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Zhang C, Verma A, Feng Y, Melo MCR, McQuillan M, Hansen M, Lucas A, Park J, Ranciaro A, Thompson S, Rubel MA, Campbell MC, Beggs W, Hirbo J, Mpoloka SW, Mokone GG, Nyambo T, Meskel DW, Belay G, Fokunang C, Njamnshi AK, Omar SA, Williams SM, Rader D, Ritchie MD, de la Fuente Nunez C, Sirugo G, Tishkoff S. Impact of natural selection on global patterns of genetic variation, and association with clinical phenotypes, at genes involved in SARS-CoV-2 infection. medRxiv 2021:2021.06.28.21259529. [PMID: 34230933 PMCID: PMC8259910 DOI: 10.1101/2021.06.28.21259529] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
We investigated global patterns of genetic variation and signatures of natural selection at host genes relevant to SARS-CoV-2 infection (ACE2, TMPRSS2, DPP4, and LY6E). We analyzed novel data from 2,012 ethnically diverse Africans and 15,997 individuals of European and African ancestry with electronic health records, and integrated with global data from the 1000GP. At ACE2, we identified 41 non-synonymous variants that were rare in most populations, several of which impact protein function. However, three non-synonymous variants were common among Central African hunter-gatherers from Cameroon and are on haplotypes that exhibit signatures of positive selection. We identify strong signatures of selection impacting variation at regulatory regions influencing ACE2 expression in multiple African populations. At TMPRSS2, we identified 13 amino acid changes that are adaptive and specific to the human lineage. Genetic variants that are targets of natural selection are associated with clinical phenotypes common in patients with COVID-19.
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Affiliation(s)
- Chao Zhang
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anurag Verma
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yuanqing Feng
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Marcelo C. R. Melo
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, Penn Institute for Computational Science, and Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael McQuillan
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew Hansen
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anastasia Lucas
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Joseph Park
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alessia Ranciaro
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Simon Thompson
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Meghan A. Rubel
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - William Beggs
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | | | | | | | - Thomas Nyambo
- Department of Biochemistry, Kampala International University in Tanzania, Dar es Salaam, Tanzania
| | - Dawit Wolde Meskel
- Addis Ababa University Department of Microbial Cellular and Molecular Biology, Addis Ababa, Ethiopia
| | - Gurja Belay
- Addis Ababa University Department of Microbial Cellular and Molecular Biology, Addis Ababa, Ethiopia
| | - Charles Fokunang
- Department of Pharmacotoxicology and Pharmacokinetics, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, Yaoundé, Cameroon
| | - Alfred K. Njamnshi
- Department of Neurology, Central Hospital Yaoundé; Brain Research Africa Initiative (BRAIN), Neuroscience Lab, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, Yaoundé, Cameroon
| | - Sabah A. Omar
- Center for Biotechnology Research and Development, Kenya Medical Research Institute, Nairobi, Kenya
| | | | - Daniel Rader
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Marylyn D. Ritchie
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Cesar de la Fuente Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, Penn Institute for Computational Science, and Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Giorgio Sirugo
- Division of Translational Medicine and Human Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104
| | - Sarah Tishkoff
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
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Araujo Sousa B, Nascimento Silva O, Farias Porto W, Lima Rocha T, Paulino Silva L, Ferreira Leal AP, Buccini DF, Oluwagbamigbe Fajemiroye J, de Araujo Caldas R, Franco OL, Grossi-de-Sá MF, de la Fuente Nunez C, Moreno SE. Identification of the Active Principle Conferring Anti-Inflammatory and Antinociceptive Properties in Bamboo Plant. Molecules 2021; 26:3054. [PMID: 34065427 PMCID: PMC8160853 DOI: 10.3390/molecules26103054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/29/2021] [Accepted: 03/31/2021] [Indexed: 11/16/2022] Open
Abstract
Early plants began colonizing earth about 450 million years ago. During the process of coevolution, their metabolic cellular pathways produced a myriad of natural chemicals, many of which remain uncharacterized biologically. Popular preparations containing some of these molecules have been used medicinally for thousands of years. In Brazilian folk medicine, plant extracts from the bamboo plant Guadua paniculata Munro have been used for the treatment of infections and pain. However, the chemical basis of these therapeutic effects has not yet been identified. Here, we performed protein biochemistry and downstream pharmacological assays to determine the mechanisms underlying the anti-inflammatory and antinociceptive effects of an aqueous extract of the G. paniculata rhizome, which we termed AqGP. The anti-inflammatory and antinociceptive effects of AqGP were assessed in mice. We identified and purified a protein (AgGP), with an amino acid sequence similar to that of thaumatins (~20 kDa), capable of repressing inflammation through downregulation of neutrophil recruitment and of decreasing hyperalgesia in mice. In conclusion, we have identified the molecule and the molecular mechanism responsible for the anti-inflammatory and antinociceptive properties of a plant commonly used in Brazilian folk medicine.
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Affiliation(s)
- Bruna Araujo Sousa
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília CEP 70790-160, DF, Brazil; (B.A.S.); (W.F.P.); (O.L.F.); (M.F.G.-d.-S.)
| | - Osmar Nascimento Silva
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande CEP 79117-900, MS, Brazil; (O.N.S.); (A.P.F.L.); (D.F.B.); (R.d.A.C.)
- Centro Universitário de Anápolis, Unievangélica, Anápolis CEP 75083-515, GO, Brazil;
| | - William Farias Porto
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília CEP 70790-160, DF, Brazil; (B.A.S.); (W.F.P.); (O.L.F.); (M.F.G.-d.-S.)
- Porto Reports, Brasília CEP 72236-011, DF, Brazil
| | - Thales Lima Rocha
- Embrapa Recursos Genéticos e Biotecnologia (Cenargen), Brasília CEP 70770-917, DF, Brazil; (T.L.R.); (L.P.S.)
| | - Luciano Paulino Silva
- Embrapa Recursos Genéticos e Biotecnologia (Cenargen), Brasília CEP 70770-917, DF, Brazil; (T.L.R.); (L.P.S.)
| | - Ana Paula Ferreira Leal
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande CEP 79117-900, MS, Brazil; (O.N.S.); (A.P.F.L.); (D.F.B.); (R.d.A.C.)
| | - Danieli Fernanda Buccini
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande CEP 79117-900, MS, Brazil; (O.N.S.); (A.P.F.L.); (D.F.B.); (R.d.A.C.)
| | - James Oluwagbamigbe Fajemiroye
- Centro Universitário de Anápolis, Unievangélica, Anápolis CEP 75083-515, GO, Brazil;
- Núcleo de Estudos e Pesquisas Tóxico-Farmacológicas, Universidade Federal de Goiás, Goiânia 74605-220, GO, Brazil
| | - Ruy de Araujo Caldas
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande CEP 79117-900, MS, Brazil; (O.N.S.); (A.P.F.L.); (D.F.B.); (R.d.A.C.)
| | - Octávio Luiz Franco
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília CEP 70790-160, DF, Brazil; (B.A.S.); (W.F.P.); (O.L.F.); (M.F.G.-d.-S.)
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande CEP 79117-900, MS, Brazil; (O.N.S.); (A.P.F.L.); (D.F.B.); (R.d.A.C.)
- Departamento de Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Brasília CEP 70910-900, DF, Brazil
| | - Maria Fátima Grossi-de-Sá
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília CEP 70790-160, DF, Brazil; (B.A.S.); (W.F.P.); (O.L.F.); (M.F.G.-d.-S.)
- Embrapa Recursos Genéticos e Biotecnologia (Cenargen), Brasília CEP 70770-917, DF, Brazil; (T.L.R.); (L.P.S.)
| | - Cesar de la Fuente Nunez
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA;
- Department of Biological Engineering, The Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Electrical Engineering and Computer Science, The Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Susana Elisa Moreno
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande CEP 79117-900, MS, Brazil; (O.N.S.); (A.P.F.L.); (D.F.B.); (R.d.A.C.)
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