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Bouafou L, Makanga BK, Rahola N, Boddé M, Ngangué MF, Daron J, Berger A, Mouillaud T, Makunin A, Korlević P, Nwezeobi J, Kengne P, Paupy C, Lawniczak MKN, Ayala D. Host preference patterns in domestic and wild settings: Insights into Anopheles feeding behavior. Evol Appl 2024; 17:e13693. [PMID: 38828055 PMCID: PMC11143308 DOI: 10.1111/eva.13693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 03/28/2024] [Accepted: 04/02/2024] [Indexed: 06/05/2024] Open
Abstract
The adaptation of Anopheles malaria vectors to domestic settings is directly linked to their ability to feed on humans. The strength of this species-habitat association is unequal across the species within the genus, with the major vectors being particularly dependent on humans. However, our understanding of how blood-feeding behavior interacts with and adapts to environmental settings, including the presence of humans, remains limited. Using a field-based approach, we first investigated Anopheles community structure and feeding behavior patterns in domestic and sylvatic settings in La Lopé National Park in Gabon, Central Africa. We characterized the preference indices using a dual-host choice sampling approach across mosquito species, habitats, and seasons. We then quantified the plastic biting behavior of mosquito species in each habitat. We collected individuals from 16 Anopheles species that exhibited significant differences in species composition and abundance between sylvatic and domestic settings. The host-seeking behavior also varied among the seven most abundant species. The general attractiveness to each host, human or animal, remained relatively constant for each species, but with significant variations between habitats across species. These variations, to more generalist and to more anthropophilic behavior, were related to seasonal changes and distance from the village, respectively. Finally, we pointed out that the host choice of major malaria vectors changed in the absence of humans, revealing a plastic feeding behavior of these species. This study highlights the effect of humans on Anopheles distribution and feeding evolution. The characterization of feeding behavior in wild and domestic settings provides opportunities to better understand the interplay between genetic determinants of host preference and ecological factors. Our findings suggest that protected areas may offer alternative thriving conditions to major malaria vectors.
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Affiliation(s)
- Lemonde Bouafou
- UMR MIVEGEC, University of Montpellier, CNRS, IRDMontpellierFrance
- CIRMFFrancevilleGabon
| | | | - Nil Rahola
- UMR MIVEGEC, University of Montpellier, CNRS, IRDMontpellierFrance
| | | | | | - Josquin Daron
- UMR MIVEGEC, University of Montpellier, CNRS, IRDMontpellierFrance
| | - Audric Berger
- UMR MIVEGEC, University of Montpellier, CNRS, IRDMontpellierFrance
| | - Theo Mouillaud
- UMR MIVEGEC, University of Montpellier, CNRS, IRDMontpellierFrance
| | | | | | | | - Pierre Kengne
- UMR MIVEGEC, University of Montpellier, CNRS, IRDMontpellierFrance
- CIRMFFrancevilleGabon
| | - Christophe Paupy
- UMR MIVEGEC, University of Montpellier, CNRS, IRDMontpellierFrance
| | | | - Diego Ayala
- UMR MIVEGEC, University of Montpellier, CNRS, IRDMontpellierFrance
- Medical Entomology UnitInstitut Pasteur de MadagascarAntananarivoMadagascar
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2
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Hong SC, Muyas F, Cortés-Ciriano I, Hormoz S. scAI-SNP: a method for inferring ancestry from single-cell data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.14.594208. [PMID: 38798590 PMCID: PMC11118306 DOI: 10.1101/2024.05.14.594208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Collaborative efforts, such as the Human Cell Atlas, are rapidly accumulating large amounts of single-cell data. To ensure that single-cell atlases are representative of human genetic diversity, we need to determine the ancestry of the donors from whom single-cell data are generated. Self-reporting of race and ethnicity, although important, can be biased and is not always available for the datasets already collected. Here, we introduce scAI-SNP, a tool to infer ancestry directly from single-cell genomics data. To train scAI-SNP, we identified 4.5 million ancestry-informative single-nucleotide polymorphisms (SNPs) in the 1000 Genomes Project dataset across 3201 individuals from 26 population groups. For a query single-cell data set, scAI-SNP uses these ancestry-informative SNPs to compute the contribution of each of the 26 population groups to the ancestry of the donor from whom the cells were obtained. Using diverse single-cell data sets with matched whole-genome sequencing data, we show that scAI-SNP is robust to the sparsity of single-cell data, can accurately and consistently infer ancestry from samples derived from diverse types of tissues and cancer cells, and can be applied to different modalities of single-cell profiling assays, such as single-cell RNA-seq and single-cell ATAC-seq. Finally, we argue that ensuring that single-cell atlases represent diverse ancestry, ideally alongside race and ethnicity, is ultimately important for improved and equitable health outcomes by accounting for human diversity.
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Affiliation(s)
- Sung Chul Hong
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Francesc Muyas
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK
| | - Isidro Cortés-Ciriano
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK
| | - Sahand Hormoz
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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3
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Martiniano R, Haber M, Almarri MA, Mattiangeli V, Kuijpers MCM, Chamel B, Breslin EM, Littleton J, Almahari S, Aloraifi F, Bradley DG, Lombard P, Durbin R. Ancient genomes illuminate Eastern Arabian population history and adaptation against malaria. CELL GENOMICS 2024; 4:100507. [PMID: 38417441 PMCID: PMC10943591 DOI: 10.1016/j.xgen.2024.100507] [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: 08/04/2023] [Revised: 11/01/2023] [Accepted: 01/31/2024] [Indexed: 03/01/2024]
Abstract
The harsh climate of Arabia has posed challenges in generating ancient DNA from the region, hindering the direct examination of ancient genomes for understanding the demographic processes that shaped Arabian populations. In this study, we report whole-genome sequence data obtained from four Tylos-period individuals from Bahrain. Their genetic ancestry can be modeled as a mixture of sources from ancient Anatolia, Levant, and Iran/Caucasus, with variation between individuals suggesting population heterogeneity in Bahrain before the onset of Islam. We identify the G6PD Mediterranean mutation associated with malaria resistance in three out of four ancient Bahraini samples and estimate that it rose in frequency in Eastern Arabia from 5 to 6 kya onward, around the time agriculture appeared in the region. Our study characterizes the genetic composition of ancient Arabians, shedding light on the population history of Bahrain and demonstrating the feasibility of studies of ancient DNA in the region.
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Affiliation(s)
- Rui Martiniano
- School of Biological and Environmental Sciences, Liverpool John Moores University, L3 3AF Liverpool, UK.
| | - Marc Haber
- Institute of Cancer and Genomic Sciences, University of Birmingham Dubai, Dubai, United Arab Emirates
| | - Mohamed A Almarri
- Department of Forensic Science and Criminology, Dubai Police GHQ, Dubai, United Arab Emirates; College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | | | - Mirte C M Kuijpers
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Berenice Chamel
- Institut Français du Proche-Orient (MEAE/CNRS), Beirut, Lebanon
| | - Emily M Breslin
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Judith Littleton
- School of Social Sciences, University of Auckland, Auckland, New Zealand
| | - Salman Almahari
- Bahrain Authority for Culture and Antiquities, Manama, Kingdom of Bahrain
| | - Fatima Aloraifi
- Mersey and West Lancashire Teaching Hospitals NHS Trust, Whiston Hospital, Warrington Road, Prescot, L35 5DR Liverpool, UK
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Pierre Lombard
- Bahrain Authority for Culture and Antiquities, Manama, Kingdom of Bahrain; Archéorient UMR 5133, CNRS, Université Lyon 2, Maison de l'Orient et de la Méditerranée - Jean Pouilloux, Lyon, France
| | - Richard Durbin
- Department of Genetics, University of Cambridge, CB2 3EH Cambridge, UK.
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Atarihuana S, Gallardo-Condor J, López-Cortés A, Jimenes-Vargas K, Burgos G, Karina-Zambrano A, Flores-Espinoza R, Coral M, Cabrera-Andrade A. Genetic basis and spatial distribution of glucose-6-phosphate dehydrogenase deficiency in ecuadorian ethnic groups: a malaria perspective. Malar J 2023; 22:283. [PMID: 37752491 PMCID: PMC10521485 DOI: 10.1186/s12936-023-04716-x] [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: 07/11/2023] [Accepted: 09/12/2023] [Indexed: 09/28/2023] Open
Abstract
BACKGROUND Glucose-6-phosphate dehydrogenase deficiency (G6PDd) is an X-linked disorder affecting over 400 million people worldwide. Individuals with molecular variants associated with reduced enzymatic activity are susceptible to oxidative stress in red blood cells, thereby increasing the risk of pathophysiological conditions and toxicity to anti-malarial treatments. Globally, the prevalence of G6PDd varies among populations. Accordingly, this study aims to characterize G6PDd distribution within the Ecuadorian population and to describe the spatial distribution of reported malaria cases. METHODS Molecular variants associated with G6PDd were genotyped in 581 individuals from Afro-Ecuadorian, Indigenous, Mestizo, and Montubio ethnic groups. Additionally, spatial analysis was conducted to identify significant malaria clusters with high incidence rates across Ecuador, using data collected from 2010 to 2021. RESULTS The A- c.202G > A and A- c.968T > C variants underpin the genetic basis of G6PDd in the studied population. The overall prevalence of G6PDd was 4.6% in the entire population. However, this frequency increased to 19.2% among Afro-Ecuadorian people. Spatial analysis revealed 12 malaria clusters, primarily located in the north of the country and its Amazon region, with relative risks of infection of 2.02 to 87.88. CONCLUSIONS The findings of this study hold significant implications for public health interventions, treatment strategies, and targeted efforts to mitigate the burden of malaria in Ecuador. The high prevalence of G6PDd among Afro-Ecuadorian groups in the northern endemic areas necessitates the development of comprehensive malaria eradication strategies tailored to this geographical region.
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Affiliation(s)
- Sebastián Atarihuana
- Facultad de Ingeniería y Ciencias Aplicadas, Universidad de Las Américas, Quito, Ecuador
| | | | - Andrés López-Cortés
- Cancer Research Group (CRG), Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Madrid, Spain
| | - Karina Jimenes-Vargas
- Grupo de Bio-Quimioinformática, Universidad de Las Américas, Quito, Ecuador
- Department of Computer Science and Information Technologies, Computer Science Faculty, CITIC, RNASA Group, University of A Coruña, A Coruña, Spain
| | - Germán Burgos
- One Health Research Group, Facultad de Medicina, Universidad de las Américas, Quito, Ecuador
- Grupo de Medicina Xenómica, Instituto de Ciencias Forenses, Universidad de Santiago de Compostela, A Coruña, Spain
| | - Ana Karina-Zambrano
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | - Rodrigo Flores-Espinoza
- Laboratório de Diagnóstico por DNA (LDD), Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marco Coral
- Grupo de Bio-Quimioinformática, Universidad de Las Américas, Quito, Ecuador
- Carrera de Medicina Veterinaria, Facultad de Ciencias de la Salud, Universidad de Las Américas, Quito, Ecuador
| | - Alejandro Cabrera-Andrade
- Grupo de Bio-Quimioinformática, Universidad de Las Américas, Quito, Ecuador.
- Escuela de Enfermería, Facultad de Ciencias de la Salud, Universidad de Las Américas, Quito, Ecuador.
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5
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Israel A, Schäffer AA, Berkovitch M, Ozeri DJ, Merzon E, Green I, Golan-Cohen A, Ruppin E, Vinker S, Magen E. Glucose-6-phosphate dehydrogenase deficiency and long-term risk of immune-related disorders. Front Immunol 2023; 14:1232560. [PMID: 37753082 PMCID: PMC10518697 DOI: 10.3389/fimmu.2023.1232560] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/29/2023] [Indexed: 09/28/2023] Open
Abstract
Introduction Glucose-6-phosphate dehydrogenase (G6PD) deficiency is an X-linked enzymatic disorder that is particularly prevalent in Africa, Asia, and the Middle East. This study aimed to assess the long-term health risks associated with G6PD deficiency. Methods A retrospective cohort study was conducted using data from a national healthcare provider in Israel (Leumit Health Services). A total of 7,473 G6PD-deficient individuals were matched with 29,892 control subjects in a 1:4 ratio, based on age, gender, socioeconomic status, and ethnic groups. The exposure of interest was recorded G6PD diagnosis or positive G6PD diagnostic test. The main outcomes and measures included rates of infectious diseases, allergic conditions, and autoimmune disorders between 2002 and 2022. Results Significantly increased rates were observed for autoimmune disorders, infectious diseases, and allergic conditions in G6PD-deficient individuals compared to the control group. Specifically, notable increases were observed for rheumatoid arthritis (odds ratio [OR] 2.41, p<0.001), systemic lupus erythematosus (OR 4.56, p<0.001), scleroderma (OR 6.87, p<0.001), pernicious anemia (OR 18.70, p<0.001), fibromyalgia (OR 1.98, p<0.001), Graves' disease (OR 1.46, p=0.001), and Hashimoto's thyroiditis (OR 1.26, p=0.001). These findings were supported by elevated rates of positive autoimmune serology and higher utilization of medications commonly used to treat autoimmune conditions in the G6PD-deficient group. Discussion In conclusion, individuals with G6PD deficiency are at a higher risk of developing autoimmune disorders, infectious diseases, and allergic conditions. This large-scale observational study provides valuable insights into the comprehensive association between G6PD deficiency and infectious and immune-related diseases. The findings emphasize the importance of considering G6PD deficiency as a potential risk factor in clinical practice and further research is warranted to better understand the underlying mechanisms of these associations.
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Affiliation(s)
- Ariel Israel
- Leumit Research Institute, Leumit Health Services, Tel Aviv-Yafo, Israel
- School of Public Health and Family Medicine Department, Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Alejandro A. Schäffer
- Cancer Data Science Laboratory, National Cancer Institute, Bethesda, MD, United States
| | - Matitiahu Berkovitch
- School of Public Health and Family Medicine Department, Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
- Clinical Pharmacology and Toxicology Unit, Shamir Medical Center, Zerifin, Israel
| | - David J. Ozeri
- Leumit Research Institute, Leumit Health Services, Tel Aviv-Yafo, Israel
- Division of Rheumatology, Sheba Medical Center, Ramat Gan, Israel
| | - Eugene Merzon
- Leumit Research Institute, Leumit Health Services, Tel Aviv-Yafo, Israel
- Adelson School of Medicine, Ariel University, Ariel, Israel
| | - Ilan Green
- Leumit Research Institute, Leumit Health Services, Tel Aviv-Yafo, Israel
- School of Public Health and Family Medicine Department, Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Avivit Golan-Cohen
- Leumit Research Institute, Leumit Health Services, Tel Aviv-Yafo, Israel
- School of Public Health and Family Medicine Department, Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Eytan Ruppin
- Cancer Data Science Laboratory, National Cancer Institute, Bethesda, MD, United States
| | - Shlomo Vinker
- Leumit Research Institute, Leumit Health Services, Tel Aviv-Yafo, Israel
- School of Public Health and Family Medicine Department, Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Eli Magen
- Leumit Research Institute, Leumit Health Services, Tel Aviv-Yafo, Israel
- Medicine A Department, Assuta Ashdod University Hospital Faculty of Health Sciences, Ben-Gurion University, Beer-Sheba, Israel
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Konner M, Eaton SB. Hunter-gatherer diets and activity as a model for health promotion: Challenges, responses, and confirmations. Evol Anthropol 2023; 32:206-222. [PMID: 37417918 DOI: 10.1002/evan.21987] [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: 09/19/2021] [Revised: 07/27/2022] [Accepted: 04/17/2023] [Indexed: 07/08/2023]
Abstract
Beginning in 1985, we and others presented estimates of hunter-gatherer (and ultimately ancestral) diet and physical activity, hoping to provide a model for health promotion. The Hunter-Gatherer Model was designed to offset the apparent mismatch between our genes and the current Western-type lifestyle, a mismatch that arguably affects prevalence of many chronic degenerative diseases. The effort has always been controversial and subject to both scientific and popular critiques. The present article (1) addresses eight such challenges, presenting for each how the model has been modified in response, or how the criticism can be rebutted; (2) reviews new epidemiological and experimental evidence (including especially randomized controlled clinical trials); and (3) shows how official recommendations put forth by governments and health authorities have converged toward the model. Such convergence suggests that evolutionary anthropology can make significant contributions to human health.
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Affiliation(s)
- Melvin Konner
- Department of Anthropology, Program in Anthropology and Human Biology, Emory University, Atlanta, Georgia, USA
| | - S Boyd Eaton
- Department of Radiology, Emory University School of Medicine (Emeritus), Adjunct Lecturer, Department of Anthropology, Emory University, Atlanta, Georgia, USA
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Iwasaki RL, Satta Y. Spatial and temporal diversity of positive selection on shared haplotypes at the PSCA locus among worldwide human populations. Heredity (Edinb) 2023:10.1038/s41437-023-00631-8. [PMID: 37353592 PMCID: PMC10382566 DOI: 10.1038/s41437-023-00631-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 05/16/2023] [Accepted: 05/17/2023] [Indexed: 06/25/2023] Open
Abstract
Selection on standing genetic variation is important for rapid local genetic adaptation when the environment changes. We report that, for the prostate stem cell antigen (PSCA) gene, different populations have different target haplotypes, even though haplotypes are shared among populations. The C-C-A haplotype, whereby the first C is located at rs2294008 of PSCA and is a low risk allele for gastric cancer, has become a target of positive selection in Asia. Conversely, the C-A-G haplotype carrying the same C allele has become a selection target mainly in Africa. However, Asian and African share both haplotypes, consistent with the haplotype divergence time (170 kya) prior to the out-of-Africa dispersal. The frequency of C-C-A/C-A-G is 0.344/0.278 in Asia and 0.209/0.416 in Africa. Two-dimensional site frequency spectrum analysis revealed that the extent of intra-allelic variability of the target haplotype is extremely small in each local population, suggesting that C-C-A or C-A-G is under ongoing hard sweeps in local populations. From the time to the most recent common ancestor (TMRCA) of selected haplotypes, the onset times of positive selection were recent (3-55 kya), concurrently with population subdivision from a common ancestor. Additionally, estimated selection coefficients from ABC analysis were up to ~3%, similar to those at other loci under recent positive selection. Phylogeny of local populations and TMRCA of selected haplotypes revealed that spatial and temporal switching of positive selection targets is a unique and novel feature of ongoing selection at PSCA. This switching may reflect the potential of rapid adaptability to distinct environments.
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Affiliation(s)
- Risa L Iwasaki
- Department of Evolutionary Studies of Biosystems, School of Advanced Science, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Kanagawa, 240-0193, Japan
- Research Center for Integrative Evolutionary Science, SOKENDAI, Hayama, Kanagawa, 240-0193, Japan
| | - Yoko Satta
- Department of Evolutionary Studies of Biosystems, School of Advanced Science, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Kanagawa, 240-0193, Japan.
- Research Center for Integrative Evolutionary Science, SOKENDAI, Hayama, Kanagawa, 240-0193, Japan.
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8
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Gu L, Xia C, Yang S, Yang G. The adaptive evolution of cancer driver genes. BMC Genomics 2023; 24:215. [PMID: 37098512 PMCID: PMC10131384 DOI: 10.1186/s12864-023-09301-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 04/08/2023] [Indexed: 04/27/2023] Open
Abstract
BACKGROUND Cancer is a life-threatening disease in humans; yet, cancer genes are frequently reported to be under positive selection. This suggests an evolutionary-genetic paradox in which cancer evolves as a secondary product of selection in human beings. However, systematic investigation of the evolution of cancer driver genes is sparse. RESULTS Using comparative genomics analysis, population genetics analysis and computational molecular evolutionary analysis, the evolution of 568 cancer driver genes of 66 cancer types were evaluated at two levels, selection on the early evolution of humans (long timescale selection in the human lineage during primate evolution, i.e., millions of years), and recent selection in modern human populations (~ 100,000 years). Results showed that eight cancer genes covering 11 cancer types were under positive selection in the human lineage (long timescale selection). And 35 cancer genes covering 47 cancer types were under positive selection in modern human populations (recent selection). Moreover, SNPs associated with thyroid cancer in three thyroid cancer driver genes (CUX1, HERC2 and RGPD3) were under positive selection in East Asian and European populations, consistent with the high incidence of thyroid cancer in these populations. CONCLUSIONS These findings suggest that cancer can be evolved, in part, as a by-product of adaptive changes in humans. Different SNPs at the same locus can be under different selection pressures in different populations, and thus should be under consideration during precision medicine, especially for targeted medicine in specific populations.
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Affiliation(s)
- Langyu Gu
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, 510275, China.
| | - Canwei Xia
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Shiyu Yang
- The Affiliated Brain Hospital, Guangzhou Medical University, Guangzhou, 510180, Guangdong, China
| | - Guofen Yang
- Department of Gynecology, First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510060, Guangdong, China.
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Israel A, Schäffer AA, Berkovitch M, Ozeri DJ, Merzon E, Green I, Golan-Cohen A, Ruppin E, Vinker S, Magen E. Glucose-6-Phosphate Dehydrogenase (G6PD) Deficiency and Long-Term Risk of Immune-Related diseases. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.23.23287616. [PMID: 37090544 PMCID: PMC10120794 DOI: 10.1101/2023.03.23.23287616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
BACKGROUND Glucose-6-phosphate dehydrogenase (G6PD) deficiency is an X-linked recessive enzymatic disorder, particularly prevalent in Africa, Asia and the Middle East. In the US, about 14% of black men are affected. Individuals with G6PD deficiency are often asymptomatic but may develop hemolysis following an infection or upon consumption of specific medications. Despite some evidence that G6PD deficiency affects the immune system, the long- term health risks associated with G6PD deficiency had not been studied in a large population. METHODS In this retrospective cohort study, health records from G6PD deficient individuals were compared to matched controls in a national healthcare provider in Israel (Leumit Health Services). Rates of infectious diseases, allergic conditions and autoimmune disorders were compared between groups. RESULTS The cohort included 7,473 G6PD deficient subjects (68.7% men) matched with 29,892 control subjects (4:1 ratio) of the same age, gender, socioeconomic status and ethnic group, followed during 14.3±6.2 years.Significantly increased rates for autoimmune disorders, infectious diseases and allergic conditions were observed throughout this period. Notable increases were observed for rheumatoid arthritis (OR 2.41, p<0.001), systemic lupus erythematosus (OR 4.56, p<0.001), scleroderma (OR 6.87, p<0.001), pernicious anemia (OR=18.70, P<0.001), fibromyalgia (OR 1.98, p<0.001), Graves' disease (OR 1.46, P=0.001), and Hashimoto's thyroiditis (OR 1.26, P=0.001). These findings were corroborated with elevated rates of positive autoimmune serology and higher rates of treatment with medications commonly used to treat autoimmune conditions in the G6PD deficient group. CONCLUSION G6PD deficient individuals suffer from higher rates of autoimmune disorders, infectious diseases, and allergic conditions.
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Affiliation(s)
- Ariel Israel
- Leumit Research Institute, Leumit Health Services, Tel Aviv-Yafo 6473817, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv-Yafo 6997801 Israel
| | - Alejandro A Schäffer
- Cancer Data Science Laboratory, National Cancer Institute, Bethesda, MD 20892, USA
| | | | - David J. Ozeri
- Leumit Research Institute, Leumit Health Services, Tel Aviv-Yafo 6473817, Israel
- Division of Rheumatology, Sheba Medical Center
| | - Eugene Merzon
- Leumit Research Institute, Leumit Health Services, Tel Aviv-Yafo 6473817, Israel
- Adelson School of Medicine, Ariel University, Ariel 4070000, Israel
| | - Ilan Green
- Leumit Research Institute, Leumit Health Services, Tel Aviv-Yafo 6473817, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv-Yafo 6997801 Israel
| | - Avivit Golan-Cohen
- Leumit Research Institute, Leumit Health Services, Tel Aviv-Yafo 6473817, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv-Yafo 6997801 Israel
| | - Eytan Ruppin
- Cancer Data Science Laboratory, National Cancer Institute, Bethesda, MD 20892, USA
| | - Shlomo Vinker
- Leumit Research Institute, Leumit Health Services, Tel Aviv-Yafo 6473817, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv-Yafo 6997801 Israel
| | - Eli Magen
- Leumit Research Institute, Leumit Health Services, Tel Aviv-Yafo 6473817, Israel
- Medicine A Department, Assuta Ashdod University Hospital Faculty of Health Sciences, Ben-Gurion University, Beer-Sheba 8410501, Israel
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10
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Wattacheril JJ, Raj S, Knowles DA, Greally JM. Using epigenomics to understand cellular responses to environmental influences in diseases. PLoS Genet 2023; 19:e1010567. [PMID: 36656803 PMCID: PMC9851565 DOI: 10.1371/journal.pgen.1010567] [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] [Indexed: 01/20/2023] Open
Abstract
It is a generally accepted model that environmental influences can exert their effects, at least in part, by changing the molecular regulators of transcription that are described as epigenetic. As there is biochemical evidence that some epigenetic regulators of transcription can maintain their states long term and through cell division, an epigenetic model encompasses the idea of maintenance of the effect of an exposure long after it is no longer present. The evidence supporting this model is mostly from the observation of alterations of molecular regulators of transcription following exposures. With the understanding that the interpretation of these associations is more complex than originally recognised, this model may be oversimplistic; therefore, adopting novel perspectives and experimental approaches when examining how environmental exposures are linked to phenotypes may prove worthwhile. In this review, we have chosen to use the example of nonalcoholic fatty liver disease (NAFLD), a common, complex human disease with strong environmental and genetic influences. We describe how epigenomic approaches combined with emerging functional genetic and single-cell genomic techniques are poised to generate new insights into the pathogenesis of environmentally influenced human disease phenotypes exemplified by NAFLD.
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Affiliation(s)
- Julia J. Wattacheril
- Department of Medicine, Center for Liver Disease and Transplantation, Columbia University Irving Medical Center, New York Presbyterian Hospital, New York, New York, United States of America
| | - Srilakshmi Raj
- Division of Genomics, Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - David A. Knowles
- New York Genome Center, New York, New York, United States of America
- Department of Computer Science, Columbia University, New York, New York, United States of America
- Department of Systems Biology, Columbia University, New York, New York, United States of America
| | - John M. Greally
- Division of Genomics, Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
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11
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Balentine CM, Bolnick DA. Parallel evolution in human populations: A biocultural perspective. Evol Anthropol 2022; 31:302-316. [PMID: 36059181 DOI: 10.1002/evan.21956] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 03/09/2022] [Accepted: 07/30/2022] [Indexed: 12/27/2022]
Abstract
Parallel evolution-where different populations evolve similar traits in response to similar environments-has been a topic of growing interest to biologists and biological anthropologists for decades. Parallel evolution occurs in human populations thanks to myriad biological and cultural mechanisms that permit humans to survive and thrive in diverse environments worldwide. Because humans shape and are shaped by their environments, biocultural approaches that emphasize the interconnections between biology and culture are key to understanding parallel evolution in human populations as well as the nuances of human biological variation and adaptation. In this review, we discuss how biocultural theory has been and can be applied to studies of parallel evolution and adaptation more broadly. We illustrate this through four examples of parallel evolution in humans: malaria resistance, lactase persistence, cold tolerance, and high-altitude adaptation.
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Affiliation(s)
- Christina M Balentine
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA.,Department of Anthropology, University of Connecticut, Storrs, Connecticut, USA
| | - Deborah A Bolnick
- Department of Anthropology, University of Connecticut, Storrs, Connecticut, USA.,Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut, USA
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12
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Sezgin E, Kaplan E. Diverse selection pressures shaping the genetic architecture of behçet disease susceptibility. Front Genet 2022; 13:983646. [PMID: 36246630 PMCID: PMC9561091 DOI: 10.3389/fgene.2022.983646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/30/2022] [Indexed: 11/13/2022] Open
Abstract
Behçet disease (BD) is a polygenic, multifactorial, multisystem inflammatory condition with unknown etiology. Global distribution of BD is geographically structured, highest prevalence observed among East Asian, Middle Eastern, and Mediterranean populations. Although adaptive selection on a few BD susceptibility loci is speculated, a thorough evolutionary analysis on the genetic architecture of BD is lacking. We aimed to understand whether increased BD risk in the human populations with high prevalence is due to past selection on BD associated genes. We performed population genetics analyses with East Asian (high BD prevalence), European (low/very low BD prevalence), and African (very low/no BD prevalence) populations. Comparison of ancestral and derived alleles’ frequencies versus their reported susceptible or protective effect on BD showed both derived and ancestral alleles are associated with increased BD risk. Variants showing higher risk to and more significant association with BD had smaller allele frequency differences, and showed less population differentiation compared to variants that showed smaller risk and less significant association with BD. Results suggest BD alleles are not unique to East Asians but are also found in other world populations at appreciable frequencies, and argue against selection favoring these variants only in populations with high BD prevalence. BD associated gene analyses showed similar evolutionary histories driven by neutral processes for many genes or balancing selection for HLA (Human Leukocyte Antigen) genes in all three populations studied. However, nucleotide diversity in several HLA region genes was much higher in East Asians suggesting selection for high nucleotide and haplotype diversity in East Asians. Recent selective sweep for genes involved in antigen recognition, peptide processing, immune and cellular differentiation regulation was observed only in East Asians. We conclude that the evolutionary processes shaping the genetic diversity in BD risk genes are diverse, and elucidating the underlying specific selection mechanisms is complex. Several of the genes examined in this study are risk factors (such as ERAP1, IL23R, HLA-G) for other inflammatory diseases. Thus, our conclusions are not only limited to BD but may have broader implications for other inflammatory diseases.
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Affiliation(s)
- Efe Sezgin
- Department of Food Engineering, Izmir Institute of Technology, Izmir, Turkey
- Biotechnology Interdisciplinary Program, Izmir Institute of Technology, Izmir, Turkey
- *Correspondence: Efe Sezgin,
| | - Elif Kaplan
- Biotechnology Interdisciplinary Program, Izmir Institute of Technology, Izmir, Turkey
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13
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Tang J, Huang M, He S, Zeng J, Zhu H. Uncovering the extensive trade-off between adaptive evolution and disease susceptibility. Cell Rep 2022; 40:111351. [PMID: 36103812 DOI: 10.1016/j.celrep.2022.111351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/13/2022] [Accepted: 08/23/2022] [Indexed: 11/03/2022] Open
Abstract
Favored mutations in the human genome may make the carriers adapt to changing environments and lifestyles but also susceptible to specific diseases. The scale and details of the trade-off between adaptive evolution and disease susceptibility are unclear because most favored mutations in different populations remain unidentified. As no statistical test can discriminate favored mutations from nearby hitchhiking neutral ones, we report a deep-learning network (DeepFavored) to integrate multiple statistical tests and divide identifying favored mutations into two subtasks. We identify favored mutations in three human populations and analyzed the correlation between favored/hitchhiking mutations and genome-wide association study (GWAS) sites. Both favored and hitchhiking neutral mutations are enriched in GWAS sites with population-specific features, and the enrichment and population specificity are prominent in genes in specific Gene Ontology (GO) terms. These provide evidence for extensive and population-specific trade-offs between adaptive evolution and disease susceptibility. The unveiled scale helps understand and investigate differences and diseases of humans.
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Affiliation(s)
- Ji Tang
- Bioinformatics Section, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Maosheng Huang
- Bioinformatics Section, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China; School of Medical Information and Engineering, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Sha He
- Bioinformatics Section, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Junxiang Zeng
- Bioinformatics Section, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Hao Zhu
- Bioinformatics Section, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China; Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Southern Medical University, Guangzhou 510515, China.
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14
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Ansari U, Bhardwaj P, Quadri H, Barnes M, George J. Diabetic Ketoacidosis Unmasking a Diagnosis of Glucose-6-Phosphate Dehydrogenase Deficiency: A Case Report and Literature Review. Cureus 2022; 14:e23842. [PMID: 35402109 PMCID: PMC8986519 DOI: 10.7759/cureus.23842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/05/2022] [Indexed: 11/05/2022] Open
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15
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Morais I, Medeiros MM, Carvalho M, Morello J, Teixeira SM, Maciel S, Nhantumbo J, Balau A, Rosa MTG, Nogueira F, Rodrigues JA, Carvalho FA, Antunes AMM, Arez AP. Synthetic Red Blood Cell-Specific Glycolytic Intermediate 2,3-Diphosphoglycerate (2,3-DPG) Inhibits Plasmodium falciparum Development In Vitro. Front Cell Infect Microbiol 2022; 12:840968. [PMID: 35372095 PMCID: PMC8967366 DOI: 10.3389/fcimb.2022.840968] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 01/21/2022] [Indexed: 11/18/2022] Open
Abstract
Mechanisms of malaria parasite interaction with its host red blood cell may provide potential targets for new antimalarial approaches. Pyruvate kinase deficiency has been associated with resistance to malaria in both experimental models and population studies. Two of the major pyruvate kinase deficient-cell disorders are the decrease in ATP and the increase in 2,3-biphosphoglycerate (2,3-BPG) concentration. High levels of this metabolite, only present in mammalian red blood cell, has an inhibitory effect on glycolysis and we hypothesized that its accumulation may also be harmful to the parasite and be involved in the mechanism of protection provided by that enzymopathy. We examined the effect of a synthetic form, 2,3-DPG, on the Plasmodium falciparum intraerythrocytic developmental cycle in vitro. Results showed an impairment of parasite growth with a direct effect on parasite maturation as significant lower progeny emerged from parasites that were submitted to 2,3-DPG. Further, adding the compound to the culture medium did not result in any effect on the host cell, but instead the metabolic profile of an infected cell became closer to that of a non-infected cell.
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Affiliation(s)
- Inês Morais
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), Lisbon, Portugal
| | - Márcia M. Medeiros
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), Lisbon, Portugal
| | - Maria Carvalho
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), Lisbon, Portugal
| | - Judit Morello
- CEDOC, NOVA Medical School, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - Sara M. Teixeira
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Suelma Maciel
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), Lisbon, Portugal
| | - Janice Nhantumbo
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), Lisbon, Portugal
| | - Ana Balau
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), Lisbon, Portugal
| | - Margarida T. G. Rosa
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), Lisbon, Portugal
| | - Fátima Nogueira
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), Lisbon, Portugal
| | | | - Filomena A. Carvalho
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Alexandra M. M. Antunes
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Ana Paula Arez
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), Lisbon, Portugal
- *Correspondence: Ana Paula Arez,
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16
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Ali Albsheer MM, Lover AA, Eltom SB, Omereltinai L, Mohamed N, Muneer MS, Mohamad AO, Abdel Hamid MM. Prevalence of glucose-6-phosphate dehydrogenase deficiency (G6PDd), CareStart qualitative rapid diagnostic test performance, and genetic variants in two malaria-endemic areas in Sudan. PLoS Negl Trop Dis 2021; 15:e0009720. [PMID: 34699526 PMCID: PMC8547650 DOI: 10.1371/journal.pntd.0009720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 08/09/2021] [Indexed: 11/24/2022] Open
Abstract
Glucose-6-phosphate dehydrogenase deficiency (G6PDd) is the most common enzymopathy globally, and deficient individuals may experience severe hemolysis following treatment with 8-aminoquinolines. With increasing evidence of Plasmodium vivax infections throughout sub-Saharan Africa, there is a pressing need for population-level data at on the prevalence of G6PDd. Such evidence-based data will guide the expansion of primaquine and potentially tafenoquine for radical cure of P. vivax infections. This study aimed to quantify G6PDd prevalence in two geographically distinct areas in Sudan, and evaluating the performance of a qualitative CareStart rapid diagnostic test as a point-of-care test. Blood samples were analyzed from 491 unrelated healthy persons in two malaria-endemic sites in eastern and central Sudan. A pre-structured questionnaire was used which included demographic data, risk factors and treatment history. G6PD levels were measured using spectrophotometry (SPINREACT) and first-generation qualitative CareStart rapid tests. G6PD variants (202 G>A; 376 A>G) were determined by PCR/RFLP, with a subset confirmed by Sanger sequencing. The prevalence of G6PDd by spectrophotometry was 5.5% (27/491; at 30% of adjusted male median, AMM); 27.3% (134/491; at 70% of AMM); and 13.1% (64/490) by qualitative CareStart rapid diagnostic test. The first-generation CareStart rapid diagnostic test had an overall sensitivity of 81.5% (95%CI: 61.9 to 93.7) and negative predictive value of 98.8% (97.3 to 99.6). All persons genotyped across both study sites were wild type for the G6PD G202 variant. For G6PD A376G all participants in New Halfa had wild type AA (100%), while in Khartoum the AA polymorphism was found in 90.7%; AG in 2.5%; and GG in 6.8%. Phenotypic G6PD B was detected in 100% of tested participants in New Halfa while in Khartoum, the phenotypes observed were B (96.2%), A (2.8%), and AB (1%). The African A- phenotype was not detected in this study population. Overall, G6PDd prevalence in Sudan is low-to-moderate but highly heterogeneous. Point-of-care testing with the qualitative CareStart rapid diagnostic test demonstrated moderate performance with moderate sensitivity and specificity but high negative predicative value. The two sites harbored primarily the African B phenotype. A country-wide survey is recommended to understand GP6PD deficiencies more comprehensively in Sudan. Malaria is caused by five species of parasites; of these Plasmodium falciparum and P. vivax cause the majority of global morbidity and mortality. Plasmodium vivax infection is an emerging public health problem in sub-Saharan Africa, including Sudan. Primaquine and other 8-aminoquinolines including tafenoquine are the primary treatments to target the silent liver stage (hypnozoites) in P. vivax infections. However, these regimens can cause severe intravascular hemolysis in patients suffering from glucose-6-phosphate dehydrogenase deficiency (G6PDd). To support safe and efficacious use of primaquine, and potentially tafenoquine in Sudan, this study aimed to estimate the prevalence of G6PDd across two sites in Sudan using spectrophotometry and a qualitative CareStart rapid diagnostic test. Subsequent genetic analysis by PCR/RFLP and sequencing of G6PD genetic variants was performed. This survey found an overall prevalence was 5.5% (27/491; 30% of adjusted male median, AMM), and 27.3% (134/491; 70% of AMM) and 13.1% (64/490) by qualitative CareStart rapid diagnostic test. Important differences in distribution of genetic variants of G6PD were found across the two sites, and the African A- was not observed. In univariate analysis a few parameters showed significant association with G6PD deficiency. In conclusion the prevalence of G6PDd was low to moderate but heterogonous, and the first-generation qualitative CareStart rapid diagnostic test showed moderate performance in both males and females.
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Affiliation(s)
- Musab M. Ali Albsheer
- Department of Parasitology and Medical Entomology, Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
- Faculty of Medical Laboratory Sciences, Sinnar University, Sennar, Sudan
| | - Andrew A. Lover
- Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts-Amherst; Amherst, Massachusetts, United States of America
| | - Sara B. Eltom
- Department of Parasitology and Medical Entomology, Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
| | - Leena Omereltinai
- Department of Parasitology and Medical Entomology, Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
| | - Nouh Mohamed
- Department of Parasitology and Medical Entomology, Faculty of Medical Laboratory Sciences, Nile University, Khartoum, Sudan
| | - Mohamed S. Muneer
- Department of Parasitology and Medical Entomology, Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
- Department of Biochemistry, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Abdelrahim O. Mohamad
- Department of Biochemistry, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Muzamil Mahdi Abdel Hamid
- Department of Parasitology and Medical Entomology, Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
- * E-mail: ,
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17
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Abstract
The prevalence of myopia, or nearsightedness, has skyrocketed in the past few decades, creating a public health crisis that is commonly attributed to lifestyle changes. Here we report an overall increase in the frequencies of myopia-associated mutant alleles over 25 years among participants of the UK Biobank. Although myopia itself appears to be selected against, many of the mutant alleles are associated with reproductive benefits, suggesting that reproduction-related selection inadvertently contributes to the myopia epidemic. We estimate that, in the UK alone, natural selection adds more than 100 000 myopia cases per generation, and argue that antagonistic pleiotropy be broadly considered in explaining the spreads of apparently disadvantageous phenotypes in humans and beyond.
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Affiliation(s)
- Erping Long
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA.,State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
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18
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Chande AT, Rishishwar L, Ban D, Nagar SD, Conley AB, Rowell J, Valderrama-Aguirre AE, Medina-Rivas MA, Jordan IK. The Phenotypic Consequences of Genetic Divergence between Admixed Latin American Populations: Antioquia and Chocó, Colombia. Genome Biol Evol 2021; 12:1516-1527. [PMID: 32681795 PMCID: PMC7513793 DOI: 10.1093/gbe/evaa154] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2020] [Indexed: 12/11/2022] Open
Abstract
Genome-wide association studies have uncovered thousands of genetic variants that are associated with a wide variety of human traits. Knowledge of how trait-associated variants are distributed within and between populations can provide insight into the genetic basis of group-specific phenotypic differences, particularly for health-related traits. We analyzed the genetic divergence levels for 1) individual trait-associated variants and 2) collections of variants that function together to encode polygenic traits, between two neighboring populations in Colombia that have distinct demographic profiles: Antioquia (Mestizo) and Chocó (Afro-Colombian). Genetic ancestry analysis showed 62% European, 32% Native American, and 6% African ancestry for Antioquia compared with 76% African, 10% European, and 14% Native American ancestry for Chocó, consistent with demography and previous results. Ancestry differences can confound cross-population comparison of polygenic risk scores (PRS); however, we did not find any systematic bias in PRS distributions for the two populations studied here, and population-specific differences in PRS were, for the most part, small and symmetrically distributed around zero. Both genetic differentiation at individual trait-associated single nucleotide polymorphisms and population-specific PRS differences between Antioquia and Chocó largely reflected anthropometric phenotypic differences that can be readily observed between the populations along with reported disease prevalence differences. Cases where population-specific differences in genetic risk did not align with observed trait (disease) prevalence point to the importance of environmental contributions to phenotypic variance, for both infectious and complex, common disease. The results reported here are distributed via a web-based platform for searching trait-associated variants and PRS divergence levels at http://map.chocogen.com (last accessed August 12, 2020).
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Affiliation(s)
- Aroon T Chande
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia.,IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, Georgia.,PanAmerican Bioinformatics Institute, Valle del Cauca, Cali, Colombia
| | - Lavanya Rishishwar
- IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, Georgia.,PanAmerican Bioinformatics Institute, Valle del Cauca, Cali, Colombia
| | - Dongjo Ban
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia.,PanAmerican Bioinformatics Institute, Valle del Cauca, Cali, Colombia
| | - Shashwat D Nagar
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia.,PanAmerican Bioinformatics Institute, Valle del Cauca, Cali, Colombia
| | - Andrew B Conley
- IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, Georgia.,PanAmerican Bioinformatics Institute, Valle del Cauca, Cali, Colombia
| | - Jessica Rowell
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia
| | - Augusto E Valderrama-Aguirre
- PanAmerican Bioinformatics Institute, Valle del Cauca, Cali, Colombia.,Biomedical Research Institute (COL0082529), Cali, Colombia.,Universidad Santiago de Cali, Colombia
| | - Miguel A Medina-Rivas
- PanAmerican Bioinformatics Institute, Valle del Cauca, Cali, Colombia.,Centro de Investigación en Biodiversidad y Hábitat, Universidad Tecnológica del Chocó, Quibdó, Colombia
| | - I King Jordan
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia.,IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, Georgia.,PanAmerican Bioinformatics Institute, Valle del Cauca, Cali, Colombia
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19
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Sirugo G, Tishkoff SA, Williams SM. The quagmire of race, genetic ancestry, and health disparities. J Clin Invest 2021; 131:e150255. [PMID: 34060479 DOI: 10.1172/jci150255] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Affiliation(s)
- Giorgio Sirugo
- Institute of Systems Pharmacology and Translational Therapeutics.,Division of Translational Medicine and Human Genetics, and
| | - Sarah A Tishkoff
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Scott M Williams
- Departments of Population and Quantitative Health Sciences, and Genetics and Genome Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, USA
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20
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Tennessen JA, Duraisingh MT. Three Signatures of Adaptive Polymorphism Exemplified by Malaria-Associated Genes. Mol Biol Evol 2021; 38:1356-1371. [PMID: 33185667 PMCID: PMC8042748 DOI: 10.1093/molbev/msaa294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Malaria has been one of the strongest selective pressures on our species. Many of the best-characterized cases of adaptive evolution in humans are in genes tied to malaria resistance. However, the complex evolutionary patterns at these genes are poorly captured by standard scans for nonneutral evolution. Here, we present three new statistical tests for selection based on population genetic patterns that are observed more than once among key malaria resistance loci. We assess these tests using forward-time evolutionary simulations and apply them to global whole-genome sequencing data from humans, and thus we show that they are effective at distinguishing selection from neutrality. Each test captures a distinct evolutionary pattern, here called Divergent Haplotypes, Repeated Shifts, and Arrested Sweeps, associated with a particular period of human prehistory. We clarify the selective signatures at known malaria-relevant genes and identify additional genes showing similar adaptive evolutionary patterns. Among our top outliers, we see a particular enrichment for genes involved in erythropoiesis and for genes previously associated with malaria resistance, consistent with a major role for malaria in shaping these patterns of genetic diversity. Polymorphisms at these genes are likely to impact resistance to malaria infection and contribute to ongoing host-parasite coevolutionary dynamics.
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21
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Abdulkareem AO, Babamale OA, Aishat LA, Ajayi OC, Gloria SK, Olatunji LA, Ugbomoiko US. Effect of sodium acetate on serum activity of glucose-6-phosphate dehydrogenase in Plasmodium berghei-infected mice. J Parasit Dis 2021; 45:121-127. [PMID: 33746396 DOI: 10.1007/s12639-020-01272-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 09/10/2020] [Indexed: 11/26/2022] Open
Abstract
Malaria is a global health problem with severe morbidity and mortality in Sub-Saharan Africa. Resistance of Plasmodium spp to the current anti-malaria drugs necessitates further search for novel effective drugs. This study, therefore, investigated the effect of sodium acetate on glucose-6-phosphate dehydrogenase in Plasmodium berghei-infected mice. Thirty male Albino mice were randomly distributed into 6 groups, A-F. Animals in Groups B-F were inoculated with P. berghei, intraperitoneally. Subsequently, Group C mice were treated with 20 mg/kg chloroquine, while groups D, E and F received 25, 50 and 100 mg/kg sodium acetate, respectively. All treatments were administered orally for 4 days. At the end of the experiment, animals were sacrificed by cervical dislocation and blood was collected via cardiac puncture for the analyses of serum glucose-6-phosphate dehydrogenase (G6PD), uric acid and lipid profile. Our results showed that Sodium acetate (50 and 100 mg/kg) significantly reduced (p < 0.05) parasitaemia (67.11% and 77.62%, respectively) than chloroquine (61.73%). Besides, body weight and serum G6PD activity in P. berghei infection were improved. Similarly, sodium acetate reduced elevated serum uric acid. Effects of sodium acetate and chloroquine on biochemical parameters were comparable (p > 0.05) but atherogenic lipid ratios were not affected by sodium acetate. These data put together suggested that activity of sodium acetate may be harnessed for development of novel anti-malaria drugs. However, more studies are required to delineate its mechanisms of action.
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Affiliation(s)
- A O Abdulkareem
- Animal Physiology Unit, Department of Zoology, University of Ilorin, Ilorin, Nigeria
- HOPE Cardiometabolic Research Research Team, University of Ilorin, Ilorin, Nigeria
| | - O A Babamale
- Parasitology Unit, Department of Zoology, University of Ilorin, Ilorin, Nigeria
| | - L A Aishat
- Animal Physiology Unit, Department of Zoology, University of Ilorin, Ilorin, Nigeria
| | - O C Ajayi
- Animal Physiology Unit, Department of Zoology, University of Ilorin, Ilorin, Nigeria
| | - S K Gloria
- Animal Physiology Unit, Department of Zoology, University of Ilorin, Ilorin, Nigeria
| | - L A Olatunji
- Cardiovascular Research Unit, Department of Physiology, College of Health Sciences, University of Ilorin, Ilorin, Nigeria
- HOPE Cardiometabolic Research Research Team, University of Ilorin, Ilorin, Nigeria
| | - U S Ugbomoiko
- Parasitology Unit, Department of Zoology, University of Ilorin, Ilorin, Nigeria
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22
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Zheng Y, Wang J, Liang X, Huang H, Ma Y, Lin L, Wang C, Zhan X, Yang L, Zha G, Yang P, Zou X, Chen Z, Chen X, Chen W, Liu X, Lin M. Epidemiology, evolutionary origin, and malaria-induced positive selection effects of G6PD-deficient alleles in Chinese populations. Mol Genet Genomic Med 2020; 8:e1540. [PMID: 33128437 PMCID: PMC7767544 DOI: 10.1002/mgg3.1540] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 09/02/2020] [Accepted: 09/17/2020] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Although glucose-6-phosphate dehydrogenase (G6PD) deficiency is the most common inherited disorder in the Chinese population, there is scarce evidence regarding the epidemiology, evolutionary origin, and malaria-induced positive selection effects of G6PD-deficient alleles in various Chinese ethnic populations. METHODS We performed a large population-based screening (n = 15,690) to examine the impact of selection on human nucleotide diversity and to infer the evolutionary history of the most common deficiency alleles in Chinese populations. RESULTS The frequencies of G6PD deficiency ranged from 0% to 11.6% in 12 Chinese ethnic populations. A frequency map based on geographic information showed that G6PD deficiency was highly correlated with historical malaria prevalence in China and was affected by altitude and latitude. The five most frequently occurring G6PD gene variants were NM_001042351.3:c.1376G>T, NM_001042351.3:c.1388G>A, NM_001042351.3:c.95A>G, NM_001042351.3:c.1311T>C, and NM_001042351.3:c.1024C>T, which were distributed with ethnic features. A pathogenic but rarely reported variant site (NM_001042351.3:c.448G>A) was identified in this study. Bioinformatic analysis revealed a strong and recent positive selection targeting the NM_001042351.3:c.1376G>T allele that originated in the past 3125 to 3750 years and another selection targeting the NM_001042351.3:c.1388G>A allele that originated in the past 5000 to 6000 years. Additionally, both alleles originated from a single ancestor. CONCLUSION These results indicate that malaria has had a major impact on the Chinese genome since the introduction of rice agriculture.
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Affiliation(s)
- Yuzhong Zheng
- School of Food Engineering and BiotechnologyHanshan Normal UniversityChaozhouGuangdong ProvinceChina
| | - Junli Wang
- Reproductive Medicine CenterThe Affiliated Hospital of Youjiang Medical University for NationalitiesBaiseChina
| | - Xueyan Liang
- Department of Medical GeneticsShantou University Medical CollegeShantouGuangdongChina
- Department of Medical LaboratoryChaozhou People’s Hospital Affiliated to Shantou University Medical CollegeChaozhouGuangdongChina
| | - Huiying Huang
- Department of Medical GeneticsShantou University Medical CollegeShantouGuangdongChina
- Department of Medical LaboratoryChaozhou People’s Hospital Affiliated to Shantou University Medical CollegeChaozhouGuangdongChina
| | - Yanbo Ma
- School of Mathematics and StatisticsHanshan Normal UniversityChaozhouGuangdongChina
| | - Liyun Lin
- School of Food Engineering and BiotechnologyHanshan Normal UniversityChaozhouGuangdong ProvinceChina
| | - Chunfang Wang
- Reproductive Medicine CenterThe Affiliated Hospital of Youjiang Medical University for NationalitiesBaiseChina
| | - Xiaofen Zhan
- Department of Medical LaboratoryChaozhou Central Hospital Affiliated to Southern Medical UniversityChaozhouGuangdongChina
| | - Liye Yang
- Department of Medical LaboratoryChaozhou Central Hospital Affiliated to Southern Medical UniversityChaozhouGuangdongChina
| | - Guangcai Zha
- School of Food Engineering and BiotechnologyHanshan Normal UniversityChaozhouGuangdong ProvinceChina
| | - Peikui Yang
- School of Food Engineering and BiotechnologyHanshan Normal UniversityChaozhouGuangdong ProvinceChina
| | - Xianghui Zou
- School of Food Engineering and BiotechnologyHanshan Normal UniversityChaozhouGuangdong ProvinceChina
| | - Zikai Chen
- School of Food Engineering and BiotechnologyHanshan Normal UniversityChaozhouGuangdong ProvinceChina
| | - Xinyao Chen
- Department of Medical LaboratoryChaozhou People’s Hospital Affiliated to Shantou University Medical CollegeChaozhouGuangdongChina
| | - Weizhong Chen
- Department of Medical LaboratoryChaozhou People’s Hospital Affiliated to Shantou University Medical CollegeChaozhouGuangdongChina
| | - Xiangzhi Liu
- Department of Medical LaboratoryChaozhou People’s Hospital Affiliated to Shantou University Medical CollegeChaozhouGuangdongChina
| | - Min Lin
- School of Food Engineering and BiotechnologyHanshan Normal UniversityChaozhouGuangdong ProvinceChina
- Department of Medical LaboratoryChaozhou People’s Hospital Affiliated to Shantou University Medical CollegeChaozhouGuangdongChina
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23
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Choudhuri A, Trompouki E, Abraham BJ, Colli LM, Kock KH, Mallard W, Yang ML, Vinjamur DS, Ghamari A, Sporrij A, Hoi K, Hummel B, Boatman S, Chan V, Tseng S, Nandakumar SK, Yang S, Lichtig A, Superdock M, Grimes SN, Bowman TV, Zhou Y, Takahashi S, Joehanes R, Cantor AB, Bauer DE, Ganesh SK, Rinn J, Albert PS, Bulyk ML, Chanock SJ, Young RA, Zon LI. Common variants in signaling transcription-factor-binding sites drive phenotypic variability in red blood cell traits. Nat Genet 2020; 52:1333-1345. [PMID: 33230299 DOI: 10.1038/s41588-020-00738-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 10/14/2020] [Indexed: 12/13/2022]
Abstract
Genome-wide association studies identify genomic variants associated with human traits and diseases. Most trait-associated variants are located within cell-type-specific enhancers, but the molecular mechanisms governing phenotypic variation are less well understood. Here, we show that many enhancer variants associated with red blood cell (RBC) traits map to enhancers that are co-bound by lineage-specific master transcription factors (MTFs) and signaling transcription factors (STFs) responsive to extracellular signals. The majority of enhancer variants reside on STF and not MTF motifs, perturbing DNA binding by various STFs (BMP/TGF-β-directed SMADs or WNT-induced TCFs) and affecting target gene expression. Analyses of engineered human blood cells and expression quantitative trait loci verify that disrupted STF binding leads to altered gene expression. Our results propose that the majority of the RBC-trait-associated variants that reside on transcription-factor-binding sequences fall in STF target sequences, suggesting that the phenotypic variation of RBC traits could stem from altered responsiveness to extracellular stimuli.
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Affiliation(s)
- Avik Choudhuri
- Harvard Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Eirini Trompouki
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA.,Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.,CIBSS Centre for Integrative Biological Signaling Studies, University of Freiburg, Freiburg, Germany
| | - Brian J Abraham
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.,Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Leandro M Colli
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, MD, USA.,Department of Medical Imaging, Hematology, and Medical Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Kian Hong Kock
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Program in Biological and Biomedical Sciences, Harvard University, Cambridge, MA, USA
| | - William Mallard
- Harvard Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,The Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Min-Lee Yang
- Division of Cardiovascular Medicine, Department of Internal Medicine and Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Divya S Vinjamur
- Division of Hematology and Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Alireza Ghamari
- Division of Pediatric Hematology-Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Audrey Sporrij
- Harvard Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Karen Hoi
- Harvard Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Barbara Hummel
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Sonja Boatman
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Victoria Chan
- Harvard Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Sierra Tseng
- Harvard Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Satish K Nandakumar
- Division of Hematology and Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Song Yang
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Asher Lichtig
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Michael Superdock
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Seraj N Grimes
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Summer Institute in Biomedical Informatics, Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Teresa V Bowman
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA.,Albert Einstein College of Medicine, Bronx, NY, USA
| | - Yi Zhou
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | | | - Roby Joehanes
- Hebrew Senior Life, Harvard Medical School, Boston, MA, USA.,Framingham Heart Study, National Heart, Blood, and Lung Institute, National Institutes of Health, Bethesda, MD, USA
| | - Alan B Cantor
- Division of Pediatric Hematology-Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Daniel E Bauer
- Division of Hematology and Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Santhi K Ganesh
- Division of Cardiovascular Medicine, Department of Internal Medicine and Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - John Rinn
- Harvard Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Paul S Albert
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Martha L Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Program in Biological and Biomedical Sciences, Harvard University, Cambridge, MA, USA.,The Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.,Summer Institute in Biomedical Informatics, Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.,Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Leonard I Zon
- Harvard Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA. .,Stem Cell Program and Division of Hematology/Oncology, Children's Hospital Boston, Harvard Stem Cell Institute, Harvard Medical School and Howard Hughes Medical Institute, Boston, MA, USA.
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24
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Rajkhowa P, Nath C, Dutta A, Misurya I, Sharma N, Barman B, Longkumer C, Lynrah KG, Sarmah D, Ruram A. Study of Glucose-6-Phosphate Dehydrogenase (G6PD) Deficiency and Genotype Polymorphism of G6PD B and G6PD (A+/A-) in Patients Treated for Plasmodium vivax Malaria in a Tertiary Care Hospital in North East India. Cureus 2020; 12:e11463. [PMID: 33214970 PMCID: PMC7671175 DOI: 10.7759/cureus.11463] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Introduction Glucose-6-phosphate dehydrogenase (G6PD) enzyme deficiency is the most common enzymopathy in humans, and its distribution has been historically described to be closely associated with that of malaria. North East India provides optimal conditions for transmission of malaria and bears a considerable burden of Plasmodium vivax (P. vivax) malaria. Primaquine, a mainstay in the treatment of vivax malaria, may trigger episodes of acute hemolysis in patients with G6PD deficiency. The present study sought to delineate the frequency and genotypes of G6PD deficiency among patients suffering from vivax malaria infections. Methods Blood specimens from 80 individuals diagnosed with vivax malaria underwent enzyme assay for G6PD deficiency. Samples with deficient phenotype underwent isolation of DNA using a genomic DNA isolation kit (Qiagen India Pvt. Ltd., New Delhi, India). The genomic DNA underwent amplification, serial denaturation, annealing, extension, final extension followed by digestion with restriction endonucleases Nla III and Fok I. The digested products were subjected to horizontal agarose electrophoresis for the separation of digested fragments. Samples without nucleotide 376 adenine→guanine (A→G) mutation were classified as G6PD B. Those with the mutation were further classified into G6PD A(+) and G6PD A(-) based on the presence of Nla III site. Results Twenty-seven out of 80 individuals (33.75%) with P. vivax malaria were found to have G6PD deficiency, of which a majority (n=24) had G6PD B genotype. Three individuals had Asparagine→Aspartic Acid mutation at position 376 (A→G), of which G6PD A(+) and G6PD A(-) were present in two and one cases, respectively. Conclusion G6PD deficiency was noted in about a third of patients with vivax malaria. Since primaquine therapy is contraindicated in this group of patients, there is a rationale for looking into screening patients with vivax malaria from the region prior to primaquine therapy. Further large scale studies may substantiate this and help in better genotypic and geographic characterization of G6PD deficiency in the region.
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Affiliation(s)
- Purnima Rajkhowa
- Department of Microbiology, Silchar Medical College, Silchar, IND
| | - Chandan Nath
- Department of Biochemistry, North Eastern Indira Gandhi Regional Institute of Health and Medical Sciences, Shillong, IND
| | - Anirban Dutta
- Department of Medicine, Dr. NMB Baruah Nursing Home, Nalbari, IND
| | - Ishita Misurya
- Department of Medicine, All India Institute of Medical Sciences, Jodhpur, IND
| | - Nalini Sharma
- Department of Obstetrics and Gynecology, North Eastern Indira Gandhi Regional Institute of Health and Medical Sciences, Shillong, IND
| | - Bhupen Barman
- Department of Medicine, North Eastern Indira Gandhi Regional Institute of Health and Medical Sciences, Shillong, IND
| | | | - K G Lynrah
- Department of Medicine, North Eastern Indira Gandhi Regional Institute of Health and Medical Sciences, Shillong, IND
| | - Devajit Sarmah
- Department of Biochemistry, Rajarshi Dashrath Autonomous State Medical College, Ayodhya, IND
| | - Alice Ruram
- Department of Biochemistry, North Eastern Indira Gandhi Regional Institute of Health and Medical Sciences, Shillong, IND
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25
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Penman BS, Gandon S. Adaptive immunity selects against malaria infection blocking mutations. PLoS Comput Biol 2020; 16:e1008181. [PMID: 33031369 PMCID: PMC7544067 DOI: 10.1371/journal.pcbi.1008181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 07/22/2020] [Indexed: 11/18/2022] Open
Abstract
The mutation responsible for Duffy negativity, which impedes Plasmodium vivax infection, has reached high frequencies in certain human populations. Conversely, mutations capable of blocking the more lethal P. falciparum have not succeeded in malarious zones. Here we present an evolutionary-epidemiological model of malaria which demonstrates that if adaptive immunity against the most virulent effects of malaria is gained rapidly by the host, mutations which prevent infection per se are unlikely to succeed. Our results (i) explain the rarity of strain-transcending P. falciparum infection blocking adaptations in humans; (ii) make the surprising prediction that mutations which block P. falciparum infection are most likely to be found in populations experiencing low or infrequent malaria transmission, and (iii) predict that immunity against some of the virulent effects of P. vivax malaria may be built up over the course of many infections.
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Affiliation(s)
- Bridget S. Penman
- Zeeman Institute and School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Sylvain Gandon
- CEFE, CNRS, University of Montpellier, Paul Valéry University of Montpellier, EPHE, IRD, Montpellier, France
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26
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Werren EA, Garcia O, Bigham AW. Identifying adaptive alleles in the human genome: from selection mapping to functional validation. Hum Genet 2020; 140:241-276. [PMID: 32728809 DOI: 10.1007/s00439-020-02206-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 07/07/2020] [Indexed: 12/19/2022]
Abstract
The suite of phenotypic diversity across geographically distributed human populations is the outcome of genetic drift, gene flow, and natural selection throughout human evolution. Human genetic variation underlying local biological adaptations to selective pressures is incompletely characterized. With the emergence of population genetics modeling of large-scale genomic data derived from diverse populations, scientists are able to map signatures of natural selection in the genome in a process known as selection mapping. Inferred selection signals further can be used to identify candidate functional alleles that underlie putative adaptive phenotypes. Phenotypic association, fine mapping, and functional experiments facilitate the identification of candidate adaptive alleles. Functional investigation of candidate adaptive variation using novel techniques in molecular biology is slowly beginning to unravel how selection signals translate to changes in biology that underlie the phenotypic spectrum of our species. In addition to informing evolutionary hypotheses of adaptation, the discovery and functional annotation of adaptive alleles also may be of clinical significance. While selection mapping efforts in non-European populations are growing, there remains a stark under-representation of diverse human populations in current public genomic databases, of both clinical and non-clinical cohorts. This lack of inclusion limits the study of human biological variation. Identifying and functionally validating candidate adaptive alleles in more global populations is necessary for understanding basic human biology and human disease.
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Affiliation(s)
- Elizabeth A Werren
- Department of Human Genetics, The University of Michigan, Ann Arbor, MI, USA
- Department of Anthropology, The University of Michigan, Ann Arbor, MI, USA
| | - Obed Garcia
- Department of Anthropology, The University of Michigan, Ann Arbor, MI, USA
| | - Abigail W Bigham
- Department of Anthropology, University of California Los Angeles, 341 Haines Hall, Los Angeles, CA, 90095, USA.
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27
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Gilchrist JJ, Uyoga S, Pirinen M, Rautanen A, Mwarumba S, Njuguna P, Mturi N, Hill AVS, Scott JAG, Williams TN. Risk of pneumococcal bacteremia in Kenyan children with glucose-6-phosphate dehydrogenase deficiency. BMC Med 2020; 18:148. [PMID: 32536341 PMCID: PMC7294654 DOI: 10.1186/s12916-020-01604-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 04/23/2020] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Glucose-6-phosphate dehydrogenase (G6PD) deficiency is the most common enzyme deficiency state in humans. The clinical phenotype is variable and includes asymptomatic individuals, episodic hemolysis induced by oxidative stress, and chronic hemolysis. G6PD deficiency is common in malaria-endemic regions, an observation hypothesized to be due to balancing selection at the G6PD locus driven by malaria. G6PD deficiency increases risk of severe malarial anemia, a key determinant of invasive bacterial disease in malaria-endemic settings. The pneumococcus is a leading cause of invasive bacterial infection and death in African children. The effect of G6PD deficiency on risk of pneumococcal disease is undefined. We hypothesized that G6PD deficiency increases pneumococcal disease risk and that this effect is dependent upon malaria. METHODS We performed a genetic case-control study of pneumococcal bacteremia in Kenyan children stratified across a period of falling malaria transmission between 1998 and 2010. RESULTS Four hundred twenty-nine Kenyan children with pneumococcal bacteremia and 2677 control children were included in the study. Among control children, G6PD deficiency, secondary to the rs1050828 G>A mutation, was common, with 11.2% (n = 301 of 2677) being hemi- or homozygotes and 33.3% (n = 442 of 1329) of girls being heterozygotes. We found that G6PD deficiency increased the risk of pneumococcal bacteremia, but only during a period of high malaria transmission (P = 0.014; OR 2.33, 95% CI 1.19-4.57). We estimate that the population attributable fraction of G6PD deficiency on risk of pneumococcal bacteremia in areas under high malaria transmission is 0.129. CONCLUSIONS Our data demonstrate that G6PD deficiency increases risk of pneumococcal bacteremia in a manner dependent on malaria. At the population level, the impact of G6PD deficiency on invasive pneumococcal disease risk in malaria-endemic regions is substantial. Our study highlights the infection-associated morbidity and mortality conferred by G6PD deficiency in malaria-endemic settings and adds to our understanding of the potential indirect health benefits of improved malaria control.
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Affiliation(s)
- James J Gilchrist
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK. .,Department of Paediatrics, University of Oxford, Oxford, OX3 9DU, UK.
| | - Sophie Uyoga
- KEMRI-Wellcome Trust Research Programme, Kilifi, 80108, Kenya
| | - Matti Pirinen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 00014, Helsinki, Finland
| | - Anna Rautanen
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Salim Mwarumba
- KEMRI-Wellcome Trust Research Programme, Kilifi, 80108, Kenya
| | | | - Neema Mturi
- KEMRI-Wellcome Trust Research Programme, Kilifi, 80108, Kenya
| | | | - Adrian V S Hill
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.,The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
| | - J Anthony G Scott
- KEMRI-Wellcome Trust Research Programme, Kilifi, 80108, Kenya.,Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Thomas N Williams
- KEMRI-Wellcome Trust Research Programme, Kilifi, 80108, Kenya. .,Department of Medicine, Imperial College, Norfolk Place, London, W2 1PG, UK.
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28
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Tsuchimatsu T, Kakui H, Yamazaki M, Marona C, Tsutsui H, Hedhly A, Meng D, Sato Y, Städler T, Grossniklaus U, Kanaoka MM, Lenhard M, Nordborg M, Shimizu KK. Adaptive reduction of male gamete number in the selfing plant Arabidopsis thaliana. Nat Commun 2020; 11:2885. [PMID: 32514036 PMCID: PMC7280297 DOI: 10.1038/s41467-020-16679-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 05/19/2020] [Indexed: 11/08/2022] Open
Abstract
The number of male gametes is critical for reproductive success and varies between and within species. The evolutionary reduction of the number of pollen grains encompassing the male gametes is widespread in selfing plants. Here, we employ genome-wide association study (GWAS) to identify underlying loci and to assess the molecular signatures of selection on pollen number-associated loci in the predominantly selfing plant Arabidopsis thaliana. Regions of strong association with pollen number are enriched for signatures of selection, indicating polygenic selection. We isolate the gene REDUCED POLLEN NUMBER1 (RDP1) at the locus with the strongest association. We validate its effect using a quantitative complementation test with CRISPR/Cas9-generated null mutants in nonstandard wild accessions. In contrast to pleiotropic null mutants, only pollen numbers are significantly affected by natural allelic variants. These data support theoretical predictions that reduced investment in male gametes is advantageous in predominantly selfing species.
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Affiliation(s)
- Takashi Tsuchimatsu
- Department of Evolutionary Biology and Environmental Studies & Zurich-Basel Plant Science Center, University of Zurich, 8057, Zurich, Switzerland
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, 8008, Zurich, Switzerland
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, A-1030, Vienna, Austria
- Department of Biology, Chiba University, Chiba, 263-8522, Japan
- Department of Biological Sciences, University of Tokyo, Tokyo, 113-0033, Japan
| | - Hiroyuki Kakui
- Department of Evolutionary Biology and Environmental Studies & Zurich-Basel Plant Science Center, University of Zurich, 8057, Zurich, Switzerland
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, 244-0813, Japan
- Graduate School of Science and Technology, Niigata University, Niigata, 950-2181, Japan
| | - Misako Yamazaki
- Department of Evolutionary Biology and Environmental Studies & Zurich-Basel Plant Science Center, University of Zurich, 8057, Zurich, Switzerland
| | - Cindy Marona
- Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Hiroki Tsutsui
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, 8008, Zurich, Switzerland
- Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan
- JST ERATO Higashiyama Live-Holonics Project, Nagoya University, Nagoya, 464-8602, Japan
| | - Afif Hedhly
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, 8008, Zurich, Switzerland
| | - Dazhe Meng
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, A-1030, Vienna, Austria
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA, 90089-0371, USA
| | - Yutaka Sato
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Thomas Städler
- Institute of Integrative Biology, ETH Zurich, 8092, Zurich, Switzerland
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, 8008, Zurich, Switzerland
| | | | - Michael Lenhard
- Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, A-1030, Vienna, Austria
| | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies & Zurich-Basel Plant Science Center, University of Zurich, 8057, Zurich, Switzerland.
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, 8008, Zurich, Switzerland.
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, 244-0813, Japan.
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29
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van Dorp L, Gelabert P, Rieux A, de Manuel M, de-Dios T, Gopalakrishnan S, Carøe C, Sandoval-Velasco M, Fregel R, Olalde I, Escosa R, Aranda C, Huijben S, Mueller I, Marquès-Bonet T, Balloux F, Gilbert MTP, Lalueza-Fox C. Plasmodium vivax Malaria Viewed through the Lens of an Eradicated European Strain. Mol Biol Evol 2020; 37:773-785. [PMID: 31697387 PMCID: PMC7038659 DOI: 10.1093/molbev/msz264] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The protozoan Plasmodium vivax is responsible for 42% of all cases of malaria outside Africa. The parasite is currently largely restricted to tropical and subtropical latitudes in Asia, Oceania, and the Americas. Though, it was historically present in most of Europe before being finally eradicated during the second half of the 20th century. The lack of genomic information on the extinct European lineage has prevented a clear understanding of historical population structuring and past migrations of P. vivax. We used medical microscope slides prepared in 1944 from malaria-affected patients from the Ebro Delta in Spain, one of the last footholds of malaria in Europe, to generate a genome of a European P. vivax strain. Population genetics and phylogenetic analyses placed this strain basal to a cluster including samples from the Americas. This genome allowed us to calibrate a genomic mutation rate for P. vivax, and to estimate the mean age of the last common ancestor between European and American strains to the 15th century. This date points to an introduction of the parasite during the European colonization of the Americas. In addition, we found that some known variants for resistance to antimalarial drugs, including Chloroquine and Sulfadoxine, were already present in this European strain, predating their use. Our results shed light on the evolution of an important human pathogen and illustrate the value of antique medical collections as a resource for retrieving genomic information on pathogens from the past.
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Affiliation(s)
- Lucy van Dorp
- UCL Genetics Institute, University College London, London, United Kingdom
| | - Pere Gelabert
- Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Adrien Rieux
- CIRAD, UMR PVBMT, St. Pierre de la Réunion, France
| | - Marc de Manuel
- Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
| | - Toni de-Dios
- Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
| | - Shyam Gopalakrishnan
- Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Christian Carøe
- Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Marcela Sandoval-Velasco
- Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Rosa Fregel
- Department of Genetics, Stanford University, Stanford, CA
- Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, La Laguna, Spain
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA
| | - Raül Escosa
- Consorci de Polítiques Ambientals de les Terres de l'Ebre (COPATE), Deltebre, Spain
| | - Carles Aranda
- Servei de Control de Mosquits, Consell Comarcal del Baix Llobregat, Sant Feliu de Llobregat, Spain
| | - Silvie Huijben
- School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ
- ISGlobal, Barcelona Institute for Global Health, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Ivo Mueller
- ISGlobal, Barcelona Institute for Global Health, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
- Population Health and Immunity Division, Walter & Eliza Hall Institute, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Tomàs Marquès-Bonet
- Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- CNAG-CRG, Barcelona Institute of Science and Technology, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain
| | - François Balloux
- UCL Genetics Institute, University College London, London, United Kingdom
| | - M Thomas P Gilbert
- Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
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Tishkoff SA. 2019 Curt Stern Award Address. Am J Hum Genet 2020. [DOI: 10.1016/j.ajhg.2020.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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Liang X, Chen J, Ma Y, Huang H, Xie D, Monte‐Nguba S, Ehapo CS, Eyi UM, Zheng Y, Liu X, Zha G, Lin L, Chen W, Zhou X, Lin M. Evidence of positively selected G6PD A- allele reduces risk of Plasmodium falciparum infection in African population on Bioko Island. Mol Genet Genomic Med 2020; 8:e1061. [PMID: 31872983 PMCID: PMC7005621 DOI: 10.1002/mgg3.1061] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 10/31/2019] [Accepted: 11/05/2019] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Glucose-6-phosphate dehydrogenase (G6PD) is an essential enzyme that protects red blood cells from oxidative damage. Although G6PD-deficient alleles appear to confer a protective effect of malaria, the link with clinical protection against Plasmodium infection is conflicting. METHODS A case-control study was conducted on Bioko Island, Equatorial Guinea and further genotyping analysis used to detect natural selection of the G6PD A- allele. RESULTS Our results showed G6PD A- allele could significantly reduce the risk of Plasmodium falciparum infection in male individuals (adjusted odds ratio [AOR], 0.43; 95% confidence interval [CI], 0.20-0.93; p < .05) and homozygous female individuals (AOR, 0.11; 95% CI, 0.01-0.84; p < .05). Additionally, the parasite densities were significantly different in the individuals with different G6PD A- alleles and individual levels of G6PD enzyme activity. The pattern of linkage disequilibrium and results of the long-range haplotype test revealed a strong selective signature in the region encompassing the G6PD A- allele over the past 6,250 years. The network of inferred haplotypes suggested a single origin of the G6PD A- allele in Africans. CONCLUSION Our findings demonstrate that glucose-6-phosphate dehydrogenase (G6PD) A- allele could reduce the risk of P. falciparum infection in the African population and indicate that malaria has a recent positive selection on G6PD A- allele.
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Affiliation(s)
- Xue‐Yan Liang
- School of Food Engineering and BiotechnologyHanshan Normal UniversityChaozhouGuangdong ProvincePeople’s Republic of China
- Department of Medical GeneticsShantou University Medical CollegeShantouGuangdong ProvincePeople’s Republic of China
| | - Jiang‐Tao Chen
- The Chinese Medical Aid Team to the Republic of Equatorial GuineaGuangzhouGuangdong ProvincePeople’s Republic of China
- Department of Medical LaboratoryHuizhou Central HospitalHuizhouGuangdong ProvincePeople’s Republic of China
| | - Yan‐Bo Ma
- School of Mathematics and StatisticsHanshan Normal UniversityChaozhouGuangdong ProvincePeople’s Republic of China
| | - Hui‐Ying Huang
- School of Food Engineering and BiotechnologyHanshan Normal UniversityChaozhouGuangdong ProvincePeople’s Republic of China
- Department of Medical GeneticsShantou University Medical CollegeShantouGuangdong ProvincePeople’s Republic of China
| | - Dong‐De Xie
- The Chinese Medical Aid Team to the Republic of Equatorial GuineaGuangzhouGuangdong ProvincePeople’s Republic of China
- Department of Medical LaboratoryHuizhou Central HospitalHuizhouGuangdong ProvincePeople’s Republic of China
| | | | - Carlos Salas Ehapo
- Department of Medical LaboratoryMalabo Regional HospitalMalaboEquatorial Guinea
| | - Urbano Monsuy Eyi
- Department of Medical LaboratoryMalabo Regional HospitalMalaboEquatorial Guinea
| | - Yu‐Zhong Zheng
- School of Food Engineering and BiotechnologyHanshan Normal UniversityChaozhouGuangdong ProvincePeople’s Republic of China
| | - Xiang‐Zhi Liu
- Department of Medical LaboratoryChaozhou People’s Hospital Affiliated to Shantou University Medical CollegeChaozhouGuangdong ProvincePeople’s Republic of China
| | - Guang‐Cai Zha
- School of Food Engineering and BiotechnologyHanshan Normal UniversityChaozhouGuangdong ProvincePeople’s Republic of China
| | - Li‐Yun Lin
- School of Food Engineering and BiotechnologyHanshan Normal UniversityChaozhouGuangdong ProvincePeople’s Republic of China
| | - Wei‐Zhong Chen
- Department of Medical LaboratoryChaozhou People’s Hospital Affiliated to Shantou University Medical CollegeChaozhouGuangdong ProvincePeople’s Republic of China
| | - Xia Zhou
- Department of Medical LaboratoryChaozhou People’s Hospital Affiliated to Shantou University Medical CollegeChaozhouGuangdong ProvincePeople’s Republic of China
| | - Min Lin
- School of Food Engineering and BiotechnologyHanshan Normal UniversityChaozhouGuangdong ProvincePeople’s Republic of China
- Department of Medical LaboratoryChaozhou People’s Hospital Affiliated to Shantou University Medical CollegeChaozhouGuangdong ProvincePeople’s Republic of China
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Devendra R, Gupta V, Biradar SS, Bhat P, Hegde S, Hoti SL, Mukherjee MB, Hegde HV. G6PD A- is the major cause of G6PD deficiency among the Siddis of Karnataka, India. Ann Hum Biol 2019; 47:55-58. [DOI: 10.1080/03014460.2019.1699954] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Rati Devendra
- ICMR-National Institute of Immunohaematology, Parel, India
| | - Vinod Gupta
- ICMR-National Institute of Immunohaematology, Parel, India
| | | | - Pradeep Bhat
- ICMR-National Institute of Traditional Medicine, Belagavi, India
| | - Shantharam Hegde
- ICMR-National Institute of Traditional Medicine, Belagavi, India
| | - S. L. Hoti
- ICMR-National Institute of Traditional Medicine, Belagavi, India
| | | | - Harsha V. Hegde
- ICMR-National Institute of Traditional Medicine, Belagavi, India
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Trumble BC, Finch CE. THE EXPOSOME IN HUMAN EVOLUTION: FROM DUST TO DIESEL. THE QUARTERLY REVIEW OF BIOLOGY 2019; 94:333-394. [PMID: 32269391 PMCID: PMC7141577 DOI: 10.1086/706768] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Global exposures to air pollution and cigarette smoke are novel in human evolutionary history and are associated with about 16 million premature deaths per year. We investigate the history of the human exposome for relationships between novel environmental toxins and genetic changes during human evolution in six phases. Phase I: With increased walking on savannas, early human ancestors inhaled crustal dust, fecal aerosols, and spores; carrion scavenging introduced new infectious pathogens. Phase II: Domestic fire exposed early Homo to novel toxins from smoke and cooking. Phases III and IV: Neolithic to preindustrial Homo sapiens incurred infectious pathogens from domestic animals and dense communities with limited sanitation. Phase V: Industrialization introduced novel toxins from fossil fuels, industrial chemicals, and tobacco at the same time infectious pathogens were diminishing. Thereby, pathogen-driven causes of mortality were replaced by chronic diseases driven by sterile inflammogens, exogenous and endogenous. Phase VI: Considers future health during global warming with increased air pollution and infections. We hypothesize that adaptation to some ancient toxins persists in genetic variations associated with inflammation and longevity.
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Affiliation(s)
- Benjamin C Trumble
- School of Human Evolution & Social Change and Center for Evolution and Medicine, Arizona State University Tempe, Arizona 85287 USA
| | - Caleb E Finch
- Leonard Davis School of Gerontology and Dornsife College, University of Southern California Los Angeles, California 90089-0191 USA
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Lo E, Zhong D, Raya B, Pestana K, Koepfli C, Lee MC, Yewhalaw D, Yan G. Prevalence and distribution of G6PD deficiency: implication for the use of primaquine in malaria treatment in Ethiopia. Malar J 2019; 18:340. [PMID: 31590661 PMCID: PMC6781416 DOI: 10.1186/s12936-019-2981-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 09/28/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND G6PD enzyme deficiency is a common enzymatic X-linked disorder. Deficiency of the G6PD enzyme can cause free radical-mediated oxidative damage to red blood cells, leading to premature haemolysis. Treatment of Plasmodium vivax malaria with primaquine poses a potential risk of mild to severe acute haemolytic anaemia in G6PD deficient people. In this study, the prevalence and distribution of G6PD mutations were investigated across broad areas of Ethiopia, and tested the association between G6PD genotype and phenotype with the goal to provide additional information relevant to the use of primaquine in malaria treatment. METHODS This study examined G6PD mutations in exons 3-11 for 344 febrile patient samples collected from seven sites across Ethiopia. In addition, the G6PD enzyme level of 400 febrile patient samples from Southwestern Ethiopia was determined by the CareStart™ biosensor. The association between G6PD phenotype and genotype was examined by Fisher exact test on a subset of 184 samples. RESULTS Mutations were observed at three positions of the G6PD gene. The most common G6PD mutation across all sites was A376G, which was detected in 21 of 344 (6.1%) febrile patients. Thirteen of them were homozygous and eight were heterozygous for this mutation. The G267+119C/T mutation was found in 4 (1.2%) individuals in South Ethiopia, but absent in other sites. The G1116A mutation was also found in 4 (1.2%) individuals from East and South Ethiopia. For the 400 samples in the south, 17 (4.25%) were shown to be G6PD-deficient. G6PD enzyme level was not significantly different by age or gender. Among a subset of 202 febrile patients who were diagnosed with malaria, 11 (5.45%) were G6PD-deficient. These 11 infected samples were diagnosed with Plasmodium vivax by microscopy. Parasitaemia was not significantly different between the G6PD-deficient and G6PD-normal infections. CONCLUSIONS The prevalence of G6PD deficiency is modest among febrile patients in Ethiopia. G6PD deficiency testing is thus recommended before administrating primaquine for radical cure of P. vivax infected patients. The present study did not indicate a significant association between G6PD gene mutations and enzyme levels.
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Affiliation(s)
- Eugenia Lo
- Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA.
| | - Daibin Zhong
- Program in Public Health, College of Health Sciences, University of California, Irvine, CA, 92697, USA
| | - Beka Raya
- School of Medical Laboratory Sciences, Jimma University, Jimma, Ethiopia
| | - Kareen Pestana
- Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Cristian Koepfli
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Ming-Chieh Lee
- Program in Public Health, College of Health Sciences, University of California, Irvine, CA, 92697, USA
| | - Delenasaw Yewhalaw
- School of Medical Laboratory Sciences, Jimma University, Jimma, Ethiopia
- Tropical and Infectious Diseases Research Center, Jimma University, Jimma, Ethiopia
| | - Guiyun Yan
- Program in Public Health, College of Health Sciences, University of California, Irvine, CA, 92697, USA.
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Glucose-6-Phosphate Dehydrogenase from the Human Pathogen Trypanosoma cruzi Evolved Unique Structural Features to Support Efficient Product Formation. J Mol Biol 2019; 431:2143-2162. [DOI: 10.1016/j.jmb.2019.03.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 03/04/2019] [Accepted: 03/24/2019] [Indexed: 12/25/2022]
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Bien SA, Wojcik GL, Hodonsky CJ, Gignoux CR, Cheng I, Matise TC, Peters U, Kenny EE, North KE. The Future of Genomic Studies Must Be Globally Representative: Perspectives from PAGE. Annu Rev Genomics Hum Genet 2019; 20:181-200. [PMID: 30978304 DOI: 10.1146/annurev-genom-091416-035517] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The past decade has seen a technological revolution in human genetics that has empowered population-level investigations into genetic associations with phenotypes. Although these discoveries rely on genetic variation across individuals, association studies have overwhelmingly been performed in populations of European descent. In this review, we describe limitations faced by single-population studies and provide an overview of strategies to improve global representation in existing data sets and future human genomics research via diversity-focused, multiethnic studies. We highlight the successes of individual studies and meta-analysis consortia that have provided unique knowledge. Additionally, we outline the approach taken by the Population Architecture Using Genomics and Epidemiology (PAGE) study to develop best practices for performing genetic epidemiology in multiethnic contexts. Finally, we discuss how limiting investigations to single populations impairs findings in the clinical domain for both rare-variant identification and genetic risk prediction.
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Affiliation(s)
- Stephanie A Bien
- Department of Public Health Science, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA; ,
| | - Genevieve L Wojcik
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, California 94305, USA;
| | - Chani J Hodonsky
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA; ,
| | - Christopher R Gignoux
- Colorado Center for Personalized Medicine, Anschutz Medical Campus, University of Colorado, Aurora, Colorado 80045, USA;
| | - Iona Cheng
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California 94158, USA;
| | - Tara C Matise
- Department of Genetics, Rutgers University, New Brunswick, New Jersey 08554, USA;
| | - Ulrike Peters
- Department of Public Health Science, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA; ,
| | - Eimear E Kenny
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
| | - Kari E North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA; ,
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Genetic Variation for Ontogenetic Shifts in Metabolism Underlies Physiological Homeostasis in Drosophila. Genetics 2019; 212:537-552. [PMID: 30975764 PMCID: PMC6553824 DOI: 10.1534/genetics.119.302052] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 04/04/2019] [Indexed: 12/28/2022] Open
Abstract
Organismal physiology emerges from metabolic pathways and structures that can vary across development and among individuals. Matoo, Julick, and Montooth found significant variation, both genetic and ontogenetic, in mitochondrial physiology in wild-type and mitochondrial-nuclear... Organismal physiology emerges from metabolic pathways and subcellular structures like the mitochondria that can vary across development and among individuals. Here, we tested whether genetic variation at one level of physiology can be buffered at higher levels of biological organization during development by the inherent capacity for homeostasis in physiological systems. We found that the fundamental scaling relationship between mass and metabolic rate, as well as the oxidative capacity per mitochondria, changed significantly across development in the fruit fly Drosophila. However, mitochondrial respiration rate was maintained at similar levels across development. Furthermore, larvae clustered into two types—those that switched to aerobic, mitochondrial ATP production before the second instar, and those that relied on anaerobic, glycolytic production of ATP through the second instar. Despite genetic variation for the timing of this metabolic shift, metabolic rate in second-instar larvae was more robust to genetic variation than was the metabolic rate of other instars. We found that larvae with a mitochondrial-nuclear incompatibility that disrupts mitochondrial function had increased aerobic capacity and relied more on anaerobic ATP production throughout development relative to larvae from wild-type strains. By taking advantage of both ways of making ATP, larvae with this mitochondrial–nuclear incompatibility maintained mitochondrial respiratory capacity, but also had higher levels of whole-body reactive oxygen species and decreased mitochondrial membrane potential, potentially as a physiological defense mechanism. Thus, genetic defects in core physiology can be buffered at the organismal level via physiological plasticity, and natural populations may harbor genetic variation for distinct metabolic strategies in development that generate similar organismal outcomes.
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Schweizer RM, Durvasula A, Smith J, Vohr SH, Stahler DR, Galaverni M, Thalmann O, Smith DW, Randi E, Ostrander EA, Green RE, Lohmueller KE, Novembre J, Wayne RK. Natural Selection and Origin of a Melanistic Allele in North American Gray Wolves. Mol Biol Evol 2019; 35:1190-1209. [PMID: 29688543 DOI: 10.1093/molbev/msy031] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Pigmentation is often used to understand how natural selection affects genetic variation in wild populations since it can have a simple genetic basis, and can affect a variety of fitness-related traits (e.g., camouflage, thermoregulation, and sexual display). In gray wolves, the K locus, a β-defensin gene, causes black coat color via a dominantly inherited KB allele. The allele is derived from dog-wolf hybridization and is at high frequency in North American wolf populations. We designed a DNA capture array to probe the geographic origin, age, and number of introgression events of the KB allele in a panel of 331 wolves and 20 dogs. We found low diversity in KB, but not ancestral ky, wolf haplotypes consistent with a selective sweep of the black haplotype across North America. Further, North American wolf KB haplotypes are monophyletic, suggesting that a single adaptive introgression from dogs to wolves most likely occurred in the Northwest Territories or Yukon. We use a new analytical approach to date the origin of the KB allele in Yukon wolves to between 1,598 and 7,248 years ago, suggesting that introgression with early Native American dogs was the source. Using population genetic simulations, we show that the K locus is undergoing natural selection in four wolf populations. We find evidence for balancing selection, specifically in Yellowstone wolves, which could be a result of selection for enhanced immunity in response to distemper. With these data, we demonstrate how the spread of an adaptive variant may have occurred across a species' geographic range.
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Affiliation(s)
- Rena M Schweizer
- Division of Biological Sciences, University of Montana, Missoula, MT.,Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA
| | - Arun Durvasula
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA
| | - Joel Smith
- Department of Ecology and Evolution, University of Chicago, Chicago, IL
| | - Samuel H Vohr
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA
| | - Daniel R Stahler
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, WY
| | | | - Olaf Thalmann
- Department of Pediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Poznan, Poland
| | - Douglas W Smith
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, WY
| | - Ettore Randi
- Department of Biology, University of Bologna, Bologna, Italy.,Department of Chemistry and Bioscience, Faculty of Engineering and Science, University of Aalborg, Aalborg, Denmark
| | - Elaine A Ostrander
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Richard E Green
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA
| | - Kirk E Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA.,Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA
| | - John Novembre
- Department of Ecology and Evolution, University of Chicago, Chicago, IL.,Department of Human Genetics, University of Chicago, IL
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA
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N’Diaye A, Haile JK, Nilsen KT, Walkowiak S, Ruan Y, Singh AK, Clarke FR, Clarke JM, Pozniak CJ. Haplotype Loci Under Selection in Canadian Durum Wheat Germplasm Over 60 Years of Breeding: Association With Grain Yield, Quality Traits, Protein Loss, and Plant Height. FRONTIERS IN PLANT SCIENCE 2018; 9:1589. [PMID: 30455711 PMCID: PMC6230583 DOI: 10.3389/fpls.2018.01589] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 10/15/2018] [Indexed: 05/21/2023]
Abstract
Durum wheat was introduced in the southern prairies of western Canada in the late nineteenth century. Breeding efforts have mainly focused on improving quality traits to meet the pasta industry demands. For this study, 192 durum wheat lines were genotyped using the Illumina 90K Infinium iSelect assay, and resulted in a total of 14,324 polymorphic SNPs. Genetic diversity changed over time, declining during the first 20 years of breeding in Canada, then increased in the late 1980s and early 1990s. We scanned the genome for signatures of selection, using the total variance Fst-based outlier detection method (Lositan), the hierarchical island model (Arlequin) and the Bayesian genome scan method (BayeScan). A total of 407 outliers were identified and clustered into 84 LD-based haplotype loci, spanning all 14 chromosomes of the durum wheat genome. The association analysis detected 54 haplotype loci, of which 39% contained markers with a complete reversal of allelic state. This tendency to fixation of favorable alleles corroborates the success of the Canadian durum wheat breeding programs over time. Twenty-one haplotype loci were associated with multiple traits. In particular, hap_4B_1 explained 20.6, 17.9 and 16.6% of the phenotypic variance of pigment loss, pasta b∗ and dough extensibility, respectively. The locus hap_2B_9 explained 15.9 and 17.8% of the variation of protein content and protein loss, respectively. All these pleiotropic haplotype loci offer breeders the unique opportunity for further improving multiple traits, facilitating marker-assisted selection in durum wheat, and could help in identifying genes as functional annotations of the wheat genome become available.
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Affiliation(s)
- Amidou N’Diaye
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jemanesh K. Haile
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Kirby T. Nilsen
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Sean Walkowiak
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Yuefeng Ruan
- Agriculture and Agri-Food Canada, Swift Current Research and Development Centre, Swift Current, SK, Canada
| | - Asheesh K. Singh
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Fran R. Clarke
- Agriculture and Agri-Food Canada, Swift Current Research and Development Centre, Swift Current, SK, Canada
| | - John M. Clarke
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Curtis J. Pozniak
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
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Tseghereda YG, Nganga JK, Kimang'a AN, Mehari TH, Weldemichael YG. Glucose-6-phosphate dehydrogenase deficiency allelic variants and their prevalence in malaria patients in Eritrea. Pan Afr Med J 2018; 31:46. [PMID: 30918572 PMCID: PMC6430948 DOI: 10.11604/pamj.2018.31.46.16527] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 08/31/2018] [Indexed: 11/23/2022] Open
Abstract
Introduction Glucose 6-phosphate dehydrogenase (G6PD) deficiency is the most common enzymopathy with a relatively high frequency in malaria-endemic regions. In Eritrea, there is scanty knowledge of G6PD deficiency. The aim of the study was to characterize and determine the prevalence of four common G6PD allelic variants. Methods Three hundred and fourteen dried blood spot samples from unrelated microscopically diagnosed malaria patient Eritrean ethnic groups living in five zobas (regions) of Eritrea were analysed by PCR-RFLP method to identify the G6PD B, G6PD A (A376G), G6PD A-(G202A), and G6PD Mediterranean (C563T) variants. To confirm the RFLP results, samples positive for A376G but negative for G202A variants were subjected to Sanger sequencing and a subset of PCR products (exon 5) directly sequenced to identify A376G and other mutations. Results For G6PD genotyping, G6PD B was detected in 87.5% and A376G detected in 12.5% of malaria patients, whereas G202A and C563T were absent. Bivariate Statistical analysis showed a statistically significant association between G6PD genotypes and zoba (P < 0.004 < 0.05). Sequencing revealed the expected A376G variant. In exon 5, four common (A376G) mutations, three uncommon mutations rs782669677 (535G→A) and one potentially new mutation (451G→C), relative to the reference, mRNA NM_001042351 were detected. Bioinformatic analysis of these mutations' potential functional impact suggests minimal effect on protein function. Conclusion This is the first report indicating that G6PD B and G6PD A genotypes are prevalent in Eritrea. Similar findings were reported in neighboring countries. Further studies including phenotype analysis are needed to corroborate the observed results.
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Shriner D, Rotimi CN. Whole-Genome-Sequence-Based Haplotypes Reveal Single Origin of the Sickle Allele during the Holocene Wet Phase. Am J Hum Genet 2018. [PMID: 29526279 PMCID: PMC5985360 DOI: 10.1016/j.ajhg.2018.02.003] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Five classical designations of sickle haplotypes are made on the basis of the presence or absence of restriction sites and are named after the ethno-linguistic groups or geographic regions from which the individuals with sickle cell anemia originated. Each haplotype is thought to represent an independent occurrence of the sickle mutation rs334 (c.20A>T [p.Glu7Val] in HBB). We investigated the origins of the sickle mutation by using whole-genome-sequence data. We identified 156 carriers from the 1000 Genomes Project, the African Genome Variation Project, and Qatar. We classified haplotypes by using 27 polymorphisms in linkage disequilibrium with rs334. Network analysis revealed a common haplotype that differed from the ancestral haplotype only by the derived sickle mutation at rs334 and correlated collectively with the Central African Republic (CAR), Cameroon, and Arabian/Indian haplotypes. Other haplotypes were derived from this haplotype and fell into two clusters, one composed of Senegal haplotypes and the other composed of Benin and Senegal haplotypes. The near-exclusive presence of the original sickle haplotype in the CAR, Kenya, Uganda, and South Africa is consistent with this haplotype predating the Bantu expansions. Modeling of balancing selection indicated that the heterozygote advantage was 15.2%, an equilibrium frequency of 12.0% was reached after 87 generations, and the selective environment predated the mutation. The posterior distribution of the ancestral recombination graph yielded a sickle mutation age of 259 generations, corresponding to 7,300 years ago during the Holocene Wet Phase. These results clarify the origin of the sickle allele and improve and simplify the classification of sickle haplotypes.
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Akbari A, Vitti JJ, Iranmehr A, Bakhtiari M, Sabeti PC, Mirarab S, Bafna V. Identifying the favored mutation in a positive selective sweep. Nat Methods 2018; 15:279-282. [PMID: 29457793 PMCID: PMC6231406 DOI: 10.1038/nmeth.4606] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 01/08/2018] [Indexed: 01/23/2023]
Abstract
Most approaches that capture signatures of selective sweeps in population genomics data do not identify the specific mutation favored by selection. We present iSAFE (for "integrated selection of allele favored by evolution"), a method that enables researchers to accurately pinpoint the favored mutation in a large region (∼5 Mbp) by using a statistic derived solely from population genetics signals. iSAFE does not require knowledge of demography, the phenotype under selection, or functional annotations of mutations.
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Affiliation(s)
- Ali Akbari
- Department of Electrical & Computer Engineering, University of California San Diego, La Jolla, California, USA
| | - Joseph J Vitti
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Arya Iranmehr
- Department of Electrical & Computer Engineering, University of California San Diego, La Jolla, California, USA
| | - Mehrdad Bakhtiari
- Department of Computer Science & Engineering, University of California San Diego, La Jolla, California, USA
| | - Pardis C Sabeti
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Siavash Mirarab
- Department of Electrical & Computer Engineering, University of California San Diego, La Jolla, California, USA
| | - Vineet Bafna
- Department of Computer Science & Engineering, University of California San Diego, La Jolla, California, USA
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Lee J, Kim TI, Kang JM, Jun H, Lê HG, Thái TL, Sohn WM, Myint MK, Lin K, Kim TS, Na BK. Prevalence of glucose-6-phosphate dehydrogenase (G6PD) deficiency among malaria patients in Upper Myanmar. BMC Infect Dis 2018; 18:131. [PMID: 29548282 PMCID: PMC5857094 DOI: 10.1186/s12879-018-3031-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 03/01/2018] [Indexed: 11/13/2022] Open
Abstract
Background Glucose-6-phosphate dehydrogenase (G6PD; EC 1.1.1.49) deficiency is one of the most common X-linked recessive hereditary disorders in the world. Primaquine (PQ) has been used for radical cure of P. vivax to prevent relapse. Recently, it is also used to reduce P. falciparum gametocyte carriage to block transmission. However, PQ metabolites oxidize hemoglobin and generate excessive reactive oxygen species which can trigger acute hemolytic anemia in malaria patients with inherited G6PD deficiency. Methods A total of 252 blood samples collected from malaria patients in Myanmar were used in this study. G6PD variant was analysed by a multiplex allele specific PCR kit, DiaPlexC™ G6PD Genotyping Kit [Asian type]. The accuracy of the multiplex allele specific PCR was confirmed by sequencing analysis. Results Prevalence and distribution of G6PD variants in 252 malaria patients in Myanmar were analysed. Six different types of G6PD allelic variants were identified in 50 (7 females and 43 males) malaria patients. The predominant variant was Mahidol (68%, 34/50), of which 91.2% (31/34) and 8.8% (3/34) were males and females, respectively. Other G6PD variants including Kaiping (18%, 9/50), Viangchan (6%, 3/50), Mediterranean (4%, 2/50), Union (2%, 1/50) and Canton (2%, 1/50) were also observed. Conclusions Results of this study suggest that more concern for proper and safe use of PQ as a radical cure of malaria in Myanmar is needed by combining G6PD deficiency test before PQ prescription. Establishment of a follow-up system to monitor potential PQ toxicity in malaria patients who are given PQ is also required.
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Affiliation(s)
- Jinyoung Lee
- Department of Parasitology and Tropical Medicine, and Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju, 52727, Republic of Korea.,Present address: Department of Tropical Medicine, and Inha Research Institute for Medical Sciences, Inha University College of Medicine, Incheon, 22212, Republic of Korea
| | - Tae Im Kim
- Department of Parasitology and Tropical Medicine, and Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju, 52727, Republic of Korea.,Present address: Planning and Management Division, Nakdonggang National Institute of Biological Resources, Sangju, 37242, Republic of Korea
| | - Jung-Mi Kang
- Department of Parasitology and Tropical Medicine, and Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju, 52727, Republic of Korea.,BK21Plus Team for Anti-aging Biotechnology and Industry, Department of Convergence Medical Science, Gyeongsang National University, Jinju, 52727, Republic of Korea
| | - Hojong Jun
- Department of Tropical Medicine, and Inha Research Institute for Medical Sciences, Inha University College of Medicine, Incheon, 22212, Republic of Korea
| | - Hương Giang Lê
- Department of Parasitology and Tropical Medicine, and Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju, 52727, Republic of Korea.,BK21Plus Team for Anti-aging Biotechnology and Industry, Department of Convergence Medical Science, Gyeongsang National University, Jinju, 52727, Republic of Korea
| | - Thị Lam Thái
- Department of Parasitology and Tropical Medicine, and Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju, 52727, Republic of Korea.,BK21Plus Team for Anti-aging Biotechnology and Industry, Department of Convergence Medical Science, Gyeongsang National University, Jinju, 52727, Republic of Korea
| | - Woon-Mok Sohn
- Department of Parasitology and Tropical Medicine, and Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju, 52727, Republic of Korea
| | - Moe Kyaw Myint
- Department of Medical Research Pyin Oo Lwin Branch, Pyin Oo Lwin, Myanmar
| | - Khin Lin
- Department of Medical Research Pyin Oo Lwin Branch, Pyin Oo Lwin, Myanmar
| | - Tong-Soo Kim
- Department of Tropical Medicine, and Inha Research Institute for Medical Sciences, Inha University College of Medicine, Incheon, 22212, Republic of Korea.
| | - Byoung-Kuk Na
- Department of Parasitology and Tropical Medicine, and Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju, 52727, Republic of Korea. .,BK21Plus Team for Anti-aging Biotechnology and Industry, Department of Convergence Medical Science, Gyeongsang National University, Jinju, 52727, Republic of Korea.
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Babalola MO, Imaga NA, Samuel TA, Diriwari IP, Kolade O, Ezeamalu I, Laoye AO, Ojewunmi OO. Genetic Polymorphisms of Glucose-6-Phosphate Dehydrogenase in Lagos, Nigeria. Hemoglobin 2018; 42:47-50. [PMID: 29493303 DOI: 10.1080/03630269.2018.1434196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Glucose-6-phosphate dehydrogenase (G6PD) is an essential enzyme in the pentose phosphate pathway that prevents oxidative damage to cells. This study determined the genotypic and allelic frequencies of G6PD G202A and A376G and also investigated correlation between G6PD polymorphisms and hemoglobin (Hb) phenotypes in children in Lagos, Nigeria. Seventy-eight children [55 with Hb AA (βΑ/βA) and 23 with Hb AS (βΑ/βS) trait] and 65 Hb SS (βS/βS) (HBB: c.20A>T) subjects in steady state with age range between 5-15 years were recruited for the study. Hemoglobin phenotypes of all study participants were carried out using alkaline electrophoresis and solubility tests. Genomic DNA was extracted from whole blood and restriction fragment length polymorphism-polymerase chain reaction (RFLP-PCR) was used to determine the G202A and the A376G mutations of the G6PD gene. The genotype and allele distributions of G6PD G202A and A376G according to the Hb phenotypes were not statistically significant (p > 0.05). The minor allele frequency 202A was 0.15 (15.0%) and 0.14 (14.0%) in cases and controls, respectively. The overall frequency of 376G allele in the case group was 0.35 (35.0%) and 0.38 (38.0%) in the control group. No statistical significance was observed in the genotype and allele distributions of A376G in both the case and control groups (p > 0.05). The G6PD A- frequency in Hb SS subjects and the control group were 6.2 and 2.6%, respectively. G6PD G202A and A376G polymorphisms were not associated with Hb phenotypes and the allele distributions of 202A and 376G in this study are typical of West African populations.
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Affiliation(s)
- Musa O Babalola
- a Department of Biochemistry, Faculty of Basic Medical Sciences, College of Medicine , University of Lagos , Lagos , Nigeria
| | - Ngozi A Imaga
- a Department of Biochemistry, Faculty of Basic Medical Sciences, College of Medicine , University of Lagos , Lagos , Nigeria
| | - Titilola A Samuel
- a Department of Biochemistry, Faculty of Basic Medical Sciences, College of Medicine , University of Lagos , Lagos , Nigeria
| | - Iyanu P Diriwari
- a Department of Biochemistry, Faculty of Basic Medical Sciences, College of Medicine , University of Lagos , Lagos , Nigeria
| | - Olajumoke Kolade
- a Department of Biochemistry, Faculty of Basic Medical Sciences, College of Medicine , University of Lagos , Lagos , Nigeria
| | - Irene Ezeamalu
- a Department of Biochemistry, Faculty of Basic Medical Sciences, College of Medicine , University of Lagos , Lagos , Nigeria
| | - Adefioye O Laoye
- a Department of Biochemistry, Faculty of Basic Medical Sciences, College of Medicine , University of Lagos , Lagos , Nigeria
| | - Oyesola O Ojewunmi
- a Department of Biochemistry, Faculty of Basic Medical Sciences, College of Medicine , University of Lagos , Lagos , Nigeria.,b Sickle Cell Foundation Nigeria , Lagos , Nigeria
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Leveraging human genetic and adverse outcome pathway (AOP) data to inform susceptibility in human health risk assessment. Mamm Genome 2018; 29:190-204. [DOI: 10.1007/s00335-018-9738-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 01/31/2018] [Indexed: 12/19/2022]
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Bigham AW, Magnaye K, Dunn DM, Weiss RB, Bamshad M. Complex signatures of natural selection at GYPA. Hum Genet 2018; 137:151-160. [PMID: 29362874 DOI: 10.1007/s00439-018-1866-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 01/06/2018] [Indexed: 01/07/2023]
Abstract
The human MN blood group antigens are isoforms of glycophorin A (GPA) encoded by the gene, GYPA, and are the most abundant erythrocyte sialoglycoproteins. The distribution of MN antigens has been widely studied in human populations yet the evolutionary and/or demographic factors affecting population variation remain elusive. While the primary function of GPA is yet to be discovered, it serves as the major binding site for the 175-kD erythrocyte-binding antigen (EB-175) of the malarial parasite, Plasmodium falciparum, a major selective pressure in recent human history. More specifically, exon two of GYPA encodes the receptor-binding ligand to which P. falciparum binds. Accordingly, there has been keen interest in understanding what impact, if any, natural selection has had on the distribution of variation in GYPA and exon two in particular. To this end, we resequenced GYPA in individuals sampled from both P. falciparum endemic (sub-Saharan Africa and South India) and non-endemic (Europe and East Asia) regions of the world. Observed patterns of variation suggest that GYPA has been subject to balancing selection in populations living in malaria endemic areas and in Europeans, but no such evidence was found in samples from East Asia, Oceania, and the Americas. These results are consistent with malaria acting as a selective pressure on GYPA, but also suggest that another selective force has resulted in a similar pattern of variation in Europeans. Accordingly, GYPA has perhaps a more complex evolutionary history, wherein on a global scale, spatially varying selective pressures have governed its natural history.
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Affiliation(s)
- Abigail W Bigham
- Department of Anthropology, The University of Michigan, 222C West Hall, 1085 S. University, Ann Arbor, MI, 48109-1107, USA.
| | - Kevin Magnaye
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA
| | - Diane M Dunn
- Department of Human Genetics, The University of Utah, Salt Lake City, UT, USA
| | - Robert B Weiss
- Department of Human Genetics, The University of Utah, Salt Lake City, UT, USA
| | - Michael Bamshad
- Departments of Pediatrics and Genome Sciences, The University of Washington, Seattle, WA, USA
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Taylor WR, Naw HK, Maitland K, Williams TN, Kapulu M, D'Alessandro U, Berkley JA, Bejon P, Okebe J, Achan J, Amambua AN, Affara M, Nwakanma D, van Geertruyden JP, Mavoko M, Lutumba P, Matangila J, Brasseur P, Piola P, Randremanana R, Lasry E, Fanello C, Onyamboko M, Schramm B, Yah Z, Jones J, Fairhurst RM, Diakite M, Malenga G, Molyneux M, Rwagacondo C, Obonyo C, Gadisa E, Aseffa A, Loolpapit M, Henry MC, Dorsey G, John C, Sirima SB, Barnes KI, Kremsner P, Day NP, White NJ, Mukaka M. Single low-dose primaquine for blocking transmission of Plasmodium falciparum malaria - a proposed model-derived age-based regimen for sub-Saharan Africa. BMC Med 2018; 16:11. [PMID: 29347975 PMCID: PMC5774032 DOI: 10.1186/s12916-017-0990-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 12/12/2017] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND In 2012, the World Health Organization recommended blocking the transmission of Plasmodium falciparum with single low-dose primaquine (SLDPQ, target dose 0.25 mg base/kg body weight), without testing for glucose-6-phosphate dehydrogenase deficiency (G6PDd), when treating patients with uncomplicated falciparum malaria. We sought to develop an age-based SLDPQ regimen that would be suitable for sub-Saharan Africa. METHODS Using data on the anti-infectivity efficacy and tolerability of primaquine (PQ), the epidemiology of anaemia, and the risks of PQ-induced acute haemolytic anaemia (AHA) and clinically significant anaemia (CSA), we prospectively defined therapeutic-dose ranges of 0.15-0.4 mg PQ base/kg for children aged 1-5 years and 0.15-0.5 mg PQ base/kg for individuals aged ≥6 years (therapeutic indices 2.7 and 3.3, respectively). We chose 1.25 mg PQ base for infants aged 6-11 months because they have the highest rate of baseline anaemia and the highest risks of AHA and CSA. We modelled an anthropometric database of 661,979 African individuals aged ≥6 months (549,127 healthy individuals, 28,466 malaria patients and 84,386 individuals with other infections/illnesses) by the Box-Cox transformation power exponential and tested PQ doses of 1-15 mg base, selecting dosing groups based on calculated mg/kg PQ doses. RESULTS From the Box-Cox transformation power exponential model, five age categories were selected: (i) 6-11 months (n = 39,886, 6.03%), (ii) 1-5 years (n = 261,036, 45.46%), (iii) 6-9 years (n = 20,770, 3.14%), (iv) 10-14 years (n = 12,155, 1.84%) and (v) ≥15 years (n = 328,132, 49.57%) to receive 1.25, 2.5, 5, 7.5 and 15 mg PQ base for corresponding median (1st and 99th centiles) mg/kg PQ base of: (i) 0.16 (0.12-0.25), (ii) 0.21 (0.13-0.37), (iii) 0.25 (0.16-0.38), (iv) 0.26 (0.15-0.38) and (v) 0.27 (0.17-0.40). The proportions of individuals predicted to receive optimal therapeutic PQ doses were: 73.2 (29,180/39,886), 93.7 (244,537/261,036), 99.6 (20,690/20,770), 99.4 (12,086/12,155) and 99.8% (327,620/328,132), respectively. CONCLUSIONS We plan to test the safety of this age-based dosing regimen in a large randomised placebo-controlled trial (ISRCTN11594437) of uncomplicated falciparum malaria in G6PDd African children aged 0.5 - 11 years. If the regimen is safe and demonstrates adequate pharmacokinetics, it should be used to support malaria elimination.
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Affiliation(s)
- W Robert Taylor
- Mahidol Oxford Tropical Medicine Research Unit (MORU), Mahidol University, 420/6 Rajvithi Road, Rajthevee, Bangkok, 10400, Thailand.
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Division of Tropical and Humanitarian Medicine, University Hospitals of Geneva, Geneva, Switzerland.
| | - Htee Khu Naw
- Mahidol Oxford Tropical Medicine Research Unit (MORU), Mahidol University, 420/6 Rajvithi Road, Rajthevee, Bangkok, 10400, Thailand
| | - Kathryn Maitland
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
- Wellcome Trust Centre for Clinical Tropical Medicine and Department of Paediatrics, Faculty of Medicine, Imperial College, London, UK
| | - Thomas N Williams
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
- Wellcome Trust Centre for Clinical Tropical Medicine and Department of Paediatrics, Faculty of Medicine, Imperial College, London, UK
| | - Melissa Kapulu
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Umberto D'Alessandro
- MRC Unit, Fajara, Banjul, The Gambia
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - James A Berkley
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Philip Bejon
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | | | | | | | | | | | | | - Muhindo Mavoko
- Department of Tropical Medicine, University of Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Pascal Lutumba
- Department of Tropical Medicine, University of Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Junior Matangila
- Department of Tropical Medicine, University of Kinshasa, Kinshasa, Democratic Republic of Congo
| | | | - Patrice Piola
- Institut Pasteur de Madagascar, BP 1274, Antananarivo, Madagascar
| | | | - Estrella Lasry
- Kinshasa Mahidol Oxford Research Unit, Kinshasa, Democratic Republic of Congo
| | - Caterina Fanello
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of Congo
| | - Marie Onyamboko
- Kinshasa Mahidol Oxford Research Unit, Kinshasa, Democratic Republic of Congo
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of Congo
| | | | - Zolia Yah
- National Malaria Control Programme, Monrovia, Sierra Leone
| | - Joel Jones
- National Malaria Control Programme, Monrovia, Sierra Leone
| | - Rick M Fairhurst
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | | | | | - Malcolm Molyneux
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | | | | | | | - Abraham Aseffa
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | | | | | - Grant Dorsey
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Chandy John
- Department of Pediatrics, Indiana University, Indianapolis, IN, USA
| | - Sodiomon B Sirima
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
- Groupe de Recherche Action en Santé (GRAS), Ouagadougou, Burkina Faso
| | - Karen I Barnes
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Peter Kremsner
- Institute of Tropical Medicine, University of Tubingen, Tubingen, Germany
| | - Nicholas P Day
- Mahidol Oxford Tropical Medicine Research Unit (MORU), Mahidol University, 420/6 Rajvithi Road, Rajthevee, Bangkok, 10400, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nicholas J White
- Mahidol Oxford Tropical Medicine Research Unit (MORU), Mahidol University, 420/6 Rajvithi Road, Rajthevee, Bangkok, 10400, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Mavuto Mukaka
- Mahidol Oxford Tropical Medicine Research Unit (MORU), Mahidol University, 420/6 Rajvithi Road, Rajthevee, Bangkok, 10400, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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Carter TE, Mekonnen SK, Lopez K, Bonnell V, Damodaran L, Aseffa A, Janies DA. Glucose-6-Phosphate Dehydrogenase Deficiency Genetic Variants in Malaria Patients in Southwestern Ethiopia. Am J Trop Med Hyg 2018; 98:83-87. [PMID: 29141760 PMCID: PMC5928732 DOI: 10.4269/ajtmh.17-0557] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 09/08/2017] [Indexed: 12/26/2022] Open
Abstract
Glucose-6-phosphate dehydrogenase (G6PD) deficiency is an X-linked erythrocyte enzyme disorder with relevance to malaria treatment policy. Treatment with the antimalarial primaquine can result in hemolytic anemia in G6PD-deficient patients. With increased interest in primaquine use, it is important to identify G6PD variants in Ethiopia to inform malaria treatment policy. In the present study, mutations in the G6PD gene are identified in a sample of patients with malaria in Jimma town in southwest Ethiopia. Plasmodium species of infection were confirmed using polymerase chain reaction (PCR) and gel electrophoresis. PCR and Sanger sequencing were performed to observe a portion of the G6PD gene where the common G6PD mutations (A376G, G202A, and C563T) are found. Molecular analysis revealed that most of the samples were single Plasmodium vivax infections (83.7%). For G6PD genotyping, A376G was detected in 23.26% of individuals, whereas G202A and C563T were absent. Three other uncommon mutations were identified: rs782669677 (535G→A), rs370658483, (485 + 37 G→T), and a new mutation at chrX:154535443(C→T). Bioinformatic analysis of these mutations' potential functional impact suggests minimal effect on protein function. The discovery of both common and uncommon G6PD mutations contributes to the discussion on G6PD deficiency and appropriate primaquine treatment in Ethiopia.
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Affiliation(s)
- Tamar E. Carter
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina
| | | | - Karen Lopez
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina
| | - Victoria Bonnell
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina
| | - Lambodhar Damodaran
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina
| | - Abraham Aseffa
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Daniel A. Janies
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina
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Ouattara AK, Yameogo P, Traore L, Diarra B, Assih M, Compaore TR, Obiri-Yeboah D, Soubeiga ST, Djigma FW, Simpore J. Prevalence, genetic variants and clinical implications of G-6-PD deficiency in Burkina Faso: a systematic review. BMC MEDICAL GENETICS 2017; 18:139. [PMID: 29169341 PMCID: PMC5701495 DOI: 10.1186/s12881-017-0496-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Accepted: 11/09/2017] [Indexed: 11/10/2022]
Abstract
BACKGROUND It is now well-known that some antimalarials such as primaquine may induce severe hemolytic anemia in people with G-6-PD deficiency. Antimalarial drug prescriptions must, therefore take into account the patient's G-6-PD status in malaria endemic areas such as Burkina Faso, where the prevalence of this genetic abnormality is relatively high. Although great clinical heterogeneity is observed depending on the molecular nature of the deficiency and the residual enzyme activity in the red blood cell, there is very poor data on the prevalence of G-6-PD deficiency and the distribution of involved genetic variants in Burkina Faso. In this systematic review, we present a synthesis of the various studies carried out on the G-6-PD deficiency in Burkina Faso in order to determine its prevalence, probable distribution of the genetic variants involved and their clinical implications for a national systematic screening policy among the groups most vulnerable to malaria. METHODS A systematic review was carried out to analyze available published data on the prevalence, phenotypes and mutations responsible for G-6-PD deficiency in Burkina Faso. The key words used were "G-6-PD deficiency AND Burkina Faso" or "Déficit en G-6-PD AND Burkina Faso" in French. To identify the relevant articles, two independent reviewers reviewed the titles, abstracts and the full text of the selected papers. RESULTS An average prevalence of 16.6% (183/1100; CI 95%: 0.145-0.190) and 6.5% (69/1066; CI 95%: 0.051-0.081) of G-6-PD deficiency was found respectively in men and women in this systematic review. Although the predominance (99.8% of G-6-PD deficient cases) of 202A/376G G-6-PD A- variant, the Santamaria and Betica Selma variants were identified in Burkina Faso. Independently of the method used, the enzymatic deficiency was significantly higher in males (2.5-20.5%) compared to females (3.3-12.3%). CONCLUSION This systematic review suggests that despite the ubiquity of the 202A/376G G-6-PD A- variant in Burkina Faso, it will be necessary to consider the Santamaria and Betica Selma variants although their frequencies remain to be specified. A systematic screening of the G-6-PD deficiency is also needed to prevent the occurrence of iatrogenic hemolytic accidents.
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Affiliation(s)
- Abdoul Karim Ouattara
- Pietro Annigoni Biomolecular Research Center (CERBA), 01 PO BOX 364, Ouagadougou 01, Burkina Faso. .,Laboratory of Molecular Biology and Molecular Genetics (LABIOGENE) UFR/SVT, University Ouaga I Prof Joseph KI-ZERBO, Ouagadougou 03, BP 7021, Burkina Faso.
| | - Pouiré Yameogo
- Laboratory of Molecular Biology and Molecular Genetics (LABIOGENE) UFR/SVT, University Ouaga I Prof Joseph KI-ZERBO, Ouagadougou 03, BP 7021, Burkina Faso
| | - Lassina Traore
- Pietro Annigoni Biomolecular Research Center (CERBA), 01 PO BOX 364, Ouagadougou 01, Burkina Faso.,Laboratory of Molecular Biology and Molecular Genetics (LABIOGENE) UFR/SVT, University Ouaga I Prof Joseph KI-ZERBO, Ouagadougou 03, BP 7021, Burkina Faso
| | - Birama Diarra
- Pietro Annigoni Biomolecular Research Center (CERBA), 01 PO BOX 364, Ouagadougou 01, Burkina Faso.,Laboratory of Molecular Biology and Molecular Genetics (LABIOGENE) UFR/SVT, University Ouaga I Prof Joseph KI-ZERBO, Ouagadougou 03, BP 7021, Burkina Faso
| | - Maléki Assih
- Pietro Annigoni Biomolecular Research Center (CERBA), 01 PO BOX 364, Ouagadougou 01, Burkina Faso.,Laboratory of Molecular Biology and Molecular Genetics (LABIOGENE) UFR/SVT, University Ouaga I Prof Joseph KI-ZERBO, Ouagadougou 03, BP 7021, Burkina Faso
| | - Tegwindé Rébéca Compaore
- Pietro Annigoni Biomolecular Research Center (CERBA), 01 PO BOX 364, Ouagadougou 01, Burkina Faso
| | - Dorcas Obiri-Yeboah
- Department of Microbiology and Immunology, University of Cape Coast, Cape Coast, Ghana
| | - Serge Théophile Soubeiga
- Pietro Annigoni Biomolecular Research Center (CERBA), 01 PO BOX 364, Ouagadougou 01, Burkina Faso.,Laboratory of Molecular Biology and Molecular Genetics (LABIOGENE) UFR/SVT, University Ouaga I Prof Joseph KI-ZERBO, Ouagadougou 03, BP 7021, Burkina Faso
| | - Florencia Wendkuuni Djigma
- Pietro Annigoni Biomolecular Research Center (CERBA), 01 PO BOX 364, Ouagadougou 01, Burkina Faso.,Laboratory of Molecular Biology and Molecular Genetics (LABIOGENE) UFR/SVT, University Ouaga I Prof Joseph KI-ZERBO, Ouagadougou 03, BP 7021, Burkina Faso
| | - Jacques Simpore
- Pietro Annigoni Biomolecular Research Center (CERBA), 01 PO BOX 364, Ouagadougou 01, Burkina Faso.,Laboratory of Molecular Biology and Molecular Genetics (LABIOGENE) UFR/SVT, University Ouaga I Prof Joseph KI-ZERBO, Ouagadougou 03, BP 7021, Burkina Faso
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Boonyuen U, Chamchoy K, Swangsri T, Junkree T, Day NPJ, White NJ, Imwong M. A trade off between catalytic activity and protein stability determines the clinical manifestations of glucose-6-phosphate dehydrogenase (G6PD) deficiency. Int J Biol Macromol 2017; 104:145-156. [PMID: 28583873 PMCID: PMC5625996 DOI: 10.1016/j.ijbiomac.2017.06.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 06/01/2017] [Accepted: 06/01/2017] [Indexed: 01/08/2023]
Abstract
Glucose-6-phosphate dehydrogenase (G6PD) deficiency is the most common polymorphism and enzymopathy in humans, affecting approximately 400 million people worldwide. It is responsible for various clinical manifestations, including favism, hemolytic anemia, chronic non-spherocytic hemolytic anemia, spontaneous abortion, and neonatal hyperbilirubinemia. Understanding the molecular mechanisms underlying the severity of G6PD deficiency is of great importance but that of many G6PD variants are still unknown. In this study, we report the construction, expression, purification, and biochemical characterization in terms of kinetic properties and stability of five clinical G6PD variants-G6PD Bangkok, G6PD Bangkok noi, G6PD Songklanagarind, G6PD Canton+Bangkok noi, and G6PD Union+Viangchan. G6PD Bangkok and G6PD Canton+Bangkok noi showed a complete loss of catalytic activity and moderate reduction in thermal stability when compared with the native G6PD. G6PD Bangkok noi and G6PD Union+Viangchan showed a significant reduction in catalytic efficiency, whereas G6PD Songklanagarind showed a catalytic activity comparable to the wild-type enzyme. The Union+Viangchan mutation showed a remarkable effect on the global stability of the enzyme. In addition, our results indicate that the location of mutations in G6PD variants affects their catalytic activity, stability, and structure. Hence, our results provide a molecular explanation for clinical manifestations observed in individuals with G6PD deficiency.
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Affiliation(s)
- Usa Boonyuen
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand.
| | - Kamonwan Chamchoy
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand.
| | - Thitiluck Swangsri
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand.
| | - Thanyaphorn Junkree
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand.
| | - Nicholas P J Day
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand; Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.
| | - Nicholas J White
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand; Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.
| | - Mallika Imwong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand; Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand.
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