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Loh L, Saunders PM, Faoro C, Font-Porterias N, Nemat-Gorgani N, Harrison GF, Sadeeq S, Hensen L, Wong SC, Widjaja J, Clemens EB, Zhu S, Kichula KM, Tao S, Zhu F, Montero-Martin G, Fernandez-Vina M, Guethlein LA, Vivian JP, Davies J, Mentzer AJ, Oppenheimer SJ, Pomat W, Ioannidis AG, Barberena-Jonas C, Moreno-Estrada A, Miller A, Parham P, Rossjohn J, Tong SYC, Kedzierska K, Brooks AG, Norman PJ. An archaic HLA class I receptor allele diversifies natural killer cell-driven immunity in First Nations peoples of Oceania. Cell 2024; 187:7008-7024.e19. [PMID: 39476840 PMCID: PMC11606752 DOI: 10.1016/j.cell.2024.10.005] [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: 06/19/2023] [Revised: 05/24/2024] [Accepted: 10/03/2024] [Indexed: 11/02/2024]
Abstract
Genetic variation in host immunity impacts the disproportionate burden of infectious diseases that can be experienced by First Nations peoples. Polymorphic human leukocyte antigen (HLA) class I and killer cell immunoglobulin-like receptors (KIRs) are key regulators of natural killer (NK) cells, which mediate early infection control. How this variation impacts their responses across populations is unclear. We show that HLA-A∗24:02 became the dominant ligand for inhibitory KIR3DL1 in First Nations peoples across Oceania, through positive natural selection. We identify KIR3DL1∗114, widespread across and unique to Oceania, as an allele lineage derived from archaic humans. KIR3DL1∗114+NK cells from First Nations Australian donors are inhibited through binding HLA-A∗24:02. The KIR3DL1∗114 lineage is defined by phenylalanine at residue 166. Structural and binding studies show phenylalanine 166 forms multiple unique contacts with HLA-peptide complexes, increasing both affinity and specificity. Accordingly, assessing immunogenetic variation and the functional implications for immunity are fundamental toward understanding population-based disease associations.
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Affiliation(s)
- Liyen Loh
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Philippa M Saunders
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Camilla Faoro
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Neus Font-Porterias
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Neda Nemat-Gorgani
- Department of Structural Biology and Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Genelle F Harrison
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Suraju Sadeeq
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Luca Hensen
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Shu Cheng Wong
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Jacqueline Widjaja
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - E Bridie Clemens
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Shiying Zhu
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Katherine M Kichula
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Sudan Tao
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO 80045, USA; Blood Center of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Faming Zhu
- Blood Center of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Gonzalo Montero-Martin
- Stanford Blood Centre, Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Marcelo Fernandez-Vina
- Stanford Blood Centre, Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Lisbeth A Guethlein
- Department of Structural Biology and Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Julian P Vivian
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Jane Davies
- Menzies School of Health Research, Charles Darwin University, Darwin, NT 0810, Australia; Department of Infectious Diseases, Royal Darwin Hospital, Casuarina, NT 0810, Australia
| | - Alexander J Mentzer
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7LF, UK
| | - Stephen J Oppenheimer
- Institute of Social and Cultural Anthropology, School of Anthropology and Museum Ethnography, University of Oxford, Oxford OX3 7LF, UK
| | - William Pomat
- Papua New Guinea Institute of Medical Research, Post Office Box 60, Goroka, Papua New Guinea
| | | | - Carmina Barberena-Jonas
- Advanced Genomics Unit, Center for Research and Advanced Studies (CINVESTAV), Irapuato 36821, Mexico
| | - Andrés Moreno-Estrada
- Advanced Genomics Unit, Center for Research and Advanced Studies (CINVESTAV), Irapuato 36821, Mexico
| | - Adrian Miller
- Jawun Research Centre, Central Queensland University, Cairns, QLD 4870, Australia
| | - Peter Parham
- Department of Structural Biology and Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Jamie Rossjohn
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, UK.
| | - Steven Y C Tong
- Victorian Infectious Diseases Service, The Royal Melbourne Hospital, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC 3000, Australia; Department of Infectious Diseases, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC 3000, Australia.
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia.
| | - Andrew G Brooks
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia.
| | - Paul J Norman
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA; Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO 80045, USA; Department of Structural Biology and Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA.
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Horwood PF, Tarantola A, Goarant C, Matsui M, Klement E, Umezaki M, Navarro S, Greenhill AR. Health Challenges of the Pacific Region: Insights From History, Geography, Social Determinants, Genetics, and the Microbiome. Front Immunol 2019; 10:2184. [PMID: 31572391 PMCID: PMC6753857 DOI: 10.3389/fimmu.2019.02184] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 08/29/2019] [Indexed: 02/06/2023] Open
Abstract
The Pacific region, also referred to as Oceania, is a geographically widespread region populated by people of diverse cultures and ethnicities. Indigenous people in the region (Melanesians, Polynesians, Micronesians, Papuans, and Indigenous Australians) are over-represented on national, regional, and global scales for the burden of infectious and non-communicable diseases. Although social and environmental factors such as poverty, education, and access to health-care are assumed to be major drivers of this disease burden, there is also developing evidence that genetic and microbiotic factors should also be considered. To date, studies investigating genetic and/or microbiotic links with vulnerabilities to infectious and non-communicable diseases have mostly focused on populations in Europe, Asia, and USA, with uncertain associations for other populations such as indigenous communities in Oceania. Recent developments in personalized medicine have shown that identifying ethnicity-linked genetic vulnerabilities can be important for medical management. Although our understanding of the impacts of the gut microbiome on health is still in the early stages, it is likely that equivalent vulnerabilities will also be identified through the interaction between gut microbiome composition and function with pathogens and the host immune system. As rapid economic, dietary, and cultural changes occur throughout Oceania it becomes increasingly important that further research is conducted within indigenous populations to address the double burden of high rates of infectious diseases and rapidly rising non-communicable diseases so that comprehensive development goals can be planned. In this article, we review the current knowledge on the impact of nutrition, genetics, and the gut microbiome on infectious diseases in indigenous people of the Pacific region.
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Affiliation(s)
- Paul F. Horwood
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, Australia
| | | | - Cyrille Goarant
- Institut Pasteur de Nouvelle-Calédonie, Noumea, New Caledonia
| | - Mariko Matsui
- Institut Pasteur de Nouvelle-Calédonie, Noumea, New Caledonia
| | - Elise Klement
- Institut Pasteur de Nouvelle-Calédonie, Noumea, New Caledonia
- Internal Medicine and Infectious Diseases Department, Centre Hospitalier Territorial, Noumea, New Caledonia
| | - Masahiro Umezaki
- Department of Human Ecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Severine Navarro
- Immunology Department, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Andrew R. Greenhill
- School of Health and Life Sciences, Federation University Australia, Churchill, VIC, Australia
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Tarantola A, Horwood PF, Goarant C, Bertrand S, Merilles OEA, Pedron T, Klement-Frutos E, Sansonetti P, Quintana-Murci L, Richard V. Counting Oceanians of Non-European, Non-Asian Descent (ONENA) in the South Pacific to Make Them Count in Global Health. Trop Med Infect Dis 2019; 4:114. [PMID: 31405081 PMCID: PMC6789437 DOI: 10.3390/tropicalmed4030114] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 07/30/2019] [Accepted: 08/06/2019] [Indexed: 01/07/2023] Open
Abstract
Several diseases and vulnerabilities associated with genetic or microbial factors are more frequent among populations of Oceanian, Non-European, Non-Asian descent (ONENA). ONENA are specific and have long been isolated geographically. To our knowledge, there are no published official, quantitative, aggregated data on the populations impacted by these excess vulnerabilities in Oceania. We searched official census reports for updated estimates of the total population for each of the Pacific Island Countries and Territories (including Australia) and the US State of Hawaii, privileging local official statistical or censual sources. We multiplied the most recent total population estimate by the cumulative percentage of the ONENA population as determined in official reports. Including Australia and the US State of Hawaii, Oceania counts 27 countries and territories, populated in 2016 by approximately 41 M inhabitants (17 M not counting Australia) among which approximately 12.5 M (11.6 M not counting Australia) consider themselves of entire or partial ONENA ancestry. Specific genetic and microbiome traits of ONENA may be unique and need further investigation to adjust risk estimates, risk prevention, diagnostic and therapeutic strategies, to the benefit of populations in the Pacific and beyond.
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Affiliation(s)
- Arnaud Tarantola
- Epidemiology unit, Institut Pasteur de Nouvelle-Calédonie, BP 61-98845 Nouméa cedex, New Caledonia.
| | - Paul F Horwood
- Virology and Viral Diseases, College of Public Health, Medical and Veterinary Sciences, Division of Tropical Health and Medicine, James Cook University, Townsville QLD 4811, Australia
| | - Cyrille Goarant
- Leptospirosis research and expertise unit, Institut Pasteur de Nouvelle-Calédonie, BP 61 - 98845 Nouméa cedex, New Caledonia
| | - Solène Bertrand
- Communauté du Pacifique/Pacific Community, 95 Promenade Roger Laroque, BP D5, Nouméa 98848, New Caledonia
| | - Onofre Edwin A Merilles
- Communauté du Pacifique/Pacific Community, 95 Promenade Roger Laroque, BP D5, Nouméa 98848, New Caledonia
| | - Thierry Pedron
- Unité de Pathogénie Microbienne Moléculaire, INSERM U1202, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris cedex 15, France
| | - Elise Klement-Frutos
- Epidemiology unit, Institut Pasteur de Nouvelle-Calédonie, BP 61-98845 Nouméa cedex, New Caledonia
- Internal Medicine and Infectious Diseases Department, Centre Hospitalier Territorial, 110 Boulevard Joseph Wamytan, Dumbéa Sur Mer 98835, New Caledonia
| | - Philippe Sansonetti
- Unité de Pathogénie Microbienne Moléculaire, INSERM U1202, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris cedex 15 ; Chaire de Microbiologie et Maladies Infectieuses, Collège de France, 11 squareMarcelin Berthelot, 75005 Paris, France
| | - Lluis Quintana-Murci
- Human Evolutionary Genetics Unit, Institut Pasteur, 25-28 Rue du Docteur Roux, 75015 Paris, France
| | - Vincent Richard
- Institut Pasteur de Nouvelle-Calédonie, BP 61-98845 Nouméa cedex, New Caledonia
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