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Le Voyer T, Maglorius Renkilaraj MRL, Moriya K, Pérez Lorenzo M, Nguyen T, Gao L, Rubin T, Cederholm A, Ogishi M, Arango-Franco CA, Béziat V, Lévy R, Migaud M, Rapaport F, Itan Y, Deenick EK, Cortese I, Lisco A, Boztug K, Abel L, Boisson-Dupuis S, Boisson B, Frosk P, Ma CS, Landegren N, Celmeli F, Casanova JL, Tangye SG, Puel A. Inherited human RelB deficiency impairs innate and adaptive immunity to infection. Proc Natl Acad Sci U S A 2024; 121:e2321794121. [PMID: 39231201 DOI: 10.1073/pnas.2321794121] [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: 12/19/2023] [Accepted: 06/24/2024] [Indexed: 09/06/2024] Open
Abstract
We report two unrelated adults with homozygous (P1) or compound heterozygous (P2) private loss-of-function variants of V-Rel Reticuloendotheliosis Viral Oncogene Homolog B (RELB). The resulting deficiency of functional RelB impairs the induction of NFKB2 mRNA and NF-κB2 (p100/p52) protein by lymphotoxin in the fibroblasts of the patients. These defects are rescued by transduction with wild-type RELB complementary DNA (cDNA). By contrast, the response of RelB-deficient fibroblasts to Tumor Necrosis Factor (TNF) or IL-1β via the canonical NF-κB pathway remains intact. P1 and P2 have low proportions of naïve CD4+ and CD8+ T cells and of memory B cells. Moreover, their naïve B cells cannot differentiate into immunoglobulin G (IgG)- or immunoglobulin A (IgA)-secreting cells in response to CD40L/IL-21, and the development of IL-17A/F-producing T cells is strongly impaired in vitro. Finally, the patients produce neutralizing autoantibodies against type I interferons (IFNs), even after hematopoietic stem cell transplantation, attesting to a persistent dysfunction of thymic epithelial cells in T cell selection and central tolerance to some autoantigens. Thus, inherited human RelB deficiency disrupts the alternative NF-κB pathway, underlying a T- and B cell immunodeficiency, which, together with neutralizing autoantibodies against type I IFNs, confers a predisposition to viral, bacterial, and fungal infections.
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Affiliation(s)
- Tom Le Voyer
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Paris 75015, France
- Imagine Institute, Paris Cité University, Paris 75015, France
- Clinical Immunology Department, Assistance Publique Hôpitaux de Paris, Saint-Louis Hospital, Paris 75010, France
| | - Majistor Raj Luxman Maglorius Renkilaraj
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Paris 75015, France
- Imagine Institute, Paris Cité University, Paris 75015, France
| | - Kunihiko Moriya
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Paris 75015, France
- Imagine Institute, Paris Cité University, Paris 75015, France
| | - Malena Pérez Lorenzo
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Paris 75015, France
- Imagine Institute, Paris Cité University, Paris 75015, France
| | - Tina Nguyen
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales Sydney, Sydney, NSW 2052, Australia
| | - Liwei Gao
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Paris 75015, France
- Imagine Institute, Paris Cité University, Paris 75015, France
| | - Tamar Rubin
- Division of Pediatric Clinical Immunology and Allergy, Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB R3A 1S1, Canada
| | - Axel Cederholm
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala SE-751 05, Sweden
| | - Masato Ogishi
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065
| | - Carlos A Arango-Franco
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Paris 75015, France
- Imagine Institute, Paris Cité University, Paris 75015, France
- Group of Inborn Errors of Immunity, Department of Microbiology and Parasitology, School of Medicine, University of Antioquia, Medellín 050010, Colombia
| | - Vivien Béziat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Paris 75015, France
- Imagine Institute, Paris Cité University, Paris 75015, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065
| | - Romain Lévy
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Paris 75015, France
- Imagine Institute, Paris Cité University, Paris 75015, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065
| | - Mélanie Migaud
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Paris 75015, France
- Imagine Institute, Paris Cité University, Paris 75015, France
| | - Franck Rapaport
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065
| | - Yuval Itan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Elissa K Deenick
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales Sydney, Sydney, NSW 2052, Australia
| | - Irene Cortese
- Experimental Immunotherapeutics Unit, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD 20892
| | - Andrea Lisco
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892
| | - Kaan Boztug
- St. Anna Children's Cancer Research Institute, Vienna 1090, Austria
- Medical University of Vienna, Department of Pediatrics and Adolescent Medicine, Vienna 1090, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna 1090, Austria
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Paris 75015, France
- Imagine Institute, Paris Cité University, Paris 75015, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065
| | - Stéphanie Boisson-Dupuis
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Paris 75015, France
- Imagine Institute, Paris Cité University, Paris 75015, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065
| | - Bertrand Boisson
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Paris 75015, France
- Imagine Institute, Paris Cité University, Paris 75015, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065
| | - Patrick Frosk
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0W2, Canada
| | - Cindy S Ma
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales Sydney, Sydney, NSW 2052, Australia
| | - Nils Landegren
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala SE-751 05, Sweden
| | - Fatih Celmeli
- Department of Allergy and Immunology, University of Medical Science, Antalya Education and Research Hospital, Antalya 07100, Türkiye
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Paris 75015, France
- Imagine Institute, Paris Cité University, Paris 75015, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065
- Pediatric Hematology-Immunology Unit, Necker Hospital for Sick Children, Paris 75015, France
- HHMI, New York, NY 10065
| | - Stuart G Tangye
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales Sydney, Sydney, NSW 2052, Australia
| | - Anne Puel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Paris 75015, France
- Imagine Institute, Paris Cité University, Paris 75015, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065
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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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Ma X, Lu Y, Xu S. Adaptive Evolution of Two Distinct Adaptive Haplotypes of Neanderthal Origin at the Immunoglobulin Heavy-chain Locus in East Asian and European Populations. Mol Biol Evol 2024; 41:msae147. [PMID: 39011558 DOI: 10.1093/molbev/msae147] [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: 11/21/2023] [Revised: 07/05/2024] [Accepted: 07/11/2024] [Indexed: 07/17/2024] Open
Abstract
Immunoglobulins (Igs) have a crucial role in humoral immunity. Two recent studies have reported a high-frequency Neanderthal-introgressed haplotype throughout Eurasia and a high-frequency Neanderthal-introgressed haplotype specific to southern East Asia at the immunoglobulin heavy-chain (IGH) gene locus on chromosome 14q32.33. Surprisingly, we found the previously reported high-frequency Neanderthal-introgressed haplotype does not exist throughout Eurasia. Instead, our study identified two distinct high-frequency haplotypes of putative Neanderthal origin in East Asia and Europe, although they shared introgressed alleles. Notably, the alleles of putative Neanderthal origin reduced the expression of IGHG1 and increased the expression of IGHG2 and IGHG3 in various tissues. These putatively introgressed alleles also affected the production of IgG1 upon antigen stimulation and increased the risk of systemic lupus erythematosus. Additionally, the greatest genetic differentiation across the whole genome between southern and northern East Asians was observed for the East Asian haplotype of putative Neanderthal origin. The frequency decreased from southern to northern East Asia and correlated positively with the genome-wide proportion of southern East Asian ancestry, indicating that this putative positive selection likely occurred in the common ancestor of southern East Asian populations before the admixture with northern East Asian populations.
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Affiliation(s)
- Xixian Ma
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Yan Lu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Department of Liver Surgery and Transplantation Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai China
| | - Shuhua Xu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Department of Liver Surgery and Transplantation Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
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Brázda V, Šislerová L, Cucchiarini A, Mergny JL. G-quadruplex propensity in H. neanderthalensis, H. sapiens and Denisovans mitochondrial genomes. NAR Genom Bioinform 2024; 6:lqae060. [PMID: 38817800 PMCID: PMC11137754 DOI: 10.1093/nargab/lqae060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 04/18/2024] [Accepted: 05/17/2024] [Indexed: 06/01/2024] Open
Abstract
Current methods of processing archaeological samples combined with advances in sequencing methods lead to disclosure of a large part of H. neanderthalensis and Denisovans genetic information. It is hardly surprising that the genome variability between modern humans, Denisovans and H. neanderthalensis is relatively limited. Genomic studies may provide insight on the metabolism of extinct human species or lineages. Detailed analysis of G-quadruplex sequences in H. neanderthalensis and Denisovans mitochondrial DNA showed us interesting features. Relatively similar patterns in mitochondrial DNA are found compared to modern humans, with one notable exception for H. neanderthalensis. An interesting difference between H. neanderthalensis and H. sapiens corresponds to a motif found in the D-loop region of mtDNA, which is responsible for mitochondrial DNA replication. This area is directly responsible for the number of mitochondria and consequently for the efficient energy metabolism of cell. H. neanderthalensis harbor a long uninterrupted run of guanines in this region, which may cause problems for replication, in contrast with H. sapiens, for which this run is generally shorter and interrupted. One may propose that the predominant H. sapiens motif provided a selective advantage for modern humans regarding mtDNA replication and function.
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Affiliation(s)
- Václav Brázda
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic
- Brno University of Technology, Faculty of Chemistry, Purkyňova 118, 612 00 Brno, Czech Republic
| | - Lucie Šislerová
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic
- Brno University of Technology, Faculty of Chemistry, Purkyňova 118, 612 00 Brno, Czech Republic
| | - Anne Cucchiarini
- Laboratoire d’Optique et Biosciences (LOB), Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91120 Palaiseau, France
| | - Jean-Louis Mergny
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic
- Laboratoire d’Optique et Biosciences (LOB), Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91120 Palaiseau, France
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5
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McMinds R, Jiang RHY, Adapa SR, Cornelius Ruhs E, Munds RA, Leiding JW, Downs CJ, Martin LB. Bacterial sepsis triggers stronger transcriptomic immune responses in larger primates. Proc Biol Sci 2024; 291:20240535. [PMID: 38917861 DOI: 10.1098/rspb.2024.0535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 04/05/2024] [Indexed: 06/27/2024] Open
Abstract
Empirical data relating body mass to immune defence against infections remain limited. Although the metabolic theory of ecology predicts that larger organisms would have weaker immune responses, recent studies have suggested that the opposite may be true. These discoveries have led to the safety factor hypothesis, which proposes that larger organisms have evolved stronger immune defences because they carry greater risks of exposure to pathogens and parasites. In this study, we simulated sepsis by exposing blood from nine primate species to a bacterial lipopolysaccharide (LPS), measured the relative expression of immune and other genes using RNAseq, and fitted phylogenetic models to determine how gene expression was related to body mass. In contrast to non-immune-annotated genes, we discovered hypermetric scaling in the LPS-induced expression of innate immune genes, such that large primates had a disproportionately greater increase in gene expression of immune genes compared to small primates. Hypermetric immune gene expression appears to support the safety factor hypothesis, though this pattern may represent a balanced evolutionary mechanism to compensate for lower per-transcript immunological effectiveness. This study contributes to the growing body of immune allometry research, highlighting its importance in understanding the complex interplay between body size and immunity over evolutionary timescales.
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Affiliation(s)
- Ryan McMinds
- Center for Global Health and Infectious Diseases Research (GHIDR), University of South Florida , Tampa, FL, USA
- USF Genomics Program, University of South Florida College of Public Health , Tampa, FL, USA
| | - Rays H Y Jiang
- Center for Global Health and Infectious Diseases Research (GHIDR), University of South Florida , Tampa, FL, USA
- USF Genomics Program, University of South Florida College of Public Health , Tampa, FL, USA
| | - Swamy R Adapa
- Center for Global Health and Infectious Diseases Research (GHIDR), University of South Florida , Tampa, FL, USA
- USF Genomics Program, University of South Florida College of Public Health , Tampa, FL, USA
| | - Emily Cornelius Ruhs
- Center for Global Health and Infectious Diseases Research (GHIDR), University of South Florida , Tampa, FL, USA
- Department of Ecology and Evolution, University of Chicago , Chicago, IL, USA
- Grainger Bioinformatics Center, Field Museum of Natural History , Chicago, IL, USA
| | - Rachel A Munds
- Center for Global Health and Infectious Diseases Research (GHIDR), University of South Florida , Tampa, FL, USA
| | - Jennifer W Leiding
- Division of Allergy and Immunology, Department of Pediatrics, Johns Hopkins Medicine , St Petersburg, FL, USA
- Institute for Clinical and Translational Research, Johns Hopkins All Children's Hospital , St Petersburg, FL, USA
| | - Cynthia J Downs
- Department of Environmental Biology, SUNY College of Environmental Science and Forestry , Syracuse, NY, USA
| | - Lynn B Martin
- Center for Global Health and Infectious Diseases Research (GHIDR), University of South Florida , Tampa, FL, USA
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6
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He K, Liang C, Ma S, Liu H, Zhu Y. Copy number and selection of MHC genes in ruminants are related to habitat, average life span and diet. Gene 2024; 904:148179. [PMID: 38242373 DOI: 10.1016/j.gene.2024.148179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/26/2023] [Accepted: 01/16/2024] [Indexed: 01/21/2024]
Abstract
The ruminants, as the main group of livestock, have been extensively studied in terms of their physiology, endocrinology, biochemistry, genetics, and nutrition. Despite the wide geographic distribution and habitat diversity of animals in this group, their ecology and evolution remain poorly understood. In this study, we analyzed the gene copy number, selection, and ecological and evolutionary processes that have affected the evolution of major histocompatibility complex (MHC) genes across ruminant lineages based on available genomic data. The 51 species analyzed represented all six families of ruminants. Our finding indicated that the architecture of the MHC region is conserved in ruminants, but with variable copy numbers of MHC-I, MHC-IIA, and MHC-IIB genes. No lineage-specific gene duplication was observed in the MHC genes. The phylogenetic generalized least squares regression (PGLS) model revealed association between ecological and biological factors (habitat and lifespan) and gene duplication in DQA and DQB, but not in DRB. The selection pressure of DQA and DQB were related with lifespan, diet, and the ratio of genetic repeat elements. These results suggest that the MHC evolution in ruminants, including copy number and selection, has been influenced by genetic repeat elements, pathogen exposure risk, and intrinsic cost of possessing multiple MHC genes.
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Affiliation(s)
- Ke He
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Hangzhou, China
| | - Chunhong Liang
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Hangzhou, China
| | - Shujuan Ma
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
| | - Hongyi Liu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Ying Zhu
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China.
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7
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Murga-Moreno J, Casillas S, Barbadilla A, Uricchio L, Enard D. An efficient and robust ABC approach to infer the rate and strength of adaptation. G3 (BETHESDA, MD.) 2024; 14:jkae031. [PMID: 38365205 PMCID: PMC11090462 DOI: 10.1093/g3journal/jkae031] [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: 10/10/2023] [Revised: 10/10/2023] [Accepted: 01/29/2024] [Indexed: 02/18/2024]
Abstract
Inferring the effects of positive selection on genomes remains a critical step in characterizing the ultimate and proximate causes of adaptation across species, and quantifying positive selection remains a challenge due to the confounding effects of many other evolutionary processes. Robust and efficient approaches for adaptation inference could help characterize the rate and strength of adaptation in nonmodel species for which demographic history, mutational processes, and recombination patterns are not currently well-described. Here, we introduce an efficient and user-friendly extension of the McDonald-Kreitman test (ABC-MK) for quantifying long-term protein adaptation in specific lineages of interest. We characterize the performance of our approach with forward simulations and find that it is robust to many demographic perturbations and positive selection configurations, demonstrating its suitability for applications to nonmodel genomes. We apply ABC-MK to the human proteome and a set of known virus interacting proteins (VIPs) to test the long-term adaptation in genes interacting with viruses. We find substantially stronger signatures of positive selection on RNA-VIPs than DNA-VIPs, suggesting that RNA viruses may be an important driver of human adaptation over deep evolutionary time scales.
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Affiliation(s)
- Jesús Murga-Moreno
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85719, USA
| | - Sònia Casillas
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
| | - Antonio Barbadilla
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
| | | | - David Enard
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85719, USA
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8
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Montenegro AFL, Clementino MAF, Yaochite JNU. Type I interferon pathway genetic variants in severe COVID-19. Virus Res 2024; 342:199339. [PMID: 38354910 PMCID: PMC10901847 DOI: 10.1016/j.virusres.2024.199339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/09/2024] [Accepted: 02/11/2024] [Indexed: 02/16/2024]
Abstract
Coronavirus Disease 2019 (COVID-19) is an infectious disease caused by SARS-CoV-2. According to the World Health Organization (WHO), there have been over 760 million reported cases and over 6 million deaths caused by this disease worldwide. The severity of COVID-19 is based on symptoms presented by the patient and is divided as asymptomatic, mild, moderate, severe, and critical. The manifestations are interconnected with genetic variations. The innate immunity is the quickest response mechanism of an organism against viruses. Type I interferon pathway plays a key role in antiviral responses due to viral replication inhibition in infected cells and adaptive immunity stimulation induced by interferon molecules. Thus, variants in type I interferon pathway's genes are being studied in different COVID-19 manifestations. This review summarizes the role of variants in type I interferon pathway's genes on prognosis and severity progression of COVID-19.
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Affiliation(s)
- A F L Montenegro
- Laboratório de Imunologia Celular e Molecular, Departamento de Análises Clínicas e Toxicológicas da Faculdade de Farmácia, Odontologia e Enfermagem, Universidade Federal do Ceará - UFC, Rua Pastor Samuel Munguba, 1210 - Rodolfo Teófilo, Fortaleza, Ceará, Brasil
| | - M A F Clementino
- Laboratório de Toxinologia Molecular, NUBIMED - Núcleo de Biomedicina, Universidade Federal do Ceará - UFC. Fortaleza, Ceará, Brasil
| | - J N U Yaochite
- Laboratório de Imunologia Celular e Molecular, Departamento de Análises Clínicas e Toxicológicas da Faculdade de Farmácia, Odontologia e Enfermagem, Universidade Federal do Ceará - UFC, Rua Pastor Samuel Munguba, 1210 - Rodolfo Teófilo, Fortaleza, Ceará, Brasil.
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9
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Voinescu CD, Mozere M, Genovese G, Downie ML, Gupta S, Gale DP, Bockenhauer D, Kleta R, Arcos-Burgos M, Stanescu HC. A Neanderthal haplotype introgressed into the human genome confers protection against membranous nephropathy. Kidney Int 2024; 105:791-798. [PMID: 38367960 DOI: 10.1016/j.kint.2024.01.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 12/27/2023] [Accepted: 01/08/2024] [Indexed: 02/19/2024]
Abstract
Class 2 HLA and PLA2R1 alleles are exceptionally strong genetic risk factors for membranous nephropathy (MN), leading, through an unknown mechanism, to a targeted autoimmune response. Introgressed archaic haplotypes (introduced from an archaic human genome into the modern human genome) might influence phenotypes through gene dysregulation. Here, we investigated the genomic region surrounding the PLA2R1 gene. We reconstructed the phylogeny of Neanderthal and modern haplotypes in this region and calculated the probability of the observed clustering being the result of introgression or common descent. We imputed variants for the participants in our previous genome-wide association study and we compared the distribution of Neanderthal variants between MN cases and controls. The region associated with the lead MN risk locus in the PLA2R1 gene was confirmed and showed that, within a 507 kb region enriched in introgressed sequence, a stringently defined 105 kb haplotype, intersecting the coding regions for PLA2R1 and ITGB6, is inherited from Neanderthals. Thus, introgressed Neanderthal haplotypes overlapping PLA2R1 are differentially represented in MN cases and controls, with enrichment In controls suggesting a protective effect.
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Affiliation(s)
- Cătălin D Voinescu
- Centre for Genetics and Genomics, Department of Renal Medicine, UCL Division of Medicine, University College London, London, UK
| | - Monika Mozere
- Department of Human and Medical Genetics, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Giulio Genovese
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Mallory L Downie
- Centre for Genetics and Genomics, Department of Renal Medicine, UCL Division of Medicine, University College London, London, UK
| | - Sanjana Gupta
- Centre for Genetics and Genomics, Department of Renal Medicine, UCL Division of Medicine, University College London, London, UK
| | - Daniel P Gale
- Centre for Genetics and Genomics, Department of Renal Medicine, UCL Division of Medicine, University College London, London, UK
| | - Detlef Bockenhauer
- Centre for Genetics and Genomics, Department of Renal Medicine, UCL Division of Medicine, University College London, London, UK
| | - Robert Kleta
- Centre for Genetics and Genomics, Department of Renal Medicine, UCL Division of Medicine, University College London, London, UK
| | - Mauricio Arcos-Burgos
- Grupo de Investigación en Psiquiatría, Departamento de Psiquiatría, Instituto de Investigaciones Médicas, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Horia C Stanescu
- Centre for Genetics and Genomics, Department of Renal Medicine, UCL Division of Medicine, University College London, London, UK.
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10
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Yeyeodu S, Hanafi D, Webb K, Laurie NA, Kimbro KS. Population-enriched innate immune variants may identify candidate gene targets at the intersection of cancer and cardio-metabolic disease. Front Endocrinol (Lausanne) 2024; 14:1286979. [PMID: 38577257 PMCID: PMC10991756 DOI: 10.3389/fendo.2023.1286979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 12/07/2023] [Indexed: 04/06/2024] Open
Abstract
Both cancer and cardio-metabolic disease disparities exist among specific populations in the US. For example, African Americans experience the highest rates of breast and prostate cancer mortality and the highest incidence of obesity. Native and Hispanic Americans experience the highest rates of liver cancer mortality. At the same time, Pacific Islanders have the highest death rate attributed to type 2 diabetes (T2D), and Asian Americans experience the highest incidence of non-alcoholic fatty liver disease (NAFLD) and cancers induced by infectious agents. Notably, the pathologic progression of both cancer and cardio-metabolic diseases involves innate immunity and mechanisms of inflammation. Innate immunity in individuals is established through genetic inheritance and external stimuli to respond to environmental threats and stresses such as pathogen exposure. Further, individual genomes contain characteristic genetic markers associated with one or more geographic ancestries (ethnic groups), including protective innate immune genetic programming optimized for survival in their corresponding ancestral environment(s). This perspective explores evidence related to our working hypothesis that genetic variations in innate immune genes, particularly those that are commonly found but unevenly distributed between populations, are associated with disparities between populations in both cancer and cardio-metabolic diseases. Identifying conventional and unconventional innate immune genes that fit this profile may provide critical insights into the underlying mechanisms that connect these two families of complex diseases and offer novel targets for precision-based treatment of cancer and/or cardio-metabolic disease.
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Affiliation(s)
- Susan Yeyeodu
- Julius L Chambers Biomedical/Biotechnology Institute (JLC-BBRI), North Carolina Central University, Durham, NC, United States
- Charles River Discovery Services, Morrisville, NC, United States
| | - Donia Hanafi
- Julius L Chambers Biomedical/Biotechnology Institute (JLC-BBRI), North Carolina Central University, Durham, NC, United States
| | - Kenisha Webb
- Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA, United States
| | - Nikia A. Laurie
- Julius L Chambers Biomedical/Biotechnology Institute (JLC-BBRI), North Carolina Central University, Durham, NC, United States
| | - K. Sean Kimbro
- Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA, United States
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11
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Wang X, Guo L, Zhang W. Extraction of Innate Immune Genes in Dairy Cattle and the Regulation of Their Expression in Early Embryos. Genes (Basel) 2024; 15:372. [PMID: 38540431 PMCID: PMC10970270 DOI: 10.3390/genes15030372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/02/2024] [Accepted: 03/15/2024] [Indexed: 06/14/2024] Open
Abstract
As more and more of the available genomic data have been published, several databases have been developed for deciphering early mammalian embryogenesis; however, less research has been conducted on the regulation of the expression of natural immunity genes during early embryonic development in dairy cows. To this end, we explored the regulatory mechanism of innate immunity genes at the whole-genome level. Based on comparative genomics, 1473 innate immunity genes in cattle were obtained by collecting the latest reports on human innate immunity genes and updated bovine genome data for comparison, and a preliminary database of bovine innate immunity genes was constructed. In order to determine the regulatory mechanism of innate immune genes in dairy cattle early embryos, we conducted weighted co-expression network analysis of the innate immune genes at different developmental stages of dairy cattle early embryos. The results showed that specific module-related genes were significantly enriched in the MAPK signaling pathway. Protein-protein interaction (PPI) analysis showed gene interactions in each specific module, and 10 of the highest connectivity genes were chosen as potential hub genes. Finally, combined with the results for differential expressed genes (DEGs), ATF3, IL6, CD8A, CD69, CD86, HCK, ERBB3, LCK, ITGB2, LYN, and ERBB2 were identified as the key genes of innate immunity in dairy cattle early embryos. In conclusion, the bovine innate immunity gene set was determined and the co-expression network of innate immunity genes in the early embryonic stage of dairy cattle was constructed by comparing and analyzing the whole genome of bovines and humans. The findings in this study provide the basis for exploring the involvement and regulation of innate immune genes in the early embryonic development of dairy cattle.
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Affiliation(s)
- Xue Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China;
| | - Lili Guo
- College of Life Science, Inner Mongolia Agricultural University, Hohhot 010018, China;
| | - Wenguang Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China;
- College of Life Science, Inner Mongolia Agricultural University, Hohhot 010018, China;
- Inner Mongolia Engineering Research Center of Genomic Big Data for Agriculture, Hohhot 010018, China
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12
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Kumar AAW, Huangfu G, Figtree GA, Dwivedi G. Atherosclerosis as the Damocles' sword of human evolution: insights from nonhuman ape-like primates, ancient human remains, and isolated modern human populations. Am J Physiol Heart Circ Physiol 2024; 326:H821-H831. [PMID: 38305751 DOI: 10.1152/ajpheart.00744.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/25/2024] [Accepted: 01/30/2024] [Indexed: 02/03/2024]
Abstract
Atherosclerosis is the leading cause of death worldwide, and the predominant risk factors are advanced age and high-circulating low-density lipoprotein cholesterol (LDL-C). However, the findings of atherosclerosis in relatively young mummified remains and a lack of atherosclerosis in chimpanzees despite high LDL-C call into question the role of traditional cardiovascular risk factors. The inflammatory theory of atherosclerosis may explain the discrepancies between traditional risk factors and observed phenomena in current literature. Following the divergence from chimpanzees several millennia ago, loss of function mutations in immune regulatory genes and changes in gene expression have resulted in an overactive human immune system. The ubiquity of atherosclerosis in the modern era may reflect a selective pressure that enhanced the innate immune response at the cost of atherogenesis and other chronic disease states. Evidence provided from the fields of genetics, evolutionary biology, and paleoanthropology demonstrates a sort of circular dependency between inflammation, immune system functioning, and evolution at both a species and cellular level. More recently, the role of proinflammatory stimuli, somatic mutations, and the gene-environment effect appear to be underappreciated elements in the development and progression of atherosclerosis. Neurobiological stress, metabolic syndrome, and traditional cardiovascular risk factors may instead function as intermediary links between inflammation and atherosclerosis. Therefore, considering evolution as a mechanistic process and atherosclerosis as part of the inertia of evolution, greater insight into future preventative and therapeutic interventions for atherosclerosis can be gained by examining the past.
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Affiliation(s)
- Annora Ai-Wei Kumar
- Medical School, The University of Western Australia, Crawley, Western Australia, Australia
| | - Gavin Huangfu
- Medical School, The University of Western Australia, Crawley, Western Australia, Australia
- Department of Cardiology, Fiona Stanley Hospital, Murdoch, Western Australia, Australia
- Harry Perkins Institute of Medical Research, Murdoch, Western Australia, Australia
| | - Gemma A Figtree
- Cardiovascular Discovery Group, Kolling Institute of Medical Research, St. Leonards, New South Wales, Australia
- Department of Cardiology, Royal North Shore Hospital, St. Leonards, New South Wales, Australia
| | - Girish Dwivedi
- Medical School, The University of Western Australia, Crawley, Western Australia, Australia
- Department of Cardiology, Fiona Stanley Hospital, Murdoch, Western Australia, Australia
- Harry Perkins Institute of Medical Research, Murdoch, Western Australia, Australia
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13
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Zeberg H, Jakobsson M, Pääbo S. The genetic changes that shaped Neandertals, Denisovans, and modern humans. Cell 2024; 187:1047-1058. [PMID: 38367615 DOI: 10.1016/j.cell.2023.12.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/20/2023] [Accepted: 12/20/2023] [Indexed: 02/19/2024]
Abstract
Modern human ancestors diverged from the ancestors of Neandertals and Denisovans about 600,000 years ago. Until about 40,000 years ago, these three groups existed in parallel, occasionally met, and exchanged genes. A critical question is why modern humans, and not the other two groups, survived, became numerous, and developed complex cultures. Here, we discuss genetic differences among the groups and some of their functional consequences. As more present-day genome sequences become available from diverse groups, we predict that very few, if any, differences will distinguish all modern humans from all Neandertals and Denisovans. We propose that the genetic basis of what constitutes a modern human is best thought of as a combination of genetic features, where perhaps none of them is present in each and every present-day individual.
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Affiliation(s)
- Hugo Zeberg
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Department of Physiology and Pharmacology, Karolinska Institutet, 17165 Stockholm, Sweden.
| | - Mattias Jakobsson
- Department of Organismal Biology, Uppsala University, 75236 Uppsala, Sweden
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Okinawa Institute of Science and Technology, Onnason 904-0495, Okinawa, Japan.
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14
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Romdhane L, Kefi S, Mezzi N, Abassi N, Jmel H, Romdhane S, Shan J, Chouchane L, Abdelhak S. Ethnic and functional differentiation of copy number polymorphisms in Tunisian and HapMap population unveils insights on genome organizational plasticity. Sci Rep 2024; 14:4654. [PMID: 38409353 PMCID: PMC10897484 DOI: 10.1038/s41598-024-54749-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 02/15/2024] [Indexed: 02/28/2024] Open
Abstract
Admixture mapping has been useful in identifying genetic variations linked to phenotypes, adaptation and diseases. Copy number variations (CNVs) represents genomic structural variants spanning large regions of chromosomes reaching several megabases. In this investigation, the "Canary" algorithm was applied to 102 Tunisian samples and 991 individuals from eleven HapMap III populations to genotype 1279 copy number polymorphisms (CNPs). In this present work, we investigate the Tunisian population structure using the CNP makers previously identified among Tunisian. The study revealed that Sub-Saharan African populations exhibited the highest diversity with the highest proportions of allelic CNPs. Among all the African populations, Tunisia showed the least diversity. Individual ancestry proportions computed using STRUCTURE analysis revealed a major European component among Tunisians with lesser contribution from Sub-Saharan Africa and Asia. Population structure analysis indicated the genetic proximity with Europeans and noticeable distance from the Sub-Saharan African and East Asian clusters. Seven genes harbouring Tunisian high-frequent CNPs were identified known to be associated with 9 Mendelian diseases and/or phenotypes. Functional annotation of genes under selection highlighted a noteworthy enrichment of biological processes to receptor pathway and activity as well as glutathione metabolism. Additionally, pathways of potential concern for health such as drug metabolism, infectious diseases and cancers exhibited significant enrichment. The distinctive genetic makeup of the Tunisians might have been influenced by various factors including natural selection and genetic drift, resulting in the development of distinct genetic variations playing roles in specific biological processes. Our research provides a justification for focusing on the exclusive genome organization of this population and uncovers previously overlooked elements of the genome.
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Affiliation(s)
- Lilia Romdhane
- Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia.
- Department of Biology, Faculty of Sciences of Bizerte, University of Carthage, Zarzouna, Tunisia.
| | - Sameh Kefi
- Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Nessrine Mezzi
- Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Najla Abassi
- Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Haifa Jmel
- Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Safa Romdhane
- Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Jingxuan Shan
- Laboratory of Genetic Medicine and Immunology, Weill Cornell Medicine-Qatar, Education City-Qatar Foundation, Doha, Qatar
- Department of Genetic Medicine, Weill Cornell Medicine, New York, NY, USA
- Genetic Intelligence Laboratory, Weill Cornell Medicine in Qatar, Education City, Qatar Foundation, Doha, Qatar
| | - Lotfi Chouchane
- Laboratory of Genetic Medicine and Immunology, Weill Cornell Medicine-Qatar, Education City-Qatar Foundation, Doha, Qatar
- Department of Genetic Medicine, Weill Cornell Medicine, New York, NY, USA
- Genetic Intelligence Laboratory, Weill Cornell Medicine in Qatar, Education City, Qatar Foundation, Doha, Qatar
| | - Sonia Abdelhak
- Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
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15
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Peyrégne S, Slon V, Kelso J. More than a decade of genetic research on the Denisovans. Nat Rev Genet 2024; 25:83-103. [PMID: 37723347 DOI: 10.1038/s41576-023-00643-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/19/2023] [Indexed: 09/20/2023]
Abstract
Denisovans, a group of now extinct humans who lived in Eastern Eurasia in the Middle and Late Pleistocene, were first identified from DNA sequences just over a decade ago. Only ten fragmentary remains from two sites have been attributed to Denisovans based entirely on molecular information. Nevertheless, there has been great interest in using genetic data to understand Denisovans and their place in human history. From the reconstruction of a single high-quality genome, it has been possible to infer their population history, including events of admixture with other human groups. Additionally, the identification of Denisovan DNA in the genomes of present-day individuals has provided insights into the timing and routes of dispersal of ancient modern humans into Asia and Oceania, as well as the contributions of archaic DNA to the physiology of present-day people. In this Review, we synthesize more than a decade of research on Denisovans, reconcile controversies and summarize insights into their population history and phenotype. We also highlight how our growing knowledge about Denisovans has provided insights into our own evolutionary history.
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Affiliation(s)
- Stéphane Peyrégne
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Viviane Slon
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Anatomy and Anthropology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- The Dan David Center for Human Evolution and Biohistory Research, Tel Aviv University, Tel Aviv, Israel
| | - Janet Kelso
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany.
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16
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Urnikyte A, Masiulyte A, Pranckeniene L, Kučinskas V. Disentangling archaic introgression and genomic signatures of selection at human immunity genes. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 116:105528. [PMID: 37977419 DOI: 10.1016/j.meegid.2023.105528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 11/04/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023]
Abstract
Pathogens and infectious diseases have imposed exceptionally strong selective pressure on ancient and modern human genomes and contributed to the current variation in many genes. There is evidence that modern humans acquired immune variants through interbreeding with ancient hominins, but the impact of such variants on human traits is not fully understood. The main objectives of this research were to infer the genetic signatures of positive selection that may be involved in adaptation to infectious diseases and to investigate the function of Neanderthal alleles identified within a set of 50 Lithuanian genomes. Introgressed regions were identified using the machine learning tool ArchIE. Recent positive selection signatures were analysed using iHS. We detected high-scoring signals of positive selection at innate immunity genes (EMB, PARP8, HLAC, and CDSN) and evaluated their interactions with the structural proteins of pathogens. Interactions with human immunodeficiency virus (HIV) 1 and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were identified. Overall, genomic regions introgressed from Neanderthals were shown to be enriched in genes related to immunity, keratinocyte differentiation, and sensory perception.
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Affiliation(s)
- Alina Urnikyte
- Faculty of Medicine, Department of Human and Medical Genetics, Institute of Biomedical Sciences, Vilnius University, Santariskiu Street 2, Vilnius LT-08661, Lithuania.
| | - Abigaile Masiulyte
- Faculty of Medicine, Department of Human and Medical Genetics, Institute of Biomedical Sciences, Vilnius University, Santariskiu Street 2, Vilnius LT-08661, Lithuania
| | - Laura Pranckeniene
- Faculty of Medicine, Department of Human and Medical Genetics, Institute of Biomedical Sciences, Vilnius University, Santariskiu Street 2, Vilnius LT-08661, Lithuania.
| | - Vaidutis Kučinskas
- Faculty of Medicine, Department of Human and Medical Genetics, Institute of Biomedical Sciences, Vilnius University, Santariskiu Street 2, Vilnius LT-08661, Lithuania.
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17
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Houldcroft CJ, Underdown S. Infectious disease in the Pleistocene: Old friends or old foes? AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 182:513-531. [PMID: 38006200 DOI: 10.1002/ajpa.24737] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 03/01/2023] [Accepted: 03/14/2023] [Indexed: 11/26/2023]
Abstract
The impact of endemic and epidemic disease on humans has traditionally been seen as a comparatively recent historical phenomenon associated with the Neolithisation of human groups, an increase in population size led by sedentarism, and increasing contact with domesticated animals as well as species occupying opportunistic symbiotic and ectosymbiotic relationships with humans. The orthodox approach is that Neolithisation created the conditions for increasing population size able to support a reservoir of infectious disease sufficient to act as selective pressure. This orthodoxy is the result of an overly simplistic reliance on skeletal data assuming that no skeletal lesions equated to a healthy individual, underpinned by the assumption that hunter-gatherer groups were inherently healthy while agricultural groups acted as infectious disease reservoirs. The work of van Blerkom, Am. J. Phys. Anthropol., vol. suppl 37 (2003), Wolfe et al., Nature, vol. 447 (2007) and Houldcroft and Underdown, Am. J. Phys. Anthropol., vol. 160, (2016) has changed this landscape by arguing that humans and pathogens have long been fellow travelers. The package of infectious diseases experienced by our ancient ancestors may not be as dissimilar to modern infectious diseases as was once believed. The importance of DNA, from ancient and modern sources, to the study of the antiquity of infectious disease, and its role as a selective pressure cannot be overstated. Here we consider evidence of ancient epidemic and endemic infectious diseases with inferences from modern and ancient human and hominin DNA, and from circulating and extinct pathogen genomes. We argue that the pandemics of the past are a vital tool to unlock the weapons needed to fight pandemics of the future.
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Affiliation(s)
| | - Simon Underdown
- Human Origins and Palaeoenvironmental Research Group, School of Social Sciences, Oxford Brookes University, Oxford, UK
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
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18
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Salazar-Tortosa DF, Huang YF, Enard D. Assessing the Presence of Recent Adaptation in the Human Genome With Mixture Density Regression. Genome Biol Evol 2023; 15:evad170. [PMID: 37713622 PMCID: PMC10563788 DOI: 10.1093/gbe/evad170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 08/30/2023] [Accepted: 09/04/2023] [Indexed: 09/17/2023] Open
Abstract
How much genome differences between species reflect neutral or adaptive evolution is a central question in evolutionary genomics. In humans and other mammals, the presence of adaptive versus neutral genomic evolution has proven particularly difficult to quantify. The difficulty notably stems from the highly heterogeneous organization of mammalian genomes at multiple levels (functional sequence density, recombination, etc.) which complicates the interpretation and distinction of adaptive versus neutral evolution signals. In this study, we introduce mixture density regressions (MDRs) for the study of the determinants of recent adaptation in the human genome. MDRs provide a flexible regression model based on multiple Gaussian distributions. We use MDRs to model the association between recent selection signals and multiple genomic factors likely to affect the occurrence/detection of positive selection, if the latter was present in the first place to generate these associations. We find that an MDR model with two Gaussian distributions provides an excellent fit to the genome-wide distribution of a common sweep summary statistic (integrated haplotype score), with one of the two distributions likely enriched in positive selection. We further find several factors associated with signals of recent adaptation, including the recombination rate, the density of regulatory elements in immune cells, GC content, gene expression in immune cells, the density of mammal-wide conserved elements, and the distance to the nearest virus-interacting gene. These results support the presence of strong positive selection in recent human evolution and highlight MDRs as a powerful tool to make sense of signals of recent genomic adaptation.
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Affiliation(s)
- Diego F Salazar-Tortosa
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA
- Department of Ecology, University of Granada, Granada, Spain
| | - Yi-Fei Huang
- Department of Biology, Pennsylvania State University, University Park, State College, Pennsylvania, PA 16801, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, State College, Pennsylvania, PA 16801, USA
| | - David Enard
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA
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19
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Murga-Moreno J, Casillas S, Barbadilla A, Uricchio L, Enard D. An efficient and robust ABC approach to infer the rate and strength of adaptation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.29.555322. [PMID: 37693550 PMCID: PMC10491248 DOI: 10.1101/2023.08.29.555322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Inferring the effects of positive selection on genomes remains a critical step in characterizing the ultimate and proximate causes of adaptation across species, and quantifying positive selection remains a challenge due to the confounding effects of many other evolutionary processes. Robust and efficient approaches for adaptation inference could help characterize the rate and strength of adaptation in non-model species for which demographic history, mutational processes, and recombination patterns are not currently well-described. Here, we introduce an efficient and user-friendly extension of the McDonald-Kreitman test (ABC-MK) for quantifying long-term protein adaptation in specific lineages of interest. We characterize the performance of our approach with forward simulations and find that it is robust to many demographic perturbations and positive selection configurations, demonstrating its suitability for applications to non-model genomes. We apply ABC-MK to the human proteome and a set of known Virus Interacting Proteins (VIPs) to test the long-term adaptation in genes interacting with viruses. We find substantially stronger signatures of positive selection on RNA-VIPs than DNA-VIPs, suggesting that RNA viruses may be an important driver of human adaptation over deep evolutionary time scales.
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Affiliation(s)
- Jesús Murga-Moreno
- University of Arizona Department of Ecology and Evolutionary Biology, Tucson, USA
| | - Sònia Casillas
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
| | - Antonio Barbadilla
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
| | | | - David Enard
- University of Arizona Department of Ecology and Evolutionary Biology, Tucson, USA
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20
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Aquino Y, Bisiaux A, Li Z, O'Neill M, Mendoza-Revilla J, Merkling SH, Kerner G, Hasan M, Libri V, Bondet V, Smith N, de Cevins C, Ménager M, Luca F, Pique-Regi R, Barba-Spaeth G, Pietropaoli S, Schwartz O, Leroux-Roels G, Lee CK, Leung K, Wu JT, Peiris M, Bruzzone R, Abel L, Casanova JL, Valkenburg SA, Duffy D, Patin E, Rotival M, Quintana-Murci L. Dissecting human population variation in single-cell responses to SARS-CoV-2. Nature 2023; 621:120-128. [PMID: 37558883 PMCID: PMC10482701 DOI: 10.1038/s41586-023-06422-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 07/11/2023] [Indexed: 08/11/2023]
Abstract
Humans display substantial interindividual clinical variability after SARS-CoV-2 infection1-3, the genetic and immunological basis of which has begun to be deciphered4. However, the extent and drivers of population differences in immune responses to SARS-CoV-2 remain unclear. Here we report single-cell RNA-sequencing data for peripheral blood mononuclear cells-from 222 healthy donors of diverse ancestries-that were stimulated with SARS-CoV-2 or influenza A virus. We show that SARS-CoV-2 induces weaker, but more heterogeneous, interferon-stimulated gene activity compared with influenza A virus, and a unique pro-inflammatory signature in myeloid cells. Transcriptional responses to viruses display marked population differences, primarily driven by changes in cell abundance including increased lymphoid differentiation associated with latent cytomegalovirus infection. Expression quantitative trait loci and mediation analyses reveal a broad effect of cell composition on population disparities in immune responses, with genetic variants exerting a strong effect on specific loci. Furthermore, we show that natural selection has increased population differences in immune responses, particularly for variants associated with SARS-CoV-2 response in East Asians, and document the cellular and molecular mechanisms by which Neanderthal introgression has altered immune functions, such as the response of myeloid cells to viruses. Finally, colocalization and transcriptome-wide association analyses reveal an overlap between the genetic basis of immune responses to SARS-CoV-2 and COVID-19 severity, providing insights into the factors contributing to current disparities in COVID-19 risk.
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Affiliation(s)
- Yann Aquino
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France
- Collège Doctoral, Sorbonne Université, Paris, France
| | - Aurélie Bisiaux
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France
| | - Zhi Li
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France
| | - Mary O'Neill
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France
| | - Javier Mendoza-Revilla
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France
| | - Sarah Hélène Merkling
- Insect-Virus Interactions Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France
| | - Gaspard Kerner
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France
| | - Milena Hasan
- Cytometry and Biomarkers UTechS, Institut Pasteur, Université Paris Cité, Paris, France
| | - Valentina Libri
- Cytometry and Biomarkers UTechS, Institut Pasteur, Université Paris Cité, Paris, France
| | - Vincent Bondet
- Translational Immunology Unit, Institut Pasteur, Université Paris Cité, Paris, France
| | - Nikaïa Smith
- Translational Immunology Unit, Institut Pasteur, Université Paris Cité, Paris, France
| | - Camille de Cevins
- Université Paris Cité, Imagine Institute, Laboratory of Inflammatory Responses and Transcriptomic Networks in Diseases, Atip-Avenir Team, INSERM UMR1163, Paris, France
| | - Mickaël Ménager
- Université Paris Cité, Imagine Institute, Laboratory of Inflammatory Responses and Transcriptomic Networks in Diseases, Atip-Avenir Team, INSERM UMR1163, Paris, France
- Labtech Single-Cell@Imagine, Imagine Institute, INSERM UMR1163, Paris, France
| | - Francesca Luca
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, USA
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Roger Pique-Regi
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, USA
| | - Giovanna Barba-Spaeth
- Structural Virology Unit, Institut Pasteur, Université Paris Cité, CNRS UMR3569, Paris, France
| | - Stefano Pietropaoli
- Structural Virology Unit, Institut Pasteur, Université Paris Cité, CNRS UMR3569, Paris, France
| | - Olivier Schwartz
- Virus and Immunity Unit, Institut Pasteur, Université Paris Cité, CNRS UMR3569, Paris, France
| | | | - Cheuk-Kwong Lee
- Hong Kong Red Cross Blood Transfusion Service, Hospital Authority, Hong Kong SAR, China
| | - Kathy Leung
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong SAR, China
| | - Joseph T Wu
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong SAR, China
| | - Malik Peiris
- Division of Public Health Laboratory Sciences, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong SAR, China
- Centre for Immunology and Infection, Hong Kong Science Park, Hong Kong SAR, China
| | - Roberto Bruzzone
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong SAR, China
- Centre for Immunology and Infection, Hong Kong Science Park, Hong Kong SAR, China
| | - Laurent Abel
- St Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, INSERM UMR1163, Necker Hospital for Sick Children, Paris, France
- Université Paris Cité, Imagine Institute, Paris, France
| | - Jean-Laurent Casanova
- St Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, INSERM UMR1163, Necker Hospital for Sick Children, Paris, France
- Université Paris Cité, Imagine Institute, Paris, France
- Department of Pediatrics, Necker Hospital for Sick Children, Paris, France
- Howard Hughes Medical Institute, New York, NY, USA
| | - Sophie A Valkenburg
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong SAR, China
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Darragh Duffy
- Translational Immunology Unit, Institut Pasteur, Université Paris Cité, Paris, France
- Centre for Immunology and Infection, Hong Kong Science Park, Hong Kong SAR, China
| | - Etienne Patin
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France
| | - Maxime Rotival
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France.
| | - Lluis Quintana-Murci
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France.
- Chair Human Genomics and Evolution, Collège de France, Paris, France.
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21
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Piccardi M, Gentiluomo M, Bertoncini S, Pezzilli R, Erőss B, Bunduc S, Uzunoglu FG, Talar-Wojnarowska R, Vanagas T, Sperti C, Oliverius M, Aoki MN, Ermini S, Hussein T, Boggi U, Jamroziak K, Maiello E, Morelli L, Vodickova L, Di Franco G, Landi S, Szentesi A, Lovecek M, Puzzono M, Tavano F, van Laarhoven HWM, Zerbi A, Mohelnikova-Duchonova B, Stocker H, Costello E, Capurso G, Ginocchi L, Lawlor RT, Vanella G, Bazzocchi F, Izbicki JR, Latiano A, Bueno-de-Mesquita B, Ponz de Leon Pisani R, Schöttker B, Soucek P, Hegyi P, Gazouli M, Hackert T, Kupcinskas J, Poskiene L, Tacelli M, Roth S, Carrara S, Perri F, Hlavac V, Theodoropoulos GE, Busch OR, Mambrini A, van Eijck CHJ, Arcidiacono P, Scarpa A, Pasquali C, Basso D, Lucchesi M, Milanetto AC, Neoptolemos JP, Cavestro GM, Janciauskas D, Chen X, Chammas R, Goetz M, Brenner H, Archibugi L, Dannemann M, Canzian F, Tofanelli S, Campa D. Exploring the Neandertal legacy of pancreatic ductal adenocarcinoma risk in Eurasians. Biol Res 2023; 56:46. [PMID: 37574541 PMCID: PMC10424372 DOI: 10.1186/s40659-023-00457-y] [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: 06/30/2022] [Accepted: 07/20/2023] [Indexed: 08/15/2023] Open
Abstract
BACKGROUND The genomes of present-day non-Africans are composed of 1-3% of Neandertal-derived DNA as a consequence of admixture events between Neandertals and anatomically modern humans about 50-60 thousand years ago. Neandertal-introgressed single nucleotide polymorphisms (aSNPs) have been associated with modern human disease-related traits, which are risk factors for pancreatic ductal adenocarcinoma (PDAC), such as obesity, type 2 diabetes, and inflammation. In this study, we aimed at investigating the role of aSNPs in PDAC in three Eurasian populations. RESULTS The high-coverage Vindija Neandertal genome was used to select aSNPs in non-African populations from 1000 Genomes project phase 3 data. Then, the association between aSNPs and PDAC risk was tested independently in Europeans and East Asians, using existing GWAS data on more than 200 000 individuals. We did not find any significant associations between aSNPs and PDAC in samples of European descent, whereas, in East Asians, we observed that the Chr10p12.1-rs117585753-T allele (MAF = 10%) increased the risk to develop PDAC (OR = 1.35, 95%CI 1.19-1.54, P = 3.59 × 10-6), with a P-value close to a threshold that takes into account multiple testing. CONCLUSIONS Our results show only a minimal contribution of Neandertal SNPs to PDAC risk.
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Affiliation(s)
- Margherita Piccardi
- Department of Biology, Unit of Genetics, University of Pisa, Via Derna 1, 56126, Pisa, Italy
| | - Manuel Gentiluomo
- Department of Biology, Unit of Genetics, University of Pisa, Via Derna 1, 56126, Pisa, Italy
| | - Stefania Bertoncini
- Department of Biology, Unit of Zoology and Anthropology, University of Pisa, Pisa, Italy
| | | | - Bálint Erőss
- Institute for Translational Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - Stefania Bunduc
- Institute for Translational Medicine, Medical School, University of Pécs, Pécs, Hungary
- Center for Translational Medicine, Semmelweis University, Budapest, Hungary
- Division of Pancreatic Diseases, Heart and Vascular Center, Semmelweis University, Budapest, Hungary
- Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Faik G Uzunoglu
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Tomas Vanagas
- Department of Surgery, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Cosimo Sperti
- Department DISCOG, Chirurgia Generale 1, University of Padova, Padua, Italy
| | - Martin Oliverius
- Department of Surgery, Third Faculty of Medicine, University Hospital Kralovske Vinohrady, Charles University, Prague, Czech Republic
| | - Mateus Nóbrega Aoki
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Curitiba, Brazil
| | - Stefano Ermini
- Blood Transfusion Service, Azienda Ospedaliero-Universitaria Meyer, Children's Hospital, Florence, Italy
| | - Tamás Hussein
- Institute for Translational Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - Ugo Boggi
- Division of General and Transplantation Surgery, University of Pisa, Pisa, Italy
| | - Krzysztof Jamroziak
- Department of Hematology, Transplantation and Internal Medicine, University of Warsaw, Warsaw, Poland
| | - Evaristo Maiello
- Department of Oncology, Fondazione IRCCS "Casa Sollievo Della Sofferenza" Hospital, San Giovanni Rotondo, Foggia, Italy
| | - Luca Morelli
- Department of Translational Research and New Technologies in Medicine and Surgery, General Surgery Unit, University of Pisa, Pisa, Italy
| | - Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Gregorio Di Franco
- Department of Translational Research and New Technologies in Medicine and Surgery, General Surgery Unit, University of Pisa, Pisa, Italy
| | - Stefano Landi
- Department of Biology, Unit of Genetics, University of Pisa, Via Derna 1, 56126, Pisa, Italy
| | - Andrea Szentesi
- Institute for Translational Medicine, Medical School, University of Pécs, Pécs, Hungary
- Center for Translational Medicine, Semmelweis University, Budapest, Hungary
- János Szentágothai Research Center, University of Pécs, Pécs, Hungary
| | - Martin Lovecek
- Department of Surgery I, University Hospital Olomouc, Olomouc, Czech Republic
| | - Marta Puzzono
- Gastroenterology and Gastrointestinal Endoscopy Unit, Vita-Salute San Raffaele University, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Francesca Tavano
- Division of Gastroenterology and Research Laboratory, Fondazione IRCCS "Casa Sollievo Della Sofferenza" Hospital, San Giovanni Rotondo, Foggia, Italy
| | - Hanneke W M van Laarhoven
- Department of Medical Oncology, Amsterdam UMC, Cancer Center Amsterdam, University of Amsterdam, Amsterdam, The Netherlands
| | - Alessandro Zerbi
- Pancreatic Unit, IRCCS Humanitas Research Hospital, Milan, Italy
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | | | - Hannah Stocker
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Network Aging Research (NAR), Heidelberg University, Heidelberg, Germany
| | - Eithne Costello
- Department of Molecular & Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | - Gabriele Capurso
- Digestive and Liver Disease Unit, S Andrea Hospital, Rome, Italy
- Pancreas Translational and Clinical Research Center, Pancreato-Biliary Endoscopy and Endoscopic Ultrasound, San Raffaele Scientific Institute IRCCS, Milan, Italy
| | - Laura Ginocchi
- Oncological Department, Oncology of Massa Carrara, ASL Toscana Nord Ovest, Massa Carrara, Italy
| | - Rita T Lawlor
- ARC-NET Research Centre and Department of Diagnostics and Public Health, Section of Pathology, University of Verona, Verona, Italy
| | - Giuseppe Vanella
- Digestive and Liver Disease Unit, S Andrea Hospital, Rome, Italy
- Pancreas Translational and Clinical Research Center, Pancreato-Biliary Endoscopy and Endoscopic Ultrasound, San Raffaele Scientific Institute IRCCS, Milan, Italy
| | - Francesca Bazzocchi
- Department of Surgery, Fondazione IRCCS "Casa Sollievo Della Sofferenza" Hospital, San Giovanni Rotondo, Foggia, Italy
| | - Jakob R Izbicki
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anna Latiano
- Division of Gastroenterology and Research Laboratory, Fondazione IRCCS "Casa Sollievo Della Sofferenza" Hospital, San Giovanni Rotondo, Foggia, Italy
| | - Bas Bueno-de-Mesquita
- Centre for Nutrition, Prevention and Health Services, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Ruggero Ponz de Leon Pisani
- Pancreato-Biliary Endoscopy and Endoscopic Ultrasound, Pancreas Translational and Clinical Research Center, San Raffaele Scientific Institute IRCCS, Milan, Italy
| | - Ben Schöttker
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Network Aging Research (NAR), Heidelberg University, Heidelberg, Germany
| | - Pavel Soucek
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Péter Hegyi
- Institute for Translational Medicine, Medical School, University of Pécs, Pécs, Hungary
- Center for Translational Medicine, Semmelweis University, Budapest, Hungary
- Division of Pancreatic Diseases, Heart and Vascular Center, Semmelweis University, Budapest, Hungary
- János Szentágothai Research Center, University of Pécs, Pécs, Hungary
| | - Maria Gazouli
- Laboratory of Biology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Thilo Hackert
- Department of General, Visceral, and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Juozas Kupcinskas
- Department of Gastroenterology and Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Lina Poskiene
- Department of Pathology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Matteo Tacelli
- Pancreato-Biliary Endoscopy and Endoscopic Ultrasound, Pancreas Translational and Clinical Research Center, San Raffaele Scientific Institute IRCCS, Milan, Italy
| | - Susanne Roth
- Department of General, Visceral, and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Silvia Carrara
- Department of Gastroenterology, Endoscopic Unit, IRCCS Humanitas Research Hospital, Milan, Italy
| | - Francesco Perri
- Division of Gastroenterology and Research Laboratory, Fondazione IRCCS "Casa Sollievo Della Sofferenza" Hospital, San Giovanni Rotondo, Foggia, Italy
| | - Viktor Hlavac
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - George E Theodoropoulos
- First Department of Propaedeutic Surgery, Hippocration General Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Olivier R Busch
- Department of Surgery, Amsterdam UMC, Cancer Center Amsterdam, University of Amsterdam, Amsterdam, the Netherlands
| | - Andrea Mambrini
- Oncological Department, Oncology of Massa Carrara, ASL Toscana Nord Ovest, Massa Carrara, Italy
| | - Casper H J van Eijck
- Department of Surgery, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Paolo Arcidiacono
- Pancreato-Biliary Endoscopy and Endoscopic Ultrasound, Pancreas Translational and Clinical Research Center, San Raffaele Scientific Institute IRCCS, Milan, Italy
| | - Aldo Scarpa
- ARC-NET Research Centre and Department of Diagnostics and Public Health, Section of Pathology, University of Verona, Verona, Italy
| | - Claudio Pasquali
- Department DISCOG, Chirurgia Generale 3, University of Padova, Padua, Italy
| | - Daniela Basso
- Department DIMED, Laboratory Medicine, University of Padova, Padua, Italy
| | - Maurizio Lucchesi
- Oncological Department, Oncology of Massa Carrara, ASL Toscana Nord Ovest, Massa Carrara, Italy
| | | | - John P Neoptolemos
- Department of General, Visceral, and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Giulia Martina Cavestro
- Gastroenterology and Gastrointestinal Endoscopy Unit, Vita-Salute San Raffaele University, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Dainius Janciauskas
- Department of Pathology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Xuechen Chen
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Roger Chammas
- Department of Radiology and Oncology, Institute of Cancer of São Paulo (ICESP) São Paulo, Sao Paulo, Brazil
- Faculty of Medicine, University of São Paulo, São Paulo, Brazil
| | - Mara Goetz
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Livia Archibugi
- Digestive and Liver Disease Unit, S Andrea Hospital, Rome, Italy
- Pancreas Translational and Clinical Research Center, Pancreato-Biliary Endoscopy and Endoscopic Ultrasound, San Raffaele Scientific Institute IRCCS, Milan, Italy
| | - Michael Dannemann
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sergio Tofanelli
- Department of Biology, Unit of Zoology and Anthropology, University of Pisa, Pisa, Italy
| | - Daniele Campa
- Department of Biology, Unit of Genetics, University of Pisa, Via Derna 1, 56126, Pisa, Italy.
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22
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Maasch JRMA, Torres MDT, Melo MCR, de la Fuente-Nunez C. Molecular de-extinction of ancient antimicrobial peptides enabled by machine learning. Cell Host Microbe 2023; 31:1260-1274.e6. [PMID: 37516110 DOI: 10.1016/j.chom.2023.07.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 05/12/2023] [Accepted: 07/06/2023] [Indexed: 07/31/2023]
Abstract
Molecular de-extinction could offer avenues for drug discovery by reintroducing bioactive molecules that are no longer encoded by extant organisms. To prospect for antimicrobial peptides encrypted within extinct and extant human proteins, we introduce the panCleave random forest model for proteome-wide cleavage site prediction. Our model outperformed multiple protease-specific cleavage site classifiers for three modern human caspases, despite its pan-protease design. Antimicrobial activity was observed in vitro for modern and archaic protein fragments identified with panCleave. Lead peptides showed resistance to proteolysis and exhibited variable membrane permeabilization. Additionally, representative modern and archaic protein fragments showed anti-infective efficacy against A. baumannii in both a skin abscess infection model and a preclinical murine thigh infection model. These results suggest that machine-learning-based encrypted peptide prospection can identify stable, nontoxic peptide antibiotics. Moreover, we establish molecular de-extinction through paleoproteome mining as a framework for antibacterial drug discovery.
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Affiliation(s)
- Jacqueline R M A Maasch
- Department of Computer and Information Science, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA; Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Bioengineering, Department of Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Marcelo D T Torres
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Bioengineering, Department of Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Institute for Computational Science, 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, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Bioengineering, Department of Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Institute for Computational Science, 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, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Bioengineering, Department of Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA 19104, USA.
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23
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Caro-Consuegra R, Lucas-Sánchez M, Comas D, Bosch E. Identifying signatures of positive selection in human populations from North Africa. Sci Rep 2023; 13:8166. [PMID: 37210386 DOI: 10.1038/s41598-023-35312-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 05/16/2023] [Indexed: 05/22/2023] Open
Abstract
Because of its location, North Africa (NA) has witnessed continuous demographic movements with an impact on the genomes of present-day human populations. Genomic data describe a complex scenario with varying proportions of at least four main ancestry components: Maghrebi, Middle Eastern-, European-, and West-and-East-African-like. However, the footprint of positive selection in NA has not been studied. Here, we compile genome-wide genotyping data from 190 North Africans and individuals from surrounding populations, investigate for signatures of positive selection using allele frequencies and linkage disequilibrium-based methods and infer ancestry proportions to discern adaptive admixture from post-admixture selection events. Our results show private candidate genes for selection in NA involved in insulin processing (KIF5A), immune function (KIF5A, IL1RN, TLR3), and haemoglobin phenotypes (BCL11A). We also detect signatures of positive selection related to skin pigmentation (SLC24A5, KITLG), and immunity function (IL1R1, CD44, JAK1) shared with European populations and candidate genes associated with haemoglobin phenotypes (HPSE2, HBE1, HBG2), other immune-related (DOCK2) traits, and insulin processing (GLIS3) traits shared with West and East African populations. Finally, the SLC8A1 gene, which codifies for a sodium-calcium exchanger, was the only candidate identified under post-admixture selection in Western NA.
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Affiliation(s)
- Rocio Caro-Consuegra
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003, Barcelona, Spain
| | - Marcel Lucas-Sánchez
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003, Barcelona, Spain
| | - David Comas
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003, Barcelona, Spain
| | - Elena Bosch
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003, Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Salud Mental, Instituto de Salud Carlos III, 28029, Madrid, Spain.
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24
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Affiliation(s)
- Gaspard Kerner
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, Centre National de la Recherche Scientifique (CNRS) UMR, 2000, Paris, France
| | - Jeremy Choin
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Lluis Quintana-Murci
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, Centre National de la Recherche Scientifique (CNRS) UMR, 2000, Paris, France. .,Chair of Human Genomics and Evolution, Collège de France, Paris, France.
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25
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Corcoran M, Chernyshev M, Mandolesi M, Narang S, Kaduk M, Ye K, Sundling C, Färnert A, Kreslavsky T, Bernhardsson C, Larena M, Jakobsson M, Karlsson Hedestam GB. Archaic humans have contributed to large-scale variation in modern human T cell receptor genes. Immunity 2023; 56:635-652.e6. [PMID: 36796364 DOI: 10.1016/j.immuni.2023.01.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 11/21/2022] [Accepted: 01/23/2023] [Indexed: 02/18/2023]
Abstract
Human T cell receptors (TCRs) are critical for mediating immune responses to pathogens and tumors and regulating self-antigen recognition. Yet, variations in the genes encoding TCRs remain insufficiently defined. Detailed analysis of expressed TCR alpha, beta, gamma, and delta genes in 45 donors from four human populations-African, East Asian, South Asian, and European-revealed 175 additional TCR variable and junctional alleles. Most of these contained coding changes and were present at widely differing frequencies in the populations, a finding confirmed using DNA samples from the 1000 Genomes Project. Importantly, we identified three Neanderthal-derived, introgressed TCR regions including a highly divergent TRGV4 variant, which mediated altered butyrophilin-like molecule 3 (BTNL3) ligand reactivity and was frequent in all modern Eurasian population groups. Our results demonstrate remarkable variation in TCR genes in both individuals and populations, providing a strong incentive for including allelic variation in studies of TCR function in human biology.
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Affiliation(s)
- Martin Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77 Stockholm, Sweden.
| | - Mark Chernyshev
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Marco Mandolesi
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Sanjana Narang
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Mateusz Kaduk
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Kewei Ye
- Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden; Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Christopher Sundling
- Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden; Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden; Department of Infectious Diseases, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Anna Färnert
- Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden; Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden; Department of Infectious Diseases, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Taras Kreslavsky
- Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden; Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Carolina Bernhardsson
- Department of Organismal Biology, Human Evolution, Norbyvägen 18C, 752 63 Uppsala, Sweden
| | - Maximilian Larena
- Department of Organismal Biology, Human Evolution, Norbyvägen 18C, 752 63 Uppsala, Sweden
| | - Mattias Jakobsson
- Department of Organismal Biology, Human Evolution, Norbyvägen 18C, 752 63 Uppsala, Sweden
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26
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Cui B, Guo Z, Cao H, Calus M, Zhang Q. The computational implementation of a platform of relative identity-by-descent scores algorithm for introgressive mapping. Front Genet 2023; 13:1028662. [PMID: 36761695 PMCID: PMC9903072 DOI: 10.3389/fgene.2022.1028662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 11/15/2022] [Indexed: 01/25/2023] Open
Abstract
With the development of genotyping and sequencing technology, researchers working in the area of conservation genetics are able to obtain the genotypes or even the sequences of a representative sample of individuals from the population. It is of great importance to examine the genomic variants and genes that are highly preferred or pruned during the process of adaptive introgression or long-term hybridization. To the best of our knowledge, we are the first to develop a platform with computational integration of a relative identity-by-descent (rIBD) scores algorithm for introgressive mapping. The rIBD algorithm is designed for mapping the fine-scaled genomic regions under adaptive introgression between the source breeds and the admixed breed. Our rIBD calculation platform provides compact functions including reading input information and uploading of files, rIBD calculation, and presentation of the rIBD scores. We analyzed the simulated data using the rIBD calculation platform and calculated the average IBD score of 0.061 with a standard deviation of 0.124. The rIBD scores generally follow a normal distribution, and a cut-off of 0.432 and -0.310 for both positive and negative rIBD scores is derived to enable the identification of genomic regions showing significant introgression signals from the source breed to the admixed breed. A list of genomic regions with detailed calculated rIBD scores is reported, and all the rIBD scores for each of the considered windows are presented in plots on the rIBD calculation platform. Our rIBD calculation platform provides a user-friendly tool for the calculation of fine-scaled rIBD scores for each of the genomic regions to map possible functional genomic variants due to adaptive introgression or long-term hybridization.
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Affiliation(s)
- Bo Cui
- School of Chemistry and Biological Engineering, University of Science and Technology, Beijing, China
- College of Water Resources and Civil Engineering, China Agricultural University, Beijing, China
- Institute of Biotechnology, Beijing Academy of Agricultural and Forestry Sciences, Beijing, China
| | - Zhongxu Guo
- School of Chemistry and Biological Engineering, University of Science and Technology, Beijing, China
- College of Water Resources and Civil Engineering, China Agricultural University, Beijing, China
- Institute of Biotechnology, Beijing Academy of Agricultural and Forestry Sciences, Beijing, China
| | - Hongbo Cao
- School of Chemistry and Biological Engineering, University of Science and Technology, Beijing, China
- College of Water Resources and Civil Engineering, China Agricultural University, Beijing, China
- Institute of Biotechnology, Beijing Academy of Agricultural and Forestry Sciences, Beijing, China
| | - Mario Calus
- Department of Animal Science, Animal Breeding and Genetics Group, Wageningen University, Wageningen, Netherlands
| | - Qianqian Zhang
- School of Chemistry and Biological Engineering, University of Science and Technology, Beijing, China
- Institute of Biotechnology, Beijing Academy of Agricultural and Forestry Sciences, Beijing, China
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27
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Genetic adaptation to pathogens and increased risk of inflammatory disorders in post-Neolithic Europe. CELL GENOMICS 2023; 3:100248. [PMID: 36819665 PMCID: PMC9932995 DOI: 10.1016/j.xgen.2022.100248] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 10/24/2022] [Accepted: 12/14/2022] [Indexed: 01/15/2023]
Abstract
Ancient genomics can directly detect human genetic adaptation to environmental cues. However, it remains unclear how pathogens have exerted selective pressures on human genome diversity across different epochs and affected present-day inflammatory disease risk. Here, we use an ancestry-aware approximate Bayesian computation framework to estimate the nature, strength, and time of onset of selection acting on 2,879 ancient and modern European genomes from the last 10,000 years. We found that the bulk of genetic adaptation occurred after the start of the Bronze Age, <4,500 years ago, and was enriched in genes relating to host-pathogen interactions. Furthermore, we detected directional selection acting on specific leukocytic lineages and experimentally demonstrated that the strongest negatively selected candidate variant in immunity genes, lipopolysaccharide-binding protein (LBP) D283G, is hypomorphic. Finally, our analyses suggest that the risk of inflammatory disorders has increased in post-Neolithic Europeans, possibly because of antagonistic pleiotropy following genetic adaptation to pathogens.
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28
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Zhang X, Kim B, Singh A, Sankararaman S, Durvasula A, Lohmueller KE. MaLAdapt Reveals Novel Targets of Adaptive Introgression From Neanderthals and Denisovans in Worldwide Human Populations. Mol Biol Evol 2023; 40:msad001. [PMID: 36617238 PMCID: PMC9887621 DOI: 10.1093/molbev/msad001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 12/25/2022] [Accepted: 12/28/2022] [Indexed: 01/09/2023] Open
Abstract
Adaptive introgression (AI) facilitates local adaptation in a wide range of species. Many state-of-the-art methods detect AI with ad-hoc approaches that identify summary statistic outliers or intersect scans for positive selection with scans for introgressed genomic regions. Although widely used, approaches intersecting outliers are vulnerable to a high false-negative rate as the power of different methods varies, especially for complex introgression events. Moreover, population genetic processes unrelated to AI, such as background selection or heterosis, may create similar genomic signals to AI, compromising the reliability of methods that rely on neutral null distributions. In recent years, machine learning (ML) methods have been increasingly applied to population genetic questions. Here, we present a ML-based method called MaLAdapt for identifying AI loci from genome-wide sequencing data. Using an Extra-Trees Classifier algorithm, our method combines information from a large number of biologically meaningful summary statistics to capture a powerful composite signature of AI across the genome. In contrast to existing methods, MaLAdapt is especially well-powered to detect AI with mild beneficial effects, including selection on standing archaic variation, and is robust to non-AI selective sweeps, heterosis from deleterious mutations, and demographic misspecification. Furthermore, MaLAdapt outperforms existing methods for detecting AI based on the analysis of simulated data and the validation of empirical signals through visual inspection of haplotype patterns. We apply MaLAdapt to the 1000 Genomes Project human genomic data and discover novel AI candidate regions in non-African populations, including genes that are enriched in functionally important biological pathways regulating metabolism and immune responses.
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Affiliation(s)
- Xinjun Zhang
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA
| | - Bernard Kim
- Department of Biology, Stanford University, Palo Alto, CA
| | - Armaan Singh
- Department of Computer Science, UCLA, Los Angeles, CA
| | - Sriram Sankararaman
- Department of Computer Science, UCLA, Los Angeles, CA
- Department of Computational Medicine, UCLA, Los Angeles, CA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA
| | - Arun Durvasula
- Department of Genetics, Harvard Medical School, Boston, MA
| | - Kirk E Lohmueller
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA
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29
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Lea AJ, Garcia A, Arevalo J, Ayroles JF, Buetow K, Cole SW, Eid Rodriguez D, Gutierrez M, Highland HM, Hooper PL, Justice A, Kraft T, North KE, Stieglitz J, Kaplan H, Trumble BC, Gurven MD. Natural selection of immune and metabolic genes associated with health in two lowland Bolivian populations. Proc Natl Acad Sci U S A 2023; 120:e2207544120. [PMID: 36574663 PMCID: PMC9910614 DOI: 10.1073/pnas.2207544120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 09/21/2022] [Indexed: 12/28/2022] Open
Abstract
A growing body of work has addressed human adaptations to diverse environments using genomic data, but few studies have connected putatively selected alleles to phenotypes, much less among underrepresented populations such as Amerindians. Studies of natural selection and genotype-phenotype relationships in underrepresented populations hold potential to uncover previously undescribed loci underlying evolutionarily and biomedically relevant traits. Here, we worked with the Tsimane and the Moseten, two Amerindian populations inhabiting the Bolivian lowlands. We focused most intensively on the Tsimane, because long-term anthropological work with this group has shown that they have a high burden of both macro and microparasites, as well as minimal cardiometabolic disease or dementia. We therefore generated genome-wide genotype data for Tsimane individuals to study natural selection, and paired this with blood mRNA-seq as well as cardiometabolic and immune biomarker data generated from a larger sample that included both populations. In the Tsimane, we identified 21 regions that are candidates for selective sweeps, as well as 5 immune traits that show evidence for polygenic selection (e.g., C-reactive protein levels and the response to coronaviruses). Genes overlapping candidate regions were strongly enriched for known involvement in immune-related traits, such as abundance of lymphocytes and eosinophils. Importantly, we were also able to draw on extensive phenotype information for the Tsimane and Moseten and link five regions (containing PSD4, MUC21 and MUC22, TOX2, ANXA6, and ABCA1) with biomarkers of immune and metabolic function. Together, our work highlights the utility of pairing evolutionary analyses with anthropological and biomedical data to gain insight into the genetic basis of health-related traits.
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Affiliation(s)
- Amanda J. Lea
- Department of Biological Sciences, Vanderbilt University, Nashville, TN37235
| | - Angela Garcia
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ85287
| | - Jesusa Arevalo
- Department of Medicine, University of California, Los Angeles, CA90095
| | - Julien F. Ayroles
- Department of Ecology and Evolution, Princeton University, Princeton, NJ08544
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ08544
| | - Kenneth Buetow
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ85287
- School of Life Sciences, Arizona State University, Tempe, AZ85287
| | - Steve W. Cole
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA90095
- Department of Medicine, University of California, Los Angeles, CA90095
| | | | | | - Heather M. Highland
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC27516
| | - Paul L. Hooper
- Economic Science Institute, Chapman University, Orange, CA92866
| | | | - Thomas Kraft
- Department of Anthropology, University of Utah, Salt Lake City, UT84112
| | - Kari E. North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC27516
| | | | - Hillard Kaplan
- Institute for Economics and Society, Chapman University, Orange, CA92866
| | - Benjamin C. Trumble
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ85287
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ85287
| | - Michael D. Gurven
- Department of Anthropology, University of California, Santa Barbara, CA93106
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30
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Ndong Sima CAA, Smith D, Petersen DC, Schurz H, Uren C, Möller M. The immunogenetics of tuberculosis (TB) susceptibility. Immunogenetics 2022; 75:215-230. [DOI: 10.1007/s00251-022-01290-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022]
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31
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Taravella Oill AM, Buetow KH, Wilson MA. The role of Neanderthal introgression in liver cancer. BMC Med Genomics 2022; 15:255. [PMID: 36503519 PMCID: PMC9743633 DOI: 10.1186/s12920-022-01405-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 11/25/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Neanderthal introgressed DNA has been linked to different normal and disease traits including immunity and metabolism-two important functions that are altered in liver cancer. However, there is limited understanding of the relationship between Neanderthal introgression and liver cancer risk. The aim of this study was to investigate the relationship between Neanderthal introgression and liver cancer risk. METHODS Using germline and somatic DNA and tumor RNA from liver cancer patients from The Cancer Genome Atlas, along with ancestry-match germline DNA from unaffected individuals from the 1000 Genomes Resource, and allele specific expression data from normal liver tissue from The Genotype-Tissue Expression project we investigated whether Neanderthal introgression impacts cancer etiology. Using a previously generated set of Neanderthal alleles, we identified Neanderthal introgressed haplotypes. We then tested whether somatic mutations are enriched or depleted on Neanderthal introgressed haplotypes compared to modern haplotypes. We also computationally assessed whether somatic mutations have a functional effect or show evidence of regulating expression of Neanderthal haplotypes. Finally, we compared patterns of Neanderthal introgression in liver cancer patients and the general population. RESULTS We find Neanderthal introgressed haplotypes exhibit an excess of somatic mutations compared to modern haplotypes. Variant Effect Predictor analysis revealed that most of the somatic mutations on these Neanderthal introgressed haplotypes are not functional. We did observe expression differences of Neanderthal alleles between tumor and normal for four genes that also showed a pattern of enrichment of somatic mutations on Neanderthal haplotypes. However, gene expression was similar between liver cancer patients with modern ancestry and liver cancer patients with Neanderthal ancestry at these genes. Provocatively, when analyzing all genes, we find evidence of Neanderthal introgression regulating expression in tumor from liver cancer patients in two genes, ARK1C4 and OAS1. Finally, we find that most genes do not show a difference in the proportion of Neanderthal introgression between liver cancer patients and the general population. CONCLUSION Our results suggest that Neanderthal introgression provides opportunity for somatic mutations to accumulate, and that some Neanderthal introgression may impact liver cancer risk.
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Affiliation(s)
- Angela M Taravella Oill
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA.
- School of Life Sciences, Arizona State University, Tempe, AZ, USA.
| | - Kenneth H Buetow
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Melissa A Wilson
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
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32
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Konopiński MK, Fijarczyk AM, Biedrzycka A. Complex patterns shape immune genes diversity during invasion of common raccoon in Europe - Selection in action despite genetic drift. Evol Appl 2022; 16:134-151. [PMID: 36699132 PMCID: PMC9850017 DOI: 10.1111/eva.13517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 11/24/2022] [Accepted: 11/28/2022] [Indexed: 12/14/2022] Open
Abstract
Rapid adaptation is common in invasive populations and is crucial to their long-term success. The primary target of selection in the invasive species' new range is standing genetic variation. Therefore, genetic drift and natural selection acting on existing variation are key evolutionary processes through which invaders will evolve over a short timescale. In this study, we used the case of the raccoon Procyon lotor invasion in Europe to identify the forces shaping the diversity of immune genes during invasion. The genes involved in the defence against infection should be under intense selection pressure in the invasive range where novel pathogens are expected to occur. To disentangle the selective and demographic processes shaping the adaptive immune diversity of its invasive and expanding populations, we have developed species-specific single-nucleotide polymorphism markers located in the coding regions of targeted immune-related genes. We characterised the genetic diversity of 110 functionally important immune genes in two invasive and one native raccoon genetic clusters, each presenting a different demographic history. Despite the strong effect of demographic processes in the invasive clusters, we detected a subset of genes exhibiting the diversity pattern suggestive of selection. The most likely process shaping the variation in those genes was balancing selection. The selected genes belong to toll-like receptors and cytokine-related genes. Our results suggest that the prevalence of selection depends on the level of diversity, that is - less genetically diverse invasive population from the Czech Republic displayed fewer signs of selection. Our results highlight the role of standing genetic variation in adapting to new environment. Understanding the evolutionary mechanisms behind invasion success would enable predicting how populations may respond to environmental change.
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Affiliation(s)
| | - Anna M. Fijarczyk
- Laval University Département de BiologieUniversité LavalQuébecQuébecCanada
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33
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Vespasiani DM, Jacobs GS, Cook LE, Brucato N, Leavesley M, Kinipi C, Ricaut FX, Cox MP, Gallego Romero I. Denisovan introgression has shaped the immune system of present-day Papuans. PLoS Genet 2022; 18:e1010470. [PMID: 36480515 PMCID: PMC9731433 DOI: 10.1371/journal.pgen.1010470] [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: 02/01/2022] [Accepted: 10/10/2022] [Indexed: 12/13/2022] Open
Abstract
Modern humans have admixed with multiple archaic hominins. Papuans, in particular, owe up to 5% of their genome to Denisovans, a sister group to Neanderthals whose remains have only been identified in Siberia and Tibet. Unfortunately, the biological and evolutionary significance of these introgression events remain poorly understood. Here we investigate the function of both Denisovan and Neanderthal alleles characterised within a set of 56 genomes from Papuan individuals. By comparing the distribution of archaic and non-archaic variants we assess the consequences of archaic admixture across a multitude of different cell types and functional elements. We observe an enrichment of archaic alleles within cis-regulatory elements and transcribed regions of the genome, with Denisovan variants strongly affecting elements active within immune-related cells. We identify 16,048 and 10,032 high-confidence Denisovan and Neanderthal variants that fall within annotated cis-regulatory elements and with the potential to alter the affinity of multiple transcription factors to their cognate DNA motifs, highlighting a likely mechanism by which introgressed DNA can impact phenotypes. Lastly, we experimentally validate these predictions by testing the regulatory potential of five Denisovan variants segregating within Papuan individuals, and find that two are associated with a significant reduction of transcriptional activity in plasmid reporter assays. Together, these data provide support for a widespread contribution of archaic DNA in shaping the present levels of modern human genetic diversity, with different archaic ancestries potentially affecting multiple phenotypic traits within non-Africans.
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Affiliation(s)
- Davide M. Vespasiani
- Melbourne Integrative Genomics, University of Melbourne, Parkville, Australia
- School of Biosciences, University of Melbourne, Parkville, Australia
| | - Guy S. Jacobs
- Department of Archaeology, University of Cambridge, Cambridge, Uniteed Kingdom
| | - Laura E. Cook
- Melbourne Integrative Genomics, University of Melbourne, Parkville, Australia
- School of Biosciences, University of Melbourne, Parkville, Australia
| | - Nicolas Brucato
- Laboratoire de Evolution et Diversite Biologique, Université de Toulouse Midi-Pyrénées, Toulouse, France
| | - Matthew Leavesley
- School of Humanities and Social Sciences, University of Papua New Guinea, Port Moresby, Papua New Guinea
- College of Arts, Society and Education, James Cook University, Cairns, Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, Australia
| | - Christopher Kinipi
- School of Humanities and Social Sciences, University of Papua New Guinea, Port Moresby, Papua New Guinea
| | - François-Xavier Ricaut
- Laboratoire de Evolution et Diversite Biologique, Université de Toulouse Midi-Pyrénées, Toulouse, France
| | - Murray P. Cox
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Irene Gallego Romero
- Melbourne Integrative Genomics, University of Melbourne, Parkville, Australia
- School of Biosciences, University of Melbourne, Parkville, Australia
- Center for Stem Cell Systems, University of Melbourne, Parkville, Australia
- Center for Genomics, Evolution and Medicine, University of Tartu, Tartu, Estonia
- * E-mail:
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34
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Ma Y, Xiang F. Discovery of genomes of Neanderthal, Denisova and its impact on modern human. CHINESE SCIENCE BULLETIN-CHINESE 2022. [DOI: 10.1360/tb-2022-1134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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35
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Integrating Single-Cell Transcriptome and Network Analysis to Characterize the Therapeutic Response of Chronic Myeloid Leukemia. Int J Mol Sci 2022; 23:ijms232214335. [PMID: 36430822 PMCID: PMC9695508 DOI: 10.3390/ijms232214335] [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: 09/12/2022] [Revised: 11/06/2022] [Accepted: 11/08/2022] [Indexed: 11/22/2022] Open
Abstract
Chronic myeloid leukemia (CML) is a myeloproliferative disease characterized by a unique BCR-ABL fusion gene. Tyrosine kinase inhibitors (TKIs) were developed to target the BCR-ABL oncoprotein, inhibiting its abnormal kinase activity. TKI treatments have significantly improved CML patient outcomes. However, the patients can develop drug resistance and relapse after therapy discontinues largely due to intratumor heterogeneity. It is critical to understand the differences in therapeutic responses among subpopulations of cells. Single-cell RNA sequencing measures the transcriptome of individual cells, allowing us to differentiate and analyze individual cell populations. Here, we integrated a single-cell RNA sequencing profile of CML stem cells and network analysis to decipher the mechanisms of distinct TKI responses. Compared to normal hematopoietic stem cells, a set of genes that were concordantly differentially expressed in various types of stem cells of CML patients was revealed. Further transcription regulatory network analysis found that most of these genes were directly controlled by one or more transcript factors and the genes have more regulators in the cells of the patients who responded to the treatment. The molecular markers including a known drug-resistance gene and novel gene signatures for treatment response were also identified. Moreover, we combined protein-protein interaction network construction with a cancer drug database and uncovered the drugs that target the marker genes directly or indirectly via the protein interactions. The gene signatures and their interacted proteins identified by this work can be used for treatment response prediction and lead to new strategies for drug resistance monitoring and prevention. Our single-cell-based findings offered novel insights into the mechanisms underlying the therapeutic response of CML.
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36
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Pick CM, Ko A, Wormley AS, Wiezel A, Kenrick DT, Al-Shawaf L, Barry O, Bereby-Meyer Y, Boonyasiriwat W, Brandstätter E, Crispim AC, Cruz JE, David D, David OA, Defelipe RP, Elmas P, Espinosa A, Fernandez AM, Fetvadjiev VH, Fetvadjieva S, Fischer R, Galdi S, Galindo-Caballero OJ, Golovina GM, Gomez-Jacinto L, Graf S, Grossmann I, Gul P, Halama P, Hamamura T, Hansson LS, Hitokoto H, Hřebíčková M, Ilic D, Johnson JL, Kara-Yakoubian M, Karl JA, Kohút M, Lasselin J, Li NP, Mafra AL, Malanchuk O, Moran S, Murata A, Ndiaye SAL, O J, Onyishi IE, Pasay-An E, Rizwan M, Roth E, Salgado S, Samoylenko ES, Savchenko TN, Sevincer AT, Skoog E, Stanciu A, Suh EM, Sznycer D, Talhelm T, Ugwu FO, Uskul AK, Uz I, Valentova JV, Varella MAC, Zambrano D, Varnum MEW. Family still matters: Human social motivation across 42 countries during a global pandemic. EVOL HUM BEHAV 2022; 43:527-535. [PMID: 36217369 PMCID: PMC9534541 DOI: 10.1016/j.evolhumbehav.2022.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 09/02/2022] [Accepted: 09/10/2022] [Indexed: 11/25/2022]
Abstract
The COVID-19 pandemic caused drastic social changes for many people, including separation from friends and coworkers, enforced close contact with family, and reductions in mobility. Here we assess the extent to which people's evolutionarily-relevant basic motivations and goals—fundamental social motives such as Affiliation and Kin Care—might have been affected. To address this question, we gathered data on fundamental social motives in 42 countries (N = 15,915) across two waves, including 19 countries (N = 10,907) for which data were gathered both before and during the pandemic (pre-pandemic wave: 32 countries, N = 8998; 3302 male, 5585 female; Mage = 24.43, SD = 7.91; mid-pandemic wave: 29 countries, N = 6917; 2249 male, 4218 female; Mage = 28.59, SD = 11.31). Samples include data collected online (e.g., Prolific, MTurk), at universities, and via community sampling. We found that Disease Avoidance motivation was substantially higher during the pandemic, and that most of the other fundamental social motives showed small, yet significant, differences across waves. Most sensibly, concern with caring for one's children was higher during the pandemic, and concerns with Mate Seeking and Status were lower. Earlier findings showing the prioritization of family motives over mating motives (and even over Disease Avoidance motives) were replicated during the pandemic. Finally, well-being remained positively associated with family-related motives and negatively associated with mating motives during the pandemic, as in the pre-pandemic samples. Our results provide further evidence for the robust primacy of family-related motivations even during this unique disruption of social life.
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Affiliation(s)
- Cari M Pick
- Arizona State University, Tempe, AZ, United States of America
| | - Ahra Ko
- Arizona State University, Tempe, AZ, United States of America
| | | | - Adi Wiezel
- Arizona State University, Tempe, AZ, United States of America
| | | | - Laith Al-Shawaf
- University of Colorado, Colorado Springs, CO, United States of America
| | - Oumar Barry
- University Cheikh Anta Diop of Dakar (UCAD), Senegal
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Ronald Fischer
- Victoria University of Wellington, New Zealand.,Instituto D'Or de Pesquisa e Ensino, Brazil
| | | | | | | | | | | | | | - Pelin Gul
- University of Groningen, Netherlands
| | | | | | - Lina S Hansson
- Stockholm University, Sweden.,Karolinska Institutet, Sweden.,Karolinska Universitetssjukhuset, Sweden
| | | | | | | | | | | | | | | | - Julie Lasselin
- Stockholm University, Sweden.,Karolinska Institutet, Sweden.,Karolinska Universitetssjukhuset, Sweden
| | | | | | | | | | | | | | - Jiaqing O
- Aberystwyth University, United Kingdom
| | | | | | | | - Eric Roth
- Universidad Católica Boliviana, Bolivia
| | | | | | | | | | | | - Adrian Stanciu
- Gesis-Leibniz Institute for the Social Sciences, Germany
| | | | | | - Thomas Talhelm
- University of Chicago, Chicago, IL, United States of America
| | - Fabian O Ugwu
- Alex Ekwueme Federal University, Ndufu-Alike, Nigeria
| | | | - Irem Uz
- TOBB University of Economics and Technology, Turkey
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37
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Li J, Zhang X, Gao Y, Jiao J, Wang C, Zhang Y, Zhang L. Signatures of positive selection are enriched in genome-wide associated allergy alleles. Allergy 2022; 77:3134-3137. [PMID: 35652364 DOI: 10.1111/all.15398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/10/2022] [Accepted: 05/21/2022] [Indexed: 01/28/2023]
Affiliation(s)
- Jingyun Li
- Department of Otolaryngology Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Nasal diseases, Beijing Institute of Otolaryngology, Beijing, China.,Department of Allergy, Beijing TongRen Hospital, Capital Medical University, Beijing, China.,Research Unit of Diagnosis and Treatment of Chronic Nasal Diseases, Chinese Academy of Medical Sciences, Beijing, China
| | - Xu Zhang
- Department of Otolaryngology Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Nasal diseases, Beijing Institute of Otolaryngology, Beijing, China.,Department of Allergy, Beijing TongRen Hospital, Capital Medical University, Beijing, China.,Research Unit of Diagnosis and Treatment of Chronic Nasal Diseases, Chinese Academy of Medical Sciences, Beijing, China
| | - Yunbo Gao
- Department of Otolaryngology Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Nasal diseases, Beijing Institute of Otolaryngology, Beijing, China.,Research Unit of Diagnosis and Treatment of Chronic Nasal Diseases, Chinese Academy of Medical Sciences, Beijing, China
| | - Jian Jiao
- Department of Otolaryngology Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Nasal diseases, Beijing Institute of Otolaryngology, Beijing, China
| | - Chengshuo Wang
- Department of Otolaryngology Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Nasal diseases, Beijing Institute of Otolaryngology, Beijing, China.,Department of Allergy, Beijing TongRen Hospital, Capital Medical University, Beijing, China.,Research Unit of Diagnosis and Treatment of Chronic Nasal Diseases, Chinese Academy of Medical Sciences, Beijing, China
| | - Yuan Zhang
- Department of Otolaryngology Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Nasal diseases, Beijing Institute of Otolaryngology, Beijing, China.,Department of Allergy, Beijing TongRen Hospital, Capital Medical University, Beijing, China.,Research Unit of Diagnosis and Treatment of Chronic Nasal Diseases, Chinese Academy of Medical Sciences, Beijing, China
| | - Luo Zhang
- Department of Otolaryngology Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Nasal diseases, Beijing Institute of Otolaryngology, Beijing, China.,Department of Allergy, Beijing TongRen Hospital, Capital Medical University, Beijing, China.,Research Unit of Diagnosis and Treatment of Chronic Nasal Diseases, Chinese Academy of Medical Sciences, Beijing, China
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38
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Reilly PF, Tjahjadi A, Miller SL, Akey JM, Tucci S. The contribution of Neanderthal introgression to modern human traits. Curr Biol 2022; 32:R970-R983. [PMID: 36167050 PMCID: PMC9741939 DOI: 10.1016/j.cub.2022.08.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Neanderthals, our closest extinct relatives, lived in western Eurasia from 400,000 years ago until they went extinct around 40,000 years ago. DNA retrieved from ancient specimens revealed that Neanderthals mated with modern human contemporaries. As a consequence, introgressed Neanderthal DNA survives scattered across the human genome such that 1-4% of the genome of present-day people outside Africa are inherited from Neanderthal ancestors. Patterns of Neanderthal introgressed genomic sequences suggest that Neanderthal alleles had distinct fates in the modern human genetic background. Some Neanderthal alleles facilitated human adaptation to new environments such as novel climate conditions, UV exposure levels and pathogens, while others had deleterious consequences. Here, we review the body of work on Neanderthal introgression over the past decade. We describe how evolutionary forces shaped the genomic landscape of Neanderthal introgression and highlight the impact of introgressed alleles on human biology and phenotypic variation.
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Affiliation(s)
| | - Audrey Tjahjadi
- Department of Anthropology, Yale University, New Haven, CT, USA
| | | | - Joshua M Akey
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
| | - Serena Tucci
- Department of Anthropology, Yale University, New Haven, CT, USA; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA.
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39
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Dubois‐Mignon T, Monget P. Gene essentiality and variability: What is the link? A within‐ and between‐species perspective. Bioessays 2022; 44:e2200132. [DOI: 10.1002/bies.202200132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/17/2022] [Accepted: 08/30/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Tania Dubois‐Mignon
- Institut de Biologie de l’École Normale Supérieure Université PSL 46 rue d'Ulm Paris 75005 France
| | - Philippe Monget
- Physiologie de la Reproduction et des Comportements, Centre Val de Loire – UMR INRAE, CNRS, IFCE Université de Tours Nouzilly France
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40
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Ferrández-Peral L, Zhan X, Alvarez-Estape M, Chiva C, Esteller-Cucala P, García-Pérez R, Julià E, Lizano E, Fornas Ò, Sabidó E, Li Q, Marquès-Bonet T, Juan D, Zhang G. Transcriptome innovations in primates revealed by single-molecule long-read sequencing. Genome Res 2022; 32:1448-1462. [PMID: 35840341 PMCID: PMC9435740 DOI: 10.1101/gr.276395.121] [Citation(s) in RCA: 1] [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: 11/16/2021] [Accepted: 07/12/2022] [Indexed: 11/24/2022]
Abstract
Transcriptomic diversity greatly contributes to the fundamentals of disease, lineage-specific biology, and environmental adaptation. However, much of the actual isoform repertoire contributing to shaping primate evolution remains unknown. Here, we combined deep long- and short-read sequencing complemented with mass spectrometry proteomics in a panel of lymphoblastoid cell lines (LCLs) from human, three other great apes, and rhesus macaque, producing the largest full-length isoform catalog in primates to date. Around half of the captured isoforms are not annotated in their reference genomes, significantly expanding the gene models in primates. Furthermore, our comparative analyses unveil hundreds of transcriptomic innovations and isoform usage changes related to immune function and immunological disorders. The confluence of these evolutionary innovations with signals of positive selection and their limited impact in the proteome points to changes in alternative splicing in genes involved in immune response as an important target of recent regulatory divergence in primates.
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Affiliation(s)
| | | | | | - Cristina Chiva
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | | | | | - Eva Julià
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain
| | - Esther Lizano
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193 Barcelona, Spain
| | - Òscar Fornas
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Eduard Sabidó
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Qiye Li
- BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tomàs Marquès-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
- CNAG-CRG, Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - David Juan
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003 Barcelona, Spain
| | - Guojie Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen 2200, Denmark
- Evolutionary and Organismal Biology Research Center, School of Medicine, Zhejiang University, Hangzhou 310058, China
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Collen EJ, Johar AS, Teixeira JC, Llamas B. The immunogenetic impact of European colonization in the Americas. Front Genet 2022; 13:918227. [PMID: 35991555 PMCID: PMC9388791 DOI: 10.3389/fgene.2022.918227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 07/07/2022] [Indexed: 11/13/2022] Open
Abstract
The introduction of pathogens originating from Eurasia into the Americas during early European contact has been associated with high mortality rates among Indigenous peoples, likely contributing to their historical and precipitous population decline. However, the biological impacts of imported infectious diseases and resulting epidemics, especially in terms of pathogenic effects on the Indigenous immunity, remain poorly understood and highly contentious to this day. Here, we examine multidisciplinary evidence underpinning colonization-related immune genetic change, providing contextualization from anthropological studies, paleomicrobiological evidence of contrasting host-pathogen coevolutionary histories, and the timings of disease emergence. We further summarize current studies examining genetic signals reflecting post-contact Indigenous population bottlenecks, admixture with European and other populations, and the putative effects of natural selection, with a focus on ancient DNA studies and immunity-related findings. Considering current genetic evidence, together with a population genetics theoretical approach, we show that post-contact Indigenous immune adaptation, possibly influenced by selection exerted by introduced pathogens, is highly complex and likely to be affected by multifactorial causes. Disentangling putative adaptive signals from those of genetic drift thus remains a significant challenge, highlighting the need for the implementation of population genetic approaches that model the short time spans and complex demographic histories under consideration. This review adds to current understandings of post-contact immunity evolution in Indigenous peoples of America, with important implications for bettering our understanding of human adaptation in the face of emerging infectious diseases.
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Affiliation(s)
- Evelyn Jane Collen
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Angad Singh Johar
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- School of Mathematics and Statistics, The University of Melbourne, Parkville, VIC, Australia
| | - João C. Teixeira
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- School of Culture History and Language, The Australian National University, Canberra, ACT, Australia
- Centre of Excellence for Australian Biodiversity and Heritage (CABAH), School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- Centre of Excellence for Australian Biodiversity and Heritage (CABAH), School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT, Australia
- Telethon Kids Institute, Indigenous Genomics Research Group, Adelaide, SA, Australia
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Kerner G, Quintana-Murci L. The genetic and evolutionary determinants of COVID-19 susceptibility. Eur J Hum Genet 2022; 30:915-921. [PMID: 35760904 PMCID: PMC9244541 DOI: 10.1038/s41431-022-01141-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 04/26/2022] [Accepted: 06/16/2022] [Indexed: 02/08/2023] Open
Abstract
Devastating pandemics, such as that due to COVID-19, can provide strong testimony to our knowledge of the genetic and evolutionary determinants of infectious disease susceptibility and severity. One of the most remarkable aspects of such outbreaks is the stunning interindividual variability observed in the course of infection. In recent decades, enormous progress has been made in the field of the human genetics of infectious diseases, and an increasing number of human genetic factors have been reported to explain, to a great extent, the observed variability for a large number of infectious agents. However, our understanding of the cellular, molecular, and immunological mechanisms underlying such disparities between individuals and ethnic groups, remains very limited. Here, we discuss recent findings relating to human genetic predisposition to infectious disease, from an immunological or population genetic perspective, and show how these and other innovative approaches have been applied to deciphering the genetic basis of human susceptibility to COVID-19 and the severity of this disease. From an evolutionary perspective, we show how past demographic and selection events characterizing the history of our species, including admixture with archaic humans, such as Neanderthals, facilitated modern human adaptation to the threats imposed by ancient pathogens. In the context of emerging infectious diseases, these past episodes of genetic adaptation may contribute to some of the observed population differences in the outcome of SARS-CoV-2 infection and the severity of COVID-19 illness.
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Affiliation(s)
- Gaspard Kerner
- Institut Pasteur, Université Paris Cité, CNRS UMR2000, Human Evolutionary Genetics Unit, F-75015, Paris, France
| | - Lluis Quintana-Murci
- Institut Pasteur, Université Paris Cité, CNRS UMR2000, Human Evolutionary Genetics Unit, F-75015, Paris, France.
- Collège de France, Chair of Human Genomics and Evolution, F-75005, Paris, France.
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43
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Garcia-Erill G, Jørgensen CHF, Muwanika VB, Wang X, Rasmussen MS, de Jong YA, Gaubert P, Olayemi A, Salmona J, Butynski TM, Bertola LD, Siegismund HR, Albrechtsen A, Heller R. Warthog Genomes Resolve an Evolutionary Conundrum and Reveal Introgression of Disease Resistance Genes. Mol Biol Evol 2022; 39:6627297. [PMID: 35779009 PMCID: PMC9250280 DOI: 10.1093/molbev/msac134] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
African wild pigs have a contentious evolutionary and biogeographic history. Until recently, desert warthog (Phacochoerus aethiopicus) and common warthog (P. africanus) were considered a single species. Molecular evidence surprisingly suggested they diverged at least 4.4 million years ago, and possibly outside of Africa. We sequenced the first whole-genomes of four desert warthogs and 35 common warthogs from throughout their range. We show that these two species diverged much later than previously estimated, 400,000–1,700,000 years ago depending on assumptions of gene flow. This brings it into agreement with the paleontological record. We found that the common warthog originated in western Africa and subsequently colonized eastern and southern Africa. During this range expansion, the common warthog interbred with the desert warthog, presumably in eastern Africa, underlining this region’s importance in African biogeography. We found that immune system–related genes may have adaptively introgressed into common warthogs, indicating that resistance to novel diseases was one of the most potent drivers of evolution as common warthogs expanded their range. Hence, we solve some of the key controversies surrounding warthog evolution and reveal a complex evolutionary history involving range expansion, introgression, and adaptation to new diseases.
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Affiliation(s)
- Genís Garcia-Erill
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Christian H F Jørgensen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Vincent B Muwanika
- Department of Environmental Management, Makerere University, PO Box 7062, Kampala, Uganda
| | - Xi Wang
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Malthe S Rasmussen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Yvonne A de Jong
- Eastern Africa Primate Diversity and Conservation Program & Lolldaiga Hills Research Programme, PO Box 149, Nanyuki 10400, Kenya
| | - Philippe Gaubert
- Laboratoire Évolution & Diversité Biologique, Université Toulouse III Paul Sabatier, 31062 Toulouse, France
| | - Ayodeji Olayemi
- Natural History Museum, Obafemi Awolowo University, HO 220005 Ile Ife, Nigeria
| | - Jordi Salmona
- Laboratoire Évolution & Diversité Biologique, Université Toulouse III Paul Sabatier, 31062 Toulouse, France
| | - Thomas M Butynski
- Eastern Africa Primate Diversity and Conservation Program & Lolldaiga Hills Research Programme, PO Box 149, Nanyuki 10400, Kenya
| | - Laura D Bertola
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Hans R Siegismund
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Anders Albrechtsen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Rasmus Heller
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
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44
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Tournebize R, Borner L, Manel S, Meynard CN, Vigouroux Y, Crouzillat D, Fournier C, Kassam M, Descombes P, Tranchant-Dubreuil C, Parrinello H, Kiwuka C, Sumirat U, Legnate H, Kambale JL, Sonké B, Mahinga JC, Musoli P, Janssens SB, Stoffelen P, de Kochko A, Poncet V. Ecological and genomic vulnerability to climate change across native populations of Robusta coffee (Coffea canephora). GLOBAL CHANGE BIOLOGY 2022; 28:4124-4142. [PMID: 35527235 DOI: 10.1111/gcb.16191] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 02/11/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
The assessment of population vulnerability under climate change is crucial for planning conservation as well as for ensuring food security. Coffea canephora is, in its native habitat, an understorey tree that is mainly distributed in the lowland rainforests of tropical Africa. Also known as Robusta, its commercial value constitutes a significant revenue for many human populations in tropical countries. Comparing ecological and genomic vulnerabilities within the species' native range can provide valuable insights about habitat loss and the species' adaptive potential, allowing to identify genotypes that may act as a resource for varietal improvement. By applying species distribution models, we assessed ecological vulnerability as the decrease in climatic suitability under future climatic conditions from 492 occurrences. We then quantified genomic vulnerability (or risk of maladaptation) as the allelic composition change required to keep pace with predicted climate change. Genomic vulnerability was estimated from genomic environmental correlations throughout the native range. Suitable habitat was predicted to diminish to half its size by 2050, with populations near coastlines and around the Congo River being the most vulnerable. Whole-genome sequencing revealed 165 candidate SNPs associated with climatic adaptation in C. canephora, which were located in genes involved in plant response to biotic and abiotic stressors. Genomic vulnerability was higher for populations in West Africa and in the region at the border between DRC and Uganda. Despite an overall low correlation between genomic and ecological vulnerability at broad scale, these two components of vulnerability overlap spatially in ways that may become damaging. Genomic vulnerability was estimated to be 23% higher in populations where habitat will be lost in 2050 compared to regions where habitat will remain suitable. These results highlight how ecological and genomic vulnerabilities are relevant when planning on how to cope with climate change regarding an economically important species.
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Affiliation(s)
- Rémi Tournebize
- DIADE, CIRAD, IRD, Univ. Montpellier, Montpellier, France
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Leyli Borner
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
- INRAE, Le Rheu, France
| | - Stéphanie Manel
- CEFE, CNRS, EPHE-PSL University, IRD, Univ Montpellier, Montpellier, France
| | - Christine N Meynard
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Yves Vigouroux
- DIADE, CIRAD, IRD, Univ. Montpellier, Montpellier, France
| | | | - Coralie Fournier
- Nestlé Research, Société des Produits Nestlé S.A., EPFL Innovation Park, Lausanne, Switzerland
- School of Medicine, University of Geneva, Geneva, Switzerland
| | - Mohamed Kassam
- Nestlé Research, Société des Produits Nestlé S.A., EPFL Innovation Park, Lausanne, Switzerland
- Danone Nutricia Research, Singapore
| | - Patrick Descombes
- Nestlé Research, Société des Produits Nestlé S.A., EPFL Innovation Park, Lausanne, Switzerland
| | | | - Hugues Parrinello
- CNRS, INSERM, Univ. Montpellier, Montpellier, France
- Montpellier GenomiX, France Génomique, Montpellier, France
| | | | | | | | - Jean-Léon Kambale
- University of Kisangani, Kisangani, Democratic Republic of the Congo
| | | | | | | | - Steven B Janssens
- Meise Botanic Garden, Meise, Belgium
- Department of Biology, KU Leuven, Leuven, Belgium
| | | | | | - Valérie Poncet
- DIADE, CIRAD, IRD, Univ. Montpellier, Montpellier, France
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45
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Hernandez-Jaimes OA, Cazares-Olvera DV, Line J, Moreno-Eutimio MA, Gómez-Castro CZ, Naisbitt DJ, Castrejón-Flores JL. Advances in Our Understanding of the Interaction of Drugs with T-cells: Implications for the Discovery of Biomarkers in Severe Cutaneous Drug Reactions. Chem Res Toxicol 2022; 35:1162-1183. [PMID: 35704769 DOI: 10.1021/acs.chemrestox.1c00434] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Drugs can activate different cells of the immune system and initiate an immune response that can lead to life-threatening diseases collectively known as severe cutaneous adverse reactions (SCARs). Antibiotics, anticonvulsants, and antiretrovirals are involved in the development of SCARs by the activation of αβ naïve T-cells. However, other subsets of lymphocytes known as nonconventional T-cells with a limited T-cell receptor repertoire and innate and adaptative functions also recognize drugs and drug-like molecules, but their role in the pathogenesis of SCARs has only just begun to be explored. Despite 30 years of advances in our understanding of the mechanisms in which drugs interact with T-cells and the pathways for tissue injury seen during T-cell activation, at present, the development of useful clinical biomarkers for SCARs or predictive preclinical in vitro assays that could identify immunogenic moieties during drug discovery is an unmet goal. Therefore, the present review focuses on (i) advances in the understanding of the pathogenesis of SCARs reactions, (ii) a description of the interaction of drugs with conventional and nonconventional T-cells, and (iii) the current state of soluble blood circulating biomarker candidates for SCARs.
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Affiliation(s)
| | - Diana Valeria Cazares-Olvera
- Instituto Politécnico Nacional, Unidad Profesional Interdisciplinaria de Biotecnología, México City 07340, México
| | - James Line
- MRC Centre for Drug Safety Science, Department of Pharmacology, University of Liverpool, Liverpool L69 3GE, United Kingdom
| | | | | | - Dean J Naisbitt
- MRC Centre for Drug Safety Science, Department of Pharmacology, University of Liverpool, Liverpool L69 3GE, United Kingdom
| | - José Luis Castrejón-Flores
- Instituto Politécnico Nacional, Unidad Profesional Interdisciplinaria de Biotecnología, México City 07340, México
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46
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Brand CM, Colbran LL, Capra JA. Predicting Archaic Hominin Phenotypes from Genomic Data. Annu Rev Genomics Hum Genet 2022; 23:591-612. [PMID: 35440148 DOI: 10.1146/annurev-genom-111521-121903] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Ancient DNA provides a powerful window into the biology of extant and extinct species, including humans' closest relatives: Denisovans and Neanderthals. Here, we review what is known about archaic hominin phenotypes from genomic data and how those inferences have been made. We contend that understanding the influence of variants on lower-level molecular phenotypes-such as gene expression and protein function-is a promising approach to using ancient DNA to learn about archaic hominin traits. Molecular phenotypes have simpler genetic architectures than organism-level complex phenotypes, and this approach enables moving beyond association studies by proposing hypotheses about the effects of archaic variants that are testable in model systems. The major challenge to understanding archaic hominin phenotypes is broadening our ability to accurately map genotypes to phenotypes, but ongoing advances ensure that there will be much more to learn about archaic hominin phenotypes from their genomes. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Colin M Brand
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA; , .,Bakar Computational Health Sciences Institute, University of California, San Francisco, California, USA
| | - Laura L Colbran
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - John A Capra
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA; , .,Bakar Computational Health Sciences Institute, University of California, San Francisco, California, USA
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47
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Caron B, Patin E, Rotival M, Charbit B, Albert ML, Quintana-Murci L, Duffy D, Rausell A. Integrative genetic and immune cell analysis of plasma proteins in healthy donors identifies novel associations involving primary immune deficiency genes. Genome Med 2022; 14:28. [PMID: 35264221 PMCID: PMC8905727 DOI: 10.1186/s13073-022-01032-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 02/15/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Blood plasma proteins play an important role in immune defense against pathogens, including cytokine signaling, the complement system, and the acute-phase response. Recent large-scale studies have reported genetic (i.e., protein quantitative trait loci, pQTLs) and non-genetic factors, such as age and sex, as major determinants to inter-individual variability in immune response variation. However, the contribution of blood-cell composition to plasma protein heterogeneity has not been fully characterized and may act as a mediating factor in association studies. METHODS Here, we evaluated plasma protein levels from 400 unrelated healthy individuals of western European ancestry, who were stratified by sex and two decades of life (20-29 and 60-69 years), from the Milieu Intérieur cohort. We quantified 229 proteins by Luminex in a clinically certified laboratory and their levels of variation were analyzed together with 5.2 million single-nucleotide polymorphisms. With respect to non-genetic variables, we included 254 lifestyle and biochemical factors, as well as counts of seven circulating immune cell populations measured by hemogram and standardized flow cytometry. RESULTS Collectively, we found 152 significant associations involving 49 proteins and 20 non-genetic variables. Consistent with previous studies, age and sex showed a global, pervasive impact on plasma protein heterogeneity, while body mass index and other health status variables were among the non-genetic factors with the highest number of associations. After controlling for these covariates, we identified 100 and 12 pQTLs acting in cis and trans, respectively, collectively associated with 87 plasma proteins and including 19 novel genetic associations. Genetic factors explained the largest fraction of the variability of plasma protein levels, as compared to non-genetic factors. In addition, blood-cell fractions, including leukocytes, lymphocytes, monocytes, neutrophils, eosinophils, basophils, and platelets, had a larger contribution to inter-individual variability than age and sex and appeared as confounders of specific genetic associations. Finally, we identified new genetic associations with plasma protein levels of five monogenic Mendelian disease genes including two primary immunodeficiency genes (Ficolin-3 and FAS). CONCLUSIONS Our study identified novel genetic and non-genetic factors associated to plasma protein levels which may inform health status and disease management.
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Affiliation(s)
- Barthelemy Caron
- Université de Paris, INSERM UMR1163, Imagine Institute, Clinical Bioinformatics Laboratory, F-75006, Paris, France
| | - Etienne Patin
- Human Evolutionary Genetics Unit, Institut Pasteur, UMR2000, CNRS, Université de Paris, F-75015, Paris, France
| | - Maxime Rotival
- Human Evolutionary Genetics Unit, Institut Pasteur, UMR2000, CNRS, Université de Paris, F-75015, Paris, France
| | - Bruno Charbit
- Cytometry and Biomarkers UTechS, CRT, Institut Pasteur, Université de Paris, F-75015, Paris, France
| | | | - Lluis Quintana-Murci
- Human Evolutionary Genetics Unit, Institut Pasteur, UMR2000, CNRS, Université de Paris, F-75015, Paris, France
- Human Genomics and Evolution, Collège de France, F-75005, Paris, France
| | - Darragh Duffy
- Cytometry and Biomarkers UTechS, CRT, Institut Pasteur, Université de Paris, F-75015, Paris, France.
- Translational Immunology Unit, Institut Pasteur, Université de Paris, F-75015, Paris, France.
| | - Antonio Rausell
- Université de Paris, INSERM UMR1163, Imagine Institute, Clinical Bioinformatics Laboratory, F-75006, Paris, France.
- Service de Médecine Génomique des Maladies Rares, AP-HP, Necker Hospital for Sick Children, F-75015, Paris, France.
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48
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Jagoda E, Xue JR, Reilly SK, Dannemann M, Racimo F, Huerta-Sanchez E, Sankararaman S, Kelso J, Pagani L, Sabeti PC, Capellini TD. Detection of Neanderthal Adaptively Introgressed Genetic Variants That Modulate Reporter Gene Expression in Human Immune Cells. Mol Biol Evol 2022; 39:msab304. [PMID: 34662402 PMCID: PMC8760939 DOI: 10.1093/molbev/msab304] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Although some variation introgressed from Neanderthals has undergone selective sweeps, little is known about its functional significance. We used a Massively Parallel Reporter Assay (MPRA) to assay 5,353 high-frequency introgressed variants for their ability to modulate the gene expression within 170 bp of endogenous sequence. We identified 2,548 variants in active putative cis-regulatory elements (CREs) and 292 expression-modulating variants (emVars). These emVars are predicted to alter the binding motifs of important immune transcription factors, are enriched for associations with neutrophil and white blood cell count, and are associated with the expression of genes that function in innate immune pathways including inflammatory response and antiviral defense. We combined the MPRA data with other data sets to identify strong candidates to be driver variants of positive selection including an emVar that may contribute to protection against severe COVID-19 response. We endogenously deleted two CREs containing expression-modulation variants linked to immune function, rs11624425 and rs80317430, identifying their primary genic targets as ELMSAN1, and PAN2 and STAT2, respectively, three genes differentially expressed during influenza infection. Overall, we present the first database of experimentally identified expression-modulating Neanderthal-introgressed alleles contributing to potential immune response in modern humans.
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Affiliation(s)
- Evelyn Jagoda
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - James R Xue
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Steven K Reilly
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael Dannemann
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Fernando Racimo
- Lundbeck GeoGenetics Centre, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Emilia Huerta-Sanchez
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, USA
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA
| | - Sriram Sankararaman
- Department of Computer Science, UCLA, Los Angeles, CA, USA
- Department of Human Genetics, UCLA, Los Angeles, CA, USA
| | - Janet Kelso
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Luca Pagani
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Department of Biology, University of Padova, Padova, Italy
| | - Pardis C Sabeti
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Terence D Capellini
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
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49
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Laval G, Patin E, Boutillier P, Quintana-Murci L. Sporadic occurrence of recent selective sweeps from standing variation in humans as revealed by an approximate Bayesian computation approach. Genetics 2021; 219:6377789. [PMID: 34849862 DOI: 10.1093/genetics/iyab161] [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: 06/20/2021] [Accepted: 09/01/2021] [Indexed: 12/14/2022] Open
Abstract
During their dispersals over the last 100,000 years, modern humans have been exposed to a large variety of environments, resulting in genetic adaptation. While genome-wide scans for the footprints of positive Darwinian selection have increased knowledge of genes and functions potentially involved in human local adaptation, they have globally produced evidence of a limited contribution of selective sweeps in humans. Conversely, studies based on machine learning algorithms suggest that recent sweeps from standing variation are widespread in humans, an observation that has been recently questioned. Here, we sought to formally quantify the number of recent selective sweeps in humans, by leveraging approximate Bayesian computation and whole-genome sequence data. Our computer simulations revealed suitable ABC estimations, regardless of the frequency of the selected alleles at the onset of selection and the completion of sweeps. Under a model of recent selection from standing variation, we inferred that an average of 68 (from 56 to 79) and 140 (from 94 to 198) sweeps occurred over the last 100,000 years of human history, in African and Eurasian populations, respectively. The former estimation is compatible with human adaptation rates estimated since divergence with chimps, and reveals numbers of sweeps per generation per site in the range of values estimated in Drosophila. Our results confirm the rarity of selective sweeps in humans and show a low contribution of sweeps from standing variation to recent human adaptation.
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Affiliation(s)
- Guillaume Laval
- Human Evolutionary Genetics Unit, Institut Pasteur, UMR 2000, CNRS, Paris 75015, France
| | - Etienne Patin
- Human Evolutionary Genetics Unit, Institut Pasteur, UMR 2000, CNRS, Paris 75015, France
| | - Pierre Boutillier
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Lluis Quintana-Murci
- Human Evolutionary Genetics Unit, Institut Pasteur, UMR 2000, CNRS, Paris 75015, France.,Human Genomics and Evolution, Collège de France, 75005 Paris, France
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50
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Human immune diversity: from evolution to modernity. Nat Immunol 2021; 22:1479-1489. [PMID: 34795445 DOI: 10.1038/s41590-021-01058-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/17/2021] [Indexed: 02/08/2023]
Abstract
The extreme diversity of the human immune system, forged and maintained throughout evolutionary history, provides a potent defense against opportunistic pathogens. At the same time, this immune variation is the substrate upon which a plethora of immune-associated diseases develop. Genetic analysis suggests that thousands of individually weak loci together drive up to half of the observed immune variation. Intense selection maintains this genetic diversity, even selecting for the introgressed Neanderthal or Denisovan alleles that have reintroduced variation lost during the out-of-Africa migration. Variations in age, sex, diet, environmental exposure, and microbiome each potentially explain the residual variation, with proof-of-concept studies demonstrating both plausible mechanisms and correlative associations. The confounding interaction of many of these variables currently makes it difficult to assign definitive contributions. Here, we review the current state of play in the field, identify the key unknowns in the causality of immune variation, and identify the multidisciplinary pathways toward an improved understanding.
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