biomedical Research Institute, Darfur College, Nyala, Sudan
| | - Alessia Ranciaro
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
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41
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Plasmodium falciparum is evolving to escape malaria rapid diagnostic tests in Ethiopia. Nat Microbiol 2021; 6:1289-1299. [PMID: 34580442 PMCID: PMC8478644 DOI: 10.1038/s41564-021-00962-4] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 08/16/2021] [Indexed: 02/07/2023]
Abstract
In Africa, most rapid diagnostic tests (RDTs) for falciparum malaria recognize histidine-rich protein 2 antigen. Plasmodium falciparum parasites lacking histidine-rich protein 2 (pfhrp2) and 3 (pfhrp3) genes escape detection by these RDTs, but it is not known whether these deletions confer sufficient selective advantage to drive rapid population expansion. By studying blood samples from a cohort of 12,572 participants enroled in a prospective, cross-sectional survey along Ethiopia's borders with Eritrea, Sudan and South Sudan using RDTs, PCR, an ultrasensitive bead-based immunoassay for antigen detection and next-generation sequencing, we estimate that histidine-rich protein 2-based RDTs would miss 9.7% (95% confidence interval 8.5-11.1) of P. falciparum malaria cases owing to pfhrp2 deletion. We applied a molecular inversion probe-targeted deep sequencing approach to identify distinct subtelomeric deletion patterns and well-established pfhrp3 deletions and to uncover recent expansion of a singular pfhrp2 deletion in all regions sampled. We propose a model in which pfhrp3 deletions have arisen independently multiple times, followed by strong positive selection for pfhrp2 deletion owing to RDT-based test-and-treatment. Existing diagnostic strategies need to be urgently reconsidered in Ethiopia, and improved surveillance for pfhrp2 deletion is needed throughout the Horn of Africa.
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42
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Amuzu DS, Rockett KA, Leffler EM, Ansah F, Amoako N, Morang'a CM, Hubbart C, Rowlands K, Jeffreys AE, Amenga-Etego LN, Kwiatkowski DP, Awandare GA. High-throughput genotyping assays for identification of glycophorin B deletion variants in population studies. Exp Biol Med (Maywood) 2020; 246:916-928. [PMID: 33325748 PMCID: PMC8022085 DOI: 10.1177/1535370220968545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Glycophorins are the most abundant sialoglycoproteins on the surface of human erythrocyte membranes. Genetic variation in glycophorin region of human chromosome 4 (containing GYPA, GYPB, and GYPE genes) is of interest because the gene products serve as receptors for pathogens of major public health interest, including Plasmodiumsp., Babesiasp., Influenza virus, Vibrio cholerae El Tor Hemolysin, and Escherichia coli. A large structural rearrangement and hybrid glycophorin variant, known as Dantu, which was identified in East African populations, has been linked with a 40% reduction in risk for severe malaria. Apart from Dantu, other large structural variants exist, with the most common being deletion of the whole GYPB gene and its surrounding region, resulting in multiple different deletion forms. In West Africa particularly, these deletions are estimated to account for between 5 and 15% of the variation in different populations, mostly attributed to the forms known as DEL1 and DEL2. Due to the lack of specific variant assays, little is known of the distribution of these variants. Here, we report a modification of a previous GYPB DEL1 assay and the development of a novel GYPB DEL2 assay as high-throughput PCR-RFLP assays, as well as the identification of the crossover/breakpoint for GYPB DEL2. Using 393 samples from three study sites in Ghana as well as samples from HapMap and 1000 G projects for validation, we show that our assays are sensitive and reliable for genotyping GYPB DEL1 and DEL2. To the best of our knowledge, this is the first report of such high-throughput genotyping assays by PCR-RFLP for identifying specific GYPB deletion types in populations. These assays will enable better identification of GYPB deletions for large genetic association studies and functional experiments to understand the role of this gene cluster region in susceptibility to malaria and other diseases.
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Affiliation(s)
- Dominic Sy Amuzu
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, GH 0233, Ghana.,Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, GH 0233, Ghana.,Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Kirk A Rockett
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK.,Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Ellen M Leffler
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK.,Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT 84112-5330, USA
| | - Felix Ansah
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, GH 0233, Ghana.,Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, GH 0233, Ghana
| | - Nicholas Amoako
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, GH 0233, Ghana.,Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, GH 0233, Ghana
| | - Collins M Morang'a
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, GH 0233, Ghana.,Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, GH 0233, Ghana
| | - Christina Hubbart
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Kate Rowlands
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Anna E Jeffreys
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Lucas N Amenga-Etego
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, GH 0233, Ghana.,Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, GH 0233, Ghana
| | - Dominic P Kwiatkowski
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK.,Wellcome Sanger Institute, Hinxton CB10 1SA, UK.,Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Gordon A Awandare
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, GH 0233, Ghana.,Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, GH 0233, Ghana
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43
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Host genetics and infectious disease: new tools, insights and translational opportunities. Nat Rev Genet 2020; 22:137-153. [PMID: 33277640 PMCID: PMC7716795 DOI: 10.1038/s41576-020-00297-6] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/14/2020] [Indexed: 12/22/2022]
Abstract
Understanding how human genetics influence infectious disease susceptibility offers the opportunity for new insights into pathogenesis, potential drug targets, risk stratification, response to therapy and vaccination. As new infectious diseases continue to emerge, together with growing levels of antimicrobial resistance and an increasing awareness of substantial differences between populations in genetic associations, the need for such work is expanding. In this Review, we illustrate how our understanding of the host–pathogen relationship is advancing through holistic approaches, describing current strategies to investigate the role of host genetic variation in established and emerging infections, including COVID-19, the need for wider application to diverse global populations mirroring the burden of disease, the impact of pathogen and vector genetic diversity and a broad array of immune and inflammation phenotypes that can be mapped as traits in health and disease. Insights from study of inborn errors of immunity and multi-omics profiling together with developments in analytical methods are further advancing our knowledge of this important area. Infectious diseases are an ever-present global threat. In this Review, Kwok, Mentzer and Knight discuss our latest understanding of how human genetics influence susceptibility to disease. Furthermore, they discuss emerging progress in the interplay between host and pathogen genetics, molecular responses to infection and vaccination, and opportunities to bring these aspects together for rapid responses to emerging diseases such as COVID-19.
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44
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Penman BS, Gandon S. Adaptive immunity selects against malaria infection blocking mutations. PLoS Comput Biol 2020; 16:e1008181. [PMID: 33031369 PMCID: PMC7544067 DOI: 10.1371/journal.pcbi.1008181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 07/22/2020] [Indexed: 11/18/2022] Open
Abstract
The mutation responsible for Duffy negativity, which impedes Plasmodium vivax infection, has reached high frequencies in certain human populations. Conversely, mutations capable of blocking the more lethal P. falciparum have not succeeded in malarious zones. Here we present an evolutionary-epidemiological model of malaria which demonstrates that if adaptive immunity against the most virulent effects of malaria is gained rapidly by the host, mutations which prevent infection per se are unlikely to succeed. Our results (i) explain the rarity of strain-transcending P. falciparum infection blocking adaptations in humans; (ii) make the surprising prediction that mutations which block P. falciparum infection are most likely to be found in populations experiencing low or infrequent malaria transmission, and (iii) predict that immunity against some of the virulent effects of P. vivax malaria may be built up over the course of many infections.
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Affiliation(s)
- Bridget S. Penman
- Zeeman Institute and School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Sylvain Gandon
- CEFE, CNRS, University of Montpellier, Paul Valéry University of Montpellier, EPHE, IRD, Montpellier, France
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45
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Algady W, Weyell E, Mateja D, Garcia A, Courtin D, Hollox EJ. Genotyping complex structural variation at the malaria-associated human glycophorin locus using a PCR-based strategy. Ann Hum Genet 2020; 85:7-17. [PMID: 32895931 DOI: 10.1111/ahg.12405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/23/2020] [Accepted: 08/15/2020] [Indexed: 02/06/2023]
Abstract
Structural variation in the human genome can affect risk of disease. An example is a complex structural variant of the human glycophorin gene cluster, called DUP4, which is associated with a clinically significant level of protection against severe malaria. The human glycophorin gene cluster harbours at least 23 distinct structural variants, and accurate genotyping of this complex structural variation remains a challenge. Here, we use a polymerase chain reaction-based strategy to genotype structural variation at the human glycophorin gene cluster, including the alleles responsible for the U- blood group. We validate our approach, based on a triplex paralogue ratio test, on publically available samples from the 1000 Genomes project. We then genotype 574 individuals from a longitudinal birth cohort (Tori-Bossito cohort) using small amounts of DNA at low cost. Our approach readily identifies known deletions and duplications, and can potentially identify novel variants for further analysis. It will allow exploration of genetic variation at the glycophorin locus, and investigation of its relationship with malaria, in large sample sets at minimal cost, using standard molecular biology equipment.
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Affiliation(s)
- Walid Algady
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Eleanor Weyell
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Daria Mateja
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - André Garcia
- UMR 261 MERIT, Institut de Recherche pour le Développement (IRD), Université de Paris, Paris, France
| | - David Courtin
- UMR 261 MERIT, Institut de Recherche pour le Développement (IRD), Université de Paris, Paris, France
| | - Edward J Hollox
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
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46
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Tennessen JA, Bollmann SR, Peremyslova E, Kronmiller BA, Sergi C, Hamali B, Blouin MS. Clusters of polymorphic transmembrane genes control resistance to schistosomes in snail vectors. eLife 2020; 9:59395. [PMID: 32845238 PMCID: PMC7494358 DOI: 10.7554/elife.59395] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 08/25/2020] [Indexed: 12/14/2022] Open
Abstract
Schistosomiasis is a debilitating parasitic disease infecting hundreds of millions of people. Schistosomes use aquatic snails as intermediate hosts. A promising avenue for disease control involves leveraging innate host mechanisms to reduce snail vectorial capacity. In a genome-wide association study of Biomphalaria glabrata snails, we identify genomic region PTC2 which exhibits the largest known correlation with susceptibility to parasite infection (>15 fold effect). Using new genome assemblies with substantially higher contiguity than the Biomphalaria reference genome, we show that PTC2 haplotypes are exceptionally divergent in structure and sequence. This variation includes multi-kilobase indels containing entire genes, and orthologs for which most amino acid residues are polymorphic. RNA-Seq annotation reveals that most of these genes encode single-pass transmembrane proteins, as seen in another resistance region in the same species. Such groups of hyperdiverse snail proteins may mediate host-parasite interaction at the cell surface, offering promising targets for blocking the transmission of schistosomiasis.
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Affiliation(s)
- Jacob A Tennessen
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, United States.,Department of Integrative Biology, Oregon State University, Corvallis, United States
| | - Stephanie R Bollmann
- Department of Integrative Biology, Oregon State University, Corvallis, United States
| | - Ekaterina Peremyslova
- Department of Integrative Biology, Oregon State University, Corvallis, United States
| | - Brent A Kronmiller
- Department of Integrative Biology, Oregon State University, Corvallis, United States.,Center for Genome Research and Biocomputing, Oregon State University, Corvallis, United States
| | - Clint Sergi
- Department of Integrative Biology, Oregon State University, Corvallis, United States
| | - Bulut Hamali
- Department of Integrative Biology, Oregon State University, Corvallis, United States
| | - Michael Scott Blouin
- Department of Integrative Biology, Oregon State University, Corvallis, United States
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47
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Werren EA, Garcia O, Bigham AW. Identifying adaptive alleles in the human genome: from selection mapping to functional validation. Hum Genet 2020; 140:241-276. [PMID: 32728809 DOI: 10.1007/s00439-020-02206-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 07/07/2020] [Indexed: 12/19/2022]
Abstract
The suite of phenotypic diversity across geographically distributed human populations is the outcome of genetic drift, gene flow, and natural selection throughout human evolution. Human genetic variation underlying local biological adaptations to selective pressures is incompletely characterized. With the emergence of population genetics modeling of large-scale genomic data derived from diverse populations, scientists are able to map signatures of natural selection in the genome in a process known as selection mapping. Inferred selection signals further can be used to identify candidate functional alleles that underlie putative adaptive phenotypes. Phenotypic association, fine mapping, and functional experiments facilitate the identification of candidate adaptive alleles. Functional investigation of candidate adaptive variation using novel techniques in molecular biology is slowly beginning to unravel how selection signals translate to changes in biology that underlie the phenotypic spectrum of our species. In addition to informing evolutionary hypotheses of adaptation, the discovery and functional annotation of adaptive alleles also may be of clinical significance. While selection mapping efforts in non-European populations are growing, there remains a stark under-representation of diverse human populations in current public genomic databases, of both clinical and non-clinical cohorts. This lack of inclusion limits the study of human biological variation. Identifying and functionally validating candidate adaptive alleles in more global populations is necessary for understanding basic human biology and human disease.
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Affiliation(s)
- Elizabeth A Werren
- Department of Human Genetics, The University of Michigan, Ann Arbor, MI, USA
- Department of Anthropology, The University of Michigan, Ann Arbor, MI, USA
| | - Obed Garcia
- Department of Anthropology, The University of Michigan, Ann Arbor, MI, USA
| | - Abigail W Bigham
- Department of Anthropology, University of California Los Angeles, 341 Haines Hall, Los Angeles, CA, 90095, USA.
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48
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Molecular study of binding of Plasmodium ribosomal protein P2 to erythrocytes. Biochimie 2020; 176:181-191. [PMID: 32717409 DOI: 10.1016/j.biochi.2020.07.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 06/13/2020] [Accepted: 07/09/2020] [Indexed: 11/23/2022]
Abstract
The ribosomal protein P2 of Plasmodium falciparum, (PfP2), performs certain unique extra-ribosomal functions. During the few hours of cell-division, PfP2 protein moves to the external surface of the infected erythrocytes (IE) as an SDS-resistant oligomer, and at that stage treatment with specific anti- PfP2 antibodies results in an arrest of the parasite cell-division. Amongst the oligomeric forms of PfP2, mainly the homo-tetramer is peripherally anchored on the external surface of the IE. To study the anchoring of PfP2 tetramer on IE-surface, we have explored the binding properties of PfP2 protein. Using NMR and erythrocyte pull-down studies, here we report that the homo-tetrameric PfP2 protein interacted specifically with erythrocytes and not leukocytes. The hydrophobic N-terminal 72 amino acid region is the major interacting domain. The binding of P2 to RBCs was neuraminidase resistant, but trypsin sensitive. The RBC binding was exclusive to the Plasmodium PfP2 protein as even the homologous protein of the closely related Apicomplexan parasite Toxoplasma gondii TgP2 protein did not interact with erythrocytes. Pull down assays, immunoprecipitation and mass spectrometry data showed that erythrocytic Band 3 protein is a possible interactor of Plasmodium PfP2 protein on the erythrocyte surface.
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49
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Gassner C, Denomme GA, Portmann C, Bensing KM, Mattle-Greminger MP, Meyer S, Trost N, Song YL, Engström C, Jungbauer C, Just B, Storry JR, Forster M, Franke A, Frey BM. Two Prevalent ∼100-kb GYPB Deletions Causative of the GPB-Deficient Blood Group MNS Phenotype S-s-U- in Black Africans. Transfus Med Hemother 2020; 47:326-336. [PMID: 32884505 PMCID: PMC7443675 DOI: 10.1159/000504946] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 11/20/2019] [Indexed: 01/11/2023] Open
Abstract
The U antigen (MNS5) is one of 49 antigens belonging to the MNS blood group system (ISBT002) carried on glycophorins A (GPA) and B (GPB). U is present on the red blood cells in almost all Europeans and Asians but absent in approximately 1.0% of Black Africans. U negativity coincides with negativity for S (MNS3) and s (MNS4) on GPB, thus be called S-s-U-, and is thought to arise from homozygous deletion of GYPB. Little is known about the molecular background of these deletions. Bioinformatic analysis of the 1000 Genomes Project data revealed several candidate regions with apparent deletions in GYPB. Highly specific Gap-PCRs, only resulting in positive amplification from DNAs with deletions present, allowed for the exact genetic localization of 3 different breakpoints; 110.24- and 103.26-kb deletions were proven to be the most frequent in Black Americans and Africans. Among 157 CEPH DNAs, deletions in 6 out of 8 African ethnicities were present. Allele frequencies of the deletions within African ethnicities varied greatly and reached a cumulative 23.3% among the Mbuti Pygmy people from the Congo. Similar observations were made for U+var alleles, known to cause strongly reduced GPB expression. The 110- and 103-kb deletional GYPB haplotypes were found to represent the most prevalent hereditary factors causative of the MNS blood group phenotype S-s-U-. Respective GYPB deletions are now accessible by molecular detection of homo- and hemizygous transmission.
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Affiliation(s)
- Christoph Gassner
- Independent at www.c-gassner.bio, Zurich, Switzerland
- Molecular Diagnostics and Research and Development, Blood Transfusion Service Zurich, Swiss Red Cross (SRC), Schlieren, Switzerland
| | | | - Claudia Portmann
- Molecular Diagnostics and Research and Development, Blood Transfusion Service Zurich, Swiss Red Cross (SRC), Schlieren, Switzerland
| | | | - Maja P. Mattle-Greminger
- Molecular Diagnostics and Research and Development, Blood Transfusion Service Zurich, Swiss Red Cross (SRC), Schlieren, Switzerland
| | - Stefan Meyer
- Molecular Diagnostics and Research and Development, Blood Transfusion Service Zurich, Swiss Red Cross (SRC), Schlieren, Switzerland
| | - Nadine Trost
- Molecular Diagnostics and Research and Development, Blood Transfusion Service Zurich, Swiss Red Cross (SRC), Schlieren, Switzerland
| | - Young-Lan Song
- Molecular Diagnostics and Research and Development, Blood Transfusion Service Zurich, Swiss Red Cross (SRC), Schlieren, Switzerland
| | - Charlotte Engström
- Molecular Diagnostics and Research and Development, Blood Transfusion Service Zurich, Swiss Red Cross (SRC), Schlieren, Switzerland
| | - Christof Jungbauer
- Blood Service for Vienna, Lower Austria, and Burgenland, Austrian Red Cross, Vienna, Austria
| | - Burkhard Just
- German Red Cross Blood Donation Service West, Hagen, Germany
| | - Jill R. Storry
- Division of Laboratory Medicine, Department of Hematology and Transfusion Medicine, Lund University, Lund, Sweden
| | - Michael Forster
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - Beat M. Frey
- Head Office, Blood Transfusion Service Zürich, Swiss Red Cross (SRC), Schlieren, Switzerland
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50
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Louzada S, Algady W, Weyell E, Zuccherato LW, Brajer P, Almalki F, Scliar MO, Naslavsky MS, Yamamoto GL, Duarte YAO, Passos-Bueno MR, Zatz M, Yang F, Hollox EJ. Structural variation of the malaria-associated human glycophorin A-B-E region. BMC Genomics 2020; 21:446. [PMID: 32600246 PMCID: PMC7325229 DOI: 10.1186/s12864-020-06849-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 06/18/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Approximately 5% of the human genome shows common structural variation, which is enriched for genes involved in the immune response and cell-cell interactions. A well-established region of extensive structural variation is the glycophorin gene cluster, comprising three tandemly-repeated regions about 120 kb in length and carrying the highly homologous genes GYPA, GYPB and GYPE. Glycophorin A (encoded by GYPA) and glycophorin B (encoded by GYPB) are glycoproteins present at high levels on the surface of erythrocytes, and they have been suggested to act as decoy receptors for viral pathogens. They are receptors for the invasion of the protist parasite Plasmodium falciparum, a causative agent of malaria. A particular complex structural variant, called DUP4, creates a GYPB-GYPA fusion gene known to confer resistance to malaria. Many other structural variants exist across the glycophorin gene cluster, and they remain poorly characterised. RESULTS Here, we analyse sequences from 3234 diploid genomes from across the world for structural variation at the glycophorin locus, confirming 15 variants in the 1000 Genomes project cohort, discovering 9 new variants, and characterising a selection of these variants using fibre-FISH and breakpoint mapping at the sequence level. We identify variants predicted to create novel fusion genes and a common inversion duplication variant at appreciable frequencies in West Africans. We show that almost all variants can be explained by non-allelic homologous recombination and by comparing the structural variant breakpoints with recombination hotspot maps, confirm the importance of a particular meiotic recombination hotspot on structural variant formation in this region. CONCLUSIONS We identify and validate large structural variants in the human glycophorin A-B-E gene cluster which may be associated with different clinical aspects of malaria.
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Affiliation(s)
- Sandra Louzada
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
- Present address: Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal
- Present address: BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Lisbon, Portugal
| | - Walid Algady
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Eleanor Weyell
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Luciana W Zuccherato
- Department of Pathology, Faculty of Medicine, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Paulina Brajer
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Faisal Almalki
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Marilia O Scliar
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Michel S Naslavsky
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Guilherme L Yamamoto
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Yeda A O Duarte
- School of Nursing, Universidade de São Paulo, São Paulo, Brazil
| | - Maria Rita Passos-Bueno
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Mayana Zatz
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | | | - Edward J Hollox
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK.
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